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UC San Diego Chancellor Pradeep Khosla honored for technical and administrative achievements

San Diego, Calif., Oct. 16, 2020 -- Pradeep K. Khosla, Chancellor of the University of California San Diego, is being honored by the Indo American Press Club for his contributions as both an engineering innovator and a university administrator.

In addition to serving as Chancellor of UC San Diego, Khosla is an internationally renowned electrical and computer engineer and member of the US National Academy of Engineering (NAE).

At UC San Diego, Khosla holds academic appointments in both the Department of Electrical and Computer Engineering (ECE) and the Department of Computer Science and Engineering (CSE) at the Jacobs School of Engineering.

The new recognition from the Indo American Press Club (IAPC) is for "outstanding contributions to the community as an academic computer scientist and university administrator." In particular, the IAPC has awarded Kosla the 2020 IAPC Prestigious Excellence Award in the field of Computer Technology.

The IAPC is a non-profit organization that aims to provide a common platform to journalists of  Indian origin living in the United States and Canada, committed to professionalism and well-being of the larger society. It has a focus on education, mentoring, recognition and networking.

Pradeep K. Khosla became UC San Diego’s eighth Chancellor on August 1, 2012. As UC San Diego’s chief executive officer, he leads a campus with more than 39,000 students, seven undergraduate colleges, five academic divisions, and seven graduate and professional schools. UC San Diego is an academic and research powerhouse, with faculty, researchers and staff attracting more than $1.45 billion in sponsored research funding a year. UC San Diego is recognized as one of the top 15 research universities in the world and is the largest civilian employer based in San Diego County.

Khosla initiated and led UC San Diego’s first-ever Strategic Plan and the ambitious $2 billion Campaign for UC San Diego. The Campaign, which is aimed at transforming the university physically and intellectually, has raised $2.31 billion in eight years. Khosla has significantly expanded college access and affordability for underserved populations, initiated interdisciplinary research initiatives to foster collaboration and solve societal challenges, and strengthened university and community relationships and partnerships. The campus is currently in the midst of a major construction plan aimed at expanding classroom and research space and doubling the number of housing units.

Khosla previously served as Dean of the College of Engineering and Philip and Marsha Dowd University Professor at Carnegie Mellon University. At Carnegie Mellon, he rose through the ranks from his first position as Assistant Professor in 1986 to his appointment as Dean in 2004. From 1994 to 1996, he also served as a Defense Advanced Research Projects Agency (DARPA) Program Manager in the Software and Intelligent Systems Technology Office, Defense Sciences Office and Tactical Technology Office, where he managed advanced research and development programs.

Khosla is an elected member of the American Academy of Arts and Sciences, National Academy of Engineering and the American Society for Engineering Education. He is a Fellow of the Institute of Electrical and Electronics Engineers, the American Society of Mechanical Engineers, the American Association for Advancement of Science, the American Association of Artificial Intelligence, the Indian Academy of Engineering and the National Academy of Inventors. He is an Honorary Fellow of the Indian Academy of Science. Khosla is also the recipient of numerous awards for his leadership, teaching, and research, including the 2012 Light of India Award, a Lifetime Achievement Award from the American Society of Mechanical Engineers, and the George Westinghouse Award for contributions to improve engineering teaching. In 2012, he was named one of the 50 most influential Indian-Americans by SiliconIndia.

We are building a more inclusive and equitable community at the Jacobs School of Engineering

Diversity is essential to innovation. The UC San Diego Jacobs School of Engineering has launched a Student and Faculty Racial Equity Task Force and is building on campus-wide initiatives as it works to ensure that all engineering and computer science students, faculty and staff can thrive and innovate.

San Diego, Calif., Oct. 13, 2020 -- Earning a degree in engineering or computer science is tough, even in the best of circumstances. Of the students in the U.S. that enroll in an engineering undergraduate program, only a third will graduate in four years, according to the American Society for Engineering Education.

For students facing one or more intersecting issues such as systemic racial discrimination, economic hardship, lackluster K-12 opportunities inside and outside the classroom, limited or no family experience with college, and a myriad of other challenges or barriers, the path to an engineering or computer science degree is often even more challenging.

For engineers and computer scientists who aspire to become professors, the path remains challenging and competitive. Aspiring professors who are traditionally underrepresented in engineering and computer science encounter additional challenges. The intersecting issues faced while earning a first degree in engineering remain, and often intensify, during graduate school, one or more postdocs, the academic job market, a job offer as a tenure-track professor, and tenure.

This year, the reality of these intersecting problems in engineering and computer science is getting much deserved renewed attention as part of a larger reckoning with systemic racism in the United States.

In this light, the University of California San Diego has launched multiple campus initiatives including two new efforts to advance faculty diversity, and a forthcoming NSF-funded effort to study bottlenecks and barriers in the computer science undergraduate pipeline. (Christine Alvarado, Associate Dean for Students and a computer science professor at the Jacobs School is part of this project. More to come in the future on this effort.)  

The UC San Diego Jacobs School of Engineering community is building on this work through targeted and complementary efforts. In particular, the Jacobs School is stepping up to assess and improve its efforts to create equitable learning and working environments for students, faculty, and staff. The Jacobs School is paying particular attention to equity for Black students and faculty, and also more broadly to all students and faculty in traditionally underrepresented groups in engineering, including LatinX, Native Americans, women, and LGBTQ+.

To listen, reflect and then move forward, the UC San Diego Jacobs School of Engineering launched the Student and Faculty Racial Equity Task Force on October 1, 2020.

"We’re committed to seeing this through and doing what’s right,” said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. "One first step to addressing racial equity issues is to really listen. It's unacceptable to be blind to the issues and claim to be faultless. Every engineer knows you can't solve a problem without first acknowledging it."

With critical input and guidance from Black students and other students of color, Christine Alvarado and Karen Christman, who are both professors and Associate Deans at the UC San Diego Jacobs School of Engineering, led the creation of the Student and Faculty Racial Equity Task Force. The task force also includes two student affairs staff members, one who works with graduate students and the other undergraduates; a representative from the Jacobs School's IDEA Engineering Student Center; a faculty representative from each department; and the Jacobs School Faculty Equity Advisor.

Crucially, four Jacobs School students who have been selected as the inaugural class of Racial Equity Fellows through a new project created by Dean Albert P. Pisano, have been invited to join the task force. These students are Muno Ogelohwohor, an undergraduate electrical engineering student and president of the National Society of Black Engineers chapter at UC San Diego; Laura Gutierrez, an undergraduate environmental engineering student, the president of the UC San Diego chapter of the Society for Hispanic Professional Engineers (SHPE) and an IDEA Scholar; Maya Rowell, a bioengineering PhD student and member of the Bioengineering Diversity Council; and Sergio Suarez, a structural engineering PhD student.

Learn more about these students here. 

Jacobs School staff are also critical to culture change within the school. The Jacobs School will launch a racial equity staff initiative in Winter Quarter 2021. This initiative will leverage the materials presented through the Chancellor's 21 Day Anti-Racism Challenge as a starting point and evolve from there. All staff are welcome to join, and Jacobs School staff who have been certified as LEAD Fellows (Tana Troke Campana, Gennie Miranda, and Jesse DeWald) will help get the initiative going. More information to come.

Student and Faculty Racial Equity Task Force

In the context of engineering and computer science education and research, equity means providing students, staff and faculty with the resources they need to succeed. Part of the mission of the Jacobs School Racial Equity task force will be to develop a comprehensive understanding of the existing programs and resources in place to do this, before suggesting solutions where gaps exist.

This will help the Task Force understand where the Jacobs School is now regarding a series of important issues including improving retention and time-to-degree for Black, Latinx and Native American students, and recruitment and retention of faculty from these same underrepresented groups.

"We are taking stock of where the Jacobs School stands both in terms of statistics and culture," said Christine Alvarado, who is Associate Dean for Students and a computer science professor at the Jacobs School. "We will be looking at how the Jacobs School compares, in terms of student and faculty diversity, to state and national statistics, and setting concrete targets for where the Jacobs School wants to be in 2025."

Once this group has a statistical baseline and also a diversity of qualitative accounts of the state of the Jacobs School, the Task Force will make concrete suggestions, with specific timelines, for strengthening what's working and addressing what's not working.

With the Racial Equity fellows at the table, the student experience will be addressed thoroughly. Student and faculty diversity are, of course, deeply interrelated. The UC San Diego campus recently announced a 10-12 person STEM cluster hire focused on racial/ethnic disparities in STEM fields with a significant focus on the Black Diaspora and African American communities. The Jacobs School is deeply engaged in this effort.

"The experiences of being a part of a shared lab, a larger research group, and an academic department are critical for any faculty member. But as an academic community, we have the added responsibility to make sure the environments we create and sustain are open and supportive for our diverse faculty. This is part of what it means to take equity seriously. We are looking at all these issues all across the Jacobs School," said Karen Christman, who is Associate Dean for Faculty Affairs and Welfare and a bioengineering professor at the Jacobs School.

When it comes to recruiting and retaining diverse faculty, the research is increasingly pointing to the importance of widespread institutional awareness of the current statistics. "Creating that awareness and then building on it is a priority," said Christman. "If an institution is not collectively aware of racial disparities, especially when it comes to faculty, it's much harder to correct them."

This new task force is not by any means the Jacobs School's first foray into student and faculty diversity issues. On the student side of things, the IDEA Engineering Student Center, and the student-focused centers that preceded IDEA, have been supporting undergraduate students at the Jacobs School, with a particular focus on students from groups underrepresented in engineering—including women, Black, Latinx and Native American students—for years. The IDEA Center is marking its 10th year in 2020-2021. The IDEA Engineering Student Center runs popular summer prep and mentorship programs, peer-led engineering learning communities, support for student diversity organizations, and more. Read more here. 

“The IDEA Engineering Student Center is here to foster an inclusive and welcoming community, increase retention rates, and promote a sustainable culture of academic excellence among all engineering students at UC San Diego,” said Olivia Graeve, a professor in the Department of Mechanical and Aerospace Engineering and faculty director of the IDEA Center.

The Jacobs School's Department of Computer Science and Engineering is also a leader in efforts to strengthen department culture and celebrate and support diversity and departments and centers across the school are making important progress as well.

The Jacobs School and UC San Diego are working together to extend this inclusive culture to the entire campus community of students, alumni, staff and faculty.  Any goals and actions recommended by the Task Force will be guided by the core tenants of UC San Diego’s Strategic Plan for Inclusive Excellence: access and success, climate and accountability. Jacobs School is working with the Office for Equity, Diversity, and Inclusion at UC San Diego on these and other projects including the accountability process, the Black Academic Excellence Initiative, and Latinx/Chicanx Academic Excellence Initiative.

"Diversity is essential to innovation," said Pisano. "We need innovators from every walk of life.”

Introducing the 2020 Jacobs School Racial Equity Fellows


San Diego, Calif., Oct. 13, 2020 -- Four engineering students with a demonstrated commitment to racial equity have been selected as the inaugural cohort of the UC San Diego Jacobs School of Engineering Racial Equity Fellows. These students, representing undergraduate and graduate perspectives from four different engineering departments, will serve as student advocates on the recently launched Jacobs School Student and Faculty Racial Equity Task Force, bringing student concerns and suggestions to the group tasked with making the Jacobs School of Engineering a truly inclusive community.

 "We’re committed to seeing this through and doing what’s right,” said Albert P. Pisano, dean of the Jacobs School of Engineering. "One first step to addressing racial equity issues is to really listen. It's unacceptable to be blind to the issues and claim to be faultless. Every engineer knows you can't solve a problem without first acknowledging it."

The students receive a $500 stipend for the yearlong fellowship and will participate in the Jacobs School Student and Faculty Racial Equity Task Force.

One of the first tasks of the Task Force is to take stock of where the Jacobs School stands in terms of both intangibles such as school climate and also develop metrics on current representation, retention and time-to-graduation for Black, Latinx, Native American, Asian and white students and faculty at the Jacobs School and how that compares across the campus, state and the country. This will help the Task Force understand where we are now, and how that compares at state and national levels. The next steps will be to develop and deliver on plans with specific outcomes and timelines.

"I am proud to introduce our first cohort of Racial Equity Fellows, and I am grateful for their openness and honesty in telling it like they see it," said Pisano.

Jacobs School 2020 Racial Equity Fellows

Laura Gutierrez: Laura Gutierrez is an undergraduate environmental engineering student, the president of the UC San Diego chapter of the Society for Hispanic Professional Engineers (SHPE), and an IDEA Scholar. She wanted to be involved in the Racial Equity Task Force to form a more welcoming culture for students from diverse backgrounds.

“There have been things that didn’t sit well with me while attending UC San Diego, and as president of SHPE I think that’s put me in a spot where I could have an impact to change the culture of the Jacobs School of Engineering,” Gutierrez said. “I want students after me to feel like they’re in a more welcoming kind of environment.”

For example, she said many students felt a lack of empathy from school faculty, staff and administrators in the wake of George Floyd’s murder and the resulting protests in the weeks leading up to finals week. One possible solution she’ll bring to the table is the Jacobs School hosting workshops on emotional intelligence and student support for faculty and staff who want to participate. Creating an environment where students feel comfortable letting faculty know about problems they’re facing is one place Gutierrez thinks could be a good start in helping students bring their whole selves to the university.

Odemuno (Muno) Ogelohwohor: Muno Ogelohwohor is an undergraduate electrical engineering student and president of the National Society of Black Engineers chapter at UC San Diego. As a Racial Equity Fellow, she hopes to find ways to increase the Black student population at the Jacobs School, and better support those students through to graduation with engineering degrees. She also sees an opportunity to increase the school’s representation of Black students, and do a better job of staying connected with alumni.

“When you walk through campus and you see all these banners and stuff, you barely see any Black people, and when you do it’s usually an arts or social sciences student,” she said. “That's something I think we need is more representation, especially within engineering. Even when you're walking through Jacobs Hall you barely see any photos of Black students anywhere, in any of the pictures. So you kind of don't really feel like you belong, but a part of you wants to belong.”

Ogelohwohor would also like to change how the diversity student organizations are viewed, which might also have long term positive consequences.

“What we're trying to do is kind of change how we not only recruit folks within the Jacobs School, but change the perception that because we're the National Society of Black Engineers folks don't think they can join if they're not Black or engineers. “That’s something we’re trying to demystify within the Jacobs community and the Black in STEM community at UC San Diego as a whole, and also for our allies who support our mission and vision.”

Maya Rowell: Maya Rowell is a bioengineering PhD student, and a member of the Bioengineering Diversity Council. She wanted to participate in the Racial Equity Task Force to share her desire to see more diverse faculty and staff within the Jacobs School. She’d also like to explore the possibility of more dedicated and well publicized resources for students from backgrounds underrepresented in engineering, for example a space for students of color.

“There's the Black Resource Center, but it's all the way across campus and not many people on this side of campus know about it or have time to go over there,” Rowell said. "And some people don’t do thorough research into the resources available for them at UC San Diego, so I wish that was more available so it doesn't need to be searched for so intensely."

Small steps like this would go a long way to making minority students feel welcome and accepted, she said.

Sergio Suarez: Sergio Suarez is a PhD student in the Department of Structural Engineering. He wanted to serve as a Racial Equity Fellow after witnessing the recent escalation in racial tensions and discrimination across the country. Some of the ideas he plans to share with the Task Force include actively working to increase the cultural and racial diversity among guest speakers; hosting info sessions to be sure students, staff and faculty are all aware of the university’s harassment and discrimination policies and how to report incidents of abuse; and to organize specific anti-racism workshops to start to tackle some of the more systemic issues.

Part of his decision to study at the Jacobs School was based on the diverse faculty he encountered, an attribute he’d like to see receive increased attention.

“To see well-renowned faculty from a variety of backgrounds leading innovative research was quite inspiring,” he said.

Celebrating 10 years of IDEA Engineering Student Center success

Students in the Transfer Prep summer program, run by the IDEA Engineering Student Center.

San Diego, Calif., Oct. 13, 2020 -- This fall marks the 10th year of the IDEA Engineering Student Center, one of the cornerstones of student life at the UC San Diego Jacobs School of Engineering. In the past decade, the IDEA— Inclusion, Diversity, Excellence, Achievement—Engineering Student Center has supported thousands of students through to graduation through its various programs, including summer prep and mentorship programs, peer-led engineering learning communities, support for student diversity organizations, and more.

The IDEA Engineering Student Center’s mission is to support all students on the challenging path of an engineering and computer science education at UC San Diego, with specific programs that build community, and provide academic and peer support for students traditionally underrepresented in engineering and computer science including Black, Latinx and Native American students, women, first generation college students, LGBTQ+ students, and low-income students.

Students say IDEA Center support and programming has been critical to their choosing to stay in engineering majors, and finding the resources they needed to thrive.

“My early undergraduate years were really difficult,” said Gladys Ornelas, a first generation college student who earned her bachelor’s degree in bioengineering at UC San Diego in 2016 and is currently working toward her PhD in bioengineering, also at UC San Diego.  “It was through IDEA that I learned about all of these programs that helped me. It’s because of IDEA that I met some of my closest mentors—they were graduate students at the time and helped me find a research position, which is a big part of why I decided to pursue graduate school.”

The IDEA Center was started in fall 2010 with a goal of supporting undergraduate students at the Jacobs School, with a particular focus on students from groups underrepresented in engineering. In 2010, Jacobs School faculty, staff, students and industry partners worked together to create and implement evidence-based programs meant to provide the community and resources for these undergraduate students to succeed through to graduation.

“The IDEA Engineering Student Center is here to foster an inclusive and welcoming community, increase retention rates, and promote a sustainable culture of academic excellence among all engineering students at UC San Diego,” said Olivia Graeve, a professor in the Department of Mechanical and Aerospace Engineering and faculty director of the IDEA Center.

The IDEA Center is home to many programs meant to accomplish these goals—Jacobs Undergraduate Mentorship Program, the Summer Engineering Institute, Engineering Learning Communities, the Engineering Overnight Program, and workshop series on both technical and career advice topics. The IDEA Center staff also run the decade-old flagship IDEA Scholars program—for students underrepresented in engineering-- and the newer ACES Scholars program—for low-income students.

IDEA Scholars participate in the Summer Engineering Institute before their freshman year, and then follow an academic enrichment plan including one-on-one mentoring with IDEA Center staff, community discussions, peer mentoring, and involvement in a student organization or research lab. IDEA Scholars get priority access to scholarships and internships, a well as networking opportunities with local companies and mentoring from Jacobs School alumni and faculty. The IDEA Scholars program serves as a model for the ACES Scholars program, which serves low-income students.

“I would definitely say that the IDEA Scholars program was helpful, especially because it kind of gave us early access to the engineering learning communities and that tutoring really did help me with my classes and kind of transitioning myself to college,” said Laura Gutierrez, an environmental engineering student, IDEA Scholar and Jacobs School Racial Equity Fellow (link). “Being an IDEA Scholar and being part of the Summer Engineering Institute did play a big role in where I am now. It was the mentors that I met during the Summer Engineering Institute who pushed me to join SHPE [Society of Hispanic Professional Engineers], and then it was kind of just the cycle of like if that hadn't happened, then this other thing wouldn’t have happened.”

And data shows that the program works. The 5-year graduation rate of underrepresented minority students from the original 2011 cohort of IDEA Scholars was 21% higher than that of their non-IDEA Scholar engineering freshmen peers from underrepresented student groups who were admitted at the same time. Furthermore, for all cohorts of IDEA Scholars since the program’s start, underrepresented minority students participating in the program have persisted in engineering at higher rates than all other underrepresented students in their respective cohorts. Among the first seven cohorts of IDEA Scholars, underrepresented minority students saw an average 11% higher retention rate by the final quarter of their third year.

 “We can see that the IDEA Center’s academic programs and avenues for community building are working,” said Gennie Miranda, director of operations for the Center. “We are excited to celebrate 10 years of success with our alumni and students this year, sharing their stories of where they are now.”

The IDEA Center is planning to host several virtual events to celebrate a decade of student success, including a panel with founding faculty director Carlos Coimbra and current faculty director Olivia Graeve, as well as virtual celebrations of their alumni’s successes.

“While we celebrate the strides we’ve made in the last 10 years, we can also see that the work of the IDEA Center alone isn’t sufficient to realize our goal of an equitable Jacobs School,” Graeve said. “We’re looking forward to being involved in the recently launched Jacobs School Racial Equity Task Force and campus-wide initiatives to continue to push for a Jacobs School and a UC San Diego that is more reflective of our broader community.”

Broadening horizons in a pandemic

A word cloud that shows some of the universities attended by the nearly 800 students participating in the Zoom REU. 

San Diego, Calif., Oct. 12, 2020-- More than 1,200 students from around the world were able to gain experience, advice and insight into their field this summer thanks to the expansion of two previously in-person only summer research programs at the UC San Diego Jacobs School of Engineering. The Biomaterials Research Experience for Undergraduates (REU) program which typically hosts 10 students in person, was expanded to accommodate nearly 800 students from 10 countries and 31 states. The Enlace binational research program expanded from 120 students to accommodate 450 students from the US and Mexico.

Traditionally, bioengineering professor Adam Engler and research scientist Roberto Gaetani host about a dozen students each summer for a paid Biomaterials Research Experience for Undergraduates program funded by the National Science Foundation. The students conduct research in various labs on campus focused on tissue engineering, nanoparticles for drug delivery, and bioinspired materials, for example, and also participate in a GRE prep course, research development workshops and field trips. 

Meanwhile, mechanical engineering professor Olivia Graeve has hosted upwards of 100 students on campus for the past seven summers through her Enlace program, bridging the US-Mexico divide through STEM research. In that program, high school and college students from both sides of the border are partnered as they conduct research together, attend college and graduate school prep workshops together, and live in the dorms together.

Instead of cancelling the programs when it became clear in the spring that in-person options would be limited, both Engler and Graeve immediately went to work to transition to virtual options, opening up the rosters to many more students from around the world than were previously able to participate.

Zoom REU

Ana Cristina Corona-Garza, a bioengineering undergraduate student at Tecnologico de Monterrey and a Zoom REU participant.

“Right now I’m in Monterrey Mexico, which is in the northern part of Mexico just a little bit south of Texas,” said Ana Cristina Corona-Garza, one of the 800 students who took part in the virtual Biomaterials REU program. She’s a bioengineering undergraduate student at Tecnologico de Monterrey. “I heard about the Zoom REU opportunity because one of my professors put it on his Facebook and I was like oh that sounds cool, you know I really don’t have anything to do this summer. It’s been a great experience. Thanks to the Zoom REU I got a better perspective about what options are out there and what I could do as an undergraduate.”

Same goes for Jacqualyn Washington, a biomedical engineering student at Rowan University, who found her summer plans dashed by the COVID-19 pandemic, but still wanted to somehow gain experience and career advice before she entered her senior year of college.

“As soon as the pandemic happened, everything shut down, no one was able to do anything,” she said. “I was so flustered, and lost. That’s a good way to describe it.

“Through the REU, I felt like I really got a firsthand experience on the opportunities available on the other side of the nation,” she added. “We had a session where we talked to industry representatives and hearing their stories we learned that everybody’s path isn’t straight and narrow, so it was nice to hear that it’s ok to take a year off to make sure you have everything you need before going into academia.”

For UC San Diego chemical engineering student Tina Reuter, the REU helped her gain clarity on her next steps after she graduates. 

“I signed up because it was so convenient since the sessions were recorded, which was nice because I was also taking classes this summer,” she said. “It was great to have this the summer before my junior year to help me figure out do I want to go to grad school, do I want to go into industry. I think that was the biggest thing that helped me, was hearing other peoples’ experiences, what they did, whether it’s a masters, or industry or even an MBA.”

Jacqualyn Washington, a biomedical engineering student at Rowan University and Zoom REU participant.

In addition to panels with biotech industry representatives and current bioengineering graduate students, the REU participants also heard directly from many biomaterials faculty at UC San Diego about their field of study and their path to professorship. In all, the program featured 25 hours of programming in 19 sessions over eight weeks. A highlight for many students was just getting to connect with so many other students interested in biomaterials from around the world.

“It was really great that there was a lot of diversity in the group,” said Corona-Garza. “Actually a few of the Spanish-speaking people from the group organized ourselves and made a WhatsApp group, so there are 26 of us from around the world—Colombia, Peru, Mexico, the US—that have been talking there.”

While Engler is excited to offer the in-person research experience again when he’s able, he said the response to the virtual program was so overwhelming that he hopes to continue to offer it in the future.

 “I think that becoming an open program was the right decision in the pandemic,” he said. “So many students lost their jobs, internships, or research experiences as a result of the pandemic, and I don’t think that we would have felt right in keeping the exclusivity of our small program with 10 students. Next summer we will likely keep as much of our program online to expand opportunities for all students, even if we are able to offer in-person experiences as well.”

Building Bridges through Zoom

Since Graeve wasn’t able to offer students the hands-on research experience that is typically a key component of Enlace, she decided instead to host weekly college and graduate school workshops to prepare high school participants to apply to college, and undergraduate students to apply for graduate school. 

UC San Diego chemical engineering student Tina Reuter.

For Jessica Tortoledo, a senior nanotechnology student at the National Autonomous University of Mexico, the Enlace program helped her not only polish her graduate school application, but firm up her future plans. 

“Because of this program I will apply to a PhD at UC San Diego in materials science and engineering,” said Tortoledo, who participated in Enlace in person last year, and found it so meaningful she wanted to join this virtual experience as well. “Initially, I was going to apply to a master´s program at a different university, but I decided to go straight into PhD because I was able to chat with PhD students through Enlace and that gave me a different perspective.”

For Graeve, the key component of Enlace has always been developing these budding friendships between aspiring scientists and engineers on both sides of the border, with a goal of building binational bridges through STEM. Would that still happen in a virtual setting? 

 “Besides all the tools we received in the program, what I enjoyed the most was the connections we were able to create between the participants despite it being a virtual event,” said Tortoledo. “I particularly enjoyed the last session because it had a student panel, and UC San Diego students talked about their experiences with grad school. I got so motivated that I finished my statement of purpose that night.”

UC San Diego Launches Institute for Materials Discovery and Design

San Diego, Calif., Oct. 9, 2020 -- Climate change, public health and equal access to food and water are some of the biggest challenges facing humanity--and materials science can help provide solutions for them all. That was the message researchers shared during the launch of the Institute for Materials Discovery and Design (IMDD) at the University of California San Diego, held virtually Sept. 29.

The IMDD is a collaboration between the Jacobs School of Engineering and Division of Physical Sciences at UC San Diego. Its goal is to leverage researchers’ cross-disciplinary expertise to discover, design and characterize advanced materials needed to address global challenges. This materials work has applications in developing zero- and low-carbon energy and transportation systems; cost-effective healthcare solutions; advances in sustainability; and next-generation information technologies. 

Stanley Whittingham was one of the recipients of the 2019 Nobel Prize in Chemistry for his work on Lithium ion batteries. He gave the keynote speech for the Institute for Materials Discovery and Design.

“We owe it to the next generation to help solve some of the world’s most pressing problems,” said Stanley Whittingham, the keynote speaker for the IMDD launch and a 2019 Nobel Laureate for his work as co-inventor of Lithium-ion batteries. “Materials science can help humanity.”

The IMDD is the ideal approach to do this kind of high-impact research, because it brings together students from different disciplines and allows them to move between research groups in chemistry, physics, engineering and more, Whittingham also said. 

“The most exciting research is done at the interface of different disciplines,” he said. “Science knows no boundaries.” 

UC San Diego Chancellor Pradeep K. Khosla echoed this. 

“ Cross-functional collaboration drives the success of our students, faculty and researchers across every division and every school of this university,” he said. “The work in materials science that is happening at UC San Diego is beyond innovative. It’s revolutionary. The IMDD will continue that tradition and accelerate collaboration, exploration and changemaking breakthroughs. ”

Professor Shirley Meng, in the UC San Diego Department of Nanoengineering, is the director of the new institute.

Materials have always defined the ages of human history, first by name, then by implication, said IMDD Director Shirley Meng, who is also a professor in the Department of Nanoengineering at the Jacobs School. For example, the Industrial Revolution would not have been possible without coal and steel; and the information age without semiconductors. It is time for researchers to discover and create the materials that will define the Anthropocene, she added. “We did not get out of the Stone Age because we ran out of stones,” said Meng.

Researchers at UC San Diego are uniquely positioned to do this because the campus, along with industry and government partners, have invested in people and cutting-edge tools for the past 15 years, Meng said. For example, UC San Diego has one of the highest resolution transmission electron microscopes in the world, which is still being used by researchers  during the COVID-19 pandemic. 

What’s more, the campus has always focused on taking discoveries from the lab into the real world. “Entrepreneurship is our DNA,” Meng said, noting that nearly 800 companies have been spun out of UC San Diego in it’s 60-year history.

One Meng's former students, Jungwoo Lee, co-founded South 8 Technologies, a company that develops liquefied gas electrolytes for next-generation Lithium batteries. Batteries fitted with this technology have many advantages including working at extreme temperatures, from the cold of space to the heat of Death Valley. “We are not letting something as simple as pressure get in the way of materials science innovation to power the future,” Lee said.

The lead team that secured a $18M NSF grant for materials science at UC San Diego: from left: professors Tod Pascal, Andrea Tao, Jon Pokorski, Nicole Steinmetz, Michael Sailor, Shirley Meng and Stacey Brydges.

$18M NSF grant for a Materials Research Science and Engineering Center

The IMDD’s research efforts are buttressed by an $18 million grant from the National Science Foundation, awarded in September of this year for the creation of a Materials Research Science and Engineering Center here on campus, said IMDD co-director Michael Sailor, who is a professor in the Division of Physical Sciences. 

“We can harness computational power to design materials from the atom up,” Sailor said. “We can also harness tools used in biotechnology to develop new materials.” 

The former MRSEC research effort is led by nanoengineering professors Andrea Tao and Tod Pascal; the latter by nanoengineering professors Nicole Steinmetz and John Pokorski.

Making materials from the ground up

Tod Pascal, a mechanical engineering professor and materials science expert, co-leads predictive assembly efforts. 

“What if we could make any and every material that we ever wanted?” Pascal asked

That is the goal he and fellow researchers, focusing on what is called predictive assembly, are working towards. Essentially, they are trying to better understand the fundamental energy landscape for small building blocks, figuring out how their surface chemistries and their shapes determine how and where they stick together. "Such detailed knowledge is critical," Pascal noted, "because it determines how these building blocks self-organize to form large scale, complex materials." 

To gain this unprecedented insight, researchers will first use powerful supercomputers and quantum theory to learn about these materials. The predictions from these calculations will then be tested and validated by materials chemists and engineers working hand-in-hand with the theorists. "We have an amazing team of computational folks, working at the quantum to the mesoscopic level, people who are experts at manipulating the atomic structure of nanomaterials and characterizing these changes using high resolution spectroscopy and microscopy. This is a one-stop shop for materials design and discovery,” Pascal added. By employing this scientific arsenal, researchers will be able to build materials that can adapt to their environment and materials with properties that change in time and in response to stimuli such as light. 

“It’s going to revolutionize material science,” Pascal added.

Plant viruses become living materials

Nicole Steinmetz, a professor of nanoengineering, works with plant viruses to create new materials.

Meanwhile, research in living materials is using the tools of the biotechnology revolution, such as genetic engineering and synthetic biology, to build new classes of materials with new kinds of abilities. For Steinmetz, that means working with plants and plant viruses. These plant viruses are harvested and repurposed as nanoparticles that fire up the immune system in mammals to attack tumors and metastases. She is also investigating how to add electronic viruses to plant tissue to create plant cyborgs that can be used for sensing molecules. “Plant viruses are scalable,” she said. “When you need more, you grow more plants.”  

Graduate program

Many of these research goals require training students to be the researchers of tomorrow, a task that will be handled by UC San Diego’s materials science and engineering graduate program, led by Prab Bandaru, a professor in the UC San Diego Department of Mechanical and Aerospace Engineering. The program includes about 100 faculty and 200 graduate students. “We are getting students together and giving them a common vocabulary,” Bandaru said. 

Hayley Hirsch is one of those students and part of Meng’s research group. 

“It is clear that there is immense passion for materials science advancement at UC San Diego,” said Hirsch when asked about the IMDD launch event. “Both the diversity of the people involved in IMDD and the resources it provides are a clear win for UC San Diego and the whole materials science field.”

Nobel Laureate Whittingham had a few words of advice for Hirsch and other graduate students: “Be willing to take risks,” he said. “What you really need are smart ideas.” 

Two UC San Diego Researchers Receive NIH High-Risk, High-Reward Awards

San Diego, Calif., October 6, 2020 -- Two University of California San Diego researchers have received prestigious awards through the 2020 National Institutes of Health (NIH) High-Risk, High-Reward Research Program.

These awards, supported by the NIH Common Fund, were created to fund highly innovative and unusually impactful biomedical or behavioral research proposed by extraordinarily creative scientists.

Sally Baxter, an assistant professor of ophthalmology and biomedical informatics.

Sally Baxter, an assistant professor of ophthalmology and biomedical informatics at the Shiley Eye Institute and Viterbi Family Department of Ophthalmology at UC San Diego Health, was awarded the Early Independence Award. This award supports exceptional junior scientists, allowing them to move immediately into independent research positions.

Duygu Kuzum, a professor of electrical and computer engineering in the UC San Diego Jacobs School of Engineering, was awarded the New Innovator Award. This award supports exceptionally creative early career investigators who propose innovative, high-impact projects in the biomedical sciences.

The High-Risk, High-Reward Research Program catalyzes scientific discovery by supporting research proposals that, due to their inherent risk, may struggle in the traditional peer-review process despite their transformative potential. Program applicants are encouraged to think “outside the box” and to pursue trailblazing ideas in any area of research relevant to the NIH’s mission to advance knowledge and enhance health.

Baxter, who received the Early Independence Award, will design and develop health information technology interventions to enhance risk stratification of patients with glaucoma, the leading cause of irreversible blindness globally. Baxter will tap into new approaches, such as big data analytics and predictive modeling using electronic health record data from the NIH All of Us Research Program, and new devices, such as 24-hour blood pressure monitoring using smartwatches, and measuring glaucoma adherence using electronic sensors.

Baxter joined the Shiley Eye Institute in 2020.  She completed her internship in internal medicine, residency in ophthalmology and fellowship training in biomedical informatics, all at UC San Diego. A particular focus of her work is finding new ways to leverage technology to improve care for special populations, such as older adults, individuals with disabilities and minority groups. 

Duygu Kuzum, a professor of electrical and computer engineering.

Kuzum, who joined UC San Diego in 2015, heads the Neuroelectronics Group in the university’s Department of Electrical and Computer Engineering. Her research applies innovations in nanoelectronics and materials science to develop new neurotechnologies to help better understand circuit-level computation in the brain. Her group develops fully transparent neural sensors based on 2D materials, which can be integrated with functional optical imaging. Kuzum’s research combines these innovative neural sensors with machine learning techniques to probe neural circuits with high spatial and temporal precision and to study circuit dynamics at the micro and macro scales. Her group also develops nanoelectronic synaptic devices for energy-efficient, brain-inspired computing. Her projects feature cross-collaboration across various fields, including the Department of Neurosciences and the School of Medicine at UC San Diego.

With funding from the New Innovator Award, Kuzum will work on creating electronic brain organoids, or “e-Organoids.” These are essentially brain tissues—formed by self-assembled, 3D structures generated from human stem cells—embedded with hundreds of individually controllable sensors.

Brain organoids are of great interest to researchers because they mimic the embryonic human brain, and thus potentially offer unprecedented opportunities for studying brain development and neuronal network dysfunctions underlying human brain diseases. They also provide an experimental platform for discovering and testing new drugs.

However, brain organoids have two key fundamental limitations: 1) they lack a functional interface that can enable researchers to monitor the activity of individual neurons and cell populations with high precision and resolution, and 2) they lack a natural brain microenvironment and blood vessels, which are critical for keeping cells in the organoids alive and healthy and enabling them to mature. Kuzum aims to overcome these challenges by creating e-Organoids that have a seamless electro-optical interface and can supply oxygen and nutrients to the cells. The ultimate goal is to create transplantable e-Organoids to restore degenerated or damaged brain regions in humans.

This 'squidbot' jets around and takes pics of coral and fish

San Diego, Calif., Oct. 5, 2020 -- Engineers at the University of California San Diego have built a squid-like robot that can swim untethered, propelling itself by generating jets of water. The robot carries its own power source inside its body. It can also carry a sensor, such as a camera, for underwater exploration. 

The researchers detail their work in a recent issue of Bioinspiration and Biomimetics

“Essentially, we recreated all the key features that squids use for high-speed swimming,” said Michael T. Tolley, one of the paper’s senior authors and a professor in the Department of Mechanical and Aerospace Engineering at UC San Diego. “This is the first untethered robot that can generate jet pulses for rapid locomotion like the squid and can achieve these jet pulses by changing its body shape, which improves swimming efficiency.”

This squid robot is made mostly from soft materials such as acrylic polymer, with a few rigid, 3D printed and laser cut parts. Using soft robots in underwater exploration is important to protect fish and coral, which could be damaged by rigid robots. But soft robots tend to move slowly and have difficulty maneuvering.

The research team, which includes roboticists and experts in computer simulations as well as  experimental fluid dynamics, turned to cephalopods as a good model to solve some of these issues. Squid, for example, can reach the fastest speeds of any aquatic invertebrates thanks to a jet propulsion mechanism. 

Their robot takes a volume of water into its body while storing elastic energy in its skin and flexible ribs. It then releases this energy by compressing its body and generates a jet of water to propel itself. 

At rest, the squid robot is shaped roughly like a paper lantern, and has flexible ribs, which act like springs, along its sides. The ribs are connected to two circular plates at each end of the robot. One of them is connected to a nozzle that both takes in water and ejects it when the robot’s body contracts. The other plate can carry a water-proof camera or a different type of sensor. 

Engineers first tested the robot in a water testbed in the lab of Professor Geno Pawlak, in the UC San Diego Department of Mechanical and Aerospace Engineering. Then they took it out for a swim in one of the tanks at the UC San Diego Birch Aquarium at the Scripps Institution of Oceanography. 

They demonstrated that the robot could steer by adjusting the direction of the nozzle. As with any underwater robot, waterproofing was a key concern for electrical components such as the battery and camera.They clocked the robot’s speed at about 18 to 32 centimeters per second (roughly half a mile per hour), which is faster than most other soft robots. 

“After we were able to optimize the design of the robot so that it would swim in a tank in the lab, it was especially exciting to see that the robot was able to successfully swim in a large aquarium among coral and fish, demonstrating its feasibility for real-world applications,” said Caleb Christianson, who led the study as part of his Ph.D. work in Tolley’s research group. He is now a senior medical devices engineer at San Diego-based Dexcom.  

Researchers conducted several experiments to find the optimal size and shape for the nozzle that would propel the robot. This in turn helped them increase the robot’s efficiency and its ability to maneuver and go faster. This was done mostly by simulating this kind of jet propulsion, work that was led by Professor Qiang Zhu and his team in the Department of Structural Engineering at UC San Diego. The team also learned more about how energy can be stored in the elastic component of the robot’s body and skin, which is later released to generate a jet. 


A new understanding of ultra long antibodies to advance vaccine research

San Diego, Calif., Oct. 5, 2020 -- The human body recombines different genes to make millions of disease-fighting antibodies. This genetic mixing and matching is essential to produce perfectly configured molecules that seek out and destroy dangerous pathogens.

As a result, each of us has around 100 million antibodies circulating through our bodies, poised to fight invaders. This huge antibody diversity is produced by three groups of genes: variable (V), diversity (D) and joining (J). VDJ recombination randomly selects one gene from each group and glues them together, generating the three-part VDJ genes that produce most antibodies. 

Understanding how these genes combine to form antibodies could inform new vaccines and other immune therapies. However, key aspects of antibody biology have remained mysterious, such as how ultralong antibodies are formed. 

Now, in a paper published in the journal Genome Research, scientists in the Department of Computer Science and Engineering at the UC San Diego Jacobs School of Engineering have answered this important question, solving a 30-year-old mystery.

“Standard antibody genes, formed by concatenating (linking) three genes, are critically important to our immune response,” said senior author Pavel Pevzner, Ronald R. Taylor Professor of Computer Science at UC San Diego. “However, the body also produces the longer, four-part variety, VDDJ through a tandem fusion of two D genes. Normal recombination signals link D genes with V and J genes but the classical recombination rule forbids linking any two D genes. So, how do these four-part antibodies even form?” 

First discovered in 1989, four-part antibody genes were initially viewed as harmless, and possibly useless, aberrations. However, in the last 10 years, researchers have shown ultralong antibodies, including D-D fusions, can deeply target HIV surface proteins, generating broadly neutralizing antibodies against the virus.

As a result, understanding VDDJ formation has become an important priority, part of an overarching effort to develop effective vaccines. But finding tandem D-D fusions in huge immuno-sequencing datasets has been a major computational challenge, as researchers must sift through multiple mutations to produce accurate results.

To solve the problem, Pevzner and coauthor Yana Safonova, a computer science postdoctoral researcher, relied on a recently developed computational tool, called IgScout, to find D-D fusions. Using this approach, they identified a distinct antibody formation process: short genomic segments called cryptic recombination signals that flank D genes and trigger tandem D-D fusions. The cryptic recombination make D genes look like V or J genes, enabling tandem D-D fusions. 

The study also showed these ultralong antibodies are much more prevalent than previously thought and have helped mammals fight disease for millions of years.

“Contrary to the previous assumption that tandem D-D fusions are rare events, our analysis shows about a quarter of ultralong antibodies, in disease-relevant antibody repertoires, may be generated through tandem fusions,” said Safonova. “These cryptic recombination signals are not limited to humans but are preserved over millions of years of evolution across multiple mammalian species. In other words, tandem D-D fusions are an important mechanism to generate ultralong antibodies.” 

Now that scientists understand how these antibodies form, they can use that knowledge to advance vaccine research.

“This paper solves the three-decade-old puzzle of aberrant tandem fusions in antibody formation,” said Pevzner. “These fusions contribute to broadly neutralizing antibodies that are important for ongoing vaccine development efforts.”



Pavel Pevzner and team unveil new algorithm designed for metagenome assembly in long-read DNA sequencing

Center for Microbiome Innovation Faculty Member Pavel Pevzner and research team unveil new algorithm designed for metagenome assembly in long-read DNA sequencing

San Diego, Calif., October 5, 2020 — Pavel Pevzner, who is a University of California San Diego computer science professor and faculty member of the UC San Diego Center for Microbiome Innovation (CMI), and a team of researchers at UC San Diego, the Dairy Research Center, St. Petersburg State University and the Bioinformatics Institute (St. Petersburg) unveiled in a paper published in Nature Methods, a new algorithm designed for metagenome assembly in long-read DNA sequencing. 

Studying complex microbial communities, such as bacteria in the human gut, is important to understand the mechanisms of various human diseases, and may help to discover new antibiotic treatments. Today, the standard short-read sequencing approaches provide only a limited view of the environmental bacteria, as the recovered bacterial genomes are highly fragmented. Long-read sequencing technologies have substantially improved the ability of researchers to sequence isolate bacterial genomes in comparison to previous fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. 

In “metaFlye: scalable long-read metagenome assembly using repeat graphs,” Pavel Pevzner and team unveil the metaFlye algorithm which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. Researchers were able to perform long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct over 60 complete or nearly-complete bacterial genomes. Additionally, they were able to demonstrate the long-read assembly of the human microbiomes, which enables the discovery of novel biosynthetic gene clusters that encode biomedically important natural products. 

Researchers were able to benchmark the metaFlye algorithm against existing state-of-the-art long-read assemblers using simulated, mock, and real bacterial community datasets. Results demonstrated that the recently introduced long-read technologies overcome limitations of the short-read sequencing, and the metaFlye algorithm is capable of reconstructing complete bacterial genomes from complex environmental communities, providing significant improvements over the other popular existing methods.

Additional co-authors include: Mikhail Kolmogorov, Derek M. Bickhart, Bahar Behsaz, Alexey Gurevich, Mikhail Rayko, Sung Bong Shin, Kristen Kuhn, Jeffrey Yuan, Evgeny Polevikov, and Timothy P.L. Smith.

The full paper is available in Nature Methods here.

About Center for Microbiome Innovation at University of California San Diego:
The UC San Diego Center for Microbiome Innovation leverages the university's strengths in clinical medicine, bioengineering, computer science, the biological and physical sciences, data sciences, and more to coordinate and accelerate microbiome research. We also develop methods for manipulating microbiomes for the benefit of human and environmental health. Learn more at cmi.ucsd.edu/ and follow @CMIDigest

UC San Diego COVID-19 Forecast Now Part of CDC Model

A schematic representation of the Global Epidemic and Mobility (GLEAM) model for the United States. The country is divided into census cells that are assigned to subpopulations centered around transportation hubs. The population layer describing the census cells is coupled with two mobility layers, the short-range commuting layer and the long-range air travel layer.
Courtesy of Nicole Samay, MOBS Lab, Northeastern University

San Diego, Calif., Oct. 2, 2020 -- A computational model that forecasts the number of COVID-19 deaths in the United States as a whole and in each state, which was developed by a team of researchers from the University of California San Diego and Northeastern University, is now part of the national mortality forecast issued by the Centers for Disease Control.

UC San Diego joins a roster of prestigious institutions who are included in the CDC’s prediction algorithms, including Harvard, Johns Hopkins and Notre Dame. Among the University of California, three institutions are part of the forecast: UC San Diego, UCLA and UC Merced.

“Our goal is to provide insights to policymakers as they make decisions about reopening,” said Yian Ma, an assistant professor at the UC San Diego Halicioglu Data Science Institute, who co-leads the UC San Diego modeling effort with Rose Yu, assistant professor in the UC San Diego Department of Computer Science and Engineering.

Currently, the model is predicting a steady increase in the number of deaths during flu season, without dramatic spikes. 

Ma and Yu are partnering with Matteo Chinazzi and Alessandro Vespignani, at the  Network Science Institute at Northeastern University, a research group that regularly consults about the pandemic for the CDC.

The UC San Diego-Northeastern model, called DeepGLEAM, is unique because it combines a physics-based model,  known as GLEAM with deep learning, a computing system made up of algorithms inspired by the way the human brain is organized. The hybrid model leverages rich data information about COVID 19 from the real world--for example when a person had been infected and where they have traveled.

Rose Yu, an assistant professor in the Department of Computer Science and Engineering, is one of the two researchers leading the UC San Diego modeling work.

“Combining the two is important,” said Yu, the computer scientist. The physics-based model is not good at handling uncertainty and unknowns in the data, for example how well people adhere to travel bans. That’s where deep learning comes in to help reduce uncertainty.   

Other research teams might have expertise in one area or the other. The UC San Diego-Northeastern team has experts in both. 

The experts

Yu is an expert in the nuts and bolts of deep learning and spatiotemporal modeling. She was an assistant professor at Northeastern University before joining UC San Diego. While at Northeastern, she worked with Vespignani. “She was our resident expert on machine learning and neural networks,” he said. “We thought she would be the perfect partner for this project.”

Yian Ma, an assistant professor at the Halicioglu Data Science Institute, co-leads the modeling effort at UC San Diego.

Ma is also a machine learning specialist, although his focus is on theory. He started working on the project right after a stint as a visiting scientist at Google Research. He and Yu asked Vespignani if it still made sense to work on a physics-deep learning hybrid forecasting model. Vespignani said yes. “So we thought: ‘we should get to work’,” Ma said. 

Vespignani is a well known physicist who leads the Network Science Institute at Northeastern. He and his team develop analytical and computational models for large-scale social, technological and biological networks. This allows them to model contagion and predict the spread of emerging diseases. He was profiled in The New York Times in March of this year for his work on predicting the spread of the coronavirus. 

Dongxia Wu, a graduate student in the UC San Diego Department of Electrical and Computer Engineering, took the lead on the deep learning day to day work. 

The model

The model Chinazzi, Ma, Vespignani and Yu developed is based on predictions from a physics-based  model using a wealth of data: death certificates, information about when the deceased contracted COVID-19 and their movements, as well as information about the various travel and opening restrictions from all 50 states. But based on this information, there is still a lot the researchers don’t know: for example, how well people adhere to restrictions. 

That’s where machine learning comes in. The algorithms and computational networks are able to handle uncertainty and make predictions. It’s tricky, Ma said, because researchers have to make sure they create their system to provide accurate and meaningful results while accounting  for uncertainty. “We want to get it right,” he said. 

For now, the model is most accurate one week out, and successively less so for two, three and four weeks.

“We want to make weekly forecasts, which can be useful to policy makers,” Vespignani said.

The CDC does use the data, which is available publicly, in a timely manner. But on average, the information you’d see today is a week old. 

Researchers’ next steps include creating forecasts for all counties in the nation, updated once a week. 

“And of course, we are always updating our model on the weekly basis to make it as accurate as possible,” Yu said. 


Robots to Help Children Touch the Outside World

UC team is developing better telepresence robots, equipped with robotic arms

San Diego, Calif., Oct. 2, 2020 -- A team of University of California researchers is working to improve telepresence robots and the algorithms that drive them to help children with disabilities stay connected to their classmates, teachers and communities. The effort is funded by a $1 million grant from the National Robotics Initiative at the National Science Foundation.

The project is unique in that the team is working with telepresence robots equipped with an arm, which will allow children at home to interact with the outside world by touch. These mobile tele-manipulator robots will also be equipped with cameras, microphones, a display and other sensors that will allow children to interact with people in places where they can’t usually go, especially schools. 

Even before COVID-19, there were over  2.5 million children in the United States who were unable to attend school in person due to medical conditions. The current pandemic has both increased this number and isolated them even further. 


The project team includes  professor Laurel Riek in the Department of Computer Science and Engineering and Emergency Medicine at University of California San Diego, and professors Veronica Ahumada-Newhart, Jacquelynne Eccles, and Mark Warschauer at the University of California, Irvine in the Schools of Education and Informatics.

"The robots we build on this project will provide an exciting, enabling technology for millions of people with disabilities and others who are isolated during the pandemic, especially children at high risk of infection," said Riek. 


Making a robotic arm available is key, Riek  added. “Children want to be able to touch the world. They want to be able to throw a ball, play games, and raise their hand in class.” 


UC Irvine’s Ahumada-Newhart has dedicated the past seven years to studying robot-mediated learning and inclusion, deploying telepresence robots in schools across the country. She  developed a framework for how to create a social telepresence for children via a robot, from both a theoretical and qualitative standpoint. Riek and her team will build new adaptive, accessible control systems  that will allow children to operate  the robot. 


Riek has  also  recently developed a system, JESSIE, which allows people with no prior programming experience to write complex, dynamic control software for robots using paper cards and taking a picture of them. This project will build on this work to create JESSIE-KIDS, which will enable controlling mobile telemanipulators in an inclusive and accessible way, to both support easily adapting the robots to meet the needs of different children, and also teach children programming concepts.  


This project’s focus is schools, which means that experiments will have to start once the COVID-19 pandemic is under control. But first, researchers will identify best practices and guidelines for the use of telepresence  in schools to best facilitate learning and social development in collaboration with key stakeholders. They will use this to inform the design of new inclusive interfaces and control modalities for homebound children to use the remotely-operated  mobile telemanipulator robots.  


They also will pioneer new inclusive robotics curricula to support children with disabilities entering the STEM workforce. This national robotics curriculum will be publicly available online and will feature introductory concepts in robotics as well as information about the evolving roles of robots in our society.


This project will yield new knowledge in multiple fields, including robotics, education, and healthcare. It will promote the progress of science by exploring how to make mobile telemanipulators accessible to people with disabilities. This work will also benefit society through insights into robot-mediated interaction, which can extend to other domains, such as telemedicine, telehealth, and others who experience barriers to remaining socially connected to their real-world communities in the physical world. 




DeepMind Gift Will Give a Boost to Machine Learning Graduate Students and Diversity Efforts at UC San Diego CSE

CSE alumnus Oriol Vinyals (M.A. ’09) is a principal scientist for DeepMind and is the brain behind some of the most important papers and ideas that have happened in artificial intelligence (AI)

San Diego, Calif., Oct. 2, 2020 -- UC San Diego Computer Science and Engineering (CSE) graduate students who are studying machine learning will receive additional support thanks to a generous gift from DeepMind, a London-based company leading artificial intelligence research and how it’s applied in the real world. UC San Diego alumnus Oriol Vinyals (M.A. ’09) is a principal scientist for the company. The gift, which contributes to the Campaign for UC San Diego, will also be used to enhance the department’s efforts to increase diversity. 

DeepMind will establish three fellowships for master’s students; those from cultural, racial, linguistic, geographic and socioeconomic backgrounds and genders that are currently underrepresented in graduate education in the field of machine learning will be encouraged to apply. The DeepMind Fellows will receive two-year fellowships that cover tuition along with a stipend, a travel grant and a DeepMind mentor. A one-time gift will be given to the CSE Diversity, Equity and Inclusion initiative.

DeepMind’s support will help strengthen the already notable reputation of CSE, currently ranked sixth in the world by csrankings.org (a metrics-based ranking for computer science institutions), and will further boost the upward trajectory of UC San Diego’s Jacobs School of Engineering, now the fifth-ranked public engineering school in the nation, according to the US News and World Report Ranking of Best Engineering Schools published in March 2020.

“To change the workforce, we must look not only at our exceptional student population but at prospective students who dream of being in the field of machine learning. DeepMind’s gift will help us to attract those students and launch them into successful careers,” said CSE Department Chair Sorin Lerner. 

“Beyond that goal, DeepMind’s philanthropic support enhances our department’s collective efforts to increase diversity in the field of computing,” Lerner said. “While always important, diversity, equity and inclusion has become a top priority for us over the last few years.” 

Obum Ekeke, education and university partnerships lead at DeepMind, said, “We’re delighted to strengthen our relationship with UC San Diego by establishing DeepMind fellowships at the university. We hope this scholarship gift will support graduate students—and we encourage those from groups currently underrepresented in AI and machine learning to apply—through not only through financial means but by providing mentors and networks to help them thrive.” 

“DeepMind’s generous gift is an investment in our most precious resource-- our students-- and a testament to their understanding that our current students are the engineers on whom we will depend in the future,” said Christine Alvarado, the associate dean of students for the Jacobs School. “It is in everyone’s best interest to see that all of our students have the opportunity to reach their full potential.” 

CSE’s Diversity, Equity and Inclusion initiative works to improve diversity, equity, and inclusion in the department and beyond. Here, students, staff and faculty participate in the inaugural “Celebration of Diversity” day last year.

CSE and DeepMind have another connection with alumnus Vinyals– he is the brain behind some of the most important papers and ideas that have happened in artificial intelligence (AI), including being a key contributor to machine translation that drives Google Translate and to the AlphaStar project where an AI defeated human professionals in a game of StarCraft. (Read more about Vinyals and his time at CSE in this story in the V6 issue of the CSE Alumni Magazine.) 

Vinyals said, “The time spent at UC San Diego was of great importance as I started doing research on natural language processing (NLP) during that time. I'm happy and glad that DeepMind is supporting the university, its students and diversity in our field."

Philanthropic gifts, like the gift from DeepMind, contribute to the Campaign for UC San Diego—a university-wide comprehensive fundraising effort concluding in 2022. Alongside UC San Diego’s philanthropic partners, the university is continuing its nontraditional path toward revolutionary ideas, unexpected answers, lifesaving discoveries and planet-changing impact. To support Computer Science and Engineering at UC San Diego’s Jacobs School of Engineering, visit: Give Now.

Researchers identify new factors for inflammation after a heart attack

Kevin King is the lead author of a paper published in Science Immunology Sept. 25.

San Diego, Calif., Sept. 30, 2020 -- A team of engineers and physicians at University of California San Diego and Massachusetts General Hospital published new work Sept. 25 in Science Immunology that provides new comprehensive single-cell datasets defining the immune response to a heart attack, from its origins in the bone marrow and its translational potential in the blood, to its diversification and regulation within the heart. They also discovered new immune cell types and regulatory mechanisms. 

In the hours and days after a heart attack, immune cells known as neutrophils and monocytes travel from the bone marrow, through the blood, and into the injured heart, where they diversify into specialized cell subsets that orchestrate repair, fibrosis and remodeling. 

Defining immune subsets has been challenging due to limitations of fluorescent antibody staining. The researchers, led by Professor Kevin King of the UC San Diego Jacobs School of Engineering and School of Medicine leverage single cell RNA-Seq technology to perform unbiased transcriptome-wide profiling of over 100,000 single cells from the heart, blood, and bone marrow at steady state and at several time points after a heart attack.

Inflammatory signaling after a heart attack was previously thought to result from immune cell interactions with biomolecules from dying cells in the heart. However, the UC San Diego team discovered that subsets of neutrophils and monocytes were pre-activated in the bone marrow before traveling to the distant heart.  These interferon-induced cells (IFNICs) express cytokines and chemokines that enhance inflammation and lead to cardiac dysfunction. 

The team found similar “priming” of neutrophils and monocytes in human blood, which they believe will enable personalized measurement of patient-specific inflammation after a heart attack. 

The team also discovered new regulators of the interferon response. They discovered a population of resident cardiac macrophages that negatively regulates the interferon response to a heart attack by expressing Nrf2-regulated genes. They also found increased bone marrow “priming” of the interferon response in mice lacking Tet2, a gene that when mutated in humans leads to increased cardiovascular events and mortality. 

Heart attacks underlie the most common cause of death in the US and the world. 

The myeloid type I interferon response to myocardial infarction begins in bone marrow and is regulated by Nrf2-activated macrophages

David M. Calcagno, Claire Zhang, Kevin R. King, UC San Diego Department of Bioengineering, Jacobs School of Engineering

Richard P. Ng Jr, Avinash Toomu, Kenneth Huang, Lor B. Daniels, Zhenxing Fu, Kevin R. King, Division of Cardiology and Cardiovascular Institute, UC San Diego School of Medicine

Aaron D. Aguirre, Ralph Weissleder, Massachusetts General Hospital/Harvard Medical School

Acute ischemic injury to the heart precipitates a strong inflammatory response including influx of myeloid cells expressing type I interferon–stimulated genes (ISGs). Calcagno et al. used single-cell RNA sequencing to probe the origin, evolution, and heterogeneity of this response in the first 4 days after myocardial infarction using human and mouse myeloid cells. Induction of ISG in myeloid cells was initially observed in bone marrow and blood. Post-infarct cardiac tissue in mice contained myeloid subsets with and without ISG expression and a steady-state macrophage population with Nrf2-dependent anti-inflammatory activity. On the basis of their findings, the authors developed an ISG score as a potential biomarker to assess how the vigor of type I interferon signaling influences clinical outcomes after a heart attack.




Material scientists learn how to make liquid crystal shape-shift

San Diego, Calif., Sept. 25, 2020 -- A new 3D-printing method will make it easier to manufacture and control the shape of soft robots, artificial muscles and wearable devices. Researchers at UC San Diego show that by controlling the printing temperature of liquid crystal elastomer, or LCE, they can control the material’s degree of stiffness and ability to contract--also known as degree of actuation.  What’s more, they are able to change the stiffness of different areas in the same material by exposing it to heat.

As a proof of concept, the researchers 3D-printed in a single print, with a single ink, structures whose stiffness and actuation varies by orders of magnitude, from zero to 30 percent. For example, one area of the LCE structure can contract like muscles; and another can be flexible, like tendons. The breakthrough was possible because the team studied LCE closely to better understand its material properties. 

The team, led by Shengqiang Cai, a professor in the Department of Mechanical and Aerospace Engineering at the UC San Diego Jacobs School of Engineering, details their work in the Sept. 25 issue of Science Advances

Researchers were inspired to create this material with different degrees of actuation by examples in biology and nature. In addition to the combination of muscle and tendon, researchers took cues from the beak of the squid, which is extremely stiff at the tip but much softer and malleable where it is connected to the mouth of the squid. 

“3D-printing is a great tool to make so many different things--and it’s even better now that we can print structures that can contract and stiffen as desired under a certain stimuli, in this case, heat,” said Zijun Wang, the paper’s first author and a Ph.D. student in Cai’s research group. 

Understanding material properties 

To understand how to tune the material properties of LCE, researchers first studied the material very closely. They determined that printed LCE filament is made of a shell and a core. While the shell cools off quickly after printing, becoming stiffer, the core cools more slowly, remaining more malleable. 

As a result, researchers were able to determine how to vary several parameters in the printing process, especially temperature, to tune the mechanical properties of LCE. In a nutshell, the higher the printing temperature, the more flexible and malleable the material. While the preparation of the LCE ink takes a few days, the actual 3D print can be done in just 1 to 2 hours, depending on the geometry of the structure being printed. 

“Based on the relationship between the properties of LCE filament and printing parameters, it’s easy to construct structures with graded material properties,” said Cai. 

Varying temperature to 3D-printing structures

For example, researchers printed an LCE disk at 40 degrees C (104 F) and heated it up to 90 degrees C (194 F) in hot water. The disk deformed into a conical shape. But an LCE disk composed of areas  that are printed at different temperatures (40, then 80 then 120 degrees Celsius, for example), deformed in a completely different shape when heated up. 

Researchers also 3D-printed structures made of two layers of LCE with different properties and showed that this gave the material even more degrees of freedom to actuate. Researchers also printed lattice structures with the material, which could be used in medical applications. 

Finally, as a proof of concept, the team 3D printed an LCE tube that they had tuned during 3D printing and showed that it could adhere to a rigid glass plate much longer when actuated at high temperatures, about 94 C (201 F), than a regular LCE tube with homogenous properties. This could lead to the manufacture of better robotic feet and grippers. 

The actuation of the material could be activated not just in hot water but also by infusing LCE with heat-sensitive particles or particles that absorb light and convert it to heat--anything from black ink powder to graphene. Another mechanism would be to 3D print the structures with electric wires that generate heat embedded in LCE. 

Next steps include finding a way to tune the material’s properties more precisely and efficiently. Researchers also are working on modifying the ink so the printed structures can be self-repairable, reprogrammable, and recyclable. 

Robots to Help Children Touch the Outside World

UC team is developing better telepresence robots, equipped with robotic arms

Two students communicate via a telepresence robot. 
Photo: UC Irvine

San Diego, Calif., Jan. 12, 2004 -- A team of University of California researchers is working to improve telepresence robots and the algorithms that drive them to help children with disabilities stay connected to their classmates, teachers and communities. The effort is funded by a $1 million grant from the National Robotics Initiative at the National Science Foundation.

The project is unique in that the team is working with telepresence robots equipped with an arm, which will allow children at home to interact with the outside world by touch. These mobile tele-manipulator  robots will also be equipped with cameras, microphones, a display and other sensors that will allow children to interact with people in places where they can’t usually go, especially schools. 

Even before COVID-19, there were over  2.5 million children in the United States who were unable to attend school in person due to medical conditions. The current pandemic has both increased this number and isolated them even further. 

The project team includes  professor Laurel Riek in the Department of Computer Science and Engineering and Emergency Medicine at University of California San Diego, and professors Veronica Ahumada-Newhart, Jacquelinne Eccles, and Mark Warschauer at the University of California, Irvine in the Schools of Education and Informatics.

"The robots we build on this project will provide an exciting, enabling technology for millions of people with disabilities and others who are isolated during the pandemic, especially children at high risk of infection," said Riek. 

Making a robotic arm available is key, Riek  added. “Children want to be able to touch the world. They want to be able to throw a ball, play games, and raise their hand in class.” 

UC Irvine’s Ahumada-Newhart has dedicated the past seven years to studying robot-mediated learning and inclusion, deploying telepresence robots in schools across the country. She  developed a framework for how to create a social telepresence for children via a robot, from both a theoretical and qualitative standpoint. Riek and her team will build new adaptive, accessible control systems  that will allow children to operate  the robot. 

Riek has  also  recently developed a system, JESSIE, which allows people with no prior programming experience to write complex control software for robots using paper cards. This project will build on this work to create JESSIE-KIDS, which will enable controlling mobile telemanipulators in an inclusive and accessible way, to both support easily adapting the robots to meet the needs of different children, and also teach children programming concepts.  

The researchers will be using Stretch, a robot manufactured by Hello Robot. Here CEO Aaron Edsinger poses with the bot. Photo courtesy of Hello Robot.

This project’s focus is schools, which means that experiments will have to start once the COVID-19 pandemic is under control. But first, researchers will identify best practices and guidelines for the use of telepresence  in schools to best facilitate learning and social development in collaboration with key stakeholders. They will use this to inform the design of new inclusive interfaces and control modalities for homebound children to use the remotely-operated  mobile telemanipulator robots.  

They also will pioneer new inclusive robotics curricula to support children with disabilities entering the STEM workforce. This national robotics curriculum will be publicly available online and will feature introductory concepts in  robotics as well as information about the evolving roles of robots in our society.

This project will yield new knowledge in multiple fields, including robotics, education, and healthcare. It will promote the progress of science by exploring how to make mobile telemanipulators accessible to people with disabilities. This work will also benefit society through insights into robot-mediated interaction, which can extend to other domains, such as telemedicine, telehealth, and others who experience barriers to remaining socially connected to their real-world communities. 

Engineering graduate students honored as Siebel Scholars

UC San Diego’s class of 2021 Siebel Scholars: (l-r) Juliane Sempionatto-Moreto, Haleh Alimohamadi, Dhruva Katrekar, Gabrielle Colvert, and Greg Poore.

San Diego, Calif., Sept. 23, 2020 --Five Jacobs School of Engineering graduate students pioneering tools to treat rare genetic disorders, studying microbes in cancer, developing noninvasive wearable biosensors, studying the physical principles underlying cell membrane deformation, and developing noninvasive methods for evaluating cardiovascular function, have been named 2021 Siebel Scholars. The Siebel Scholars program recognizes the most talented students in the world’s leading graduate schools of business, computer science, bioengineering and energy science. The students are selected based on outstanding academic performance and leadership, and each receive a $35,000 award toward their final year of study.

Three of these students are pursuing research through the UC San Diego Department of Bioengineering, while one conducts biomedical research through the Department of NanoEngineering and one in the Department of Mechanical and Aerospace Engineering. UC San Diego’s Department of Bioengineering was ranked the No. 1 bioengineering doctoral program in the nation according to the National Research Council rankings, while the Department of Mechanical and Aerospace Engineering was ranked the No. 1 public university program in the country by the Academic Ranking of World Universities. The Department of NanoEngineering at UC San Diego was the first in the country to offer undergraduate and graduate courses of study in nanoengineering.

“These students are shining examples of the power of engineering for the public good,” said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. “The research that these Siebel Scholars are doing will have profound impacts on human health in the future. My hearty congratulations on this prestigious recognition and honor.”

The five 2021 Siebel Scholars from UC San Diego and some of their accomplishments are outlined below.

Haleh Alimohamadi

Haleh Alimohamadi is a Ph.D. candidate in the Department of Mechanical Engineering working with Professor Padmini Rangamani. Her research focuses on developing theoretical frameworks that can tightly integrate experiments with computational models to study the physical principles underlying the cell membrane deformation by subcellular force generating mechanisms. In addition to research, Alimohamadi is passionate about STEM education, and has volunteered with multiple programs that aim to increase undergraduate and minority research in engineering, including the ENLACE program, the JUMP mentorship program, and the MAE Graduate Women’s Group. 



Gabrielle Colvert

Gabrielle Colvert is a bioengineering graduate student in the Cardiovascular Imaging Lab under the mentorship of Dr. Elliot McVeigh. Her PhD research is dedicated to developing noninvasive methods for evaluating cardiovascular function using four-dimensional computed tomography. Colvert has established successful collaborations with physicians, researchers, and industry partners both in the US and internationally which have led to multiple co-authored manuscripts and conference presentations. She was nominated by her department to be an ARCS Scholar and awarded an NIH F31 Predoctoral fellowship. At UC San Diego she has trained and served as a mentor to several undergraduate students. Outside of UC San Diego, she is involved with organizations that empower girls to become leaders, creators, and problem-solvers.


Dhruva Katrekar

Dhruva Katrekar is a Ph.D. candidate in the department of Bioengineering at UC San Diego, and works towards addressing some of the key challenges of in vivo gene therapy. During his graduate studies, advised by professor Prashant Mali, Katrekar has pioneered the development of an RNA editing tool for the treatment of rare genetic disorders. He has won awards for presentations at premier gene therapy conferences and garnered acclaim for his work in the broad research community. In addition to a strong publication record, he has been granted multiple provisional patents for his inventions. In the near future, Katrekar aims to enable clinical translation of his research as a novel therapeutic agent to positively impact the lives of patients suffering from rare genetic disorders.


Greg Poore

Gregory Poore is in his fifth year of the UC San Diego Medical Scientist Training Program (MSTP), having completed two years each of medical school and of the Bioengineering Ph.D. program. He has a unique background in oncology and microbiology, with his PhD research focused on building the most comprehensive survey of microbes in cancer to date, and studying the three-way interactions between intratumoral microbes, cancer cells, and immune cells. Poore is also an entrepreneur and has co-founded two companies: a medical device company for managing respiratory diseases (Vigor Medical Systems) and a cancer diagnostic company (Micronoma). Outside of academia, Poore is a triathlete—he completed his first Ironman in 2019-- and a servant leader, who founded and has actively mentored a food recovery initiative at his alma mater Duke University that has donated more than 100,000 lbs of food since 2013.

Juliane Sempionatto-Moreto

Juliane Sempionatto-Moreto is a Ph.D. candidate in the Department of Nanoengineering working in profesor Joseph Wang’s Laboratory for Nanobioelectronics. Her research aims to develop muchh needed non-invasive wearable biosensors with a focus on real-life applications. Her research has broadened the field of wearable sensors with her significant contribution and innovation. Sempionatto-Moreto’s innovative ideas have resulted in five patents, two of which were licensed to a company exclusively focused on the development of her device. She is also strongly committed to diversity and mentorship.



Siebel Foundation

The Siebel Scholars program was established by the Thomas and Stacey Siebel Foundation in 2000 to recognize the most talented students at the world’s leading graduate schools of business, computer science, bioengineering, and energy science. Each year, more than 90 graduate students at the top of their class are selected during their final year of studies based on outstanding academic performance and leadership to receive a $35,000 award toward their final year of studies. Today, the active community of over 1,400 Siebel Scholars serves as advisors to the Siebel Foundation and works collaboratively to find solutions to society’s most pressing problems.

Roboticist coaches middle school team to victory

San Diego, Calif., Sept. 23, 2020-- A team of middle and high school students from San Diego made history when they became the youngest team ever to win the annual RoboSub International underwater robotics competition. The team has been coached by Jack Silberman, a lecturer in UC San Diego’s Contextual Robotics Institute, for the past decade.

The competition was held virtually this year, but that didn’t stop Team Inspiration from earning 1st place in the overall standings, as well as 1st place for their technical design report and website, and 2nd place for their video.

Silberman said he hopes seeing the team’s success will encourage other STEM professionals to get involved in outreach activities with young students.

Learn more about Team Inspiration in this 10 News video: https://www.10news.com/news/local-news/local-robotics-team-ranks-1-in-international-competition


L'Oreal Joins UC San Diego Center for Microbiome Innovation (CMI) as Industry Partner

San Diego, Calif., September 22, 2020 - UC San Diego Center for Microbiome Innovation (CMI) announced today that the L’Oreal Group, the world’s leading beauty company, has joined CMI as an Industry Partner. Founded by a chemist in 1909, L’Oreal has a more than 110-year heritage rooted in scientific innovation, delivering the highest quality cosmetic, skincare and beauty products to meet evolving consumer needs around the world.  

Human skin is home to a large number and wide variety of microorganisms such as bacteria, fungi, and viruses, collectively known as the skin microbiome, and varies by each individual. Given the heightened focus on skin health and the need to understand the characteristics of different skin types, learning about the complex composition of microbial communities on the skin will provide critical learnings to the cosmetic and skincare industry. 

A world leader in microbiome research and expertise, CMI exists to inspire, nurture, and sustain dynamic collaborations between UC San Diego Microbiome experts and the industry. As CMI’s first cosmetic industry partner, L’Oreal will have the opportunity to expand upon their 15 years of microbiome research and leverage the latest studies and most advanced technologies while sharing their insights into how this research can be applied to the field. This innovative collaboration will bring forth multidisciplinary research to influence and accelerate microbiome discovery and integrate learnings into future skincare products. 

“Embracing the science of microbiome can introduce new insights to support the development of technologies, actives, and products that have the potential to deliver skin transformation,” said CMI Faculty Director Dr. Rob Knight. “We are thrilled to welcome L’Oreal as the first cosmetic industry partner to join the Center for Microbiome Innovation.”

Together with the CMI team, L’Oreal intends to extend the frontiers of knowledge in skin microbiome research—going beyond the description of microbial composition to microbial function and skin appearance, as well as the more limitedly explored compounds. 

“CMI is at the forefront of research into the human microbiome, and together, we have a unique opportunity to influence the future of microbiome research,” said Magali Moreau, who leads L’Oreal Microbiome research in North America. “We are excited to dive more deeply into microbial function and uncover new ways to promote long-term skin wellness and beauty and deliver new levels of product performance.”  

By partnering with CMI, L’Oreal will  be able to provide essential consumer and market insights to CMI researchers, while ensuring the focus remains on the importance of understanding the science behind any potential products developed. “L’Oreal brings significant expertise in beauty technology, personalization, Artificial Intelligence, and other areas as it relates to cosmetics and skincare” said CMI Executive Director Dr. Andrew Bartko. “Partnering with our first industry member in this field will provide critical advancements to the field of skin microbiome research.”


About L’Oréal
L’Oréal has devoted itself to beauty for over 100 years. With its unique international portfolio of 36 diverse and complementary brands, the Group generated sales amounting to 29.87 billion euros in 2019 and employs 88,000 people worldwide. As the world’s leading beauty company, L’Oréal is present across all distribution networks: mass market, department stores, pharmacies and drugstores, hair salons, travel retail, branded retail and e-commerce. Research and Innovation, and a dedicated research team of 4,100 people, are at the core of L’Oréal’s strategy, working to meet beauty aspirations all over the world.

About Center for Microbiome Innovation at University of California San Diego:
The UC San Diego Center for Microbiome Innovation leverages the university's strengths in clinical medicine, bioengineering, computer science, the biological and physical sciences, data sciences, and more to coordinate and accelerate microbiome research. We also develop methods for manipulating microbiomes for the benefit of human and environmental health. Learn more at cmi.ucsd.edu/ and follow @CMIDigest.

Toward all-solid-state lithium metal batteries

San Diego, Calif., September 17, 2020 -- Battery researchers know that solid-state electrolytes, such as lithium phosphorus oxynitride (LiPON), remain electrochemically stable against Lithium (Li) metal. But they don't know why exactly.

Figuring out why and how specific solid-state electrolytes like LiPON remain stable and cycleable when in contact with lithium metal anodes is an important step toward finally incorporating lithium metal anodes into next generation all-solid-state lithium metal batteries.

Lithium metal batteries, which have anodes made of lithium metal, are an essential part of the next generation of battery technologies. They promise twice the energy density of today’s lithium-ion batteries (which usually have anodes made of graphite), so they could last longer and weigh less. This could potentially double the range of electric vehicles.

New work published in September 2020 in the journal Joule, led by researchers in the lab of UC San Diego nanoengineering professor Shirley Meng, will help explain this stability. In particular, the work unravels some of the mystery of the interface between lithium metal and LiPON.

"This research provides new insights for interface engineering aimed at stabilizing the lithium metal anode," said Diyi Cheng, a nanoengineering PhD student in Shirley Meng's lab at the UC San Diego Jacobs School of Engineering.

The team uncovered an 80-nm-thick interface comprising nanocrystals embedded in an amorphous matrix. Analyzing its chemical distribution is leading to a mechanistic understanding of solid-solid interface formation in lithium metal batteries.

This work combines cryogenic electron microscopy and cryogenic focused ion beam (FIB). The methodology in this work can be then extended to the interface studies in other battery systems using either organic liquid or solid-state electrolytes.

Paper title: Unveiling the Stable Nature of the Solid Electrolyte Interphase between Lithium Metal and LiPON via Cryogenic Electron Microscopy

Authors: Diyi Cheng, Thomas A. Wynn, Xuefeng Wang, Shen Wang, Minghao Zhang, Ryosuke Shimizu, Shuang Bai, Han Nguyen, Chengcheng Fang, Min-cheol Kim, Weikang Li, Bingyu Lu, Suk Jun Kim, and Ying Shirley Meng.

Materials Science and Engineering Program, University of California San Diego, La Jolla, CA 92121, USA
Department of NanoEngineering, University of California San Diego, La Jolla, CA 92121, USA
School of Energy, Materials and Chemical Engineering, Korea University of Technology and Education, Cheonan 31253, Republic of Korea

Making space weather forecasts faster and better

Power grid failures, massive blackouts, widespread damage to the satellites that enable GPS and telecommunication — space plasma phenomena like coronal mass ejections cause geomagnetic storms that interact with Earth’s atmosphere, wreaking havoc on the systems and technologies that enable modern society.
Image courtesy of NASA.

UC San Diego engineer Boris Kramer is part of a team that will develop software to forecast space storms.

San Diego, Calif., Sept. 16, 2020 --In August 1859, a massive solar storm knocked out the global telegraph system. Some telegraph operators were hit by electric shocks; others saw sparks flying from cable pylons. Telegraph transmissions were halted for days.

The damage was due to a geomagnetic storm caused by a series of coronal mass ejections--giant bursts from the sun’s surface--that raced across the solar system and saturated Earth’s atmosphere with magnetic solar energy. 

If a solar storm of similar scale occurred today, it would cause worldwide blackouts, massive network failures and widespread damage to the satellites that enable GPS and telecommunication. Worse still, it would threaten human health due to increased levels of radiation. 

The arrival and intensity of these solar storms can be difficult to predict. To improve the ability to forecast space weather, a multidisciplinary team of researchers, including Professor Boris Kramer at the University of California San Diego, received $3.1 million from the National Science Foundation. The researchers, led by Professor Richard Linares at the Massachusetts Institute of Technology, will also work on speeding up the forecasting abilities that are currently available. 

Speeding up forecasts

"Space weather models often need to be evaluated rather quickly, for example when they are used for control of satellites, so I am excited to contribute with new data-driven reduced-order modeling approaches to this overall goal, and make space weather models not only better, but also faster," said Kramer, who is part of the Department of Mechanical and Aerospace Engineering at the UC San Diego Jacobs School of Engineering. 

The algorithms for complex space weather models that Kramer will develop will speed up the time it takes to execute the models’ simulations and lead to real-time estimations. As a result, decision makers will have real-time information to make sure satellites avoid collisions. The project will also improve satellite navigation overall.

Making forecasts more accurate

"A second big issue are the massive uncertainties that weather, and here specifically space weather, is subject to,” he added. “There are so many parameters we don't know well, or can't measure in outer space. Our work here at UC San Diego will help tell us what uncertainties are present in our computed, predicted weather simulations, given that there are so many inputs that are uncertain. I am excited to work with the MIT Haystack Observatory to get high-quality data of the ionosphere that we can use to calibrate our predictions."

Kramer will develop theory and multifidelity algorithms to quantify the uncertainty in space weather models. The goal is to at least match the accuracy of the models that predict hurricanes, which include a likely path and an estimate of other areas where hurricanes could be headed. Researchers want to be able to predict a likely path for a solar storm, for example, and also draw a cone around that path, showing the other areas it might be headed to instead. 

Powerful software platform

The team, which also includes researchers at the University of Michigan, will create a powerful, flexible software platform using cutting-edge computational tools to collect and analyze huge sets of observational data that can be easily shared and reproduced among researchers. The platform will also be designed to work even as computer technology rapidly advances and new researchers contribute to the project from new places, using new machines. Using Julia, a high-performance programming language developed by Professor Alan Edelman at MIT, researchers from all over the world will be able to tailor the software for their own purposes to contribute their data without having to rewrite the program from scratch.

The grant is part of a $17 million, three-year effort by NSF and NASA to expand the nation's space weather prediction capabilities. 

"Space weather involves intricate interactions between the sun, the solar wind, Earth's magnetic field and Earth's atmosphere," said Jim Spann, the space weather lead for NASA's heliophysics division at NASA headquarters in Washington, D.C. "Our ability to understand the sun-Earth system is of growing importance to economies, national security, and our society as it increasingly depends on technology. NASA and NSF through this program enable the operational organizations, NOAA and the Department of Defense, to incorporate that understanding into operational models and space weather predictions to better prepare us for potential impacts."


Add human-genome produced RNA to the list of cell surface molecules

(Left) A hypothetical model of the relative positions of FISH probes (red arrowheads) on a membrane-bound RNA fragment. (Right) A single molecule RNA fluorescence in situ hybridization image of maxRNAs (yellow arrows).

San Diego, Calif., September 10, 2020 -- Bioengineers at UC San Diego have shown that human-genome produced RNA is present on the surface of human cells, suggesting a more expanded role for RNA in cell-to-cell and cell-to-environment interactions than previously thought. This new type of membrane-associated extracellular RNA (maxRNA) is found in human cells that are not undergoing cell death, shedding light on the contribution of nucleic acids—particularly RNA—to cell surface functions.

The maxRNAs and the molecular technologies developed to inspect the cell surface to detect them, are detailed in a paper in Genome Biology published Sept. 10. 

“The cell’s surface is to a cell like the face is to a person,” said Sheng Zhong, bioengineering professor at the UC San Diego Jacobs School of Engineering and corresponding author of the study. “It is the most important part for recognizing what type of cell it is, for example a good actor – like a T cell — or a bad actor— like a tumor cell—and it aids in communication and interactions.”

While much is known about other components of a cell’s surface, including proteins, glycans, and lipids, little was known about RNA; with a few exceptions, the RNA produced by the human nuclear genome was not thought to exist on the surface of human cells with intact cell membranes. The discovery that RNA does in fact naturally occur as a cell surface molecule could play a role in better understanding the genome and developing more effective therapeutics.

“This discovery expands our ability to interpret the human genome, because we now know a portion of the human genome may also regulate how a cell presents itself and interacts with other cells through the production of maxRNA,” said Norman Huang, a bioengineering PhD and the first author of this paper. 

Better understanding maxRNA could also lead to new strategies for therapeutics development. MaxRNA is easier for therapeutics to reach since it’s on the outside surface of the cell, and because RNA can be targeted by specific antisense oligonucleotides, which are easier to develop than other agents such as antibodies. 

In order to test for RNA on the surface of mouse and human cells, bioengineers in Zhong’s lab designed a nanotechnology called Surface-seq. They based this off a method used by UC San Diego Professor Liangfang Zhang to create microscopic nanosponges cloaked in natural cell membranes, a process that involves extracting the plasma membrane from cells and assembling it around polymeric cores. 

This maintains the right-side-out orientation of the cell membrane by keeping the surface molecules on the membrane facing outwards. The process of cell membrane purification and the stable coating onto the polymeric core ensures the removal of intracellular contents, allowing researchers to detect RNA that is stably associated with the extracellular layer of the cell membrane. Researchers then characterized the sequences, cell-type specificity, and functional attributes of these maxRNA molecules, which were used as the input of the Surface-seq library construction and sequencing.

In addition to collaborating with Zhang, Zhong collaborated with professor Zhen Chen’s lab in the Beckman Research Institute at City of Hope.  

The collaborative team plan to further study how the maxRNA is transported to the cell surface and anchored there, as well as further investigate the diversity of cell types, genes, environmental cues and biogenesis pathways for maxRNA expression and their contribution to cellular functions. 

UC San Diego Jacobs School of Engineering Hires 24 Faculty in Fall 2020

San Diego, Calif., September 9, 2020 --The University of California San Diego Jacobs School of Engineering is proud to introduce the 24 new professors hired in Fall 2020. These professors are among the more than 130 faculty who have joined the UC San Diego Jacobs School of Engineering in the last seven years. 

2020 New Faculty brochure available here.

These new faculty, and the communities of scholarship and innovation they are creating and building on, point to an exciting future for everyone here at the Jacobs School of Engineering. 

"I'm honored to welcome all our new faculty to the Jacobs School. My job is to help empower each of our new faculty to have lasting positive impacts. Engineering and computer science for the public good is what we do at the Jacobs School," said Albert P. Pisano. "Given that we have hired more than 130 faculty in the last seven years, we will see an incredible jump in positive impact in the coming years as their labs and research groups further grow and strengthen." 

This is part of an overall upward trajectory for the School. In March 2020, UC San Diego Jacobs School of Engineering jumped to the #9 spot in the influential U.S. News and World Report Rankings of Best Engineering Schools. This is up from #11 last year and #17 four years ago. It’s the first time the UC San Diego Jacobs School of Engineering has broken into the top 10 of this closely watched ranking.

Jacobs School new faculty


Brian Aguado, Assistant Professor

Aguado’s goal is to develop precision biomaterials that enable the evaluation of a patient's unique biology to diagnose and treat a variety of health disorders as a function of sex, age, and/or ancestry. Specifically, Aguado aims to develop sex-specific biomaterial technologies to treat cardiovascular diseases, including aortic valve disease and heart failure.

Previously: Postdoctoral Fellow, University of Colorado at Boulder

Ph.D.: Northwestern University


Andrew Bartko, Professor of Practice

Bartko’s goal is to inspire, nurture, and sustain vibrant collaborations between UC San Diego’s microbiome experts and industry partners in the life science, nutrition, energy, information technology, clinical and healthcare industries. Specifically, Bartko aims to focus on creating and commercializing innovative technologies to accelerate microbiome discoveries and healthcare breakthroughs across academic and industry collaborations.

Previously: Research Leader, Battelle 

Ph.D.: Georgia Institute of Technology


Benjamin Smarr, Assistant Professor

Smarr’s research focuses on time series analysis in biological systems, with an emphasis on practical information extraction for translational applications. His main project is TemPredict, which brings together wearable device data from 50K people with over 2 million daily symptom reports and is used to identify signs of COVID-19 onset, progression, and recovery.

Previously: Postdoctoral Fellow, UC Berkeley

Ph.D.: University of Washington



Carlos Jensen, Associate Vice Chancellor, Educational Innovation

Jensen’s research lies at the intersection between usability and software engineering, with an emphasis on studying how Open Source communities operate and organize, and the tools and processes needed to make them more efficient. His recent work uses automated testing techniques to help developers improve the reliability of large and complex open source software.

Previously: Associate Dean, Oregon State University

Ph.D.: Georgia Institute of Technology


Tzu-Mao Li, Assistant Professor

Li connects classical computer graphics and image processing algorithms with modern data-driven methods to facilitate physical exploration. His work added 3D understanding to computer vision models; used data to improve camera imaging pipeline quality; and made light transport simulation faster by using information implicitly defined by rendering programs.

Previously: Postdoctoral Researcher, UC Berkeley and MIT

Ph.D.: Massachusetts Institute of Technology


Kristen Vaccaro, Assistant Professor

Vaccaro focuses on how to design machine learning systems to give users a sense of agency and control. She found that some existing ways of providing control for social media can function as placebos, increasing user satisfaction even when they do not work. She will help develop systems to give users control and oversight, and ethical guidelines and policies.

Previously: Research assistant, University of Illinois at Urbana-Champaign

Ph.D.: University of Illinois at Urbana-Champaign


Rose Yu, Assistant Professor

The goal of Yu’s research is to advance machine learning and enable interpretable, efficient and robust large-scale spatiotemporal reasoning. Her work has been successfully applied to solve challenging domain problems in sustainability, health and physical sciences.

Previously: Assistant professor, Northeastern University

Ph.D.: University of Southern California



Nick Antipa, Assistant Professor

Antipa’s research aims to develop design frameworks that merge optical models with algorithms, allowing optimization of both components and enabling the development of cutting-edge imaging and display systems. By considering both the hardware and digital domains, new computational optical systems emerge that extend capability beyond what is available.

Previously: Ph.D. Candidate, UC Berkeley

Ph.D.: UC Berkeley


Mingu Kang, Assistant Professor

Kang researches vertically-integrated VLSI information processing for machine learning and signal processing algorithms. His research focuses on energy- and latency-efficient integrated circuits, architectures and systems by leveraging novel computing paradigms including in-memory, in-sensor and neuromorphic computing with both CMOS and emerging devices.

Previously: Research Scientist, IBM Research

Ph.D: University of Illinois at Urbana-Champaign

Florian Meyer, Assistant Professor

Meyer researches statistical signal processing for navigation, mapping and multiobject tracking in applications including maritime situational awareness, autonomous driving, and indoor localization. He investigates efficient and scalable high-dimensional nonlinear estimation using graphical models where the number of states to be estimated may also be unknown.

Previously: Postdoctoral Fellow and Associate, MIT

Ph.D.: Vienna University of Technology


Karcher Morris, Assistant Teaching Professor

Morris’s teaching aims to embed project-based learning throughout the undergraduate electrical and computer engineering curriculum, complementing theoretical foundations. By connecting students with application-oriented coursework and industry-relevant challenges, Morris promotes an early engagement between students and their research/industry goals.

Previously: Ph.D. Candidate, UC San Diego

Ph.D.: UC San Diego


Yuanyuan Shi, Assistant Professor

Shi's research interests are in the area of energy systems and cyber-physical systems, spanning from machine learning to optimization and control. She works on data-driven control for complex networked systems and market mechanism design under multi-agent learning dynamics.

Previously: Postdoctoral Researcher, Caltech

Ph.D: University of Washington


Yatish Turakhia, Assistant Professor

Turakhia develops algorithms and hardware accelerators to enable faster and cheaper progress in biology and medicine. He also develops computational methods that enable biological discoveries, such as new genotype-phenotype relationships.

Previously: Postdoctoral Researcher, UC Santa Cruz

Ph.D.: Stanford University


Yang Zheng, Assistant Professor

Zheng develops methods and frameworks for the optimization and control of network systems and their applications to cyber-physical systems, especially autonomous vehicles and traffic systems. His goal is to develop computationally efficient and distributed solutions for large-scale network systems by exploring and exploiting real-world system structures.

Previously: Postdoctoral Researcher, Harvard

Ph.D.: University of Oxford



Sylvia Herbert, Assistant Professor

Herbert focuses on developing new techniques for safety and efficiency in autonomous systems. She has developed methods for scalable safety and real-time decision making that draw from control theory, cognitive science and reinforcement learning, which are backed by both rigorous theory and physical testing on robotic platforms.

Previously: Graduate Researcher, UC Berkeley

Ph.D.: UC Berkeley


Patricia Hidalgo-Gonzalez, Assistant Professor

Hidalgo-Gonzalez focuses on high penetration of renewable energy using optimization, control theory and ML. She co-developed a power system expansion model for Western North America’s grid under climate change uncertainty.  She is interested in power dynamics, energy policy, electricity market redesign, and learning for dynamical systems with safety guarantees.

Previously: Ph.D. Candidate, UC Berkeley

Ph.D: UC Berkeley


Stephanie Lindsey, Assistant Professor

Lindsey’s work lies at the interface of fluid mechanics, numerical analysis and cardiovascular developmental biology. She seeks to determine causal-effect relationships for the creation of cardiac malformations and address important challenges in clinical treatment of congenital heart defects through a combined computational-experimental approach.

Previously: Postdoctoral Researcher, Stanford University

Ph.D.: Cornell University


Marko Lubarda, Assistant Teaching Professor

Lubarda is dedicated to engineering pedagogy and enriching students' learning experiences through curriculum design, teaching innovations and support of undergraduate student research. He works in the areas of computational analysis, engineering mathematics, materials science, solid mechanics, device physics, and magnetic nanotechnologies.

Previously: Assistant Professor, University of Donja Gorica, Montenegro

Ph.D.: UC San Diego


Lonnie Petersen, Assistant Professor

Dr. Petersen is a physician scientist specializing in space and aviation physiology and development of countermeasure devices for use in space. During the COVID-19 pandemic, she co-lead a team that developed a low-cost, easy-to-use ventilator and other ways to support critically ill COVID19 patients and mitigate the spread of disease.

Previously: Postdoctoral Researcher, UC San Diego School of Medicine

Ph.D.: University of Copenhagen


Lisa Poulikakos, Assistant Professor

Poulikakos harnesses nanophotonics, the study and manipulation of light on the nanoscale, to bridge engineering and biomedicine. The resulting in-vivo and ex-vivo nanophotonic probes aim to elucidate the origin and propagation of a range of diseases, leading to low-cost medical diagnostics; rapid, on-chip biochemical drug testing; or in-situ biomedical imaging.

Previously: Postdoctoral Researcher, Stanford University
Ph.D.: ETH Zurich


Aaron Rosengren, Assistant Professor

Rosengren conducts fundamental and applied research in astrodynamics, space situational awareness and space traffic management to define perennial, ad-hoc practices and policies to make space a sustainable resource. His contributions are in the fields of celestial mechanics and nonlinear dynamics, with a strong focus on space debris and small Solar-System bodies.

Previously: Assistant Professor, University of Arizona

Ph.D.: University of Colorado, Boulder


Jon Wade, Professor of Practice

Wade’s objective is to ensure that the research conducted and the curriculum developed in systems engineering has the greatest impact on addressing the critical challenges that face our global society and nation. He leads research in the area of complex, evolving systems engineering methods, processes, tools, and education.

Previously: Research Professor, Stevens Institute of Technology

Ph.D: Massachusetts Institute of Technology



Zeinab Jahed, Assistant Professor

Jahed designs electronics that integrate intelligently with biological systems at the nanoscale. She designs non-invasive and high-throughput bio-electronic tools to record and manipulate biological activities and uses AI and ML techniques to interpret the large data sets from these nano-bio-electronic tools to answer important biological questions.

Previously: Postdoctoral Researcher, Stanford University

Ph.D.: UC Berkeley



Georgios Tsampras, Assistant Professor

Tsampras’ research goal is to improve the seismic response and simplify the lifetime management of structures and civil infrastructures. He conducts integrated experimental and analytical research on components, connections, and systems that enhance the safety and reliability of structures and civil infrastructures against earthquakes.

Previously: Falcon Vehicle Structures Engineer, SpaceX

Ph.D.: Lehigh University


New anode material could lead to safer fast-charging batteries

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Researchers Haodong Liu and Ping Liu hold batteries made with the disordered rocksalt anode material they discovered, standing in front of a device used to fabricate battery pouch cells.

San Diego, Calif., Sept. 2, 2020--Scientists at UC San Diego have discovered a new anode material that enables lithium-ion batteries to be safely recharged within minutes for thousands of cycles. Known as a disordered rocksalt, the new anode is made up of earth-abundant lithium, vanadium and oxygen atoms arranged in a similar way as ordinary kitchen table salt, but randomly. It is promising for commercial applications where both high energy density and high power are desired, such as electric cars, vacuum cleaners or drills.

The study, jointly led by nanoengineers in the labs of Professors Ping Liu and Shyue Ping Ong, was published in Nature on September 2.

Currently, two materials are used as anodes in most commercially available lithium-ion batteries that power items like cell phones, laptops and electric vehicles. The most common, a graphite anode, is extremely energy dense—a lithium ion battery with a graphite anode can power a car for hundreds of miles without needing to be recharged. However, recharging a graphite anode too quickly can result in fire and explosions due to a process called lithium metal plating. A safer alternative, the lithium titanate anode, can be recharged rapidly but results in a significant decrease in energy density, which means the battery needs to be recharged more frequently.

This new disordered rocksalt anode—Li3V2O5 —sits in an important middle ground: it is safer to use than graphite, yet offers a battery with at least 71% more energy than lithium titanate. 

The capacity and energy will be a little bit lower than graphite, but it’s faster, safer and has a longer life. It has a much lower voltage and therefore much improved energy density over current commercialized fast charging lithium-titanate anodes,” said Haodong Liu, a postdoctoral scholar in Professor Ping Liu’s lab and first author of the paper. “So with this material we can make fast-charging, safe batteries with a long life, without sacrificing too much energy density.”

The researchers formed a company called Tyfast in order to commercialize this discovery. The startup’s first markets will be electric buses and power tools, since the characteristics of the Li3V2O5 disordered rocksalt make it ideal for use in devices where recharging can be easily scheduled. 

The crystal structure of disordered rocksalt -Li3V2O5. The red balls represent O, the blue tetrahedron represents Li in tetrahedral sites, and the green octahedron represents the Li/V shared octahedral sites

Researchers in Professor Liu’s lab plan to continue developing this lithium-vanadium oxide anode material, while also optimizing other battery components to develop a commercially viable full cell.  

“For a long time, the battery community has been looking for an anode material operating at a potential just above graphite to enable safe, fast charging lithium-ion batteries. This material fills an important knowledge and application gap,” said Ping Liu. “We are excited for its commercial potential since the material can be a drop-in solution for today’s lithium-ion battery manufacturing process.”

Why try this material?

Researchers first experimented with disordered rocksalt as a battery cathode six years ago. Since then, much work has been done to turn the material into an efficient cathode. Haodong Liu said the UC San Diego team decided to test the material as an anode based on a hunch. 

“When people use it as a cathode they have to discharge the material to 1.5 volts,” he said. “But when we looked at the structure of the cathode material at 1.5 volts, we thought this material has a special structure that may be able to host more lithium ions—that means it can go to even lower voltage to work as an anode.”

In the study, the team found that their disordered rocksalt anode could reversibly cycle two lithium ions at an average voltage of 0.6 V—higher than the 0.1 V of graphite, eliminating lithium metal plating at a high charge rate which makes the battery safer, but lower than the 1.5 V at which lithium-titanate intercalates lithium, and therefore storing much more energy. 

The researchers showed that the Li3V2O5  anode can be cycled for over 6,000 cycles with negligible capacity decay, and can charge and discharge energy rapidly, delivering over 40 percent of its capacity in 20 seconds.  The low voltage and high rate of energy transfer are due to a unique redistributive lithium intercalation mechanism with low energy barriers.

Postdoctoral scholar Zhuoying Zhu, from Professor Shyue Ping Ong’s Materials Virtual Lab, performed theoretical calculations to understand why the disordered rocksalt Li3V2O5 anode works as well as it does.



The corresponding and first authors on a Zoom call. From top left clockwise: Professor Ping Liu, Professor Shyue Ping Ong, Haodong Liu, Jun Lu, Professor Huolin Xin, and Zhuoying Zhu. 

“We discovered that Li3V2O5 operates via a charging mechanism that is different from other electrode materials. The lithium ions rearrange themselves in a way that results in both low voltage as well as fast lithium diffusion,” said Zhuoying Zhu.

“We believe there are other electrode materials waiting to be discovered that operate on a similar mechanism,” added Ong.

The experimental studies at UC San Diego were funded by awards from the UC San Diego startup fund to Ping Liu, while the theoretical studies were funded by the Department of Energy and the National Science Foundation’s Data Infrastructure Building Blocks (DIBBS) Local Spectroscopy Data Infrastructure program, and used resources at the San Diego Supercomputer Center provided under the Extreme Science and Engineering Discovery Environment (XSEDE).

The team also collaborated with researchers at Oak Ridge National Lab, who used neutron diffraction to determine the atomic structure of the Li3V2O5 material. Researchers at UC Irvine and Brookhaven National Lab led by Professor Huolin Xin performed high resolution microscopic studies to resolve the structural changes after lithium insertion. Finally, the teams at Argonne National Lab led by Jun Lu, and Lawrence Berkeley National Lab, conducted X-ray diffraction and X-ray absorption studies to reveal the crystal structural change and charge compensation mechanisms of the material during (de)lithiation. This study used national lab facilities including the beamline VULCAN (Spallation Neutron Source at Oak Ridge National Lab), beamline 17-BM (Advanced Photon Source at Argonne National Lab), beamline 5.3.1 (Advanced Light Source at Lawrence Berkeley National Lab).

Paper Title: “A disordered rock salt anode for fast-charging lithium-ion batteries.” Co-authors include Haodong Liu, Zhuoying Zhu, Qizhang Yan, Sicen Yu, Yiming Chen, Yejing Li, Xing Xing, Yoonjung Choi, Shyue Ping Ong and Ping Liu, UC San Diego; Xin He, Jun Feng, Robert Kostecki, Lawrence Berkeley National Laboratory; Yan Chen, Ke An, Oak Ridge National Laboratory; Rui Zhang, Huolin L. Xin, University of California; Lu Ma, Ruoqian Lin, Brookhaven National Laboratory; Tongchao Liu, Matthew Li, Khalil Amine, Tianpin Wu, Jun Lu, Argonne National Laboratory; Lucy Gao, Del Norte High School; Helen Sung-yun Cho, Canyon Crest Academy.

Dr. Rob Knight and CMI researchers develop tool to identify patterns driving differences in microbial composition

Compositional tensor factorization that allows control for individuality across time or space will enable significant advancements in field of microbiome research

San Diego, Calif., August 31, 2020 —Dr. Rob Knight, Faculty Director for the Center for Microbiome Innovation (CMI), and a team of researchers at UC San Diego, UCLA and the Flatiron Center for Computational Biology unveiled in a paper published today in Nature Biotechnology, a new tool developed to identify patterns driving differences in microbial composition and allow control in research studies across time or space. 

Genetically speaking, humans are 99% the same, but the trillions of microbes that live in, on and around a person makes each of us microbially unique. Microbiomes play a significant role in who we are as humans, in sickness and in health. Research has shown that microbes help us digest and process nutrients, and also constantly interact with — and help shape — our immune systems. To date, the makeup of our gut microbiomes has been associated with diseases and conditions such as food allergies, obesity, inflammatory bowel disease and colon cancer. 

Not only do the community of trillions of microbes vary dramatically from person to person, but they can significantly change over the course of individual’s lifetime as well. This microbial variation can be on the scale of hours — from eating a meal to over the course of a night’s sleep — to over a number of years due to aging or other changes in one’s health.

While a great deal of research has advanced our understanding of microbiomes and how they interact with, and affect one’s overall health, to date there has been lack of available research tools to help account for the significant amount of microbial variation from person to person that are reproduceable across data sets to help enable broader research advancements in the field.

In “Context-aware dimensionality reduction deconvolutes gut microbial community dynamics,” the new method is compositional tensor factorization (CTF), built specifically to control for individuality in studies with repeated measures of the same subject across time or space. The tool incorporates information from the same host across multiple samples to reveal patterns driving differences in microbial composition. 

Research findings using CTF included reproducible longitudinal microbial “signatures” for infant birth mode (i.e. vaginal v. caesarean section). Using tools such as CTF will enable researchers to understand how the combination of microbial “signatures” developed across an individual’s lifetime results in a unique set of microbes. 

Tools such as CTF will widely enable and advance the field of microbiome research as the number of repeated measurable microbiome datasets will greatly increase with the goal to bring researchers one step closer to individualized precision medicine for the microbiome.

Additional co-authors include: Cameron Martino, Liat Shenhav, Clarisse A. Marotz, George Armstrong, Daniel McDonald, Yoshiki Vázquez-Baeza, James T. Morton, Lingjing Jiang, Maria Gloria Dominguez-Bello, Austin D. Swafford, and Eran Halperin.

The full paper is available in Nature Biotechnology here.

About Center for Microbiome Innovation at University of California San Diego:
The UC San Diego Center for Microbiome Innovation leverages the university's strengths in clinical medicine, bioengineering, computer science, the biological and physical sciences, data sciences, and more to coordinate and accelerate microbiome research. We also develop methods for manipulating microbiomes for the benefit of human and environmental health. Learn more at cmi.ucsd.edu/ and follow @CMIDigest.

Wearable Electrochemical Sensors for the Monitoring and Screening of Drugs

ECCV 20 Honorable Mention

Brina Lee '13 Forges Another Frontier, This Time in Audio

San Diego, Calif., August 21, 2020 -- Brina Lee (MA ’13) has learned a thing or two about overcoming fear. It’s been a necessity for someone who has blazed a career path that includes being Instagram’s first female engineer and co-founding a company. As she works toward growing her startup, Hamul, the UC San Diego Computer Science and Engineering Department (CSE) graduate can summarize the most important lesson she’s learned in one short phrase.

“Don’t let you hold yourself back,” she says. “It’s as simple as that.”

"If you tell me I can’t do it, I’m one hundred percent committed to proving you wrong."

Ahead of the curve

Lee grew up in Orange County, California, and graduated from UC San Diego with a bachelor’s degree in communications in 2008. Just as the Great Recession hit, she snagged a marketing position at a tiny startup, where she was handed a book on HTML and asked to build a website from scratch.

To her surprise, Lee found herself staying up late to pursue this newfound form of creative freedom. Typing in a line of code and watching the website change as a result seemed inexplicable and surprising, “literally like magic,” she says. And she wanted to see where it could take her.

In the 2000s, however, switching from a nontechnical field like communications to computer science was almost unheard of. Websites like Coursera did not yet exist, and as a college graduate, Lee couldn’t return to university for a new bachelor’s degree.

Undeterred, she visited UC San Diego Extension to meet with Rick Ord, a CSE lecturer leading an introductory course in computer science. She still remembers his bewildered reaction. He had just given a test that had weeded out students in mathematics and engineering. What was a communications student doing on his doorstep?

Lee placed within the ninety-ninth percentile in Ord’s class and went on to tutor other students. Her work began turning heads, even as she burned through her savings paying for classes and access to laboratory resources.

With persistence, time, and the support of mentors like Ord, Lee was accepted into a master’s program in computer science at UC San Diego. She found a community that encouraged teamwork instead of competition, and saw doors opening for her at companies like Facebook and Google. In the workplace, students from other universities expressed admiration for the tight bond between her and her UC San Diego classmates.

“UC San Diego is very team-based,” says Lee. “It brings up the entire class of people, versus everyone competing against each other.”

Shortly after Lee graduated with her master’s, she made news as Instagram’s first female engineer. It was there that she worked on initiatives to improve user experience and met the two graduates who would someday become her cofounders.

Audio as the next social frontier

Lee met Joshua Li and Hendri (no surname) while the three worked as software engineers at Instagram during the social media giant’s early years. Together, they worked hard to connect people and capture meaningful moments in their lives, an effort they’re continuing at their new business, Hamul.

Hamul curates a collection of audio clips, or voice lines, from popular culture to create social tools for gamers. The team’s goal is to allow gamers to customize their online presence and contribute to a more positive gaming environment through audio.

“Through Hamul, we hope that people have more ways to express themselves and connect to like-minded gamers,” says Lee. “We want to blaze the way for positive community spaces and improve the quality of relationships made online. If we can do this in the gaming industry, I would be very happy and excited.”

With team-based online gaming on the rise, Lee and her cofounders also see an opportunity to provide a healthy example of social networking. Lee says this will be especially important for younger generations, who might try their hand at online, team-based games before they enter the world of social media. Hamul hopes to contribute to the gaming community, first through audio clips, then through other means in the future. The team is striving to publish their first product in the coming weeks.

Hamul isn’t the end point for Lee. Now that she’s had a taste of the entrepreneur’s journey, she sees herself starting “over and over again.” In interviews with students interested in launching their own companies, she warns that the most difficult part of their undertaking will not be logistical, but personal. They’ll have to push past their own doubts to truly invest themselves in their business and product.

Luckily, Lee has had a strong role model to look to. Her father — a NASA engineer who specialized in shuttle launches and missile defense — showed her the lengths one could go with hard work and perseverance. His example taught her that nothing is truly impossible.

“It’s the biggest driving force in what makes me, me,” says Lee.

Eight teams of engineers and physicians work to tackle COVID-19 related challenges

San Diego, Calif., Aug. 20,2020 -- The Galvanizing Engineering in Medicine program at UC San Diego is supporting eight COVID-19 related projects in early stages with microgrants. 

The program is a collaboration between the Altman Clinical and Translational Research Institute and the Institute of Engineering in Medicine launched in 2013 to bring engineers and clinicians together to develop innovative technologies and solve challenging problems in medical care.

The eight projects funded by the COVID-19 rapid response grants were:

  •  The vacuum exhausted isolation locker, or VEIL, developed in the Medically Advanced Devices Laboratory at the Jacobs School of Engineering is essentially a large bubble that goes over a patient’s head and upper body, giving a patient an oxygen-rich environment that also prevents air—and possible droplets contaminated with COVID-19—from leaving the enclosure. The enclosure extracts exhaled aerosols and droplets from COVID-19 patients, providing health care workers with a safety barrier. The device also helps reduce the need for ventilators while also providing a solution to help patients breathe without suffering the long-term health issues from a ventilator such as lung scarring.The project is led by engineering professor James Friend and Dr. Timothy Morris from the UC San Diego School of Medicine. http://friend.ucsd.edu/veil/

  • Prof. Karen Christman in the Department of Bioengineering is partnering with Dr. Mark Hepokoski to develop a treatment for Acute Respiratory Distress System, or ARDS, a life-threatening lung injury found in COVID 19 patients when fluid leaks into the lungs. Christman and her team will develop extracellular matrix-based hydrogels, which provide a scaffold for surrounding cells to grow. The goal is to create a treatment that can be delivered directly to the site of injury, where the hydrogel would recruit stem cells, treat lung inflammation and promote lung healing. The project also received $250,000 in funding from the California Institute for Regenerative Medicine. 

  • A disposable wearable for tracking the vitals of COVID-19 positive ICU patients is being developed by engineering Professor Todd Coleman and Dr. Robert Owens, director of the ICU at the Thornton Medical Center. The device aims to protect healthcare workers providing care for COVID-19 patients from exposure. The device is 3 cm by 3 cm (roughly one square inch) and can be applied with medical-grade Band-Aid like materials.

  • Nanoengineering Prof. Sheng Xu is partnering with Dr. Jinghong Li to develop a customized wearable wireless sensor for remote monitoring of COVID-19 patients. The goal is to build a sensor that can acquire the five vital signs of COVID-19 patients--temperature, heart rate, blood pressure, respiratory rate and oxygen saturation. The wearable would reduce exposure of healthcare workers to patients while also providing early warning signs of dangerous silent hypoxia. 

  • Bioengineers and physicians are also partnering to develop a tool to assess the risk for arrhythmia after a COVID-19 infection. This tool is important to lower mortality from cardiac arrhythmias in COVID-19 patients. In addition, the project will help reduce the risks caused by certain medications, which alter electrical activity in the heart. The team includes Professor Jeff Omens, in the Department of Bioengineering, and Professors David Krummen, Kurt Hoffmayer and Gordon Ho at the UC San Diego School of Medicine.

  • Low-cost telehealth robots to improve healthcare safety and patient wellbeing are being developed by Professor Laurel Riek in the Department of Computer Science and Engineering, and Drs. Leslie Oyama, Alan Card, and Lesley Wilson in UC San Diego Health. The researchers will design, deploy, and evaluate a new fleet of telehealth robots to 1) Help healthcare workers provide better and safer care to patients with COVID-19, 2) Help patients connect with families remotely. The robots are made of open-source, low-cost parts, to make them accessible and affordable to hospitals worldwide. Riek and colleagues will assess the impact of the robot's use for patient visits on: the quality and safety of care, patient well-being, and healthcare worker well-being. "Ultimately this work has the potential to reduce burnout, which most substantially impacts frontline healthcare workers, particularly during the pandemic. We also expect use of the robot will improve patient well-being by reducing social isolation,” Riek says.

  • A medical electronic command center for COVID-19 crisis management is a collaboration between Drs. Sonia Ramamoorthy and Shanglei Liu and Professor Ryan Kastner and Ph.D. student Michael Barrow in the UC San Diego Department of Computer Science and Engineering. The project is designed to enhance hospital-wide communications in a crisis and help medical specialists care for more patients. Clinicians with the most acute care experience can focus on the sickest patients while having a telecommunications conduit to advise their colleagues. This way, technology can multiply expertise.

  • Electrical engineering Prof. Sujit Dey is working with a team in the Department of Psychiatry to build a personalized mental wellness platform to serve clinicians during COVID-19. The project’s goal is to prevent mental health crises in frontline healthcare providers during the pandemic. In addition to Dry, the project involves Profs. Jyoti Mishra, Steve Koh and Dhakshin Ramanathan.


Diamonds, Pencils Inspire Scientists to Create Multipurpose Protein Tool

UC San Diego named 4th best public research university in prestigious global rankings

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San Diego, Calif., August 17, 2020 -- The University of California San Diego has been named the fourth best public university in the United States for the second consecutive year by the 2020 Academic Ranking of World Universities (ARWU).

The overall rankings list the campus as the country’s 14th best university, up one spot from last year, and 18th in the world.

UC San Diego has consistently been included among the top 20 higher education institutions in the annual Academic Ranking of World Universities list since it was established in 2003.  Each year, the rankings are released by the Center for World-Class Universities at Shanghai Jiao Tong University, a public research university considered one of the most prestigious universities in China.

The annual Academic Ranking of World Universities list is based on six objective indicators including the number of alumni and faculty winning Nobel Prizes and Fields Medals; the number of highly cited researchers; the number of articles published in journals of Nature and Science; the number of articles indexed in Science Citation Index - Expanded and Social Sciences Citation Index; and per capita performance.

“UC San Diego’s multidisciplinary, collaborative approach to teaching, research and patient care makes it one of the most innovative and influential universities in the world,” said Chancellor Pradeep K. Khosla. “This year especially, our faculty and scholars have demonstrated strength, grace and ingenuity as they rise to new challenges to ensure the safety of our campus and surrounding community while continuing breakthrough research to address the global health crisis.”

Jacobs School of Engineering disciplines earned high marks in the ARWU Academic Subject Rankings, as well.

  • Mechanical Engineering at UC San Diego ranks 1st among public universities and 5th in the USA overall, and 9th in the world
  • Biotechnology at UC San Diego ranks 6th in the country and 9th in the world, and Biomedical Engineering at UC San Diego ranks 11th in the USA
  • Structural Engineering at UC San Diego ranks 7th in the USA among Civil Engineering programs
  • Electrical Engineering at UC San Diego ranks 12th in the country
  • Nanoenginering ranks 15th in the USA among Nanoscience and Nanotechnology programs
  • Computer Science and Engineering is tied for 19th in the country

UC San Diego’s world-renowned research has been critical during the global COVID-19 pandemic. The university currently is involved in three national trials evaluating the effectiveness of a vaccine to protect against SARS-CoV-2, the novel coronavirus that causes COVID-19. Other potentially life-saving research from the campus’ Jacobs School of Engineering includes the development of a low-cost, easy-to-use emergency ventilator for COVID-19 patients that is built around a ventilator bag most often found in ambulances. Additionally, an economic study from the university revealed how South Korea’s efficacy in containing COVID-19 is largely due to the country’s ability to notify people with detailed text messages whenever someone in their neighborhood is newly diagnosed with information on the businesses that person recently visited.

The campus’ cutting-edge research around the COVID-19 pandemic is at the foundation of its Return to Learn program, which is guided by scientific evidence and expertise from the UC San Diego School of Medicine and Wertheim School of Public Health and Longevity Science, as well as healthcare experts from UC San Diego Health. The continually evolving university-wide strategy enables a safe return to campus based on results from regular COVID-19 testing, wastewater monitoring and contact tracing, in addition to comprehensive facial covering requirements, and isolation housing for on-campus residents, among other measures.

For more information about the UC San Diego Return to Learn program, go to the program’s website

For more information on the 2020 Academic Ranking of World Universities, go to the Shanghai rankings website. More information on UC San Diego’s rankings can be found at the Campus Profile.

Extrachromosomal DNA is common in human cancer and drives poor patient outcomes

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In this scanning electron micrograph of inside the nucleus of a cancer cell, chromosomes are indicated by blue arrows and circular extra-chromosomal DNA are indicated by orange arrows. Image courtesy of Paul Mischel, UC San Diego.

San Diego, Calif.,Aug. 17. 2020 -- The multiplication of genes located in extrachromosomal DNA that have the potential to cause cancer drives poor patient outcomes across many cancer types, according to a Nature Genetics study published Aug. 17, 2020 by a team of researchers including Professors Vineet Bafna and Dr.Paul Mischel of the University of California San Diego  and Professor Roel Verhaak of Jackson Laboratories.

This is the first time that a study has shown that the multiplication of these extrachromosomalDNA (ecDNA) genes--a phenomenon called ecDNA oncogene amplification-- is present in a broad range of cancer tumor types. The researchers found that ecDNA is a common event in human cancer, occuring at minimum in 14% of human tumors, with far, far higher frequencies in the most malignant forms of cancer, including glioblastoma, sarcoma, esophageal, ovarian, lung, bladder, head and neck, gastric, and many others. The findings demonstrate that ecDNA plays a critical role in cancer. 

“We also find that patients whose cancers have ecDNA have significantly shorter survival than all other cancer patients, whose tumors are driven by other molecular lesions, even when grouped by tumor type,” said Dr. Mischel, one of the study’s authors and a distinguished professor at the UC San Diego School of Medicine and a member of the Ludwig Institute for Cancer Research. 

The shorter overall survival raises the possibility that cancer patients whose tumors are driven by ecDNA may not be as responsive to current therapies and may be in need of new forms of treatment. The researchers’ hope is that these findings will be applied to the development of powerful anti-cancer therapies for individuals with ecDNA-driven cancers. 

“This study provides a new window into the molecular epidemiology of ecDNA in cancer, providing a unique opportunity to study patients longitudinally to better understand how and why they respond poorly to treatment,” Dr. Mischel said.

The researchers observed that ecDNA amplification occurs in many types of cancers, but not in normal tissue or in whole blood, and that the most common recurrent oncogene amplifications frequently arise on ecDNA. Notably, ecDNA-based circular markers of amplification were found in 25 of 29 cancer types analyzed, and at high frequency in many cancers that are considered to be among the most aggressive histological types, such as glioblastoma, sarcoma, and esophageal carcinoma. 

“It seems that cancers have pulled an ancient evolutionary trick. Oncogenes and surrounding regulatory regions untether themselves from their chromosomal constraints, driving high oncogene copy number, accelerating tumor evolution, contributing to therapeutic resistance, and endowing tumors with the ability to rapidly change their genomes in response to rapidly changing environments, thereby accelerating tumor evolution and contributing to therapeutic resistance,” Dr. Mischel said.

To get to this finding, the research team used intensive computational analysis of whole-genome sequencing data from more than 3,200 tumor samples in The Cancer Genome Atlas (TCGA) and the Pan-Cancer Analysis of Whole Genomes (PCAWG), totaling over 400 terabytes of raw sequencing data, to observe the impact of ecDNA amplification on patient outcomes. 

We developed a powerful computational approach called Amplicon Architect, which identifies ecDNA based on three key features– circularity, high copy number, and “reuse of breakpoints,” said paper coauthor Bafna,a professor in the UC San Diego Department of Computer Science and Engineering. 

Dr. Mischel and Bafna are cofounders of Boundless Bio, a company developing innovative new therapies directed to extrachromosomal DNA (ecDNA) in aggressive cancers. 

“These results point to the urgent need for therapies that can target ecDNA and interfere with their ability to drive aggressive cancer growth, resistance, and recurrence,” said Jason Christiansen, chief technology officer of Boundless Bio.

What is ecDNA?

Extrachromosomal DNA, or ecDNA, are distinct circular units of DNA containing functional genes that are located outside cells’ chromosomes and can make many copies of themselves. ecDNA rapidly replicate within cancer cells, causing high numbers of oncogene copies, a trait that can be passed to daughter cells in asymmetric ways during cell division. Cancer cells have the ability to upregulate or downregulate oncogenes located on ecDNA to ensure survival under selective pressures, including chemotherapy, targeted therapy, immunotherapy, or radiation, making ecDNA one of cancer cells’ primary mechanisms of recurrence and treatment resistance. ecDNA are rarely seen in healthy cells but are found in many solid tumor cancers. They are a key driver of the most aggressive and difficult-to-treat cancers, specifically those characterized by high copy number amplification of oncogenes.

Frequent extrachromosomal oncogene amplification drives aggressive tumors

Nam-phuong Nguyen and Kristen Turner, Boundless Bio scientists 

Paul Mischel, M.D., Distinguished Professor at the University of California San Diego (UC San Diego) School of Medicine and a member of the Ludwig Institute for Cancer Research

Vineet Bafna, Ph.D., Professor of Computer Science & Engineering, UC San Diego

Howard Chang, M.D., Ph.D., Virginia and D.K. Ludwig Professor of Cancer Genomics and Genetics, Stanford University

Roel Verhaak, Ph.D., Professor and Associate Director of Computational Biology, The Jackson Laboratory


CMI Researcher Receives $7.3M DOE Grant to Address National Crop Productivity Through Soil Microbes

Multi-year research project will explore how to reduce microbial competition for organic Nitrogen and increase plant efficiency for long-term sustainable bioenergy production

SAN DIEGO, CA – August 14, 2020 -- UC San Diego Center for Microbiome Innovation (CMI) Faculty Member Karsten Zengler and a team of researchers have been awarded a $7.3 million grant over a five-year period from the U.S. Department of Energy (DOE) with a goal of making bioenergy feedstock crops more productive and resilient.

With a shortage of suitable land for growing feedstock crops that are necessary for sustainable bioenergy production, the DOE grants will accelerate research to develop crops with greater productivity and survivability in stressful environments. The grant awards will focus on the complex interactions among crops, soil, and soil microbes that impact productivity and stress resistance.

Zengler, a professor of pediatrics and bioengineering at UC San Diego, in collaboration with co-principal investigators, was awarded the grant in August by competitive peer review under a DOE Funding Opportunity Announcement for Systems Biology Research to Advance Sustainable Bioenergy Crop Developmentand sponsored by the Office of Biological and Environmental Research (BER) within DOE’s Office of Science.

Co-principal investigators include Trent Northen and John Vogel of Lawrence Berkeley National Laboratory and Amélie Gaudin of UC Davis.

“To avoid competition with food crops and maximize economic and environmental benefits, bioenergy crops should be grown on marginal soils with minimal inputs, especially energy-intensive synthetic nitrogen fertilizer,” said Zengler. “For long-term sustainability, we need bioenergy crops to be more reliant on microbial-driven organic nitrogen for nutrition. Principles identified for bioenergy crops might also translate to food crops, increasing land that can be use agriculture in general.”

Root exudates, the variety of substances secreted by the roots of living plants and exist in the surrounding soil called the rhizosphere, are thought to play a critical role in recruiting and maintaining beneficial microbes, including those that make nitrogen available to the plant and provide a critical source of nutrition for diverse microorganisms. 

Using funds from the multi-year grant, Zengler and team will explore if this exchange of exudates for plant benefits continues through the night when plants are not photosynthesizing with initial research that exudate composition indicates strong circadian rhythms. Understanding the nature of plant and microbial drivers behind these dynamic interactions is crucial for putting together a complete picture of nitrogen cycling and the uptake process in the rhizosphere.

“By using predictive models to understand the complexity of these processes and optimize sustainable bioenergy systems, exudate and bacterial community engineering will enable enhanced nitrogen supplies,” said Zengler. “Our goal is to reduce microbial competition for organic nitrogen and thereby increase plant nitrogen use efficiency.”

Zengler is one of over 130 CMI Faculty Members working to advance innovative collaborations between UC San Diego Microbiome experts and industry partners that will accelerate microbiome discovery and create innovative technologies to advance the field and enable major clinical breakthroughs. 

“Zengler’s highly innovative and interdisciplinary study will unveil findings in plant productivity at a very mechanistic level and advance microbiome knowledge that is currently lacking,” said CMI Executive Director Andrew Bartko, Ph.D. “The Center for Microbiome Innovation is committed to this work to develop new methods for manipulating microbiomes that will benefit the environment and ultimately improve human health.”

The study will unveil new knowledge in the field and greatly improve the ability to increase the productivity of bioenergy and other crops grown under low input conditions. Research efforts will be enabled by advanced techniques developed by this group, which include model ecosystems, absolute microbial abundance measurements, community modeling, 24,000 grass mutant lines, state-of-the-art metabolomics, and isotope dilution methods. 

Using these systems biology and multi-omics tools, the researchers will further weave together the intricate network between plants and microbes across time and space and allow for the first genome-scale computational model of the rhizosphere. Additionally, it will enable design of nutrient and microbial variants that are optimized for specific plant lines and provide a significant research advancement for the field of biosustainable biotechnology.

Zengler’s research focus at UC San Diego is using omics tools to understand how microbes interact with their partners, and the use of computational models to analyze and integrate the data.


About Center for Microbiome Innovation at University of California San Diego:
The UC San Diego Center for Microbiome Innovation leverages the university's strengths in clinical medicine, bioengineering, computer science, the biological and physical sciences, data sciences, and more to coordinate and accelerate microbiome research. We also develop methods for manipulating microbiomes for the benefit of human and environmental health. Learn more at cmi.ucsd.edu/ and follow @CMIDigest

Media Contact:
Erin Bateman
Communications Officer
Center for Microbiome Innovation, Jacobs School of Engineering
UC San Diego

UC San Diego engineers selected for DARPA Secure Silicon program

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San Diego, Calif., August 13, 2020 -- Engineers at UC San Diego have been selected by DARPA to participate in the Automatic Implementation of Secure Silicon (AISS) program to increase the security of our nation’s semiconductor supply chain. Through a team of academic, government and industry partners, the AISS program aims to automate the process of incorporating scalable defense mechanisms into semiconductor chip designs, while allowing designers to explore chip economics versus security trade-offs based on the expected application.

AISS is composed of two teams of researchers and engineers who will explore the development of a novel design tool and IP ecosystem – which includes tool vendors, chip developers, and IP licensors – allowing defenses to be incorporated efficiently into chip designs. The expected AISS technologies could enable hardware developers to not only integrate the appropriate level of state-of-the-art security based on the target application, but also balance security with economic considerations like power consumption, die area, and performance.

UC San Diego engineers will work on the team led by Synopsys, an electronic design automation company, as prime contractor. Engineers led by Sujit Dey, a professor of Electrical and Computer Engineering and director fo the Center for Wireless Communications at the Jacobs School, will create a framework to allow developers of new machine vision and artificial intelligence algorithms to more efficiently take advantage of both embedded software and hardware accelerators, resulting in optimized system-on-chip architectures which can meet desired power, area and speed metrics, with security built in to the process.

 “We are developing a framework which ultimately will let developers of new machine vision and machine learning algorithms specify their application at a high level, and our methodology will come up with a very efficient hardware-software co-design implementation for them to use,” said Dey.

Dey and his team will collaborate with Anand Raghunathan from Purdue University on this task. The rest of the larger Synopsys-led team includes Arm, Boeing, Florida Institute for Cybersecurity Research at the University of Florida, Texas A&M University, and UltraSoC.

The AISS program is part of DARPA’s larger Electronics Resurgence Initiative, which engineers at the Jacobs School are also part of; electrical engineering Professor Andrew Kahng is leading a multi-institution project which aims to develop electronic design automation tools for 24-hour, no-human-in-the-loop hardware layout generation.


This research was, in part, funded by the U.S. Government. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the U.S. Government.

Nanoengineers, radiologists work toward immunotherapy for liver cancer

San Diego, Calif., August 13, 2020-- A team of nanoengineers and interventional radiologists at UC San Diego and the VA San Diego Healthcare System received a $575,000 grant from the Congressionally Directed Medical Research Programs (CDMRP) to develop a new method to treat liver cancer by combining ablation—a treatment to destroy tumors—with an immunotherapy derived from a plant virus.

Liver cancer is the second leading cause of cancer-related death in the country, in part because few patients are eligible for curative treatments such as a liver transplant. Instead, many patients will be treated with a minimally invasive procedure called ablation, which uses a wand inserted via a pinhole in the skin to destroy small tumors using extreme temperatures. Even with this treatment, however, the cancer can recur.

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Structure of the Cowpea mosaic virus

Nanoengineers led by Professor Nicole Steinmetz, director of the UC San Diego Center for Nano-ImmunoEngineering, plan to improve the long-term results of ablation for liver cancer by combining it with a nanotechnology developed from a plant virus called the cowpea mosaic virus (CPMV). This plant virus has been shown to safely stimulate the immune system of humans. Since it is a plant virus, it is non-toxic and does not infect humans.

In collaboration with a team of interventional radiologists and VA scientists led by Dr. Isabel Newton, they will combine cryoablation, which destroys tumors with ice, with injections of the CPMV nanoparticle into the tumor. CPMV acts as a flare inside the tumor, stimulating the immune system to recognize and fight the tumor. Once activated, the immune system makes specialized cells that can patrol the body for tumor cells, even if they are at distant sites or if they appear in the future. This combined treatment is designed to treat the liver tumor and any tumor cells that may have spread throughout the body, protecting against cancer recurrence.

Steinmetz and her team have used the cowpea mosaic virus to successfully treat melanoma in dogs, and are using it to develop an ovarian cancer immunotherapy, thanks to a grant from the National Institutes of Health.


Flipping a metabolic switch to slow tumor growth

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Schematic describing in vivo sphingolipid physiology under high- and low-dose myriocin treatments

San Diego, Calif., Aug. 12, 2020-- The enzyme serine palmitoyl-transferase can be used as a metabolically responsive “switch” that decreases tumor growth, according to a new study by a team of San Diego scientists, who published their findings Aug. 12 in the journal Nature.

By restricting the dietary amino acids serine and glycine, or pharmacologically targeting the serine synthesis enzyme phosphoglycerate dehydrogenase, the team induced tumor cells to produce a toxic lipid that slows cancer progression in mice. Further research is needed to determine how this approach might be translated to patients.

Over the last decade researchers have learned that removing the amino acids serine and glycine from animal diets slows the growth of some tumors. However, most research teams have focused on how these diets impact epigenetics, DNA metabolism, and antioxidant activity. In contrast, the researchers from the University of California San Diego and the Salk Institute for Biological Studies identified a dramatic impact of these interventions on tumor lipids, particularly those found on the surface of cells. 

“Our work highlights the beautiful complexity of metabolism as well as the importance of understanding physiology across diverse biochemical pathways when considering such metabolic therapies,” said Christian Metallo, a professor of bioengineering at the Jacobs School of Engineering at UC San Diego and the paper’s corresponding author.

In this case, serine metabolism was the researchers’ focus. The enzyme serine palmitoyl-transferase, or SPT, typically uses serine to make fatty molecules called sphingolipids, which are essential for cell function. But if serine levels are low, the enzyme can act “promiscuously” and use a different amino acid such as alanine, which results in the production of toxic deoxysphingolipids. 

The team decided on this research direction after examining the affinity that certain enzymes have to serine and comparing them to the concentration of serine in tumors. These levels are known as Km or the Michaelis constant, and the numbers pointed to SPT and sphingolipids. 

“By linking serine restriction to sphingolipid metabolism, this finding may enable clinical scientists to better identify which patients’ tumors are most sensitive to serine-targeting therapies,” Metallo said. 

These toxic deoxysphingolipids are most potent at decreasing the growth of cells in “anchorage-independent” conditions--a situation where cells cannot easily adhere to surfaces that better mimics tumor growth in the body. Further studies are necessary to better understand the mechanisms through which deoxysphingolipids are toxic to cancer cells and what effects they have on the nervous system.

In the Nature study, the research team fed a diet low on serine and glycine to xenograft model mice. They observed that SPT turned to alanine to produce toxic deoxysphingolipids instead of normal sphingolipids. In addition, researchers used the amino-acid based antibiotic myriocin to inhibit SPT and deoxysphingolipid synthesis in mice fed low serine and glycine diets and found that tumor growth was improved. 

Depriving an organism of serine for long periods of time leads to neuropathy and eye disease, Metallo pointed out. Last year, he co-lead an international team that identified reduced levels of serine and accumulation of deoxysphingolipids as a key driver of a rare macular disease called macular telangiectasia type 2, or MacTel. The work was published in the New England Journal of Medicine. However, serine restriction or drug treatments for tumor therapy would not require the prolonged treatments that induce neuropathy in animals or age-related diseases.

This work was supported by the National Institutes of Health (R01CA188652 and R01CA234245; U54CA132379), a Camille and Henry Dreyfus Teacher-Scholar Award, the National Science Foundation Faculty Early Career Development (CAREER) Program, the Helmsley Center for Genomic Medicine and funding from Ferring Foundation. This work was also supported by NIH grants to the Salk Institute Mass Spectrometry Core (P30CA014195, S10OD021815).

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Schematic depicting synthesis of canonical sphingolipids from serine (blue) and deoxysphingolipids from alanine (red) via promiscuous SPT activity and ceramide synthase (CERS).

Serine restriction alters sphingolipid diversity to constrain tumour growth


UC San Diego Department of Bioengineering: Thangaselvam Muthusamy, Thekla Cordes, Michal K. Handzlik,  Le You, Esther W. Lim, Jivani Gengatharan,  Mehmet G. Badur, Christian M. Metallo. Professor Metallo is also affiliated with the UC San Diego Moores Cancer Center

Salk Institute for Biological Studies: , Antonio F. M. Pinto, Matthew J. Kolar, Alan Saghatelian

Thekla Cordes, Michal K. Handzlik and Le You contributed equally to the work. 


Nanoengineering and chemical engineering at UC San Diego in the spotlight

San Diego, Calif., August 10, 2020 -- A creative group of faculty, students and staff within the University of California San Diego are taking innovative approaches to develop breakthroughs in nanomedicine, flexible electronics, and energy storage. Together, this group makes up the Department of NanoEngineering and the Chemical Engineering Program at the UC San Diego Jacobs School of Engineering. 

A virtual issue of the journal ACS Nano highlights the wide ranging research, educational and workforce-development contributions of this extraordinary group. A group of UC San Diego nanoengineering faculty led by professor Darren Lipomi wrote the editorial for this virtual issue, which serves to organize a number of recent papers from the department that have been published in ACS Nano.

The nanoengineering department is highly interdisciplinary and known internationally for its many strengths in research areas that are leading to innovations in nanomedicine, flexible electronics, and energy storage. Leadership in computational materials science cuts across the entire department. Chemical engineering is also integral to the department. As theoretical and computational strengths within the department grow, the connections between chemical engineering, nanoengineering and materials science continue to multiply. The results will shape multiple fields for years to come.

Just this summer, UC San Diego won a prestigious $18 million Materials Research Science and Engineering Center (MRSEC) from the National Science Foundation. All four of the faculty co-leading the two research thrusts within this MRSEC -- predictive assembly and living materials -- are nanoengineering professors. In addition, the MRSEC director and associate director hold secondary and primary appointments in nanoengineering, respectively. 

Winning this MRSEC speaks to the forward-looking moves at UC San Diego to connect nanoengineering and chemical engineering. The MRSEC is also the first big win for the UC San Diego Institute for Materials Discovery and Design (IMDD), which focuses on bridging the gap between physical scientists and engineers on the campus to enable cross-disciplinary research. The IMDD is also led by a nanoengineering professor. 

In the editorial introducing the virtual issue, the editorial authors highlight recent contributions from department research groups in the areas of nanomedicine, biomaterials, flexible and stretchable electronics, complex alloys and heterointerfaces, theory and computation, energy storage, nanophotonics and nanomagnetics, and photovoltaics.

Education is also central to the mission of the department, which offers BS, MS, and PhD degrees in two programs: nanoengineering and chemical engineering. Both BS degrees are ABET certified. 

The department faculty include four professors who are specialists in the pedagogy of chemical engineering. These core chemical engineering teaching faculty lead the way well-established curricula that are consistent with other top programs. 

The nanoengineering curriculum, on the other hand, is more unique. Given its interdisciplinarity and newness, faculty design nanoengineering curricula in ways that can respond to new developments in the field and at the same time provide relevant theoretical and practical grounding for students to allow them to develop satisfying careers while meeting the needs of employers. 

Input from the department's Industrial Advisory Board, exit surveys with students, internal teaching working groups, and external feedback from auditors and review committees are used to improve our program in a continuous manner. 

Faculty and students in the department are engaged with industry partners on projects of shared interest across many application areas. Nanoengineering faculty play key roles in industry focused centers and institutes across the Jacobs School of Engineering including: the Sustainable Power and Energy Center (SPEC), the Center for Wearable Sensors (CWS), the Center for NanoImmunoEngineering (NanoIE), the Contextual Robotics Institute (CRI), and the Institute for Materials Discovery and Design (MRSEC)

Engineer Earns Presidential Award for Improving Underrepresented Student Access to STEM Experiences

Olivia Graeve, a materials science expert, is being recognized by the White House for her outreach work in STEM.

San Diego, Calif., Aug. 7, 2020 -- Olivia Graeve, a UC San Diego professor of mechanical and aerospace engineering, has received the Presidential Award for Excellence in Science, Mathematics and Engineering Mentoring from the White House.

The award was created in 1995 to honor extraordinary individuals whose efforts have helped provide underrepresented groups with access to opportunities in STEM.

Graeve is recognized for her role as the director of the IDEA Engineering Student Center at the Jacobs School of Engineering; her work promoting binational research opportunities for high school and college students across the U.S–Mexico border; and her efforts within the Society of Hispanic Professional Engineers (SHPE) to increase opportunities for Hispanic students and faculty. She received the award virtually on Monday.

“As I build programs for students, I am filled with hope that we can build something extraordinary, with kindness, compassion and respect for others,” Graeve said. “I hope that we will eliminate borders and bring down walls.”

Graeve, a Tijuana native and UC San Diego undergraduate engineering alumna, conducts research on novel materials in the Xtreme Materials Laboratory, which she leads.

Graeve is an expert in materials science research.

As founding director of the CaliBaja Center for Resilient Materials and Systems at UC San Diego, Graeve has made the center the home of bi-national materials research, with scientists and engineers developing advanced materials for extreme environments such as high temperatures, extreme strain rates and deformations, and radiation.

She also serves as faculty director of the IDEA Engineering Student Center, creating programs to support students from underrepresented backgrounds in engineering through graduation and beyond.

For the past eight years, Graeve has been leading a binational summer research program for high school and undergraduate students called ENLACE. The program gives students from underrepresented backgrounds in engineering in the United States and Mexico the opportunity to work together to promote the development of cross-border friendships in a research setting.

She is also the driving force behind the CaliBaja Education Consortium, a collaboration between UC San Diego and 20 institutions in Mexico. The consortium, launched in June 2017, helps researchers and students work together across the border. Through the consortium, students from high school to graduate school are able to do research and take classes both at UC San Diego and at various Baja California institutions.

In 2018, Graeve conducted a survey of engineering Latinx faculty members in the United States and found that only 48 out of 600 were born in the United States. This, Graeve says, is due to the virtual lack of pipeline to academia for Latinx in the United States.

As a result, Graeve worked with SHPE to boost the attendance of Latinx faculty members at the annual meetings, leading to the creation of a new Latinx engineering faculty cohort dedicated to Hispanic engineering education. Graeve’s support also helped transform part of the SHPE National Conference into a successful mentoring event for both students and faculty.

Graeve is a member of the Mexican Academy of Engineering, the Mexican Academy of Sciences and a Fellow of the American Ceramic Society. She was named one of the 100 Most Powerful Women of Mexico by Forbes in 2017.

Qualcomm Institute-based Startup Receives Funding to Continue Development of Opioid Sensor

San Diego, Calif., August 6, 2020 -- CARI Therapeutics, a member of UC San Diego’s Qualcomm Institute Innovation Space, has received additional funding from the National Institute of Drug Abuse (NIDA) to refine their tiny implantable biosensor that could help combat the deadly and destructive opioid crisis in the United States.

The second phase of funding from the NIDA’s Small Business Innovation Research and Small Business Technology Transfer programs will allow CARI Therapeutics to continue developing a biosensor called “BioMote” that can continuously monitor opioid use in a patient and send data to health care providers who can intervene quickly if opioids are detected. It can be used along with other treatment options to help reduce relapses and overdoses. 

CARI Therapeutics’s biosensor (depicted next to a United States penny) is about the size of a grain of rice and is implanted under the skin on the wrist.  

“Substance misuse is an immense problem for our society. Beyond the heavy costs from loss of work productivity, health care needs and an increased burden on the judicial system, the human costs from lost lives, broken families and unfulfilled potential is devastating,” said CARI Therapeutics CEO Patrik Schmidle.

“Current treatment strategies are not keeping pace with the growing opioid crisis and new solutions are urgently needed, particularly given the high relapse rates of opioid users,” he said.

Substance use disorders are estimated to cause $400 billion worth of financial damage annually to the U.S. economy, according to the National Institutes of Health (NIH). The number of deaths related to drug overdose has more than quadrupled over the last decade, from 16,000 in 2006 to more than 70,000 in 2017. More than 3 million U.S. citizens and more than 16 million people worldwide are estimated to be suffering from opioid use disorders, according to data from the NIDA, which is a subdivision of the NIH.

Patients who have a previous history of overdose, who have recently been discharged from detoxification programs or who are beginning or ending opioid maintenance therapy tend to be at a high risk of opioid overdose, according to a study published in the NIH’s National Library of Medicine. And with the current COVID-19 pandemic causing even more distress and anxiety for those patients, resulting in an increase in drug and alcohol misuse, the risk is even greater.

“Our BioMote has the potential to save insurance companies billions in dollars in claim costs by reducing high relapse rates and ensuring patients in treatment programs use their prescribed medication appropriately. And more importantly, it could also have an enormous social impact by helping to save thousands of lives every year,” Schmidle said.

The wrist-worn wearable device is located above the sensor and transmits opioid measurements. 

Dr. Gregory Polston, a pain medicine physician at both UC San Diego Heath and the Veteran’s Administration who will advise on the development of the BioMote, agrees.

“By getting real data, from real patients, we will be better able to follow patients, confirm that they are taking their medications and maybe even warn or identify patients if they are in trouble,” he said. “Aggregating this data, we will be able to recommend best practices with these medications. Think of trying to recommend insulin to patients with diabetes without knowing their glucose levels.”

Precision medicine helping to “close the loop”

CARI Therapeutics’s current work builds on the first phase of the BioMote project that successfully demonstrated the viability of a microscale biosensor system that integrates the ability to detect, measure and track the use of opioids to help treat those with opioid use disorders.

The sensor—about the size of a grain of rice— is injected subcutaneously, where it can detect the presence of opioids in interstitial fluid. Measurements are taken throughout the day and the results are communicated wirelessly to a device such as a smartphone or smartwatch. The device can warn users of risky behavior and intervene by alerting healthcare providers if a patient is at risk of dying because of a significant increase in opioid levels in their system.

The information detected by the sensor is then shared with patients, loved ones and health care providers

Drew Hall, an associate professor in the Electrical and Computer Engineering Department at the Jacobs School of Engineering, is one of the principal investigators on the project and developed the injectable sensor technology and the assays used to detect opioids.

“This technology is important because it ‘closes the loop’ in the treatment paradigm by providing quantitative, real-time data rather than relying solely on self-reporting,” he said. “This fits within the broader precision-medicine initiative that is changing how physicians tailor a treatment to individuals rather than using a one-size-fits-all approach.” 

The next phase of research funded by this award will focus on:

  • Further expanding the functionality of the sensor
  • Refining the tools and procedures for inserting and extracting the sensor
  • Testing the biosensor in swine and humans

A “game changer” in dealing with increased overdoses

Dr. Carla Marienfeld, a clinical professor of psychiatry and medical director of the Addiction Recovery and Treatment Program at UC San Diego School of Medicine, said medical personnel are seeing signs of increased substance use as well as increased overdoses due to the COVID-19 pandemic.

Marienfeld, who is an advisor on the project, sees first-hand the needs and struggles in people who are trying to recover from substance misuse. “This device will help bring advanced, private, and specific care to the people struggling with substance use disorders that may be worsening during the pandemic,” she said.

Clinicians can remotely keep track of opioid use to inform patient treatment.

Dr. Krishnan Chakravarthy, an assistant clinical professor of anesthesiology and pain medicine at UC San Diego Health, said the current pandemic has highlighted the growing difficulties for addiction patients and the problem of opiate dependence.

“With lack of consistent access to care, these patients find themselves in a tough situation,” he said. “In addition, due to a lack of effective ways to measure addiction and opiate use and issues surrounding diversion, the BioMote technology could be a game changer in how we address these patients.”

This is the fourth federal award, totaling more than $4 million, that CARI Therapeutics has received for its efforts to develop biosensors to monitor and report alcohol and opioid use. (A previous project led to the creation of a technology platform for alcohol monitoring.)  Schmidle credits the resources of the Qualcomm Institute and the partnerships with UC San Diego engineering, psychiatry and pain management experts in helping to prepare the grant proposals and ultimately earn the funding.

Other UC San Diego collaborators on the “BioMote” project include the Institute of the Global Entrepreneur (IGE), which has been supporting the development of the commercialization strategy.

Biomedical Engineering Society earns Outstanding Chapter Award

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Members of the BMES leadership team.

By Gabby Gracida

San Diego, Calif., July 31, 2020 -- UC San Diego’s chapter of the Biomedical Engineering Society (BMES) was recognized with the Chapter Outstanding Achievement Award for their 2019-2020 efforts. This is the second time the undergraduate BMES chapter received this prestigious award, after earning the honor in 2017.

The 150+ person UC San Diego chapter offers a variety of events that serve as a resource to bioengineering students, the UC San Diego campus, and the San Diego community. They were recognized for their “ability to be well-rounded, hardworking, and efficient in their chapter activities.”

“I think what makes us unique is that we’re focused on building something great together,” said Michael Bennington, the incoming 2020-2021co-president. “Members are not competing with each other; they can come together and contribute to BMES and build friendships.”

“We’re not about outshining each other or other events or workshops,” said Elisabette Tapia, 2020-2021 co-president. “We very much have a ‘how can we grow together?’ format of thinking, which is why we’re able to to do more. Our members want each other to put their best foot forward.”

BMES’s mission is to be a resource for undergraduate bioengineering students and anyone who is interested in learning more about the field. They offer technical workshops focused on a variety of topics, while also connecting people with lab and research opportunities, hosting outreach events, networking opportunities, and social events for bioengineering students.

The chapter also offers campus-wide events that are open to all students and majors. Though their large events were held virtually this year due to COVID-19, the online format allowed them to reach more attendees than in years past. Lab Expo, an annual research exposition, hosted over 75 student researchers who presented on various bioengineering research efforts.

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The Bioengineering Day leadership team.

Bioengineering Day was also held virtually, and celebrated UC San Diego's consistently top ranked bioengineering department, current research by students, and advances in the field itself. The online event was an opportunity for undergraduates, graduate students, faculty, and members from industry to form valuable connections with one another.

BMES’s outreach efforts extend far beyond UC San Diego. Students host bioengineering demonstrations for K-12 classrooms, mentor and advise high school students, and connect with local teachers to share resources. In just under five weeks, BMES students were able to reach over 100 high school students through a college advising program they hosted, where undergraduate BMES members connected with high school classrooms via Zoom and answered questions about college.

“I’m glad that all the hard work that the executive board, officer board, and our members put in is being recognized as something positive,” said Reo Yoo, 2019-2020 chapter president. “We spend a lot of time planning things, leading events, and being present in all aspects of the organization -- almost like a second job. It feels nice that apart from doing good for the community, our efforts are something that other people also see as impactful.”

As they enter the 2020-2021 school year, BMES plans to continue incorporating virtual event opportunities to broaden their reach, and focus on serving as a resource to both UC San Diego and the community.

“A large part of my college experience has been defined by BMES. To me, I think of UC San Diego and BMES as something truly special and truly great in our community. This award helps reassure us that we’re on the right track and that we are doing something important,” Bennington said.

The UC San Diego bioengineering department is regarded as the No. 1 bioengineering doctoral program in the nation according to the National Research Council, and U.S. News & World Report ranks it the No. 4 graduate program in the country. Bioengineering has ranked among the top four programs in the nation every year for more than a decade.

New fabrication method brings single-crystal perovskite devices closer to viability

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A single-crystal thin perovskite film during the transfer process. Photos by Yusheng Lei

San Diego, Calif., July 29, 2020 --Nanoengineers at UC San Diego developed a new method to fabricate perovskites as single-crystal thin films, which are more efficient for use in solar cells and optical devices than the current state-of-the-art polycrystalline forms of the material.

Their fabrication method—which uses standard semiconductor fabrication processes—results in flexible single-crystal perovskite films with controlled area, thickness, and composition. These single-crystal films showed fewer defects, greater efficiency, and enhanced stability than their polycrystalline counterparts, which could lead to the use of perovskites in solar cells, LEDs, and photodetectors.

Researchers in Professor Sheng Xu’s Jacobs School of Engineering nanoengineering lab published their findings on July 29 in Nature.

“Our goal was to overcome the challenges in realizing single-crystal perovskite devices”, said Yusheng Lei, a nanoengineering graduate student and first author of the paper. “Our method is the first that can precisely control the growth and fabrication of single-crystal devices with high efficiency. The method doesn’t require fancy equipment or techniques—the whole process is based on traditional semiconductor fabrication, further indicating its compatibility with existing industrial procedures.”

Perovskites are a class of semiconductor materials with a specific crystalline structure that demonstrate intriguing electronic and optoelectronic properties, which make perovskites appealing for use in devices that channel, detect, or are controlled by light—solar cells, optical fiber for communication, or LED-based devices, for example.

“Currently, almost all perovskite fabrication approaches are focused on polycrystalline structures since they’re easier to produce, though their properties and stability are less outstanding than single-crystal structures”, said Yimu Chen, a nanoengineering graduate student and co-first author of the paper.   

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Single-crystal perovskite films could enable more efficient flexible solar cells such as the one pictured here.

Controlling the form and composition of single-crystal perovskites during fabrication has been difficult. The method invented in Xu’s lab was able to overcome this roadblock by taking advantage of existing semiconductor fabrication processes including lithography.

“Modern electronics such as your cell phone, computers, and satellites are based on single-crystal thin films of materials such as silicon, gallium nitride, and gallium arsenide,” said Xu. “Single crystals have less defects, and therefore better electronic transport performance, than polycrystals. These materials have to be in thin films for integration with other components of the device, and that integration process should be scalable, low cost, and ideally compatible with the existing industrial standards. That had been a challenge with perovskites.”

In 2018, Xu’s team was the first to successfully integrate perovskites into the industrial standard lithography process; a challenge, since lithography involves water, which perovskites are sensitive to. They got around this issue by adding a polymer protection layer to the perovskites followed by dry etching of the protection layer during fabrication. In this new research, the engineers developed a way to control the growth of the perovskites at the single crystal level by designing a lithography mask pattern that allows control in both lateral and vertical dimensions.

In their fabrication process, the researchers use lithography to etch a mask pattern on a substrate of hybrid perovskite bulk crystal. The design of the mask provides a visible process to control the growth of the ultra-thin crystal film formation.  This single-crystal layer is then peeled off the bulk crystal substrate, and transferred to an arbitrary substrate while maintaining its form and adhesion to the substrate. A lead-tin mixture with gradually changing composition is applied to the growth solution, creating a continuously graded electronic bandgap of the single-crystal thin film.

The perovskite resides at the neutral mechanical plane sandwiched between two layers of materials, allowing the thin film to bend. This flexibility allows the single-crystal film to be incorporated into high-efficient flexible thin film solar cells, and into wearable devices, contributing toward the goal of battery-free wireless control.

Their method allows researchers to fabricate single-crystal thin films up to  5.5 cm by 5.5 cm squares, while having control over the thickness of the single-crystal perovskite—ranging from 600 nanometers to 100 microns—as well as the composition gradient in the thickness direction.

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Graded single crystal perovskites

 “Further simplifying the fabrication process and improving the transfer yield are urgent issues we’re working on,” said Xu. “Alternatively, if we can replace the pattern mask with functional carrier transport layers to avoid the transfer step, the whole fabrication yield can be largely improved.”

Instead of working to find chemical agents to stabilize the use of polycrystalline perovskites, this study demonstrates that it’s possible to make stable and efficient single-crystal devices using standard nanofabrication procedures and materials. Xu’s team hopes to further scale this method to realize the commercial potential of perovskites.


This work was supported by the start-up fund by University of California San Diego; California Energy Commission award no. EPC-16-050; the microfabrication involved in this work was in part performed at the San Diego Nanotechnology Infrastructure (SDNI) of UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which was supported by the National Science Foundation (grant number ECCS-1542148); the characterization work was performed, in part, at the Center for Integrated Nanotechnologies, an Office of Science User Facility operated for the US Department of Energy (DOE) Office of Science by Los Alamos National Laboratory (contract 89233218CNA000001) and Sandia National Laboratories (contract DE-NA-0003525).

Computer Scientist Receives NSF Grant to Identify Antibody Responses Against SARS-COV-2

Pavel Pevzner, a professor in the Department of Computer Science and Engineering, is the lead researcher on an NSF grant for COVID-19 research. 

San Diego, Calif., July 27, 2020 -- Pavel Pevzner, Ronald R. Taylor Professor of Computer Science in UC San Diego’s Computer Science and Engineering Department, has been awarded a $300,000 grant, through the National Science Foundation’s EArly-concept Grants for Exploratory Research (EAGER) program, to investigate immune system genes in humans, bats and other mammals and identify successful antibody responses against SARS-COV-2.

The project, called Assembling the Immunoglobulin Loci Across Mammalian Species and Across the Human Population, seeks to generate immunoglobulin (Ig) locus sequences, which vary across human populations. The project will also analyze this genomic region in mammals to better understand how different species generate antiviral antibodies. 

“The immunoglobulin locus is complex, making it difficult to assemble its genomic sequence and find all the immune genes hiding there,” said Pevzner. “Since these genes represent a template to generate antibodies, the lack of Ig assemblies has been a barrier to antibody engineering and vaccine testing. This project seeks to develop the first specialized software tools to assemble and annotate the immunoglobulin locus in humans and other mammalian species.” 

To illuminate the genomics behind antiviral immune responses, Pevzner’s team will develop a new algorithm to analyze personalized immune genes that have shown strong immunological responses. 

The Ig locus contains variable immune genes – called V, D and J – that can rearrange in different configurations to encode around 100 million unique, circulating human antibodies. Each one is a mosaic of V, D, and J genes, making it virtually impossible to study an organism’s antibody repertoire and infection response without decoding the nucleotide sequences in the locus.  Personalized immunogenomics seeks to analyze how V, D, and J gene variations affect individual immune responses.

Other mammals may also provide important insights. Bats have much greater immune gene diversity than humans, but still have no accurate Ig loci assemblies, making it difficult to study how they generate antibodies to cope with multiple viruses. The group will also analyze the Ig locus in llamas, which could provide promising antibodies against COVID-19.  

The Pevzner group will also work with immunogenomics experts to analyze Ig loci in COVID-19 patients, looking for helpful mutations. To disseminate the team’s findings, the grant will also fund a new Coursera class: Bioinformatics of SARS-COV-2.

“The deadly COVID-19 pandemic has shown that we need to develop novel bioinformatic techniques to understand how different mammals respond to various viruses to help us develop better therapeutics,” said Pevzner. “These tools will support ongoing efforts to sequence Ig loci in COVID-19 patients and to understand why some patients are able to generate effective anti-viral antibodies and others fail.”

Rare Glassy Metal Discovered During Quest to Improve Battery Performance

San Diego, Calif., July 27, 2020 -- Materials scientists studying recharging fundamentals made an astonishing discovery that could open the door to better batteries, faster catalysts and other materials science leaps.

Scientists from the University of California San Diego and Idaho National Laboratory scrutinized the earliest stages of lithium recharging and learned that slow, low-energy charging causes electrodes to collect atoms in a disorganized way that improves charging behavior. This noncrystalline “glassy” lithium had never been observed, and creating such amorphous metals has traditionally been extremely difficult.

The findings suggest strategies for fine-tuning recharging approaches to boost battery life and—more intriguingly—for making glassy metals for other applications. The study was published on July 27 in Nature Materials.

Charging knowns, unknowns

New research describes the evolution of nanostructural lithium atoms (blue) depositing onto an electrode (yellow) during the battery charging operation.
New research describes the evolution of nanostructural lithium atoms (blue) depositing onto an electrode (yellow) during the battery charging operation.(Image courtsey of Idaho National Laboratory)

Lithium metal is a preferred anode for high-energy rechargeable batteries. Yet the recharging process (depositing lithium atoms onto the anode surface) is not well understood at the atomic level. The way lithium atoms deposit onto the anode can vary from one recharge cycle to the next, leading to erratic recharging and reduced battery life.

The INL/UC San Diego team wondered whether recharging patterns were influenced by the earliest congregation of the first few atoms, a process known as nucleation.

“That initial nucleation may affect your battery performance, safety and reliability,” said Gorakh Pawar, an INL staff scientist and one of the paper’s two lead authors.

Watching lithium embryos form
The researchers combined images and analyses from a powerful electron microscope with liquid-nitrogen cooling and computer modeling. The cryo-state electron microscopy allowed them to see the creation of lithium metal “embryos,” and the computer simulations helped explain what they saw.

In particular, they discovered that certain conditions created a less structured form of lithium that was amorphous (like glass) rather than crystalline (like diamond).

“The power of cryogenic imaging to discover new phenomena in materials science is showcased in this work,” said Shirley Meng, corresponding author and researcher who led UC San Diego’s pioneering cryo-microscopy work. Meng is a professor of NanoEngineering, and Director of UC San Diego’s Sustainable Power and Energy Center, and the Institute for Materials Discovery and Design. The imaging and spectroscopic data are often convoluted, she said. “True teamwork enabled us to interpret the experimental data with confidence because the computational modeling helped decipher the complexity.”

A glassy surprise
Pure amorphous elemental metals had never been observed before now. They are extremely difficult to produce, so metal mixtures (alloys) are typically required to achieve a “glassy” configuration, which imparts powerful material properties.

During recharging, glassy lithium embryos were more likely to remain amorphous throughout growth. While studying what conditions favored glassy nucleation, the team was surprised again.

“We can make amorphous metal in very mild conditions at a very slow charging rate,” said Boryann Liaw, an INL directorate fellow and INL lead on the work. “It’s quite surprising.”

That outcome was counterintuitive because experts assumed that slow deposition rates would allow the atoms to find their way into an ordered, crystalline lithium. Yet modeling work explained how reaction kinetics drive the glassy formation. The team confirmed those findings by creating glassy forms of four more reactive metals that are attractive for battery applications.

What’s next?
The research results could help meet the goals of the Battery500 consortium, a Department of Energy initiative that funded the research. The consortium aims to develop commercially viable electric vehicle batteries with a cell level specific energy of 500 Wh/kg. Plus, this new understanding could lead to more effective metal catalysts, stronger metal coatings and other applications that could benefit from glassy metals.

(Story written by Idaho National Laboratory (INL) / INL media contact: Sarah Neumann, 208-520-1651, sarah.neumann@inl.gov)

A Prototype for Help in the Fight Against COVID-19

From face masks and test swabs to protective boxes for patients and caregivers, Qualcomm Institute’s Prototyping Lab has been lending its equipment and expertise to help combat COVID-19

San Diego, Calif., July 23, 2020 -- In the midst of the unprecedented COVID-19 pandemic that had UC San Diego researchers racing to understand the complexities around the virus’s spread and to find ways to combat it, engineers and fabrication specialists at the Qualcomm Institute’s Prototyping Lab leapt into action.

Vacuum exhaused isolation lockers, or VEILs, produced in the Prototyping Lab are ready to be delivered to local hospitals.

The lab’s 3D printers, laser cutters and other machinery along with in-house expertise in mechanical and electrical engineering design, have been tapped by researchers across campus as they seek to protect patients and healthcare workers and provide mass testing for the virus.

“It’s exciting and gratifying to see how much the community has pulled together to help in every way possible during this time,” said Qualcomm Institute (QI) mechanical engineer Alex Grant, who along with Prototyping Lab Director Jeffrey Sandubrae has been stretching the lab’s capacity to help several important initiatives move forward.

“We are pleased to be able to lend our resources in this time of crisis. We have the unique benefit of collaborating with our campus partners and industry to bring an idea to life and create potential solutions that could benefit our community, our region and our world,” Sandubrae said.

Qualcomm Institute Director Ramesh Rao said, “Within our Atkinson Hall, we have developed an infrastructure that can accommodate many diverse projects and groups. We offer not only a unique facility in our Prototyping Lab but the unique expertise of our technical and professional staff.”

Helping meet the need for testing

The request from Rady Children’s Hospital to the Prototyping Lab began with a simple need for rayon fibers to make testing swabs for COVID-19.

Grant started procuring materials to help the hospital meet the heavy demand for testing, and the lab’s involvement quickly expanded to brainstorming ways to manufacture the swabs themselves.

“The intent was to make as many swabs to meet the needs of Rady’s to begin with, and it’s since evolved. We did some brainstorming and prototypes of different swab geometries using our 3D Markforged printer,” he recalled.

Trays QI mechanical engineer Alex Grant designed and manufactured to hold the swabs in easy-to-count rows to streamline the process throughout the production line.

What resulted was a model of the swab stick that would eventually be wrapped with the rayon fibers at the tip. That prototype of the swab stick then jumpstarted an effort to bring much-needed testing swabs to the area, and possibly the state.

With only so much capacity available in the Prototyping Lab, a local startup with multiple 3D Markforged printers was brought into the fold to begin producing the swab sticks in greater numbers. Grant continued to work with the company on improving the workflow where appropriate and identify any bottlenecks to their process. He designed and manufactured more than 100 trays to hold the swabs in easy-to-count rows to streamline the process throughout the production line.

And what began as just a request for material has turned into a partnership between academia and industry that is providing 5,000 to 6,000 swabs per day to boost Rady’s COVID-19 testing efforts and to support UC San Diego’s Return to Learn initiative that aims to test students, faculty and staff on campus on a recurring basis for the virus. Sandubrae said the company has also been in talks to supply the state with swabs.

The Prototyping Lab is also helping to support the university's Return to Learn program by creating and printing initial prototypes for test tube caps on the lab’s resin-based 3D printer. The caps will be needed for the tubes that will hold the COVID-19 tests conducted on campus. The lab is currently evaluating its potential involvement and making recommendations about production needs and logistics.

Protecting medical staff and patients during procedures

With two different Polycarbonate boxes developed in the Prototyping Lab, engineers and doctors are seeking to protect patients and their caregivers.

Grant and the Prototyping Lab were enlisted to help design and develop two enclosures for COVID-19 patients as a part of research teams trying to make treating those patients safer for medical staff and patients themselves.

With the vacuum exhaused isolation locker, or VEIL, researchers have designed and built an enclosure that extracts exhaled aerosols and droplets from COVID-19 patients, providing health care workers with a safety barrier. Grant describes it as a large bubble that goes over a patient’s head and upper body, giving a patient an oxygen-rich environment that also prevents air—and possible droplets contaminated with COVID-19—from leaving the enclosure.

The device helps reduce the need for ventilators while also providing a solution to help patients breathe without suffering the long-term health issues from a ventilator such as lung scarring.

COSIE boxes in the Prototyping Lab hall during production.

Grant was first approached by a graduate student working on the research team and together they worked through 11 different iterations and several small modifications as the team tested the device in local hospitals and clinics. Two versions, one for a hospital bed and the other for a gurney, have been developed.

Twenty-five of these boxes are currently in use at UC San Diego clinics in Hillcrest and La Jolla. The project has been supported by the Qualcomm Institute’s rapid response initiative.

The VEIL team is led by UC San Diego professors Dr. Timothy Morris, a pulmonologist, and James Friend in the Department of Mechanical and Aerospace Engineering. In addition to Sandubrae and Grant from QI, other team members include Mechanical and Aerospace Engineering Ph.D. student Gopesh Tivawala and other physicians and researchers at the Jacobs School of Engineering and the UC San Diego School of Medicine.

Grant helped develop another box—what he describes as a glove box—where a doctor can put his or her hands through two openings and intubate a patient. Called Coronavirus Safety during Intubation and Extubation (or COSIE), the enclosure protects medical staff from aerosols and droplets from COVID-19 patients during intubation and extubation. Grant and Sandubrae again worked with Friend and his Ph.D. student Tivawala as well as Dr. Alexander Girgis, a UC San Diego anesthesiologist, and others to build this device.

Graduate students also approached Grant for his involvement on the COSIE project. Luckily, Grant, whose expertise is in robotics and manufacturing, had made this type of box before and had a decade of experience working with the type of plastic used to construct it.

The group went through six iterations, adjusting the arm holes a couple inches to make it more comfortable and functional and making other modifications.

Between 20 and 30 boxes were built in the Prototyping Lab that were then taken by a San Diego anesthesiologist group to several area hospitals for trials. The team’s findings were recently published in the Journal of Cardiothoracic and Vascular Anesthesia.

Helping to Protect Across Borders

The Prototyping Lab has also worked with students and researchers in a project led by Nadir Weibel, an associate professor in the Department of Computer Science and Engineering and head of the Human-Centered and Ubiquitous Computing Lab, to create face masks for hospitals in Tijuana, Mexico.

Facemasks bound for Tijuana hospitals are being cut on the laser cutter in Prototyping Lab.

Weibel and a team of students have created multi-layered fabric face masks fabricated with guidance from Grant and Sandubrae using one of the laser cutters available in their lab.

Sandubrae said a process was developed on the laser cutter that seals the edges as it cuts through the layers of fabric, like cauterizing a wound, and reduces the amount of work needed to create the masks.

“We have been able to produce a surgical mask that has better protection than any other DIY masks out there,” said Weibel, whose team has produced about 1,500 masks to supply hospitals in Tijuana.

A hand in developing emergency ventilators

Grant and colleague Mark Stambaugh, a QI electrical engineer, were enlisted to help on another project led by Friend to develop low-cost, easy-to-use emergency ventilators for COVID-19 patients.

Grant helped the team with design consulting on the ventilator and then worked with the lab’s 3D printing capabilities to produce several early prototypes. Panels for the ventilator were cut with the lab’s laser cutter and a type of air flow valve was 3D printed, he said. Stambaugh stepped in to work on the microcontroller and help adjust the stroke cycle and control the speed and volume of the compressions to help patients breathe. Stambaugh also designed the circuit, wrote the code and designed the prototype circuit board, Friend noted.

Supporting ARC

The Prototyping Lab has also been lending its capabilities to support the work of another Atkinson Hall resident, the Additive Rocket Corporation (ARC), which is known for creating 3D printed metal rocket engines. Part of the Qualcomm Institute Innovation Space (or QIIS), ARC is using the lab’s machine shop to create parts for ventilators for a medical device company.

ARC has also used its own 3D metal printer to make ventilator components that are redesigned to allow for rapid production and increased performance and flexibility in hospital settings. ARC's 3D metal printer is among the many resources in Atkinson Hall available for use by the broader community.

Visit Qualcomm Institute’s Prototyping Lab to learn more about its capabilities and services.

Engineer and mathematician receive Newton Award for Transformative Ideas during COVID-19 pandemic

Boris Kramer UCSD
Boris Kramer, a professor in the Department of Mechanical and Aerospace Engineering received a Newton Award from the Department of Defense. 

San Diego, Calif., July 21, 2020-- The years between 1665 and 1667, during the bubonic plague in England, have been called the “Years of Wonder” for Sir Isaac Newton, the famous scientist-mathematician who developed the principles of modern physics, including the laws of motion. While the plague raged, Newton sheltered in the countryside where he focused on work that ultimately changed the world. Years later, he referred to that time as the most productive of his life.

Fast forward more than 350 years, to 2020 and the novel coronavirus pandemic, when the U.S. Department of Defense (DOD) is recognizing Newtonian excellence with its Newton Award for Transformative Ideas during the COVID-19 Pandemic. Two UC San Diego professors—Melvin Leok from the Department of Mathematics (Division of Physical Sciences) and Boris Kramer from the Department of Mechanical and Aerospace Engineering (Jacobs School of Engineering) are among the 13 award recipients. They were selected from a pool of 548 applicants for their vision to study and efficiently simulate complex interconnected systems for long-term analysis.  

For example, most mathematical descriptions of complex systems such as an aircraft, smart robots, the Internet-of-Things, satellites, etc., end up with large-scale models that are interconnected systems-of-systems, explained Kramer. “Imagine you want to simulate these systems for long periods of time to do analysis and learn more about their reliability and to control them—it’s impossible at that scale,” he said, adding that researchers have tried making these simulations cheaper for decades by making many approximations but without a good solution. “That’s where Melvin Leok and I connected. Melvin is an expert in the structure of interconnected systems, and my expertise is in approximating very expensive computational models with accurate but much cheaper surrogate models.”

he tandem approach matched up with the DOD’s challenge to applicants to propose novel conceptual frameworks or theory-based approaches that utilized analytical reasoning, calculations, simulations and thought experiments. Together, Leok and Kramer submitted a two-part proposal titled, “Geometric Structure-Preserving Model Reduction for Large-Scale Interconnected Systems.” With the Newton Award, the UC San Diego researchers can now dive deep into the fundamentals of what “a good approximation” means and the ways to design it.

“We were blown away by the overwhelming response and the ingenuity and creativity in the proposals we reviewed,” said JihFen Lei, acting director of defense research and engineering for research and technology. “We look forward to seeing where the development of these ideas leads us.”

To that end, Leok will use his expertise in developing accurate, structure-preserving models of simpler mechanical interconnected systems, evolving on curved spaces, and extend them to larger scale engineering systems.

“By synthesizing this with Boris Kramer’s expertise in surrogate models for large-scale systems, we aim to develop systematic methods for constructing scalable models of more complex engineered systems, while respecting the interconnection and geometric structure, so that they are computationally tractable on a range of hardware platforms,” said Leok, adding that first they will reexamine the characteristics of a good surrogate model for a geometric interconnected system. “Then we’ll develop metrics for quantifying this.”

All Newton Award recipients will receive $50,000 over a six-month period of performance. At the end of the award period, the researchers will brief the Office of the Under Secretary of Defense for Research and Engineering leadership.

Leok explained that while the award is intended to support the principal investigators’ work, he and Kramer hope follow-up funding will support student involvement in their research.

The hundreds of proposals for the Newton Award came from 184 U.S.-affiliated and accredited universities and research centers across 41 states and the District of Columbia. Forty-one of the proposals came from historically black colleges and universities or other minority-serving institutions. Proposals spanned topic areas ranging from applied mathematics and quantum physics to the social sciences and disease ecology, and were reviewed by subject-matter experts in the DOD, other U.S. government agencies and the academic community. For the full list of the Newton Award funded projects, click here. Additional Newton Award recipients may be announced as funds become available.

The Office of the Under Secretary of Defense for Research and Engineering (OUSD(R&E)) is responsible for the research, development and prototyping activities across the Department of Defense. OUSD(R&E) fosters technological dominance across the DOD ensuring the unquestioned superiority of the American joint force. 

Non-invasive blood test can detect cancer four years before conventional diagnosis methods

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Professor Kun Zhang is one of the corresponding authors of the July 21, 2020 Nature Communications and the chair of the UC San Diego Department of Bioengineering.

San Diego, Calif., July 21, 2020 -- An international team of researchers has developed a non-invasive blood test that can detect whether an individual has one of five common types of cancers, four years before the condition can be diagnosed with current methods. The test detects stomach, esophageal, colorectal, lung and liver cancer. 

Called PanSeer, the test detected cancer in 91% of samples from individuals who had been asymptomatic when the samples were collected and were only diagnosed with cancer one to four years later. In addition, the test accurately detected cancer in 88% of samples from 113 patients who were already diagnosed when the samples were collected. The test also recognized cancer-free samples 95% of the time. 

In addition, the test accurately detected cancer in 88% of samples from 113 patients who already diagnosed with five common cancer types. The test also recognized cancer-free samples 95% of the time. 

The study is unique in that researchers had access to blood samples from patients who were asymptomatic and had not yet been diagnosed. This allowed the team  to develop a test that can find cancer markers much earlier than conventional diagnosis methods. The samples were collected as part of a 10-year longitudinal study launched in 2007 by Fudan University in China. 

“The ultimate goal would be performing blood tests like this routinely during annual health checkups,” said Kun Zhang, one of the paper’s corresponding authors and professor and chair of the Department of Bioengineering at the University of California San Diego. “But the immediate focus is to test people at higher risk, based on family history, age or other known risk factors.”

Early detection is important because the survival of cancer patients increases significantly when the disease is identified at early stages, as the tumor can be surgically removed or treated with appropriate drugs. However, only a limited number of early screening tests exist for a few cancer types.

Zhang and colleagues present their work in the July 21, 2020 issue of Nature Communications. The team includes researchers at Fudan University and at Singlera Genomics, a San Diego and Shanghai based startup that is working to commercialize the tests based on advances originally made in Zhang's bioengineering lab at the UC San Diego Jacobs School of Engineering.

The researchers emphasize that the PanSeer assay is unlikely to predict which patients will later go on to develop cancer. Instead, it is most likely identifying patients who already have cancerous growths, but remain asymptomatic for current detection methods. The team concluded that further large-scale longitudinal studies are needed to confirm the potential of the test for the early detection of cancer in pre-diagnosis individuals.

Taizhou Longitudinal Study

Blood samples in the Nature Communications study were collected as part of the Taizhou Longitudinal Study, which has collected plasma samples from over 120,000 individuals between 2007 and 2017. Each individual gave blood samples over a 10-year period and underwent regular check-ins with physicians. In all, over 1.6 million specimens have been collected and archived to date.  

Once a person was diagnosed with cancer, the researchers had access to blood samples taken one to four years before these patients even started to show symptoms. 

The team was able to examine samples from both healthy and sick individuals from the same cohort. The authors performed an analysis on plasma samples obtained from 605 asymptomatic individuals, 191 of whom were later diagnosed with cancer. They also profile plasma samples from an additional 223 diagnosed cancer patients as well as 200 primary tumour and normal tissue samples.

DNA methylation based diagnosis method

Zhang and his lab have been developing for over a decade methods to detect cancer based on a biological process called DNA methylation analysis. The method screens for a particular DNA signature called CpG methylation, which is the addition of methyl groups to multiple adjacent CG sequences in a DNA molecule. Each tissue in the body can be identified by its unique signature of methylation haplotypes. They did an early-stage proof-of-concept study that was published in a 2017 paper in Nature Genetics.

Zhang cofounded Singlera Genomics, which licensed technology he developed at UC San Diego. In the past few years, Singlera Genomics has been working to improve and eventually commercialize early cancer detection tests, including the PanSeer test, which was used in the Nature Communications study. Zhang is now the company’s scientific advisor. 

Zhang, Singlera Genomics and additional collaborators have been working to make a formal demonstration that cancer can be detected in the blood prior to conventional diagnosis. The July 2020 Nature Communications publication is the outcome of that effort. 

Conflict of interest statement:

Jeffrey Gole, Athurva Gore, Qiye He, Jun Min, Xiaojie Li, Lei Cheng, Zhenhua Zhang, Hongyu Niu, Zhe Li, Zhe Li, Han Shi, Justin Dang, Catie McConnell, and Rui Liu are employees of Singlera Genomics. Yuan Gao and Rui Liu are board members of Singlera Genomics. Jeffrey Gole, Athurva Gore, and Rui Liu are inventors on a patent (US62/657,544) held by Singlera Genomics that covers basic aspects of the library preparation method used in this paper. Kun Zhang is a co-founder, equity holder, and paid consultant of Singlera Genomics. The terms of these arrangements are being managed by the University of California San Diego in accor- dance with its conflict of interest policies. 


The Taizhou Longitudinal Study study was supported by the National Key Research and Development Program of China (grant number: 2017YFC0907000, 2017YFC0907500, 2019YFC1315800, 2019YF101103, and 2016YFC0901403), the National Natural Science Foundation of China (grant number: 91846302 and 81502870), the Key Basic Research grants from the Science and Technology Commission of Shanghai Municipality (grant number: 16JC1400501), the International S&T Cooperation Program of China (grant number: 2015DFE32790), the Shanghai Municipal Science and Technology Major Pro- ject program (grant number: 2017SHZDZX01), the International Science and Technol- ogy Cooperation Program of China (grant number: 2015DFE32790), and the 111 Project (B13016). Funding for the DNA methylation assays was provided by Singlera Genomics.

Non-invasive early detection of cancer four years before conventional diagnosis using a blood test


Xingdong Chen1,2,3,12, Jeffrey Gole4,12, Athurva Gore4,12, Qiye He5,12, Ming Lu2,6,12, Jun Min4, Ziyu Yuan2, Xiaorong Yang2,6, Yanfeng Jiang1,2, Tiejun Zhang7, Chen Suo7, Xiaojie Li5, Lei Cheng5, Zhenhua Zhang5, Hongyu Niu5, Zhe Li5, Zhen Xie5, Han Shi4, Xiang Zhang8, Min Fan9, Xiaofeng Wang1,2, Yajun Yang1,2, Justin Dang4, Catie McConnell4, Juan Zhang2, Jiucun Wang1,2,3, Shunzhang Yu2,7, Weimin Ye2,10✉,

Yuan Gao4, Kun Zhang 11, Rui Liu4,5 & Li Jin1,2,3

1 State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 200438 Shanghai, China. 2 Taizhou Institute of Health Sciences, Fudan University, 225300 Taizhou, Jiangsu, China. 3 Human Phenome Institute, Fudan University, 201203 Shanghai, China. 4 Singlera Genomics Inc., La Jolla, CA 92037, USA. 5 Singlera Genomics (Shanghai) Ltd., 201203 Shanghai, China.

6 Clinical Epidemiology Unit, Qilu Hospital of Shandong University, 250012 Jinan, Shandong, China. 7 Department of Epidemiology, School of Public Health, Fudan University, 200032 Shanghai, China. 8 Taizhou Disease Control and Prevention Center, 225300 Taizhou, Jiangsu, China. 9 Taixing Disease Control and Prevention Center, 225400 Taizhou, Jiangsu, China. 10 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177

Stockholm, Sweden. 11 Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093, USA. 12These authors contributed equally: Xingdong Chen, Jeffrey Gole, Athurva Gore, Qiye He, Ming Lu. ✉email: weimin.ye@ki.se; gary.gao@singleragenomics.com; kzhang@bioeng.ucsd.edu; rliu@singleragenomics.com; lijin@fudan.edu.cn


New model connects respiratory droplet physics with spread of Covid-19

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A droplet suspended in an acoustic levitator. Photo courtesy of Abhishek Saha

San Diego, Calif., July 20, 2020 --Respiratory droplets from a cough or sneeze travel farther and last longer in humid, cold climates than in hot, dry ones, according to a study on droplet physics by an international team of engineers. The researchers incorporated this understanding of the impact of environmental factors on droplet spread into a new mathematical model that can be used to predict the early spread of respiratory viruses including COVID-19, and the role of respiratory droplets in that spread. 

The team developed this new model to better understand the role that droplet clouds play in the spread of respiratory viruses. Their model is the first to be based on a fundamental approach taken to study chemical reactions called collision rate theory, which looks at the interaction and collision rates of a droplet cloud exhaled by an infected person with healthy people. Their work connects population-scale human interaction with their micro-scale droplet physics results on how far and fast droplets spread, and how long they last.

Their results were published June 30 in the journal Physics of Fluids.

“The basic fundamental form of a chemical reaction is two molecules are colliding. How frequently they’re colliding will give you how fast the reaction progresses,” said Abhishek Saha, a professor of mechanical engineering at the University of California San Diego, and one of the authors of the paper. “It’s exactly the same here; how frequently healthy people are coming in contact with an infected droplet cloud can be a measure of how fast the disease can spread.”

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A flow-diagram outlining the interconnections of the model

They found that, depending on weather conditions, some respiratory droplets travel between 8 feet and 13 feet away from their source before evaporating, without even accounting for wind. This means that without masks, six feet of social distance may not be enough to keep one person’s exhalated particles from reaching someone else.

“Droplet physics are significantly dependent on weather,” said Saha. “If you’re in a colder, humid climate, droplets from a sneeze or cough are going to last longer and spread farther than if you’re in a hot dry climate, where they’ll get evaporated faster. We incorporated these parameters into our model of infection spread; they aren’t included in existing models as far as we can tell.”

The researchers hope that their more detailed model for rate of infection spread and droplet spread will help inform public health policies at a more local level, and can be used in the future to better understand the role of environmental factors in virus spread.

They found that at 35C (95F) and 40 percent relative humidity, a droplet can travel about 8 feet. However, at 5C (41F) and 80 percent humidity, a droplet can travel up to 12 feet. The team also found that droplets in the range of 14-48 microns possess higher risk as they take longer to evaporate and travel greater distances. Smaller droplets, on the other hand, evaporate within a fraction of a second, while droplets larger than 100 microns quickly settle to the ground due to weight. 

This is further evidence of the importance of wearing masks, which would trap particles in this critical range.

The team of engineers from the UC San Diego Jacobs School of Engineering, University of Toronto and Indian Institute of Science are all experts in the aerodynamics and physics of droplets for applications including propulsion systems, combustion or thermal sprays. They turned their attention and expertise to droplets released when people sneeze, cough or talk when it became clear that COVID-19 is spread through these respiratory droplets. They applied existing models for chemical reactions and physics principles to droplets of a salt water solution—saliva is high in sodium chloride—which they studied in an ultrasonic levitator to determine the size, spread, and lifespan of these particles in various environmental conditions.

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Experimental setup showing the acoustic levitation of a droplet illuminated by a cold LED source. A diffuser plate is used for uniform imaging of the droplet. A CCD camera fitted with the zoom lens assembly is used for illumination. The schematic is not to scale.

Many current pandemic models use fitting parameters to be able to apply the data to an entire population. The new model aims to change that.

“Our model is completely based on “first principles” by connecting physical laws that are well understood, so there is next to no fitting involved,” said Swetaprovo Chaudhuri, professor at University of Toronto and a co-author. “Of course, we make idealized assumptions, and there are variabilities in some parameters, but as we improve each of the submodels with specific experiments and including the present best practices in epidemiology, maybe a first principles pandemic model with high predictive capability could be possible.”

 There are limitations to this new model, but the team is already working to increase the model's versatility.

 "Our next step is to relax a few simplifications and to generalize the model by including different modes of transmission,” said Saptarshi Basu, professor at the Indian Institute of Science and a co-author. "A set of experiments are also underway to investigate the respiratory droplets that settle on commonly touched surfaces.”

Wearable device company named Spinoff Prize finalist

Ron Graham, mathematician, computer scientist, juggler and magician: 1935-2020

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Ronald Graham, a professor in the Department of Computer Science and Engineering passed away July 6, 2020. He was 84.
Photos courtesy of the Graham family. 

San Diego, Calif., July 16, 2020 -- Ron Graham, a professor of computer science and mathematics at the University of California San Diego, perhaps best known for the discovery of Graham’s number, passed away July 6, 2020 at his home in La Jolla, from complications due to bronchiectasis, a chronic lung condition. He was 84. 

During a career that spanned six decades, Graham served as the president of both principal mathematical associations in the United States, and of the International Jugglers’ Association. He once said that he considered juggling a physical form of mathematics. He was also known for mathematics-based card tricks that he described in “Magical Mathematics,” a book he co-authored with Stanford mathematician and long-time collaborator Persi Diaconis. Graham was sometimes referred to as the “mathemagician.” 

“He was a true giant among researchers, but also one of the nicest human beings I have known,” said Larry Smarr, founding director of the California Institute for Telecommunications and Information Technology (Calit2) and the Harry E. Gruber Professor in Computer Science and Engineering at UC San Diego. “He was one of my most important mentors, particularly during the early days of bringing up Calit2. But Ron's diverse interests were as legendary as his deep role in mathematics.  That a mind of his caliber also focused on what the body could accomplish, in juggling, trampoline, and a wide array of exercise, was always a model for me.”

As a mathematician, Graham’s work helped enable the expansion of phone networks and later of Internet networks. He worked at Bell Labs for 37 years, primarily as director of information sciences. He later served as chief scientist for AT&T Labs. His research led him to focus on the complexity of routing telephone calls across U.S. time zones for AT&T. He explored the creation of a worldwide network of routers with mathematician Tom Leighton, now CEO of web and cyber security services provider Akamai Technologies. Graham joined the company’s board of directors from 2001 to 2010 and used his shares to endow the Akamai Professor in Internet Mathematics chair at UC San Diego. 

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Graham with his wife and main research partner, Fan Chung Graham, in an undated photo.

His main research partner over the years was his wife, Fan Chung Graham, with whom he authored more than 100 papers. She is on faculty in the UC San Diego Department of Mathematics as an emerita. 

“In our married life, most of the time we are doing mathematics together. It’s like our toy. And it’s particularly fun to do it with Ron. It’s why we have so many joint papers,”  Fan said in the 2015 documentary “Something New Every Day,” released for her husband’s 80th birthday. “In mathematics, we usually like to see the pursuit of truth. It’s actually a very romantic goal. So you want to know what the essence of things is. It’s inherent curiosity.”    

Graham joined the UC San Diego Jacobs School of Engineering in 1999 and held the Irwin and Joan Jacobs Endowed Chair in Computer and Information Science. He also served as chief scientist at Calit2 since the institute’s early days. 

“Through Ron, we learned first hand what made Bell Labs such an extraordinary place," said Ramesh Rao, interim director of Calit2 and director of the Qualcomm Institute, the UC San Diego Division of Calit2. "He taught us to seek out and gather the best scholars and trust them to explore  the future. That has been a guiding principle for us at Calit2."  

In 2015, the university honored Graham’s legacy and contributions by establishing an endowed chair in his name: the Ronald L. Graham Chair of Computer Science, now held by Professor Ravi Ramamoorthi. That same year Graham earned a teacher of the year award at the Jacobs School. Among all the honors and accolades he received during his career, it was the only award on display in his office. Graham was a performer and enjoyed teaching because it allowed him to connect with students, said friend and research partner Steve Butler.

Graham taught Mathematics for Algorithms and Systems Analysis, also known as CSE 21, a large two-section class with more than 400 students, at the request of Rajesh Gupta, who was then the chair of the UC San Diego Department of Computer Science and Engineering. 

“Students would post something like, ‘OMG, Ron Graham of Graham number/Guinness Book’ is teaching,” Gupta recalls. “And that, as I explained to Ron then, was the point of having him teach our lower division students, to catch the moments of inspiration early on for our students, a task he did with amazing stamina and effectiveness.”

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Graham's number, as handwritten by its author. 

Graham came up with the eponymous number in 1977 as an approximate solution to a complex problem in a field of mathematics known as “Ramsey’s Theory.” That area of mathematics shows that in large enough amounts of data, however random or arbitrary, local patterns will emerge. Graham’s number was at the time the largest specific positive integer ever to have been used in a published mathematical proof, and was recorded as such in the Guinness Book of World Records in 1980. (It has since been surpassed.)

Before becoming a researcher, Graham served in the Air Force for four years in Fairbanks, Alaska, with the Alaska Air Command at the Eielson Air Base. 

He earned a PhD in Mathematics from UC Berkeley in 1962. He put himself through graduate school by performing in a circus trampoline act. He would still do complex trampoline tricks well into his 60s. He bought himself a hoverboard before his 80th birthday. 

His long friendship with influential mathematician Paul Erdős, with whom he co-authored nearly 30 papers, also resulted in Graham’s 1979 paper that introduced the concept of an “Erdős number,” showing how closely other mathematicians were tied to Erdős based on the number of publications they co-authored with Erdős. Ron Graham’s Erdős number: 1 (reserved for Erdos’s immediate coauthors.) This concept later took hold in Hollywood as the basis of the popular “Six Degrees of Separation” game calculating how close an actor got to appearing in a movie with Kevin Bacon. 

Erdős travelled a lot and never had a home of his own. So Graham always had a room available for him when he lived in New Jersey. This is a great example of Graham's generosity and willingness to share, which was experienced by everyone who interacted with him, Butler said. 

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Graham, unicycling, photographed by his daughter, Ché Graham.

According to the American Mathematical Society (AMS), of which he served as a past president, Graham was “one of the principal architects of the rapid development worldwide of discrete mathematics in recent years." Akamai CEO Leighton described discrete mathematics as the basis of computer science. In addition to his role with the AMS, he also served as president of Mathematical Association of America (MAA)--  the two largest associations of mathematicians-- and was selected as a member of the inaugural class of Fellows of the Society for Industrial and Applied Mathematics (SIAM) in 2009.

Among his many other prestigious appointments and honors, he received the Steele Prize for Lifetime Achievement (2003) from the AMS; the Euler Medal of the Institute of Combinatorics and its Applications (1994); the Carl Allendorfer Award (1990); and the Polya Prize in Combinatorics (1972). He also was a fellow of the inaugural class of the American Mathematical Society in 2013, the same year that he received the Euler book prize. He was a member of and served as treasurer of the National Academy of Sciences and was a fellow of the Association of Computing Machinery (ACM) and of the American Academy of Arts and Sciences. Graham also holds six honorary doctorates.

Survivors include his wife, Fan Chung Graham, and four children, Ché Graham, Marc Graham, Christy Newman and Laura Lindauer, as well as his two stepchildren,  Dean and Laura May, 11 grandchildren and his brother, Jerry Graham. 

In lieu of flowers, the family requests that donations be made to the Cystic Fibrosis Foundation: https://www.cff.org/


Computer Scientists Brings Us Closer to Complete Genomic Sequences

San Diego, Calif., July 16, 2020 -- In a paper that brings scientists measurably closer to assembling the entire human genome, UC San Diego Department of Computer Science and Engineering Professor Pavel Pevzner has outlined an algorithm, called centroFlye, that uses long, error-prone DNA reads to assemble centromeres, the DNA that connects chromosome arms. This is the first time an accurate centromere sequence has been automatically assembled. The paper was co-authored with graduate student Andrey Bzikadze and published this week in Nature Biotechnology.

Though quite comprehensive, the first draft of the human genome had many missing sequences. Centromeres were the largest of these gaps. Working with data produced by the Telomere-to-Telomere (T2T) Consortium, Pevzner and Bzikadze have developed an approach that could close these gaps.

In addition to their Nature Biotechnology work, Bzikadze and Pevzner contributed to a landmark paper, also published this week, in the journal Nature that reported the first-ever complete assembly of a human chromosome. CentroFlye played an important role in this work.

“Human centromeres have remained the dark matter of the human genome, evading all attempts to sequence them since the Human Genome Project was completed,” says Pevzner, the Ronald R. Taylor Professor of Computer Science and senior author on the paper. “This is the first automated way to assemble centromeres. Now, we have to generate the first gapless assembly of the human genome.”

Centromeres make up around 3 percent of the human genome and are thought to play important roles in human health. However, without accurate sequences, it remains challenging to precisely assess how they contribute to disease.

“Centromeres are associated with various diseases, including cancer, and maybe there are more, but we know so little about them,” says Bzikadze. “These assemblies will allow us to systematically study variations in centromeres and their associations with disease.”

To uncover the secrets of human centromere DNA sequences, Pevzner modified his long read assembly algorithm, called Flye. Based on the Seven Bridges of Konigsberg puzzle, in which participants traverse the city while walking across each bridge only once, Flye models genome assembly as a large city. Each read is a bridge and the genome represents a path traversing each bridge. However, centromere sequences are highly repetitive, a challenge that dogged previous efforts.

“They’re like a jigsaw puzzle on steroids where most of the puzzle is a blue sky with some clouds” says Pevzner. “How do you assemble blue sky?”

Although the centromeres in each human chromosome are different, they are all formed by segments (called higher-order repeats or HORs), which can be repeated thousands of times with little variation.

Since HORs are so repetitive, almost all short centromere substrings (called k-mers for strings of length k) are repeated many times, turning the assembly into a computational nightmare – not unlike assembling a puzzle with just 16 pieces where each frog appears just four times (figure below). However, Bzikadze and Pevzner found rare k-mers in the centromere (i.e, k-mers that appear only once) that become anchors for assembly.


These rare k-mers are like small, wispy clouds in that flawless blue sky, providing small bits of contrast, which the researchers used to guide the assembly algorithm.

In addition to providing new insights into disease, sequencing centromeres could deliver a wealth of information about human biology, such as illuminating how these structures evolved, how they are maintained and why they have such different sequences, even between the 23 human chromosomes.

“Centromeres hold many biological secrets that are waiting to be solved,” says Pevzner. “The time has come, 20 years after the completion of the Human Genome Project, to read the compete genome.”

In memoriam: electrical engineering professor Elias Masry

July 16, 2020 -- Elias Masry, a pioneer in the theory and application of stochastic processes and professor emeritus at the University of California San Diego, passed away on March 17, 2020 in La Jolla, California. He was 83.

Professor Masry was born January 7, 1937, and grew up in Israel. He received B.Sc. and M.Sc. degrees in Electrical Engineering from the Technion-Israel Institute of Technology, in 1963 and 1965 respectively, and an M.S. in Electrical Engineering from Princeton in 1966. He earned his Ph.D. in Electrical Engineering in 1968 from Princeton University, and he joined the UC San Diego faculty that same year. He was a member of the Communications Theory and Systems group in the Electrical and Computer Engineering Department at the UC San Diego Jacobs School of Engineering and remained on the faculty until his retirement in 2009.

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Elias Masry

Professor Masry’s distinguished research career spanned four decades and his work covered a wide range of topics in communication systems, signal processing, and mathematical statistics. He was a meticulous researcher whose work was rigorous and precise. The first two decades of Professor Masry’s research made seminal contributions to the fundamental aspects of stochastic processes and involved questions of representations, modeling and estimation. His work made extensive contributions in the areas of covariance, spectral, and probability density estimation, inverse problems in nonlinear systems, optimal sampling designs, Monte Carlo integration, deconvolution methods in probability density and regression functions estimation, to mention a few. In addition to developing novel methods for estimation, his work always involved a rigorous analysis characterizing the quality of the estimation method, usually as a function of the number of samples. In the last two decades of his research work, he continued to make contributions to the theory of representing and processing of stochastic processes. A sampling of his contributions include local polynomial regression fitting for short-range and long-range dependent data, wavelet representation of stochastic processes and applications to function estimation, estimation and identification of stationary nonlinear ARCH and ARX systems, and sampling theorems for stochastic processes. In addition to the theoretical work, his work addressed important problems in digital communications and signal processing which clearly benefited from his expertise in stochastic processes. This included interference rejection in spread-spectrum communication systems, analysis of adaptive filtering algorithms, and the design and analysis of multi-antenna wireless communication systems.

Professor Masry was elected a Fellow of IEEE in 1986 for his contributions to the theory of stochastic processes and time series analysis in sampled data systems and digital communication systems. He served as Associate Editor for Stochastic Processes for the IEEE Transactions on Information Theory 1980-83 and was the Publications Chairman of the 1990 International Symposium on Information Theory in San Diego. He was honored by his students in Electrical and Computer Engineering with the Graduate Teaching Award in 2000 and the Undergraduate Teaching Award in 2001.

He will be deeply missed by his family, his colleagues and friends, and the UC San Diego community. He is survived by his sister Rachel Shasha and her two daughters and five grandchildren, and by his brother Sami Metser and his wife, two sons and two grandchildren.

An event celebrating his life will be organized when campus can resume large social gatherings again.



BluBLE: Estimating Your COVID-19 Risk with Accurate Contact Tracing

Dinesh Bharadia, lead scientist on the new BluBLE contact tracing application.

San Diego, Calif., Jan. 12, 2004 -- Motivated by the prospect of creating protective, social-distancing “bubbles” around members of the public, researchers in the UC San Diego Wireless Communications Sensing and Networking Laboratory are developing BluBLE, a new app for contact tracing during the COVID-19 pandemic.

BluBLE employs ubiquitous Bluetooth Low Energy (BLE) technology and personalized algorithms to ensure intelligent and accurate contact tracing. The app aims to provide each user with a personalized risk score by considering their various social and physical interactions. Risk scores update in real time, offering a faster, more efficient means of alerting individuals to exposure than current methods.

“BluBLE would enable core algorithms to provide accurate contact determination by leveraging my team’s expertise in determining robust locations indoors with WiFi and Bluetooth,” said Dinesh Bharadia, an assistant professor in the Electrical and Computer Engineering Department and the project’s Principal Investigator. “Our vision is to not only create accurate contact tracing, but to enable real-time feedback to warn users about potential physical spaces to avoid (germ-zones), which would be necessary to re-open our economy.”

BluBLE builds on existing contact tracing apps by addressing a key challenge posed by BLE technology. BLE’s range of 150 feet creates a contact tracing radius much larger than the six-feet standard, raising the chances that an app will register contact between two people when no such contact occurred. An app might consider neighbors separated by a wall, for example, as “in contact” with one another if they are within 150 feet.

BluBLE provides users with real-time warnings and updates to their personalized risk scores in each case of potential contact with the novel coronavirus.

Furthermore, most COVID-19 contact tracing apps identify a person’s exposure to the novel coronavirus as a binary “yes” or “no.” With more context, Bharadia’s team says, BluBLE can better estimate the user’s likelihood of contracting a virus from social interactions. Engaging in an extended conversation in a poorly ventilated room, for instance, would carry a higher probability of transmission as compared to briefly passing by on the street. By considering input from various common sensors available on the phone (chiefly Bluetooth, infrared and motion sensors), BluBLE can provide more accurate estimates of each contact’s potential risk.

BluBLE also plans to encourage effective quarantine while respecting the user’s privacy. The application would provide polite notifications to quarantined users tempted to venture outside. Furthermore, should an individual break quarantine, BluBLE would advise them to avoid nearby smartphone users unafflicted by COVID-19, thereby respecting the quarantined person’s privacy.

The team released BluBLE through android and iOS widely to the UC San Diego community in April. A second release is around the corner. Members of the community can support the team by visiting the BluBLE website and performing a few short experiments to make the platform even more robust.

The project is supported by electrical and computer engineering graduate students Aditya Arun and Agrim Gupta, and electrical and computer engineering undergraduate students Saikiran Komatineni and Shivani Bhakta.

Researchers Discover Two Paths of Aging and New Insights on Promoting Healthspan

Identifying a master aging circuit allows biologists to genetically engineer prolonged life

Yeast cells with the same DNA under the same environment show different structures of mitochondria (green) and the nucleolus (red), which may underlie the causes of different aging paths. Single and double arrowheads point to two cells with distinct mitochondrial and nucleolar morphologies.

San Diego, Calif., July 16, 2020 -- Molecular biologists and bioengineers at the University of California San Diego have unraveled key mechanisms behind the mysteries of aging. They isolated two distinct paths that cells travel during aging and engineered a new way to genetically program these processes to extend lifespan.

The research is described July 17 in the journal Science.

Our lifespans as humans are determined by the aging of our individual cells. To understand whether different cells age at the same rate and by the same cause, the researchers studied aging in the budding yeast Saccharomyces cerevisiae, a tractable model for investigating mechanisms of aging, including the aging paths of skin and stem cells.

The scientists discovered that cells of the same genetic material and within the same environment can age in strikingly distinct ways, their fates unfolding through different molecular and cellular trajectories. Using microfluidics, computer modeling and other techniques, they found that about half of the cells age through a gradual decline in the stability of the nucleolus, a region of nuclear DNA where key components of protein-producing “factories” are synthesized. In contrast, the other half age due to dysfunction of their mitochondria, the energy production units of cells.

The cells embark upon either the nucleolar or mitochondrial path early in life, and follow this “aging route” throughout their entire lifespan through decline and death. At the heart of the controls the researchers found a master circuit that guides these aging processes.

“To understand how cells make these decisions, we identified the molecular processes underlying each aging route and the connections among them, revealing a molecular circuit that controls cell aging, analogous to electric circuits that control home appliances,” said Nan Hao, senior author of the study and an associate professor in the Section of Molecular Biology, Division of Biological Sciences.

Having developed a new model of the aging landscape, Hao and his coauthors found they could manipulate and ultimately optimize the aging process. Computer simulations helped the researchers reprogram the master molecular circuit by modifying its DNA, allowing them to genetically create a novel aging route that features a dramatically extended lifespan.

UC San Diego biologists and bioengineers identified a master aging circuit that opens the door to genetically engineered prolonged life. Erik Jepsen/UC San Diego Publications

“Our study raises the possibility of rationally designing gene or chemical-based therapies to reprogram how human cells age, with a goal of effectively delaying human aging and extending human healthspan,” said Hao.

The researchers will now test their new model in more complex cells and organisms and eventually in human cells to seek similar aging routes. They also plan to test chemical techniques and evaluate how combinations of therapeutics and drug “cocktails” might guide pathways to longevity.

“Much of the work featured in this paper benefits from a strong interdisciplinary team that was assembled,” said Biological Sciences Professor of Molecular Biology Lorraine Pillus, one of the study’s coauthors. “One great aspect of the team is that we not only do the modeling but we then do the experimentation to determine whether the model is correct or not. These iterative processes are critical for the work that we are doing.”

The research team included Yang Li (postdoctoral scholar, Biological Sciences), Yanfei Jiang (postdoctoral scholar, Biological Sciences), Julie Paxman (graduate student, Biological Sciences), Richard O’Laughlin (former bioengineering graduate student, Jacobs School of Engineering), Stephen Klepin (laboratory assistant, Biological Sciences), Yuelian Zhu (visiting scholar), Lorraine Pillus (professor, Biological Sciences and Moores Cancer Center), Lev Tsimring (research scientist, BioCircuits Institute), Jeff Hasty (professor, Biological Sciences, Jacobs School of Engineering and BioCircuits Institute) and Nan Hao (associate professor, Biological Sciences and BioCircuits Institute).

The National Institutes of Health–National Institute on Aging (AG056440) and National Science Foundation Molecular and Cellular Biosciences (1616127 and 1716841) supported the research. Julie Paxman was supported by UC San Diego’s Cellular and Molecular Genetics training program, (5T32GM007240).

UC San Diego’s Studio Ten 300 offers radio and television connections for media interviews with our faculty. For more information, email studio@ucsd.edu.

UC San Diego News on the web at: https://ucsdnews.ucsd.edu



A nanomaterial path forward for COVID-19 vaccine development

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San Diego, Calif., July 15, 2020 -- From mRNA vaccines entering clinical trials, to peptide-based vaccines and using molecular farming to scale vaccine production, the COVID-19 pandemic is pushing new and emerging nanotechnologies into the frontlines and the headlines. 

Nanoengineers at UC San Diego detail the current approaches to COVID-19 vaccine development, and highlight how nanotechnology has enabled these advances, in a review article in Nature Nanotechnology published July 15

“Nanotechnology plays a major role in vaccine design,” the researchers, led by UC San Diego Nanoengineering Professor Nicole Steinmetz, wrote. Steinmetz is also the founding director of UC San Diego’s Center for Nano ImmunoEngineering. “Nanomaterials are ideal for delivery of antigens, serving as adjuvant platforms, and mimicking viral structures. The first candidates launched into clinical trials are based on novel nanotechnologies and are poised to make an impact.”

Steinmetz is leading a National Science Foundation-funded effort to develop—using a plant virus— a stable, easy to manufacture COVID-19 vaccine patch that can be shipped around the world and painlessly self-administered by patients. Both the vaccine itself and the microneedle patch delivery platform rely on nanotechnology. This vaccine falls into the peptide-based approach described below. 

 “From a vaccine technology development point of view, this is an exciting time and novel technologies and approaches are poised to make a clinical impact for the first time. For example, to date, no mRNA vaccine has been clinically approved, yet Moderna’s mRNA vaccine technology for COVID-19 is making headways and was the first vaccine to enter clinical testing in the US.”

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Nanoengineering Professor Nicole Steinmetz is using a plant virus to develop a COVID-19 vaccine. Photo by David Baillot/UC San Diego Jacobs School of Engineering

As of June 1, there are 157 COVID-19 vaccine candidates in development, with 12 in clinical trials.

“There are many nanotechnology platform technologies put toward applications against SARS-CoV-2; while highly promising, many of these however may be several years away from deployment and therefore may not make an impact on the SARS-CoV-2 pandemic,” Steinmetz wrote. “Nevertheless, as devastating as COVID-19 is, it may serve as an impetus for the scientific community, funding bodies, and stakeholders to put more focused efforts toward development of platform technologies to prepare nations for readiness for future pandemics,” Steinmetz wrote.

To mitigate some of the downsides of contemporary vaccines—namely live-attenuated or inactivated strains of the virus itself-- advances in nanotechnology have enabled several types of next-generation vaccines, including:

Peptide-based vaccines: Using a combination of informatics and immunological investigation of antibodies and patient sera, various B- and T-cell epitopes of the SARS-CoV-2 S protein have been identified. As time passes and serum from convalescent COVID-19 patients are screened for neutralizing antibodies, experimentally-derived peptide epitopes will confirm useful epitope regions and lead to more optimal antigens in second-generation SARS-CoV-2 peptide-vaccines. The National Institutes of Health recently funded La Jolla Institute for Immunology in this endeavor.

Peptide-based approaches represent the simplest form of vaccines that are easily designed, readily validated and rapidly manufactured. Peptide-based vaccines can be formulated as peptides plus adjuvant mixtures or peptides can be delivered by an appropriate nanocarrier or be encoded by nucleic acid vaccine formulations. Several peptide-based vaccines as well as peptide-nanoparticle conjugates are in clinical testing and development targeting chronic diseases and cancer, and OncoGen and University of Cambridge/DIOSynVax are using immunoinformatics-derived peptide sequences of S protein in their COVID-19 vaccine formulations.

An intriguing class of nanotechnology for peptide vaccines is virus like particles (VLPs) from bacteriophages and plant viruses. While non-infectious toward mammals, these VLPs mimic the molecular patterns associated with pathogens, making them highly visible to the immune system. This allows the VLPs to serve not only as the delivery platform but also as adjuvant. VLPs enhance the uptake of viral antigens by antigen-presenting cells, and they provide the additional immune-stimulus leading to activation and amplification of the ensuing immune response. Steinmetz and Professor Jon Pokorski received an NSF Rapid Research Response grant to develop a peptide-based COVID-19 vaccine from a plant virus: https://jacobsschool.ucsd.edu/news/news_releases/release.sfe?id=3005. Their approach uses the Cowpea mosaic virus that infects legumes, engineering it to look like SARS-CoV-2, and weaving antigen peptides onto its surface, which will stimulate an immune response.

Their approach, as well as other plant-based expression systems, can be easily scaled up using molecular farming. In molecular farming, each plant is a bioreactor. The more plants are grown, the more vaccine is made. The speed and scalability of the platform was recently demonstrated by Medicago manufacturing 10 million doses of influenza vaccine within one month. In the 2014 Ebola epidemic, patients were treated with ZMapp, an antibody cocktail manufactured through molecular farming. Molecular farming has low manufacturing costs, and is safer since human pathogens cannot replicate in plant cells. 

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COVID-19 vaccine candidates in the clinical development pipeline.

Nucleic-acid based vaccines: For fast emerging viral infections and pandemics such as COVID-19, rapid development and large scale deployment of vaccines is a critical need that may not be fulfilled by subunit vaccines. Delivering the genetic code for in situ production of viral proteins is a promising alternative to conventional vaccine approaches. Both DNA vaccines and mRNA vaccines fall under this category and are being pursued in the context of the COVID-19 pandemic. 

  • DNA vaccines are made up of small, circular pieces of bacterial plasmids which are engineered to target nuclear machinery and produce S protein of SARS-CoV-2 downstream. 
  • mRNA vaccines on the other hand, are based on designer-mRNA delivered into the cytoplasm where the host cell machinery then translates the gene into a protein – in this case the full-length S protein of SARS-CoV-2. mRNA vaccines can be produced through in vitro transcription, which precludes the need for cells and their associated regulatory hurdles

While DNA vaccines offer higher stability over mRNA vaccines, the mRNA is non-integrating and therefore poses no risk of insertional mutagenesis. Additionally, the half-life, stability and immunogenicity of mRNA can be tuned through established modifications. 

Several COVID-19 vaccines using DNA or RNA are undergoing development: Inovio Pharmaceuticals has a Phase I clinical trial underway, and Entos Pharmeuticals is on track for a Phase I clinical trial using DNA. Moderna’s mRNA-based technology was the fastest to Phase I clinical trial in the US, which began on March 16th, and BioNTech-Pfizer recently announced regulatory approval in Germany for Phase 1/2 clinical trials to test four lead mRNA candidates.

Subunit vaccines: Subunit vaccines use only minimal structural elements of the pathogenic virus that prime protective immunity-- either proteins of the virus itself or assembled VLPs. Subunit vaccines can also use non-infectious VLPs derived from the pathogen itself as the antigen. These VLPs are devoid of genetic material and retain some or all of the structural proteins of the pathogen, thus mimicking the immunogenic topological features of the infectious virus, and can be produced via recombinant expression and scalable through fermentation or molecular farming. The frontrunners among developers are Novavax who initiated a Phase I/II trial on May 25, 2020. Also Sanofi Pasteur/GSK, Vaxine, Johnson & Johnson and the University of Pittsburgh have announced that they expect to begin Phase I clinical trials within the next few months. Others including Clover Biopharmaceuticals and the University of Queensland, Australia are independently developing subunit vaccines engineered to present the prefusion trimer confirmation of S protein using the molecular clamp technology and the Trimer-tag technology, respectively.

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Nanoengineering Professor Nicole Steinmetz is using a plant virus to develop a COVID-19 vaccine. Photo by David Baillot/UC San Diego Jacobs School of Engineering

Delivery device development

Lastly, the researchers note that nanotechnology’s impact on COVID-19 vaccine development does not end with the vaccine itself, but extends through development of devices and platforms to administer the vaccine. This has historically been complicated by live attenuated and inactivated vaccines requiring constant refrigeration, as well as insufficient health care professionals where the vaccines are needed.

“Recently, modern alternatives to such distribution and access challenges have come to light, such as single-dose slow release implants and microneedle-based patches which could reduce reliance on the cold chain and ensure vaccination even in situations where qualified health care professionals are rare or in high demand,” the researchers write.  “Microneedle-based patches could even be self-administered which would dramatically hasten roll-out and dissemination of such vaccines as well as reducing the burden on the healthcare system.”

Pokorski and Steinmetz are co-developing a microneedle delivery platform with their plant virus COVID-19 vaccine for both of these reasons. 

This work is supported by a grant from the National Science Foundation (NSF CMMI-2027668)

“Advances in bio/nanotechnology and advanced nanomanufacturing coupled with open reporting and data sharing lay the foundation for rapid development of innovative vaccine technologies to make an impact during the COVID-19 pandemic,” the researchers wrote. “Several of these platform technologies may serve as plug-and-play technologies that can be tailored to seasonal or new strains of coronaviruses. COVID-19 harbors the potential to become a seasonal disease, underscoring the need for continued investment in coronavirus vaccines.”

$18M Boost to Materials Science Research at UC San Diego

The UC San Diego MRSEC center provides sustained research and educational opportunities for both graduate and undergraduate students, with a particular focus on transfer students. Photos by Erik Jepsen/University Communications

San Diego, Calif., July 9, 2020 -- The National Science Foundation has awarded University of California San Diego researchers a six-year $18 million grant to fund a new Materials Research Science and Engineering Center (MRSEC).

These research centers are transformative for the schools that earn them, putting their materials science research efforts into the global spotlight. In addition to research and facilities funding, MRSEC centers provide sustained research opportunities for both graduate and undergraduate students, and resources to focus on diversifying the pool of students studying materials science.

The UC San Diego labs funded by this new MRSEC will focus on two important, emerging approaches to build new materials aimed at improving human lives.

The first research theme is all about developing new ways to control the properties of materials during their synthesis by controlling how they transition, from the smallest atomic building blocks to materials that are large enough to see with the human eye.

Improved materials for batteries and other technologies that help societies increase renewable energy use will emerge from UC San Diego MRSEC center projects.

The second research theme is focused on creating hybrid materials that incorporate living substances—microbes and plant cells—in order to create materials with new properties.

The new materials developed at UC San Diego will be used to improve the speed and accuracy of medical diagnostic tests, enable more effective therapeutics for disease treatment, quickly and efficiently decontaminate chemical or biological hazards, improve batteries, and reduce the cost of key industrial processes.

"This MRSEC grant is a wonderful affirmation of what we've known all along—that UC San Diego is a world-class research and education powerhouse in materials science. This grant is going to enable researchers and students from different disciplines to work together and chart the course for important new avenues for innovation in materials science," said UC San Diego Chancellor Pradeep K. Khosla.

At the heart of the new MRSEC are student programs designed to diversify materials science and a strong partnership with the educational arm of San Diego's Fleet Science Center.

The team weaves 19 UC San Diego faculty members and their labs from the Division of Physical Sciences, the Jacobs School of Engineering and the Division of Biological Sciences into a large community of computational and materials science researchers.

A true UC San Diego collaboration

“Our MRSEC capitalizes on three specific strengths at UC San Diego—our leadership in materials science, our leadership in the life sciences and our position as a national resource in high performance computing,” said Michael Sailor, professor of chemistry and biochemistry at UC San Diego and the leader of the center. “We are weaving the life sciences and high performance computing into materials science. That really makes our center unique.”

The MRSEC is the first big win for the UC San Diego Institute for Materials Discovery and Design (IMDD), which focuses on bridging the gap between physical scientists and engineers on the campus to enable cross-disciplinary research.

The UC San Diego professors who make up the leadership team of the UC San Diego MRSEC center are, left to right: Tod Pascal, Andrea Tao, Jon Pokorski, Nicole Steinmetz, Michael Sailor, Shirley Meng and Stacey Brydges.

"Many of tomorrow's life-changing discoveries will happen at the intersection of engineering, physical sciences and biological sciences. This is why we pursue such interdisciplinarity here at UC San Diego, and this MRSEC is a tangible result of that effort. It is a tribute to the vision of Mike Sailor, Shirley Meng, Andrea Tao and Jon Pokorski to make the connections necessary to build this world-class team across such varied disciplines,” said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering.

This world-class research will directly serve UC San Diego graduate and undergraduate students, including transfer students. According to Sailor, one of the unique challenges for transfer students is that they often do not have the time or the training to participate in the rich research enterprise at UC San Diego.

“Our MRSEC summer schools have a specific focus on bringing transfer students into the materials science research community—the intensive workshops are intended to bring them up to speed so that they can seamlessly enter a research lab. Exposure of undergraduates to cutting-edge research is one of the most important activities of the MRSEC, because fluency in research concepts, tools, and techniques is a key element of a well-trained STEM workforce,” said Steven Boggs, dean of the Division of Physical Sciences at UC San Diego.

Research thrust: predictive assembly

The "predictive assembly" research team is working to bring the computational and predictive tools that the pharmaceutical industry has used successfully to design "small molecule" drugs with particular properties and behaviors into the realm of materials science. The team is led by UC San Diego nanoengineering professors Andrea Tao and Tod Pascal.

Learn more about the predictive assembly project.

Research thrust: living materials

The living materials research team is using the tools of biotechnology to build new classes of materials that help make people healthier and safer.

The second UC San Diego team is using the tools of the biotechnology revolution—in particular, genetic engineering and synthetic biology—to build new classes of materials with new kinds of abilities. Materials that can repair themselves are just one example. The team's big idea is to incorporate living organisms, either from plants or microbes, into their new materials. UC San Diego nanoengineering professor Jonathan Pokorski co-leads this research team, along with co-leader Nicole Steinmetz, also a UC San Diego nanoengineering professor.

Learn more about the living materials project.

Diversifying the materials science education pipeline

As part of its core educational mission, the UC San Diego MRSEC team is developing a suite of education programs aimed at growing and diversifying the pipeline for materials scientists in the United States. Summer school workshops, for example, are designed to provide trainees with immersive experience in laboratory procedures, advanced instrumentation and computational methods, explained Stacey Brydges, a professor in the Department of Chemistry & Biochemistry at UC San Diego who oversees the educational elements of the MRSEC.

“We view the summer schools as a transformative mechanism to enhance the training of participants from a broad range of educational levels—from high school to post-graduate," said Brydges. "We will offer high school and undergraduate students, with particular opportunities for our transfer students, their first introduction to research. The programs will also give incoming graduate students a quick start on their thesis projects."

Programs will also provide established industrial and international scientists with an update on the “hot topics” by engaging UC San Diego MRSEC researchers.

MRSEC facilities

One of the most important drivers of success in materials research today is the availability of cutting-edge instrumentation. The UC San Diego MRSEC will bring two new, exciting elements to the campus' research-facilities ecosystem: the Engineered Living Materials Foundry and the MesoMaterials Design Facility.

The predictive assembly research team is weaving computational and predictive tools into the realm of materials science in order to create materials with new, useful properties.

“High-end computation and synthetic biology are both under-represented in the materials science field, and these are areas where we see our MRSEC facilities poised to make a big impact,” said UC San Diego nanoengineering professor Shirley Meng.

She leads the facilities thrust of the MRSEC and is also director of the IMDD. “A major task for our MRSEC is not just to build out the facilities ecosystem but also to train scientists and engineers on how to deploy these tools to enable their research.”

Public outreach

To reach out to the public in new ways, the UC San Diego MRSEC team partnered with San Diego's Fleet Science Center.

“The goals of many of our community programs and initiatives dovetail nicely with the MRSEC goals," said Kris Mooney, director of education at the Fleet Science Center.

The MRSEC leverages the Fleet Science Center's community engagement model, which relies on local community-articulated needs to guide the design and delivery of educational programming.

"When we were setting up the MRSEC, we paid close attention to the diversity of our program at all levels," said Sailor. "We are particularly focused on diversifying the pipeline for materials science. This is a field that touches the lives of everyone. It's critical that the people developing the future of materials science reflect society at large."

UC San Diego NanoEngineers to lead MRSEC research thrust on Predictive Assembly

Professors Andrea Tao (left) and Tod Pascal lead the predictive assembly research thrust of the $18 million grant. 

San Diego, Calif., July 8, 2020 -- In some ways, the field of materials science is where the pharmaceutical sciences were twenty years ago. A team of University of California San Diego researchers is working to change that. The team makes up the "predictive assembly" research thrust of the new $18M Materials Research Science and Engineering Center (MRSEC) funded by the National Science Foundation (NSF).

Today, computational and predictive tools are used in the pharmaceutical industry in order to design "small molecule" drugs with particular properties and behaviors. The challenge is that the design-before-you-synthesize approach hasn't worked for the larger-scale materials that are critical for many applications beyond small-molecule drugs. That's the work that will be done by the team led by nanoengineering professors Andrea Tao and Tod Pascal from the UC San Diego Jacobs School of Engineering.

Andrea Tao uses surface chemistry and self-assembly concepts to build mesoscale materials. Tod Pascal couples theory with high performance computing to predict structure, properties, and microscopic signatures of complex materials.

Together, Tao and Pascal tapped into a diverse set of expertise at UC San Diego in order to create a team that will change the way advanced materials are designed and synthesized. The team includes UC San Diego experts in inorganic chemistry, condensed matter physics, nanoengineering, and computational and data sciences.

“Many of the life-saving drugs we have today were born in computer simulations from twenty years ago—those calculations revealed key interactions of molecules with their cellular targets, providing insights into how they might perform in the body,” said Tao. “We’d like to do the same for nanoscale molecules and particles, not just to understand how they perform on their own, but also to understand how we can use these objects like building blocks to construct new types of materials.”

“Many of the properties of a material that might be useful in building something like an enzyme-selective membrane for energy storage applications or a switchable optical metamaterial for holographic displays do not emerge until that material gets to a size much larger than a typical drug molecule,” said UC San Diego nanoengineering professor Tod Pascal. He leads the computational effort of the MRSEC and is co-director of the predictive assembly team.

“Indeed, we are only now starting to appreciate that the collective behavior of systems with lots of smaller subunits is quite different than systems with only two or three of these building blocks, a phenomenon known as emergent behavior,” said Pascal.  

With the unparalleled capabilities within UC San Diego's San Diego Supercomputer Center, Halicioglu Data Sciences Institute, and the NSF-funded Science Gateways Community Institute, Tao, Pascal, and their team are deploying the most advanced computational tools available to understand and design materials assembly processes from the ground up. This is an ambitious endeavor that has previously been intractable.

“Our strategy is to start with simulations based on accurate quantum mechanics, so that we are confident we can describe the microscopic interactions in these building blocks correctly,” Pascal continued. “Research in the lab of Francesco Paesani in the chemistry department has pioneered efficient approaches for doing this, with the latest advances using artificial intelligence and machine learning to accelerate these calculations.

"From there, we construct more approximate models that still retain the critical physics, such as those being developed in the lab of Gaurav Arya in the mechanical engineering department of Duke University. These models allows us to consider larger, more elaborate systems and before you know it, we can accurately describe assemblies of proteins with tunable catalytic sites, such as those currently being studied in the labs of  professors Joshua Figueora and Akif Tezcan in the chemistry department, or viral capsid proteins currently being developed in the lab of Nicole Steinmetz in the nanoengineering department,” said Pascal.

Another unique capability of the Predictive Assembly research thrust of the new UC San Diego MRSEC is the tight connection to spectroscopy.

“Time-resolved scattering techniques, such as those being developed by Alex Frano in the physics department, is one of the cornerstones of our efforts, as it allows us to investigate the dynamics of complex assemblies in real time. What’s even more exciting is that we are now developing methods to directly simulate these spectra on the computer,” said Pascal.

Two world renowned experts in spectroscopy, Susan Habas at the National Renewable Energy Laboratory (NREL) and Tony van Burren at Lawrence Livermore National Lab (LLNL), will join the effort and expand the available spectroscopic tools that will be used to characterize these complex materials systems.  


The predictive assembly team will work closely with the larger UC San Diego MRSEC team to create a MesoMaterials Design Facility.

“This is an effort to bring the two cultures of theory and synthesis together,” said Tao. “The MesoMaterials Design Facility will also serve as a resource to the larger materials science community across the country and across the world—providing a portal for others to design new properties into new materials.” 

The predictive assembly team is focusing on the assembly of materials at the so-called mesoscale—sizes just larger than molecular and nanometer dimensions—where some of the most interesting properties of materials and their behavior are determined. More familiar properties such as strength, flexibility, and reactivity, and more esoteric behaviors such as quantum mechanical confinement and plasmonic coupling are mostly determined by the mesoscale structure of a material. 

“Take metal nanoparticles as an example," said Tao. "Many of the catalysts used in the petrochemical industry, the sensor elements used in medical diagnostic kits, and the electrodes in rechargeable batteries rely on assemblies of metal nanoparticles to perform their functions. However, such metal nanoparticle ensembles have properties that are very different from an isolated metal nanoparticle. Very subtle changes in seemingly minor factors, like the orientation of the particles relative to each other, can exert profound changes in the properties of a material. The efficiency of a catalyst, the sensitivity of a medical diagnostic test, how many times a battery can be recharged, even the color of a material are all determined by these mesoscale interactions. So learning the rules for how matter can be put together on this scale will allow us to rationally design and predict new materials with revolutionary properties.”

Predictive assembly team

Co-Lead of predictive assembly team

Andrea Tao
nanoengineering professor, UC San Diego

Co-Lead of predictive assembly team
Tod Pascal
nanoengineering professor, UC San Diego

Founding professors on the predictive assembly team
Francesco Paesani, chemistry and biochemistry professor, UC San Diego
Joshua Figueroa, chemistry and biochemistry professor, UC San Diego
Akif Tezcan, chemistry and biochemistry professor, UC San Diego
Alex Frano, physics professor, UC San Diego
Guarav Arya, mechanical engineering and materials professor, Duke University

External National Lab Collaborators
Susan Habas, Nanoscience & Materials Chemistry, NREL
Tony van Buuren, Materials Science Division, LLNL



UC San Diego NanoEngineers to lead MRSEC research thrust on Living Materials

Nanoengineering professors Jonathan Pokorski (right( and Nicole Steinmetz lead the living materials thrust on the $18 million grant. 

San Diego, Calif., July 8, 2020 -- University of California San Diego researchers are using the tools of the biotechnology revolution—in particular, genetic engineering and synthetic biology—to build new classes of materials with novel kinds of abilities. Materials that can repair themselves are just one example of the applications of the "living materials" research thrust that is a key component of the new $18M Materials Research Science and Engineering Center (MRSEC) funded by the National Science Foundation (NSF).

The team's big idea is to incorporate living organisms, either from plants or microbes, into their new materials. Living organisms have evolved over billions of years to perform complex functions and to sense the environment around them. Synthetic materials still lag far behind what biological systems can accomplish. The UC San Diego researchers are asking: why not use biology to program materials?

Nanoengineering professors Jonathan Pokorski and Nicole Steinmetz from the UC San Diego Jacobs School of Engineering co-lead this research team.

Pokorski's lab incorporates living cells into engineering polymers to improve their performance. Steinmetz's lab engineers components of plants and plant viruses to generate functional materials. To meet their ambitious goals, they assembled a team of scientists and engineers from UC San Diego with a wide range of expertise including polymer chemistry, biology, nanoengineering, genetic engineering, and materials characterization.

The COVID-19 pandemic provides a good example of the limitations of many materials we encounter in our everyday lives.

"Why can’t the materials in our clothing and in our masks be more efficient at filtering out, or even killing a deadly virus?” asked Pokorski. “And wouldn’t it be great if that mask could automatically repair a small tear in its fabric before it lets a virus particle leak through?”

Materials that incorporate living, adaptive elements provide one possible solution. 

“Living systems have been making materials to suit their own purposes for eons,” said Pokorski. “Some of those are useful to us unintentionally—for example an oak tree makes strong wood that we can use to construct a table or a chair. What our MRSEC is trying to do is engineer organisms so they will make materials useful to us by design, not by accident.”

A major element of their effort is not just to make materials, but to engineer into them living properties that can respond to environmental cues.

“When a branch breaks on a live tree, it just grows a new one. However, a board made from a tree will not repair itself if you break it,” says Steinmetz. “A unique feature of our approach is that we are designing the materials to include live organisms directly into their structure—so they can respond to events just as other living systems can.”

The team assembled by Pokorski and Steinmetz is using plants, algae, and harmless soil bacteria as the live elements in their materials. They are engineering their living materials with capabilities to generate industrially important chemicals, polymers, and electronic materials, or to change their shape, their electronic properties or to repair themselves, in response to external stimuli.

The team is composed of UC San Diego researchers that span a unique spectrum from responsive biology through materials biology to polymeric materials.

Co-lead of living materials team
Jon Pokorski, nanoengineering professor, UC San Diego

Co-lead of living materials team
Nicole Steinmetz, nanoengineering professor, UC San Diego

Founding professors on the Living Materials team
Susan Golden, biological sciences professor, UC San Diego
Jim Golden, biological sciences professor, UC San Diego
Rachel Dutton, biological sciences professor, UC San Diego
Mike Burkart, chemistry and biochemistry professor, UC San Diego
Steve Mayfield, biological sciences professor, UC San Diego
Darren Lipomi, nanoengineering professor, UC San Diego
Jinhye Bae, nanoengineering professor, UC San Diego


UC San Diego receives $1.6 million to better prepare young adults for engineering and technical careers

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By Debra Bass and Judy Piercey

San Diego, Calif., July 2, 2020 -- Longtime University of California San Diego supporter Buzz Woolley has pledged $1.6 million over the next three years to fund an innovative new initiative that will significantly expand the region’s engineering and technical workforce.

Woolley’s support will help initiate a partnership between UC San Diego’s Jacobs School of Engineering and UC San Diego Extension to meet the growing need for a talent pool of workers with advanced technical and engineering skills. Woolley is a retired venture capitalist and entrepreneur, with a focus on supporting K-12 programs in San Diego. This philanthropic gift contributes to the Campaign for UC San Diego.

The initiative, provisionally titled Problem-Solving and Skill-Building for the Technical Workplace, promises to increase youth success in entry-level jobs in technical and engineering industries, as well as better prepare them for postsecondary university engineering degrees.

With this support, the Jacobs School and Extension at UC San Diego will develop an immersive course for high school students and first-year undergraduates offering foundations for success in the workplace of the future and in advanced engineering education based on doing, failing and succeeding. Simultaneously, the effort will create professional development opportunities for secondary teachers to support a pipeline of skilled problem-solvers who are ready-to-work, ready-to-learn high school graduates.

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Buzz Woolley. Photo credit: Voice of San Diego

Woolley said that it is crucial for the next generation to have an unprecedented level of comfort, curiosity and proficiency with universal engineering principles. For that to happen, teachers need enhanced teaching skills.

“The times demand accelerated educational opportunities in these rapidly and continually evolving fields,” Woolley said. “Industries need well-trained technical workers and young people deserve good jobs.

Mary Walshok, associate vice chancellor for Public Programs and dean of UC San Diego Extension, said that a large number of innovative educational programs at the university have been supported by “angel investors” like Woolley. These are people who have been quietly providing seed money, program capital and scholarship funding to support progressive, often experimental efforts, throughout the university’s rich history, she said.

“We do not take his investment in this joint program lightly,” said Edward Abeyta, associate dean for Education and Community Outreach (ECO), including pre-collegiate programming at UC San Diego Extension. “We consider it an honor and welcome challenge, because we know he’s going to be watching the results closely. Our wide-reaching Pre-College programs have a well-established reputation of exceeding his expectations, and we take pride in his support.”

Given the unique landscape of technical employers in California, and in San Diego particularly, Woolley agreed that UC San Diego is the ideal home for this initiative. He is also excited that the program is committed to expanding inroads into the region’s underrepresented intellectual pool of first-generation students.

“This program will make technical jobs with growth potential accessible to a larger and more diverse group of people in San Diego," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. “Technical problem solving is a transferable skill that everyone deserves access to. We will expand this access through new, transformative classes and teaching tools."

Much of the work to create inclusive problem-solving materials for students and teachers will be based in the EnVision Arts and Engineering Maker Studio at UC San Diego.

“Most people have a friend or family member who can take anything apart, make some small adjustments and put it back together so that it works even better than in the beginning. This reverse engineering is a perfect example of a systematic approach to solving a problem and it’s an incredibly valuable and teachable skill,” said Jesse DeWald, director of the EnVison Arts and Engineering Maker Studio at UC San Diego. “These are the kinds of skills that will set you up for success throughout your life, whether in good technical jobs that you can get right out of high school or in engineering courses in college.”

By the end of the first year, hundreds of high school students will benefit from a cohort of up to 40 teachers taking part in the program. Within the initial three-year phase, a total of 2,000 high school students are expected to take part in this dynamic change in instruction.

Abeyta and Jesse Dewald will be joined by assistant dean of ECO Morgan Appel and senior program manager for ECO Maysoon Lehmeidi Dong from UC San Diego Extension; Curt Schurgers, faculty member from electrical engineering at the Jacobs School of Engineering, and a new R&D engineer and a curriculum specialist to spearhead the execution of this project.

This generous gift from Buzz Woolley contributes to the Campaign for UC San Diego—a university-wide comprehensive fundraising effort concluding in 2022. To learn more, visit campaign.ucsd.edu.


Women who mean business

By Michelle Franklin

San Diego, Calif., July 2, 2020 -- Women are on the rise. According to the latest U.S. census data, they make up more than 50% of the population. They also earn more degrees at every level (associate’s, bachelor’s, master’s and doctoral) than men. And Kauffman Fellows Research Center states that between 2000-2018, the number of startups with at least one female founder rose from 4% to 20%.

The University of California San Diego is proud to have been named a top 25 undergraduate university for female-founded startups by Pitchbook, a financial data and software company.

Pitchbook tracked companies that raised their first round of funding between January 1, 2006 and August 31, 2019. UC San Diego landed in the No. 22 spot with 45 female founders whose companies raised over $580 million in first-round funding.

UC San Diego Chancellor Pradeep Khosla isn’t surprised by those statistics. “This ranking from Pitchbook affirms UC San Diego women excel in entrepreneurship. They learn the Triton way, under excellent instructors. Over the years, we have developed really strong programs on campus, including our student start-up incubator, The Basement, and Entrepreneurs-in-Residence mentor program. Triton women are solving real-world problems, impacting communities, and driving economic development,” he said.

Paul Roben, associate vice chancellor for Innovation and Commercialization is encouraged to see the number of female alumni who have found success as entrepreneurs, saying, “As we continue to expand our innovation ecosystem on campus, we are also looking for ways to ensure that underrepresented minorities have equal access to programs and opportunities for success. This is one indication that we are moving in the right direction and providing everyone the support they need to succeed in the startup world.”

Here is a peek into the busineses of some of the 45 outstanding founders.

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Ronald Graham -- Click Here to visit JSOE Flickr

Rachel Dreilinger, ’99, Bioengineering
Co-founder and CEO, NeuraMedica Inc.

NeuraMedica is developing a bioabsorbable surgical clip that can help neurosurgeons and orthopedic spine surgeons more quickly and easily repair the dura mater during spinal surgery. The dura is the membrane that covers and protects the brain, spinal cord and cerebrospinal fluid. It is a small device that can have a big impact, with product launch slated for early 2021. Dreilingeris proud of her resiliency and determination despite the obstacles she has faced as a Native female entrepreneur: “I didn’t quit, and now I can use my influence to create more inclusive companies and environments that value and respect diversity.”

Full story: https://ucsdnews.ucsd.edu/feature/women-who-mean-business

Creating an engineering senior design project...at home

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The SonoHand team—Mayuki Sasagawa, Barry Cheung, Brandon Chung, and Simon Kim—with their prototype and project sponsor at the UC San Diego School of Medicine Simulation Training Center.

San Diego, Calif., July 2, 2020 -- Curbside delivery of 3D-printed parts, the cooperation of roommates, weekend build sessions in Riverside and communication, communication, communication. This is what it took for graduating engineering students, staff and faculty at UC San Diego to transition the hands-on, team-based capstone mechanical engineering design course to remote instruction in the age of COVID-19.

“How do we get the student teams to make something that’s a functional prototype or better? This was the worry on my end, and I was very pessimistic in the beginning about whether or not we could achieve anything meaningful for the students,” said David Gillett, one of four instructors for the mechanical engineering capstone design course at the Jacobs School of Engineering. “The reality has proven amazingly positive. I am so impressed. These students are creative, resilient and adaptive.”

Normally, teams of four to five students spend 10 weeks creating a solution to a real-world problem put forth and sponsored by a local company or research lab. They meet regularly with each other, with their instructor and with their project sponsor to design and build a physical product that meets the sponsor’s needs. Students normally have access to a full machine shop, electronics shop, rapid prototyping tools, and advice from engineering staff. In past years, students have developed an elbow orthotic device to help a 5-year-old regain use of his arms; a neonatal simulation system for a complicated medical procedure; and a “mouse lickometer” to help scientists better study alcoholism.

What were students and staff to do when, a mere week before spring quarter, the state of California was put under shelter in place restrictions, most students moved off campus, and students and staff weren’t able to access the campus design studio, maker space, and tools that they would normally take advantage of to build their projects?

“As instructors, we briefly considered switching to a paper exercise, but we decided that student motivation was the most important factor,” said Nathan Delson, another of the course instructors. “The students had already started learning about their projects in November and were motivated to solve real-world problems for their sponsors.”

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Students designed and built a prototype of a robotic brusher that will be used to study nerve fibers called C-tactile afferents.

“We had these long conversations and decided that the best decision was to try and get the students to access outside resources to actually make things,” said Gillett. “I have to give huge props to the engineering staff because we had a number of staff individuals that took 3D printers home and became a service bureau, printing parts for students in a day or two.”

For the students, it was all about getting creative. One team resorted to the kindness of an uninvolved roommate in order to manufacture their automatic brushing device, sponsored by a professor at the UC San Diego Department of Anesthesiology who studies the sensations of pleasure and plain derived from stimulating C-tactile fibers.

“I got a 3D printer last quarter as a Black Friday sale purchase, and that turned out to be really helpful,” said mechanical engineering student Andrew Ma. “Most of the quarter, my teammates were in San Diego and I was at home in the Bay Area. So, it was complicated because I was sending our design files to my roommate and having him print the stuff. Then he would leave them outside, and someone from our team would come over and pick up the 3D-printed parts from the doorstep.”

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The SonoHand is a robotic arm meant to hold ultrasound probes of different sizes in a precise location on a patient during a procedure.

Another project, team SonoHand, was tasked with developing a robotic arm that doctors could use to hold an ultrasound probe in place on a patient during a procedure. The students were spread out around the San Diego and Riverside areas, and in order to develop a prototype, used the manufacturing facility of one team member’s family company on the weekends.

“Throughout the week, we all helped design and do Functional Data Analysis,” said team member Simon Kim. “On weekends, we’d come together, meet up in Riverside, and build it together. We wanted to make something physical out of this project; that was the main goal,” said Kim.

This put extra pressure on the team during the week, ensuring that the components they’d be building would work, and scheduling their design and build sessions with these couple of weekend marathons in mind.

With their expected manufacturing sites and tools no longer accessible, students turned to purchasing more off-the-shelf components for their projects, which added a challenge to staying within the budget set by their sponsor, and accounting for COVID-related shipping delays for these parts.

“I think the biggest challenge, but also kind of a good way of thinking, is this innovative way of thinking that if there are problems that persist, there’s always a way to work around it,” Kim said. “You don’t have to rely on one methodology of thinking.”

There were some teams that, due to location, size or other constraints, weren’t able to build physical prototypes. Instead, they conducted thorough simulations and analysis to ensure their designs would work, and developed manuals detailing the sourcing, manufacturing and assembly of their product.

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A rendering of the 13-foot centrifuge students designed to study the effect of a rocket launch on brain organoids being sent to space.

One team of students, sponsored by the Arthur C. Clarke Center for Human Imagination and Space Tango, was tasked with designing a way for researchers to study the effects of a rocket launch on brain organoids being sent to the International Space Station.

“They’re performing research on the effect of low gravity on neurological development, so they’re sending these little brains up to the Space Station to see how gravity affects them,” said team member Nicholas Blischak. “As a result of having to send something to the Space Station you have to put it on a rocket, and they really want to see what the effects of that acceleration that the experiments are going to experience in the process of being sent into space are. Our project was to come up with a way to simulate that acceleration.”

To accomplish this, the team decided to design a 13-foot centrifuge that will mimic the acceleration and movement the brain organoids will experience on the Falcon 9 rocket. It will also be used as a control here on Earth to compare against the organoids in space.

This was too large of a product to build from home, so the team resorted to putting together a detailed blueprint of how exactly to build it.

“We’ve been told that our sponsor is going to manufacture it after we complete our designs, and work on it over the summer,” said team member Clara Blatchley. “So, it will be built this year, most likely.”

At the end of the quarter, the student teams all participated in a virtual poster presentation as part of a Mechanical and Aerospace Engineering Senior Project Day. Judges from the engineering community and guests stopped be each team’s Zoom room for short presentations and Q&A.

While the students and staff were successful in finding ways to make this hands-on course a reality from afar, they’re hoping they can resume in-person meetings and use the Jacobs School of Engineering machine and prototyping lab resources again soon.

“I have an engineer brain that says I need to touch it, I want to feel it, can the device do this,” said Gillett. “And you just can’t do that remotely.”

Center for Microbiome Innovation names Dr. Andrew Bartko as Executive Director

UC San Diego Center for Microbiome Innovation names Dr. Andrew Bartko, a veteran research leader from Battelle Memorial Institute, as its new Executive Director

Bartko embarks on new role as founding executive director Dr. Sandrine Miller-Montgomery departs to lead Micronoma, a San Diego-based startup spawned out of the Center

SAN DIEGO, CA – June 30, 2020 – The University of California San Diego Center for Microbiome Innovation (CMI) has named Dr. Andrew Bartko as its incoming Executive Director. Bartko was most recently a Research Leader at Battelle Memorial Institute, a nonprofit global research and development organization committed to science and technology for the greater good.

"We are excited Andrew has joined CMI to support our efforts to accelerate microbiome research," said CMI Faculty Director Dr. Rob Knight. "He is passionate about our work and has a long track record of success in forging impactful academic and industry partnerships, making him an important asset to CMI as we continue our critical work to push the boundaries of human understanding of microbiomes." In addition to his role at CMI, Knight is a UC San Diego professor of pediatrics, computer science, and bioengineering and Co-Director of the IBM-UCSD Artificial Intelligence Center for Healthy Living. 

CMI exists to inspire, nurture, and sustain vibrant collaborations between UC San Diego Microbiome experts and industry partners. In his new role, Bartko will be responsible for leading a team focused on fostering and expanding industry and academic collaborations to accelerate microbiome discovery and create innovative technologies to advance the field and enable major clinical breakthroughs.

"It is a privilege and an honor to join this team of inspired microbiome researchers dedicated to improving human health and expanding disease prevention," said Bartko. "I hope to leverage my experience building interdisciplinary collaborations and industrial partnerships to create impactful innovations that advance CMI's mission."

In addition, Bartko holds the title of Professor of Practice in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering. 

Bartko starts his new position this month, and succeeds Dr. Sandrine Miller-Montgomery as Executive Director of CMI. Miller-Montgomery departs the Center after nearly four successful years to become the President and CEO of Micronoma, a San Diego-based startup born from research advancements made at CMI and UC San Diego. Micronoma, co-founded with Dr. Rob Knight and Gregory Poore, is initially focused on its liquid biopsy technology to detect and predict early cancer with clinical-grade accuracy. 

"I am thrilled to lead Micronoma in its work to advance an accessible tool for cancer diagnostics through tumor-related Microbial biomarkers," said Miller-Montgomery. "Our work is the epitome of what the CMI stands for - combining the expertise of a research university with the applied power of industry to foster innovation to improve human health and benefit the environment."

Bartko has extensive business development, technical knowledge, and application development experience and significant expertise in developing innovative technologies and building industrial research partnerships. He brings over seventeen years of progressive leadership experience in various roles at Battelle and Los Alamos National Laboratory. Bartko received his Bachelor of Science in Physical Chemistry from the University of Pittsburgh and his Ph.D. in Physical Chemistry from the Georgia Institute of Technology.

About Center for Microbiome Innovation at University of California San Diego:
The UC San Diego Center for Microbiome Innovation leverages the university's strengths in clinical medicine, bioengineering, computer science, the biological and physical sciences, data sciences, and more to coordinate and accelerate microbiome research. We also develop methods for manipulating microbiomes for the benefit of human and environmental health. Learn more at cmi.ucsd.edu/ and follow @CMIDigest.

Media Contact:
Erin Bateman
Communications Officer
Center for Microbiome Innovation, Jacobs School of Engineering
UC San Diego


Jacobs School of Engineering Launches Research Ethics Project

Pranjali Beri, who recently completed her Ph.D. in bioengineering, was part of a group of students and engineering department chairs who provided input on the ethics guideline documents.

San Diego, Calif., June 25, 2020 -- How can faculty encourage conversations about ethical research in their labs? What are reasonable expectations for mentoring? How do you decide who is the first author on a paper? Who should students turn to if they feel they’re being asked to publish unrepeatable results? How do we foster diversity in all areas of research, from topics studied, to testing, to creating an inclusive environment for diverse research teams?

Building a sustained culture where students, faculty and staff have the resources and comfort level to engage in these kinds of ethical conversations on an ongoing basis is the goal of the Research Ethics Project at the UC San Diego Jacobs School of Engineering. The project, which is funded by the National Science Foundation (NSF), entered phase two in May.

“I don’t know of any other systemic approach such as we’re developing here,” said Michael Kalichman, founding director of the UC San Diego Research Ethics Program, and director of the Jacobs School Research Ethics Project. “This is very different than more formal approaches people typically use; we’re trying to do something in a widespread, informal way that uses a variety of different approaches to encourage conversations. This is an experiment, but we have good reason to believe it will work.”

The project, co-led by Jacobs School of Engineering Dean Albert P. Pisano and Executive Vice Chancellor Elizabeth H. Simmons, aims to infuse ethics conversations into research labs, the curriculum and the life of the engineering and computer science community at UC San Diego. Instead of mandating a one-time course, the project aims to empower faculty, and the community at large, to find ways to incorporate ethics into their labs, courses, and conversations.

The project is underpinned by four evolving guideline documents shaped by Jacobs School graduate students, postdocs and faculty. These guidelines are focused on principles of responsible research, mentorship, data management and authorship.

“This project is a unique opportunity for faculty, staff, and students to participate in important dialogues about the ethical conduct of research,” said Simmons. “I value the conversations I joined as part of this initiative, and look forward to additional engagement across our campus community.”

The intent is for the guideline documents to serve as living records to be updated as needed, and to be used as starting points for conversations about ethical questions.

This is important work. Talking about ethics and the practice of engineering research is directly relevant to creating an anti-racist academic community," said Pisano. "I encourage our faculty, students and staff to engage with this program. It is a unique opportunity to participate in structured dialogue on topics that can be hard to talk about, especially if you are a student or a postdoc."

Graduate students engage

Ross Turner, a materials science graduate student and Gordon Scholar, helped shape the draft documents. He and a group of Gordon Scholars were one of several groups of students that met to review the draft guidelines, and ensure issues important to students were included.

“I have always seen ethics as a skill that you need—you always need to be working on doing better and raising standards for those around you,” Turner said. “People make mistakes, but we can prevent a lot of them by just thinking through some of this, which is what this project will enable.”

Issues of mentorship, authorship on papers, and repeatability of data and experiments are important to students. Pranjali Beri, who recently completed her Ph.D. in bioengineering and was part of a group of students and engineering department chairs who also provided input on the guidelines, agreed that mentorship was a key component of research ethics, and not just for students.

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“Mentorship is not just for students but also for young faculty,” said Beri, who was recognized as a 2020 Siebel Scholar for her research into biomarkers to identify the most aggressive cells in tumors. “New faculty don’t often receive this sort of training on how to manage grad students or post docs, and it’s been just a little while since they’ve been grad students themselves. This project’s guidelines on mentoring help define mentorship and provide suggestions for new faculty mentoring.”

Beri added that for students, having a mentor outside of their advisor can be helpful to get more perspectives on career and management styles, and as a trusted source to raise concerns about any issues happening in their lab.

“If students feel they need to suffer through grad school to please their advisor, I think talking about it with other faculty and knowing that that’s not what it’s supposed to be, would help those students succeed,” Beri said. “Some of these graduate students will go on to become professors themselves, so if they have just only one mentor experience that’s exactly what they’ll do when they become mentors themselves—it’s fostering a chain of poor mentorship.”

Overall, the goal of the Jacobs School Research Ethics Program is to empower faculty and students to feel comfortable having these conversations through structured support—including resources for faculty interested in teaching a designated course on ethics or incorporating it into existing courses—as well as unstructured means, like ongoing movie and discussion events, or incorporating questions on ethical dilemmas into guest lecturers’ remarks.

Building a culture of ethics requires a clear framework to govern the ways research mentors and mentees interact with each other and share our work with the outside world,” said John McCartney, professor and chair of the Department of Structural Engineering at UC San Diego. “The lessons learned from our collaboration with the Research Ethics Program have been very helpful and educational in the development of a framework that is specific to the Jacobs School. As faculty, we need to also work hard to instill ethical principles into our teaching and learning environment, as ethical behavior developed in the classroom can affect ethical behavior in practice or in research.”


This story ran in the ThisWeek@UCSanDiego newsletter

Nature Nanotechnology webinar with Nicole Steinmetz

Researchers develop low-cost, easy-to-use emergency ventilator for COVID-19 patients

San Diego, Calif., June 23, 2020 --A team of engineers and physicians at the University of California San Diego has developed a low-cost, easy-to-use emergency ventilator for COVID-19 patients that is built around a ventilator bag usually found in ambulances.

The team built an automated system around the bag and brought down the cost of an emergency ventilator to just $500 per unit--state of the art models cost at least $50,000. The device's components can be rapidly fabricated  and the ventilator can be assembled in just 15 minutes. The device’s electronics and sensors rely on a robust supply chain from fields not related to healthcare that are unlikely to be affected by shortages. 

The UCSD MADVent Mark V is also the only device offering pressure-controlled ventilation equipped with alarms that can be adjusted to signal that pressure is too low or too high. This is especially important because excessive pressure can cause lung injury in COVID-19 patients that often experience rapid decreases in lung capacity as the disease progresses.  

Most ventilators measure the volume of air that is being pumped into the patient’s lungs, which requires expensive airflow sensors. By contrast, the UCSD MADVent Mark V measures pressure and uses that data to deduct and control the airflow to the lungs. This was key to lowering the device’s price. 

The team from UC San Diego and industry partners will be seeking approval for the device from the Food and Drug Administration. They detail their work in an upcoming issue of Medical Devices and Sensors

The device’s plans and specifications are available at http://MADVent.ucsd.edu/

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The UCSD MADVent Mark V is a ventilator built around a bag used by EMTs, which is pressed by a machined paddle. The ventilator was tested on a lung simulator (right in the back). 

“The MADVent can safely meet the diverse requirements of COVID-19 patients because it can adjust over the broad ranges of respiration parameters needed to treat acute respiratory distress syndrome,” said James Friend, a professor at the UC San Diego Jacobs School of Engineering and one of the paper’s two corresponding authors. “The combination of off-the-shelf components and readily machined parts with mechanically driven pressure control makes our design both low cost and rapidly manufacturable.” 

 Researchers also wanted to make sure that the device could be used by healthcare workers with limited experience with ventilators and no experience with this type of system, said Dr. Casper Petersen, co-author of the study and a project scientist in the Department of Anesthesiology at the UC San Diego School of Medicine. As a result, the MADVent Mark V is safe to use, easy to assemble and easy to repair, thre searchers said. 

“This device could be a great option for use in situations where materials are scarce, such as when  the normal supply chain breaks down, or in developing nations and hard-to-reach rural areas,” Dr. Casper Petersen said. 

The device is not meant as a substitute for the highly complex ventilators used in Intensive Care Units.
“Rather, our low-cost ventilator is meant to bridge an urgent gap in situations of a large surge in patients where we may not have enough life sustaining equipment”, said Dr. Lonnie Petersen, an assistant professor at the Jacobs School of Engineering, adjunct professor at UC San Diego Health and the paper’s other corresponding author. “Safety is our main priority; while the MADVent is a low-tech and low-cost device, it actually offers robust and patient tailored ventilationThis really increases the safety for the patients suffering from the complex pulmonary infection and respiratory distress associated with COVID-19”. 

The UCSD MADVent Mark V

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The ventilator is controlled by pressure sensors, rather than volume sensors, which allowed researchers to lower the device's price dramatically. 

The UC San Diego team built their device around a ventilator bag usually found in ambulances and designed to be manually squeezed to help patients breathe. In the UCSD MADvent Mark V, a machined paddle squeezes the bag instead. The paddle is controlled by a series of pressure sensors to make sure the patients get the appropriate flow of air into their lungs. The team deliberately integrated as many standard hospital items as possible into the design because those have already undergone rigorous testing for safety, longevity and compatibility. 

To measure pressure, the researchers developed an algorithm that deduces how much the bag was compressed based on how many turns the device’s motor has made and calculates the volume of air sent into the patient’s lungs as a result.

“The elasticity of the lungs changes very quickly, so it’s important to be able to sense the feedback from the patient,” said Dr. Lonnie Petersen.

Researchers tested their system more than 200 times and for days on end on a lung simulator, adhering to standards for the International Standards Organization and FDA guidelines to ensure it functioned correctly. The device was also tested on a medical mannequin simulator.

One of the keys for cost savings was developing computer models of the volume of air delivered through the ambulance bag when it is compressed. This allowed researchers to do away with expensive airflow sensors and the complex algorithms that control them.

The materials on the ventilator can be sanitized with conventional disinfectants such as 1.5% hydrogen peroxide and 70% ethanol.  

“The system, in its current state of development, can easily accommodate new modules that enable more sophisticated features, such as flow monitoring, which can enable additional ventilation modes and provide healthcare operators more information regarding a patient’s breathing,” said Aditya Vasan, a Ph.D. student in Friend’s research group and the paper’s first author. 

Collaboration across disciplines

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A schematic of the UCSD MADVent Mark V

A close collaboration between clinicians and engineers enabled the team to put together a crude prototype in just three days. They then spent countless hours refining and testing the ventilator.  A lot of work went into making sure it was safe and could be manufactured with simple parts at a large scale.

Engineers with the UC San Diego Qualcomm Institute Prototyping Lab provided engineering design and fabrication support.  Electrical engineer Mark Stambaugh stepped in to work on the microcontroller and help adjust the stroke cycle and control the speed and volume of the compressions to help patients breathe. Mechanical engineer Alex Grant provided design support and guidance.

Seed funding for the project came from several organizations: San Diego-based Kratos Defense & Security Solutions, Inc., which develops fields systems, platforms and products for national security and communications needs; the US Office of Naval Research in the Department of Defense; and the Catalyst initiative at the UC Institute for Global Conflict and Cooperation.

MADVent: A low-cost ventilator for patients with COVID-19

Corresponding authors: James Friend, Dr. Lonnie Petersen

UC San Diego Jacobs School of Engineering: Medically Advanced Devices Laboratory: James Friend, Aditya Vasan, Reiley Weekes, William, Connacher, 

UC San Diego School of Medicine: Dr. Casper Petersen, Dr. Sidney Merritt, Dr. Preetham Suresh, Dr. Daniel E. Lee, Dr. William Mazzei, Theodore Vallejos, Jeremy Sieker, 

Qualcomm Institute: Mark Stambaugh, Alex Grant 

Eric Schlaepfer, independent researcher


IEEE Spectrum Cover Story

NIH grant to bioprint nanoparticles for ovarian cancer immunotherapy

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Professor Nicole Steinmetz

San Diego, Calif., June 19, 2020 -- Nanoengineers at UC San Diego received a five-year, $2.9 million grant from the National Institutes of Health to develop an immunotherapy for ovarian cancer using plant virus nanoparticles. The particles will be produced using 3D-bioprinting, enabling them to be released at specified intervals, instead of a continuous slow release.

High grade serous ovarian cancer (HGSOC) is the most common and severe form of ovarian cancer, accounting for an estimated 70 percent of all ovarian cancer diagnoses. To provide an effective and long lasting treatment for HGSOC, Professor Nicole Steinmetz plans to use a patient’s own irradiated tumor cells, coupled with a virus-like particle (VLP) from a plant virus that has been shown to boost the body’s immune response, to trigger the body to attack the tumor cells. The irradiated tumor cells will serve as the foreign agent telling the body’s immune response exactly what cells to attack. The co-released VLP will boost the natural immune response in reaction to these tumor cells. This is meant to create a cellular memory against these tumor antigens, creating a long-lasting and adaptive anti-tumor immunity and preventing relapse.

“We have already demonstrated that our VLP nanotechnology is highly effective as a cancer immunotherapy,” said Steinmetz. “The innovation here lies in the advanced manufacturing coupled with the novel nanotechnology to produce a personalized immunotherapy to protect women with ovarian cancer from recurrence of this disease.”

Steinmetz’ team developed the VLP nanotechnology from the same non-infectious, non-toxic plant virus they used to successfully treat melanoma in dogs, and has shown that these plant virus-like particles generate anti-tumor immunity in mice with ovarian cancer. 

The biopolymer immunotherapy will be delivered via an implant, produced using a 3D bioprinting technique developed in Professor Shaochen Chen’s 3D Bioprinting lab at the Jacobs School of Engineering. Known as rapid, microscale, continuous optical bioprinting, Chen’s team has used this 3D bioprinting method to create a spinal cord implant that could be used to promote nerve growth and treat spinal cord injury, as well as life-like liver tissue and intricate blood vessel networks. His lab will collaborate with Steinmetz to bioprint these immunotherapy implants incorporating the nanoparticles and irradiated tumor cells. 

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These 3D printed implants were used to heal severe spinal cord injury in rat models. They were developed in Professor Shaochen Chen's 3D Bioprinting lab using the same method they'll use for this cancer immunotherapy implant. 

“Our 3D bioprinting platform enables manufacturing of patient specific implants with precise control over both the topographical complexity and the cellular and material composition,” said Chen. “The engineering design space and tunability of this approach is impeccable; in particular the implant will be designed so that therapeutic doses are released in programmed intervals.”

Ultimately, the researchers envision this immunotherapy implant being seamlessly added in to the existing ovarian cancer treatment process. During surgery to remove the bulk of the tumor, the biocompatible, biodegradable implant would be inserted in the cavity lining the patient’s abdomen, where it would release the engineered immunotherapy particles at timed intervals.

This work is carried out at UC San Diego’s Center for Nano-ImmunoEngineering (Steinmetz is the founding director and Chen is also a member) and at Dartmouth College, where the UC San Diego team collaborates with Steve Fiering, a professor of Microbiology and Immunology and of Genetics at the Geisel School of Medicine at Dartmouth. Fiering is also a member of the Immunology and Cancer Immunotherapy Research Program at Dartmouth's Norris Cotton Cancer Center.

Fiering and Steinmetz have been working as a team toward the translation of the VLP cancer immunotherapy since 2015; this new grant will pave the way for applications in ovarian cancer. Dr. Stephen Howell, Professor of Medicine at UC San Diego, is contributing to the project by providing a clinical perspective.

Using LEGO to test children's ability to visualize and rotate 3D shapes in space

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Students work on assembling LEGO pieces without instructions while being timed. 

Spatial visualization is tied to increased GPA and graduation rates in STEM

San Diego, Calif., June 18, 2020 -- Researchers at the University of California San Diego have developed a test that uses children’s ability to assemble LEGO pieces to assess their spatial visualization ability. Spatial visualization is the ability to visualize 3D shapes in one’s mind, which is tied to increased GPAs and graduation rates in STEM college students.

One tool to increase spatial visualization skills among college students is a mobile app, called Spatial Vis, which allows students to sketch 2D and 3D shapes on a touchscreen and was developed based on  research at UC San Diego. 

However, the researchers Lelli Van Den Einde and Nathan Delson, both teaching professors at the UC San Diego Jacobs School of Engineering, feel that it would be beneficial to start teaching spatial visualization skills at younger ages. Indeed, during the COVID19 pandemic  they have seen increased requests for use of Spatial Vis by middle school and high school teachers because it works well  for remote instruction. One challenge to overcome to enable the teaching of these skills is how to assess spatial visualization ability at lower grade levels.

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This student is done.

At the college level, a widely used assessment is the Purdue Spatial Visualization Test: Rotations, or PSVT:R, which is a 20-minute timed test consisting of a series of multiple-choice questions that are geared towards students 13 and older. Van Den Einde and Delson wanted to develop an assessment that would be more suitable and engaging for students at lower grade levels. They turned to LEGO, which was designed with that younger age range in mind and is familiar  to many children. To pass the test, students have to assemble a set of LEGO pieces into a specific shape, such as a whale or a small plane, while only being given a picture of the final shape but no step-by-step instructions. The time it takes students to build the correct solution is the metric used for assessment.

Van Den Einde and Delson, along with Jessica Tuazon, Development Engineer, and Daniel Yang, PhD student, will present the LEGO Assembly test at the American Society for Engineering Education conference, held virtually June 22 to 26. In order to validate the test, the researchers had students in two freshman engineering graphics courses take both the LEGO assembly test and the PSVT:R. Students took the tests both at the beginning and end of the quarter. During the course, they were trained with the Spatial Viz app. Test results show a statistically significant correlation between outcomes on the LEGO test and the PSVT:R. 

“We think the LEGO assembly test is a suitable way to assess spatial visualization ability for elementary school age students,” Van Den Einde said. 

Delson added that the LEGO test shows that younger students get a tangible benefit from  using Spatial Vis  and improve  their spatial visualization skills. 

Van Den Einde and Delson cofounded eGrove Education Inc. to commercialize spatial visualization training. The Spatial Vis app is used by over 120 schools and 2000 students. The two UC San Diego teaching professors are now working on a version for lower grade levels to meet the demand which has increased due to remote instruction. 

The app includes automatic grading of student sketches, and hints when students are stuck. The researchers will be modifying their hint feedback, so the app is more suitable for K-12 students and encourages students to be persistent and solve assignments with only minimal hints. 



How long would it take you to go from the pieces on the left to the finished product on the right? That's what the LEGO assessment UC San Diego researchers developed is based on. The result determines your spatial visualization abilities. 






Nanosponges Could Intercept Coronavirus Infection

San Diego, Calif., June 17, 2020 --Nanoparticles cloaked in human lung cell membranes and human immune cell membranes can attract and neutralize the SARS-CoV-2 virus in cell culture, causing the virus to lose its ability to hijack host cells and reproduce.

The first data describing this new direction for fighting COVID-19 were published on June 17 in the journal Nano Letters. The "nanosponges" were developed by engineers at the University of California San Diego and tested by researchers at Boston University.

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Illustration credit: David Baillot, UC San Diego Jacobs School of Engineering

The UC San Diego researchers call their nano-scale particles "nanosponges" because they soak up harmful pathogens and toxins.

In lab experiments, both the lung cell and immune cell types of nanosponges caused the SARS-CoV-2 virus to lose nearly 90% of its "viral infectivity" in a dose-dependent manner. Viral infectivity is a measure of the ability of the virus to enter the host cell and exploit its resources to replicate and produce additional infectious viral particles.

Instead of targeting the virus itself, these nanosponges are designed to protect the healthy cells the virus invades.

“Traditionally, drug developers for infectious diseases dive deep on the details of the pathogen in order to find druggable targets. Our approach is different. We only need to know what the target cells are. And then we aim to protect the targets by creating biomimetic decoys," said Liangfang Zhang, a nanoengineering professor at the UC San Diego Jacobs School of Engineering.

His lab first created this biomimetic nanosponge platform more than a decade ago and has been developing it for a wide range of applications ever since. When the novel coronavirus appeared, the idea of using the nanosponge platform to fight it came to Zhang “almost immediately,” he said. 

In addition to the encouraging data on neutralizing the virus in cell culture, the researchers note that nanosponges cloaked with fragments of the outer membranes of macrophages could have an added benefit: soaking up inflammatory cytokine proteins, which are implicated in some of the most dangerous aspects of COVID-19 and are driven by immune response to the infection.

Making and testing COVID-19 nanosponges

Each COVID-19 nanosponge—a thousand times smaller than the width of a human hair—consists of a polymer core coated in cell membranes extracted from either lung epithelial type II cells or macrophage cells. The membranes cover the sponges with all the same protein receptors as the cells they impersonate—and this inherently includes whatever receptors SARS-CoV-2 uses to enter cells in the body. 

The researchers prepared several different concentrations of nanosponges in solution to test against the novel coronavirus. To test the ability of the nanosponges to block SARS-CoV-2 infectivity, the UC San Diego researchers turned to a team at Boston University's National Emerging Infectious Diseases Laboratories (NEIDL) to perform independent tests. In this BSL-4 lab--the highest biosafety level for a research facility--the researchers, led by Anthony Griffiths, associate professor of microbiology at Boston University School of Medicine, tested the ability of various concentrations of each nanosponge type to reduce the infectivity of live SARS-CoV-2 virus—the same strains that are being tested in other COVID-19 therapeutic and vaccine research.

At a concentration of 5 milligrams per milliliter, the lung cell membrane-cloaked sponges inhibited 93% of the viral infectivity of SARS-CoV-2. The macrophage-cloaked sponges inhibited 88% of the viral infectivity of SARS-CoV-2. Viral infectivity is a measure of the ability of the virus to enter the host cell and exploit its resources to replicate and produce additional infectious viral particles.

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Researcher Anna Honko prepares the assay in the BSL-4 in the National Emerging Infectious Diseases Laboratories (NEIDL). Courtesy of the Griffiths lab at Boston University's NEIDL.

“From the perspective of an immunologist and virologist, the nanosponge platform was immediately appealing as a potential antiviral because of its ability to work against viruses of any kind. This means that as opposed to a drug or antibody that might very specifically block SARS-CoV-2 infection or replication, these cell membrane nanosponges might function in a more holistic manner in treating a broad spectrum of viral infectious diseases. I was optimistically skeptical initially that it would work, and then thrilled once I saw the results and it sunk in what this could mean for therapeutic development as a whole,” said Anna Honko, a co-first author on the paper and a Research Associate Professor, Microbiology at Boston University's National Emerging Infectious Diseases Laboratories (NEIDL).

In the next few months, the UC San Diego researchers and collaborators will evaluate the nanosponges’ efficacy in animal models. The UC San Diego team has already shown short-term safety in the respiratory tracts and lungs of mice. If and when these COVID-19 nanosponges will be tested in humans depends on a variety of factors, but the researchers are moving as fast as possible.

"Another interesting aspect of our approach is that even as SARS-CoV-2 mutates, as long as the virus can still invade the cells we are mimicking, our nanosponge approach should still work. I'm not sure this can be said for some of the vaccines and therapeutics that are currently being developed," said Zhang.

The researchers also expect these nanosponges would work against any new coronavirus or even other respiratory viruses, including whatever virus might trigger the next respiratory pandemic.

Mimicking lung epithelial cells and immune cells

Since the novel coronavirus often infects lung epithelial cells as the first step in COVID-19 infection, Zhang and his colleagues reasoned that it would make sense to cloak a nanoparticle in fragments of the outer membranes of lung epithelial cells to see if the virus could be tricked into latching on it instead of a lung cell.

Macrophages, which are white blood cells that play a major role in inflammation, also are very active in the lung during the course of a COVID-19 illness, so Zhang and colleagues created a second sponge cloaked in macrophage membrane.

The research team plans to study whether the macrophage sponges also have the ability to quiet cytokine storms in COVID-19 patients.

“We will see if the macrophage nanosponges can neutralize the excessive amount of these cytokines as well as neutralize the virus,” said Zhang.

Using macrophage cell fragments as cloaks builds on years of work to develop therapies for sepsis using macrophage nanosponges.

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Qiangzhe Zhang, a graduate student at the Jacobs School of Engineering, and first author of the Nano Letters paper. Courtesy of Weiwei Gao, UC San Diego Jacobs School of Engineering

In a paper published in 2017 in Proceedings of the National Academy of Sciences, Zhang and a team of researchers at UC San Diego showed that macrophage nanosponges can safely neutralize both endotoxins and pro-inflammatory cytokines in the bloodstream of mice.

A San Diego biotechnology company co-founded by Zhang called Cellics Therapeutics is working to translate this macrophage nanosponge work into the clinic.

A potential COVID-19 therapeutic

The COVID-19 nanosponge platform has significant testing ahead of it before scientists know whether it would be a safe and effective therapy against the virus in humans, Zhang cautioned. But if the sponges reach the clinical trial stage, there are multiple potential ways of delivering the therapy that include direct delivery into the lung for intubated patients, via an inhaler like for asthmatic patients, or intravenously, especially to treat the complication of cytokine storm.

A therapeutic dose of nanosponges might flood the lung with a trillion or more tiny nanosponges that could draw the virus away from healthy cells. Once the virus binds with a sponge, “it loses its viability and is not infective anymore, and will be taken up by our own immune cells and digested,” said Zhang.

“I see potential for a preventive treatment, for a therapeutic that could be given early because once the nanosponges get in the lung, they can stay in the lung for some time,” Zhang said. “If a virus comes, it could be blocked if there are nanosponges waiting for it.”

Growing momentum for nanosponges

Zhang’s lab at UC San Diego created the first membrane-cloaked nanoparticles over a decade ago. The first of these nanosponges were cloaked with fragments of red blood cell membranes. These nanosponges are being developed to treat bacterial pneumonia and have undergone all stages of pre-clinical testing by Cellics Therapeutics, the San Diego startup cofounded by Zhang. The company is currently in the process of submitting the investigational new drug (IND) application to the FDA for their lead candidate: red blood cell nanosponges for the treatment of methicillin-resistant staphylococcus aureus (MRSA) pneumonia. The company estimates the first patients in a clinical trial will be dosed next year.

The UC San Diego researchers have also shown that nanosponges can deliver drugs to a wound site; sop up bacterial toxins that trigger sepsis; and intercept HIV before it can infect human T cells.

The basic construction for each of these nanosponges is the same: a biodegradable, FDA-approved polymer core is coated in a specific type of cell membrane, so that it might be disguised as a red blood cell, or an immune T cell or a platelet cell. The cloaking keeps the immune system from spotting and attacking the particles as dangerous invaders.

"I think of the cell membrane fragments as the active ingredients. This is a different way of looking at drug development," said Zhang. "For COVID-19, I hope other teams come up with safe and effective therapies and vaccines as soon as possible. At the same time, we are working and planning as if the world is counting on us."

Paper reference

"Cellular Nanosponges Inhibit SARS-CoV-2 Infectivity," published in the journal Nano Letters.


Qiangzhe Zhang, Jiarong Zhou, Hua Gong, Ronnie H. Fang, Weiwei Gao and Liangfang Zhang from the Department of NanoEngineering, Chemical Engineering Program, Jacobs School of Engineering and Moores Cancer Center, University of California San Diego

Anna N. Honko, Sierra N. Downs, Jhonatan Henao Vasquez and Anthony Griffiths from the Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine


Qiangzhe Zhang, Jiarong Zhou and Anna N. Honko contributed equally to the work


This work is supported by the Defense Threat Reduction Agency Joint Science and Technology Office for Chemical and Biological Defense under Grant Number HDTRA1‐18‐1‐0014.

Conflict of Interest statement

Liangfang Zhang discloses financial interest in Cellics Therapeutics. All other authors declare no competing interests.

Intellectual Property

Patents for macrophage nanosponges are held by Cellics Therapeutics.

Nano-scale sponges for COVID-19 are already a win for San Diego

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Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering

A commentary by Albert P. Pisano
Dean, UC San Diego Jacobs School of Engineering

San Diego, Calif., June. 17, 2020 -- A team of nanoengineers at the University of California San Diego is taking a unique approach to COVID-19 drug discovery. Their strategy is to intercept virus particles and neutralize them with nano-scale sponges before the virus can enter healthy human cells and replicate.

On June 17, 2020 the team, which is led by UC San Diego nanoengineering professor Liangfang Zhang, published the first set of data on this new approach to COVID-19 therapeutics. The experiments, described in the peer-reviewed journal Nano Letters, show that the nano-scale sponges reduce the infectivity of SARS-CoV-2 by about 90%. (Collaborators at Boston University's National Emerging Infectious Diseases Laboratories tested the nano-scale sponges with live SARS-CoV-2 virus.) Watch our animation here. Visit the nanosponge website.

It’s far too early to know if these nanosponges will make the leap from bench to bedside. But given the global need, these researchers are working as intently as possible.

I am hopeful for any and all safe and effective drugs and vaccines that will help us to reduce and eventually stop the human suffering this global pandemic is causing. As we focus on these immediate medical needs, we must also reverse the underlying inequities in the communities that are suffering disproportionately from this pandemic.

As the dean of the #9 engineering school in the USA, I have additional reasons to be talking about these nanosponges.

As an engineer and a problem solver, I like the big idea behind these nanosponges. 

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Making nanosponges infographic. Image credit: UC San Diego Jacobs School of Engineering / David Baillot

The engineers repurpose fragments of human cell membranes to create decoys. These decoys then bind to the virus, which prevents the virus from entering live cells where it will replicate and continue the infection.  

There's another aspect of this story that I'm drawing attention to in order to make a larger point. These nanosponges did not appear out of thin air back in January when troubling reports started coming in.

Professor Liangfang Zhang leveraged a platform technology his team has been developing and methodically maturing for a decade. When Liangfang understood the origins of COVID-19, he almost immediately decided to pivot not just his research efforts but his whole technology platform. A platform that his lab here at the UC San Diego Jacobs School of Engineering is leveraging to develop solutions for HIV, sepsis, rheumatoid arthritis, bacterial pneumonia, antibiotic-resistant infections and more. The startup company Zhang founded to transfer this work into the clinic, called Cellics Therapeutics, aims to start clinical trials on red blood cell nanosponges for antibiotic-resistant bacterial pneumonia next year.

This is the larger point that I'm trying to draw attention to. As a nation, we need to get better at developing, improving and leveraging platform technologies that have the potential to have outsized positive impacts compared to the investments required to create them.

As an electronics guy of a certain age, it's easy to point out, as something to emulate, platform technologies like low-cost chip design tools. These tools were critical for the birth of the micro-electronics and personal computer revolutions here in the United States.

Indeed, much of the innovation and technological successes of the past have been based on the development of platform technologies. We can’t afford to miss out on the benefits bestowed on the nations that have the foresight, trained teams, and support needed to develop and leverage the platform technologies of the future.

We can’t predict the future, but we know that our societies will need to be far more resilient than they are today. At the same time, the horrific events of the last few weeks remind us just how much work we must do to make our societies more just as well.

Having a deep bench of home-grown platform technologies that can be repurposed to address emerging and changing needs in society will go a long way towards both resilience and economic growth. In parallel, it is our responsibility to make sure our future technologists fully reflect the true diversity of our nation.

We need to be strategic about creating and supporting the innovation and education ecosystems that will give rise to the next generations of platform technologies and the people who will invent these platform technologies. I’m actively working to develop these ideas here at the Jacobs School of Engineering. I am also engaged in this project through committee work for various national organizations including the National Academy of Engineering and the U.S. Council on Competitiveness.

In the meantime, I am anxiously following the progress of all many innovators around the nation and the world who are building on what we know and what we don't know to solve the COVID-19 pandemic. 



How Stimulus Dollars are Spent will Affect Emissions for Decades

To tackle COVID-19 and climate change, government spending must deliver jobs and growth alongside deep decarbonization

Key in determining post-pandemic emissions is how governments choose to spend stimulus monies—whether they use it to prop up fossil fuel incumbents or bolster clean energy transitions already underway. iStock.com/angkhan

San Diego, Calif., June 11, 2020 -- The COVID-19 pandemic and subsequent lockdowns have led to a record crash in emissions. But it will be emission levels during the recovery—in the months and years after the pandemic recedes—that matter most for how global warming plays out, according to a new Nature commentary from researchers at the University of California San Diego.

While the skies have been noticeably cleaner, countries like the U.S., Mexico, Brazil, South Africa and others have recently relaxed laws controlling pollution and vehicle energy efficiency standards.

“This trend is worrisome because policy decisions being made now about how to save economies will determine how much CO2 enters the atmosphere over the coming decade,” said Ryan Hanna, lead author of the Nature piece and an assistant research scientist at UC San Diego, who earned his Ph.D. in the Department of Mechaincal and Aerospace Engineering here.

Some economies are already ticking upward, and so too emissions. Coal consumption in China, for example, has already returned to pre-pandemic levels.

History shows that recoveries can spur green or dirty industrial turning points

Key in determining post-pandemic emissions is how governments choose to spend stimulus monies—whether they use it to prop up fossil fuel incumbents or bolster clean energy transitions already underway, according to Hanna and co-authors David Victor, professor of international relations at UC San Diego’s School of Global Policy and Strategy, and Yangyang Xu, assistant professor of atmospheric sciences at Texas A&M University.

Economic shocks, the authors note, can be critical industrial turning points. Past shocks have led to both increases and decreases in the growth of CO2 emissions. After the 1998 Asian financial crisis, emissions doubled largely due to growth of China’s heavy manufacturing and exports, all fueled by coal. By contrast, after the global financial crash of 2008, emissions growth halved over the next decade, aided by stimulus for green technologies—up to $530 billion in 2020 USD, or 15 percent of the total global stimulus. That’s promising as it shows that structural change and lower emissions are possible if governments provide support.

Whether the coming recovery is green or dirty will have an outsized effect on climate. According to the authors’ analysis, this year’s crash in emissions, by itself, would lead to levels of  atmospheric CO2 in 2050 about 10 PPM lower than the trajectory the world was on before the pandemic. By comparison, whether the recovery is green or dirty amounts to a difference of 19 PPM in the atmosphere by 2050—nearly double the impact on the climate.

Ensuring a green recovery will require government action. Yet, government responses have so far been mixed. The European Union and South Korea remain largely committed to their respective “Green New Deals,” while other governments are falling short.

The Trump Administration in March rolled back U.S. auto fuel economy rules, committing the nation to higher transport emissions—now the largest source of warming gases in the U.S. In the same month, China authorized more coal power plants than it did in all of 2019.

Indeed, many governments have signaled a narrow focus on immediate concerns of the pandemic, such as securing health, jobs and the economy, rather than protecting the planet.

That’s bad news for planetary warming. As the authors note, meeting the goals of the Paris agreement—limiting warming to well below 2ºC above pre-industrial levels—would require cutting emissions by an amount similar to that delivered by the current economic catastrophe every year for the next decade.

Charting a course that protects both jobs and the climate

How do you align the public’s urgent needs with the need to also limit warming? “Political leaders—and climate activists who want to help them succeed—should filter policy actions for the climate by what’s politically viable,” said Hanna. “In short, that means coming up with projects that deliver jobs and revenues quickly.”

Investing in sectors like renewables, energy efficiency and preserving the existing feat of zero emission nuclear plants can set the economy on track and deepen cuts to future emissions. Bolstering these sectors can deliver and save hundreds of thousands of jobs.

At the start of this year, more than 250,000 people worked in solar energy in the U.S. The pandemic has since wiped out five years of job growth in that sector — jobs that could return quickly if credible investment incentives were in place.

Investing in energy efficiency and infrastructure construction, such as erecting power lines and conducting energy retrofits for buildings and public transportation, is another large potential employer.

“The trillions devoted to stimulus, so far, have been about stabilizing economies and workers,” said Victor. “With a fresh focus that looks further into the future, the next waves of spending must also help to protect the climate.”

The EU Green Deal as a model for stimulus

Hanna, Victor and Xu write, “The European Green Deal is a good model for stimulus packages. It is a massive, €1-trillion (U.S. $1.1-trillion) decade-long investment plan that combines industrial growth with deep decarbonization and efficiency and has maintained political support throughout the pandemic.”

Existing firms will need to be involved in a green recovery because they are ready to restart, the authors recommend.  And a savvy political strategy would isolate only those companies whose actions egregiously undermine climate goals, such as conventional coal, and would ensure their workers are treated justly and retrained in new areas of employment.

The authors also recommend a sector by sector approach to decarbonizing the economy, as the policies needed to rein in the largest emitters in each sector differ.

“On our current path, emissions are likely to tick upwards, as they have after each recession since the first oil shock of the early 1970s,” said Victor. “The historic drop in recent months was too hard won to be so easily lost.”

To read the full Nature piece, go to the Nature website.

Graduating students honored with engineering Awards of Excellence

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By Daniel Li

San Diego, Calif., June 11, 2020-- While graduation celebrations for the Class of 2020 may be different than usual, some things will remain the same, including the high caliber and character of students graduating from UC San Diego with baccalaureate degrees in engineering. 

All of these students have contributed to our Jacobs School of Engineering community in ways big and small, but six students were selected from among their peers to receive an Award of Excellence for their outstanding academic, leadership and community contributions. They received these awards virtually from Dean Albert P. Pisano at the livestreamed Ring Ceremony on Saturday, June 13. Watch a replay of the ceremony here the Jacobs School of Engineering website.

At the Ring Ceremony, graduating seniors also received their class ring, and recited together the Jacobs School of Engineering oath, vowing to practice engineering with integrity and high ethical standards. 

Distinguished student speaker Laura Alejandra Morejon Ramirez, an aerospace engineering graduate, shared the following remarks.

Here are some highlights from the 2020 Jacobs School of Engineering student award winners.

Award for Excellence in Bioengineering

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Almudena Prieto Prieto

Almudena Prieto Prieto’s favorite part about bioengineering is its impact on improving the lives of others through drug treatments and medical devices. Throughout her four years at UC San Diego, Prieto Prieto has been a part of the Biomedical Engineering Society and served as the Translational Medicine Day co-chair her junior year. 

“As TMD co-chair I was able to organize a conference-style event displaying the field of translational medicine and its bench-to-bedside approach that ensures that medical innovation reaches patients and benefits them sooner rather than later,” she said. “Organizing and learning about this event made me realize the importance of timely impact and made me want to focus on practical healthcare innovations that put the patient first.”

While at UC San Diego, Prieto Prieto completed two internships: She worked abroad in Australia and at Tandem Diabetes Care in the research and development department. After graduating, Prieto Prieto will continue her studies at Rice University, pursuing a master’s degree in Medical Innovation to dive deeper into medical technologies, particularly for low resource communities. She hopes to use this knowledge to pursue medical technology development focused on global health to make an impact in communities around the world.

Prieto Prieto explained the importance of branching outside of one’s major and exploring seemingly unrelated topics.

“Many times, I feel like engineering students will not try different specialties or projects because it doesn’t fit their cookie-cutter definition of what they think they are supposed to do based on all these labels,” Prieto Prieto said. “However, in reality, most projects are so interdisciplinary that everyone’s background knowledge can contribute so much. I wished I had had someone tell me that when I began my college career, and that I’d listened because I truly think that one can only learn when they step out of their comfort zone.”

Award for Excellence in Computer Science and Engineering

Goto FlickrWeiyang Wang

Weiyang Wang is obsessed with solving complex problems, which is why he decided to double major in computer science and physics. He spent the majority of his time at UC San Diego conducting circuit-switching research under Professor Alex Snoeren, an experience that helped him discover his interests in research and computer networking. 

At the same time, Wang was a tutor for several computer science classes, including CSE 132A with Professor Victor Vianu and CSE 8B with Professors Paul Cao and Alex Snoeren.

“Our tutoring program is awesome — it gives us a chance to help fellow students to learn, consolidate our knowledge, and meet other amazing peer tutors,” Wang said. 

In the fall, Wang will enroll at MIT for his Ph.D. in computer science, with hopes of becoming a professor. To be successful, Wang explained that it is important to be willing to dive deep into a subject and take advantage of all the resources that the department offers. 

“I never run out of fun things to think about in computer science (and physics), and these interesting problems motivate me to keep exploring,” Wang said. “Hence, my advice would be to realize your motivation and carry on with it.”

Award for Excellence in Electrical and Computer Engineering

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Keshav Rungta

Keshav Rungta was immediately hooked on electrical engineering after taking one of his first ECE classes, ECE5: Making, Breaking and Hacking Stuff. The class reinforced his passion for robotics, and after earning his master’s degree next year as part of the BS/MS program at the Jacobs School, he hopes to enter the robotics industry.  

On campus, Rungta was involved in a variety of organizations, including UC San Diego’s Eta Kappa Nu chapter, and IEEE. He also conducted research under Professor Truong Nguyen on a 3D Scene Reconstruction project, and Professor Dinesh Bharadia on an All Weather Radar Imaging for Autonomous Driving project. His most memorable experience: running H.A.R.D. Hack, one of the largest hardware hackathons. 

“I believe it is the people I met along the way that really made these activities meaningful; it was all of these relationships and the support from all my friends that allowed me to work in so many things,” Rungta said. 

He encourages students to step out of their comfort zones and try something new to gain more experiences.

“The one thing that I would want everyone to keep in mind is to always try something new,” Rungta said. “It will allow one to get out of their comfort zone, meet new people, learn new perspectives, learn new ideas, and gain new experiences.”

Award for Excellence in Mechanical and Aerospace Engineering

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Barry Lawlor

Mechanical engineering was an attractive major for Barry Lawlor to study in college because he loved working with his hands, understanding mechanisms, and excelled in math and physics. For Lawlor, one of the most rewarding aspects of the field is the ability to study the function of different aspects of the world, and then apply that in practical ways through technology. 

After graduation, Lawlor will be attending California Institute of Technology for his Ph.D. in Mechanical and Civil Engineering. According to Lawlor, his time in Professor Veronica Eliasson's Shocks & Impacts Lab conducting research on experimental mechanics is what inspired him to pursue a Ph.D. 

“Throughout the course of the years, I had the chance to see the full development of an experimental system from initial concept to fine tuning and producing results,” Lawlor said. “Ultimately this was the most instrumental opportunity that led to my pursuit of a Ph.D. after undergrad. I'm so thankful to Dr. Eliasson for her great investment in me and the other undergrads in her lab. I don't know of any other faculty that cares so much about their students and seeks to set them up for success like Dr. Eliasson does!”

His advice to students?

“Seek out challenges early in your career! Eventually, they'll come to you regardless. But struggling through difficult problems and projects early on provides so much more valuable experience than taking things easy on yourself: making future challenges after undergraduate that much more manageable,” Lawlor said. “For sure, there are times to rest, but you have to know that it will never seem convenient to take on these extra challenges.”

Award for Excellence in Nanoengineering

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Leilani Kwe

Leilani Kwe was drawn to nanoengineering because of its interdisciplinary nature and the field’s cutting-edge technology and research. At UC San Diego, Kwe worked in Professor Shaochen Chen's Tissue Engineering Lab for two years, working with engineers to create 3D-bioprinted objects. 

Kwe will be interning at Intel this summer and then returning to UC San Diego to start her master’s degree. She stressed the importance of communicating with peers, mentors, and experienced engineers. For Kwe, reaching out to these more experienced engineers and advisors for advice helped her get a clearer picture of her future goals, and she encourages students to do the same.

“For me, it was difficult to figure out what kind of path I wanted to take with my degree, and many times I wasn't even sure how to set myself apart from other students,” Kwe said. “A previous teaching assistant, Cody Carpenter, nudged me to get into research and build more skills; he explained how I could approach a PI and gave me the confidence to do so. And once in a lab, my Ph.D. mentor showed me how to communicate scientific ideas in a cooperative manner, how to write a resume and answer interview questions, and most importantly, how to better manage a work/life balance.”

Award for Excellence in Structural Engineering

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Jessica Chan

When Jessica Chan started at UC San Diego, she was an engineering science major looking to switch into mechanical engineering. However, after attending a Triton Unmanned Aerial Systems meeting with a friend and joining a project team, she became interested in aerospace composites and structural design. She decided to pursue structural engineering, and the rest is history. 

Since joining Triton UAS, Chan has held multiple leadership roles: Airframe subteam co-lead and project manager. She emphasized that on top of developing hands-on technical skills, Triton UAS has allowed her to gain experience in leadership, management, and communications.

“Most notably, I have also learned how to work with a diverse and interdisciplinary team of students from the computer science, data science, mechanical and aerospace engineering, and structure engineering departments to integrate software, embedded, and airframe systems to create a competitive platform for competition,” Chan said. “Our team provides an opportunity for students to have hands-on experience by making sure that the barrier for entry is low - we don't have any applications or attendance requirements.”

At UC San Diego, Chan also conducted research in Professor Hyonny Kim’s lab, studied abroad in Rome, and participated in Los Alamos Dynamic Summer School. She urges students to get involved on campus right away, and to talk to both professors and teaching assistants. 

“There's a lot of different engineering student project teams to choose from and many professors are happy to offer undergraduate students lab assistant positions in their labs,” Chan said. “If you can, figure out how to do a study abroad program. The effort is really worth the experience. For engineers, one good study abroad program is the Global Seminars, many of which fulfill college specific general education requirements.”

After graduation, Chan looks forward to working at General Atomics as a stress engineer. She hopes to take some time and figure out if she would like to pursue graduate school to branch off either to academia or a federally funded research and development center like NASA.

Pioneering Scientist and Innovator Larry Smarr Retires

Pioneering scientist and innovator Larry Smarr retires. Photo credit: Erik Jepsen/UC San Diego

San Diego, Calif., June 11, 2020 -- After 20 years at UC San Diego, Larry Smarr will step down as the director of the California Institute for Telecommunications and Information Technology (Calit2) and retire as a distinguished professor from the Jacobs School of Engineering’s Computer Science and Engineering Department at the end of this month. Dr. Ramesh Rao, professor of electrical and computer engineering at the Jacobs School of Engineering, will serve as interim director of Calit2, in addition to his current position as the director of the Qualcomm Institute.

During these two decades, Smarr grew the two-campus Calit2 into a collaborative discovery system that engaged hundreds of faculty, staff, students and companies.

“As a pioneer in scientific computing, supercomputer applications, and Internet infrastructure, Larry’s work helped shape the modern world,” said Chancellor Pradeep K. Khosla. “His commitment to interdisciplinary collaboration, unique vision on how information technology can enhance life science research, and leadership of Calit2 propelled research to new heights at UC San Diego and beyond.”

Pioneering a Path of Discovery

Smarr joined UC San Diego in 2000 and later that year was appointed the founding director of Calit2, an interdisciplinary research and education institute with two divisions — the Qualcomm Institute at UC San Diego and Calit2@UC Irvine.

Smarr worked closely with the Calit2 division directors, as well as countless collaborators, to develop a wide range of Calit2 multidisciplinary research efforts in health, energy, environment, and culture, all driven by exponential advances in information technologies, telecommunications, nanotechnology and biomedical technologies.

“Larry has been a great source of inspiration for me,” said Rao, who has served as the director of the Qualcomm Institute since its inception. “I feel fortunate to be one of the many faculty and researchers from numerous disciplines who Larry was able to deeply influence with his knowledge, understanding and intellectual sensibility.”

“I am honored to have had the opportunity to collaborate with Larry, a leader, mentor and visionary in multiple fields of science and technology, and to advance many successful joint research programs between our two campuses,” said G.P. Li, the director of Calit2@UC Irvine since 2007.

With 20 years of National Science Foundation funding, Smarr and his colleagues at Calit2 and the San Diego Supercomputer Center demonstrated how to use optical fiber networks to create distributed computer, storage, and visualization systems to empower data-intensive research, not only on the UC San Diego and UC Irvine campuses, but then extending to connect campuses across California and outward to campuses around the world.

Over the last decade, Smarr has become a pioneer in the quantified-self movement, including personalized surgery. He has developed a unique, multi-year time series of over 100 biomarkers and gut microbiome genomics, using his own body as a laboratory, which is now being analyzed by many UC San Diego faculty, staff and students. He is also currently a lead investigator on research supported by the Helmsley Charitable Trust on a 3D Medical Imaging Pilot to Improve Surgical Outcomes for Patients with Crohn’s Disease.

“Larry is a true engineering leader, pioneer and visionary. He has made many contributions in both the development of new technologies and the application of engineering and computing advances for the good of humanity,” said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. “At the same time, Larry is a role model for how to collaborate across disciplines and how to communicate the work to key constituents in government and industry and to the general public.”

“Larry Smarr is an innovator in every sense of the word.” said Dean Tullsen, Chair of the Computer Science and Engineering Department at UC San Diego. “His commitment to building strong, lasting scientific collaborations coupled with his dedication to education and public service have led to numerous scientific and technological advances that touch a variety of fields - from health and medicine to art and culture. It has been an honor to work with him.” 

Smarr received his BA and MS from the University of Missouri and earned his PhD at the University of Texas at Austin in 1975. He then completed postdoctoral research at Princeton, Harvard and Yale. Prior to joining UC San Diego, Smarr was a professor of Physics and of Astronomy at the University of Illinois at Urbana-Champaign (UIUC) for 20 years where he conducted observational, theoretical and computational-based research in relativistic astrophysics. During that time, he served as the founding director of the UIUC National Center for Supercomputing Applications and later the National Computational Science Alliance, headquartered on the UIUC campus.

Dedication to Science and Public Service 

Smarr has been a strong believer in public service throughout his career. For eight years he was a member of the NIH Advisory Committee to the NIH Director, serving three directors. Smarr served on the NASA Advisory Council to four NASA Administrators, was chair of the NASA Information Technology Infrastructure Committee and the NSF Advisory Committee on Cyberinfrastructure. He also served on Governor Schwarzenegger’s California Broadband Task Force in 2007. He currently serves on the Advisory Board to the Director of the Lawrence Berkeley National Laboratory.

Smarr was elected a Fellow of the American Physical Society in 1988, received the Franklin Institute’s Delmer S. Fahrney Gold Medal for Leadership in Science or Technology in 1990, was named a Fellow of the American Academy of Arts and Sciences in 1994, was elected a member of the National Academy of Engineering in 1995, and a Fellow of the American Association for the Advancement of Science in 2017. In 2002, he was named the Harry E. Gruber Professor of Computer Science and Information Technologies at the UC San Diego Jacobs School of Engineering. In 2006, he received the IEEE Computer Society Tsutomu Kanai Award for his lifetime achievements in distributed computing systems and in 2014 the Golden Goose Award. In May 2008 he was awarded an honorary Ph.D. by his alma mater, the University of Missouri-Columbia.


Virtual Q&A: nanotech and COVID-19

Sunmi Shin Wins 2020 Chancellor's Dissertation Medal

Sunmi Shin, a Materials Science and Engineering PhD student, recently won the 2020 Chancellor’s Dissertation Medal which recognizes outstanding doctoral research at UCSD. Sunmi's research focuses on how to better control heat. The heat conduction process is often difficult to control due to its diffusive nature. This feature is distinct from optical and electrical energy transport with highly advanced technologies. If one could engineer the transport of thermal energy,  which is arguably the most ubiquitous form of energy, a variety of energy transport and conversion technologies could be improved. Active control of thermal transport is of significant interest for a wide range of applications, such as thermoregulation of individuals, buildings, vehicles and batteries, renewable energy conversion, bio/chemical sensing, and micro/nanomanufacturing. Sunmi's work aims to actively manipulate heat transport using multidisciplinary approaches, including thermo-electric and thermo-photonic engineering.

Class Acts: 2020 Grads Step into the Spotlight

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By Lily Chen

San Diego, Calif., June 4, 2020 -They’ve worked hard, made an impact, inspired their communities, and most of all, they’ve demonstrated incredible resilience in challenging times. Help celebrate the class of 2020’s remarkable achievements by reading their stories of hope as these new alumni create better futures for themselves and the world.

Varun Govil: Undergraduate Expanding the Horizons of Cancer Diagnosis

Major: Bioengineering: Biotechnology

College: Earl Warren College

When Varun Govil was in high school, he became fascinated with biology after learning about the large-scale living systems and how they were all integrated together. In particular, he was interested in cancer mechanisms, especially the Darwinian evolution of tumors, and the research process scientists have utilized in their attempts to defeat cancer. Combining his interests in engineering and the ability to experiment with biological systems in the lab led him to study bioengineering at UC San Diego. Govil was awarded the Irwin Jacobs Scholarship, a full merit-based scholarship for top engineering students, which has opened up other avenues for mentorship and growth as an undergraduate researcher.

Govil was involved with several synthetic biology research projects during his time as undergraduate, including working in the School of Medicine to help develop and patent Epinoma, a blood test to screen for liver cancer. “It’s by far one of the most intriguing ideas that I’ve been fortunate to work on,” he said. “Our discussions with various oncologists and cancer patients highlighted some of the most pressing challenges in cancer diagnostics today, mainly the issue of cost, invasiveness and limited accuracy.” Those discussions were used as a launching point to create a protein that could be applied to blood samples and give off a fluorescent signal that would then be used to assess patient health. Govil led a team of 11 undergraduates as part of an independent research team in the School of Medicine and together, they built a set of unique machine learning algorithms to identify the biomarkers for liver cancer. The algorithms characterized the properties of a nanomaterial for better sensitivity and created a digital platform for patients to monitor their own health. “Looking back, I think our team was really driven by the desire to positively impact others’ lives and the desire to just perform good science,” Govil said.

In 2018, Govil and his team earned a second-place win at the International Genetically Engineered Machine (iGEM) competition earned additional funding to keep developing Epinoma for the appropriate levels of sensitivity. “For me, being a part of this competition was just absolutely incredible,” he said. “It was so exciting to see our vision grow from an initial set of experiments to unfolding into a much more useful technology.”

Govil was also awarded the Strauss Scholarship, a generous $15,000 grant, to develop Verde Lux, a pilot program for low-income and underprivileged San Diego high school students with an emphasis on STEM engagement. Working together with a team, he researched relevant case studies to build a virtual classroom. Their primary focus is providing underrepresented minority students the opportunities to pursue nontraditional research pathways and get them excited about a career in science and engineering. “It’s been really rewarding to be able to share the joy of science and learning with others,” Govil said. “It’s given me a completely different perspective about educational pedagogy.” Verde Lux was recognized by Imperial College’s School of Business QSReimagine Education competition for its innovation in the education space and shortlisted for the Top K12 Project award.

After graduation, Govil will be attending the Masters in Translational Medicine program, a joint program between UC San Francisco and UC Berkeley, where he hopes to continue working on next-generation cancer diagnostics and gain hands-on experience with medtech devices. “I think that we as scientists and researchers should realize the enormous privilege we have been given, to be at the front lines of driving change, and to make the most of that opportunity,” he said.

Full story: https://ucsdnews.ucsd.edu/feature/class-acts-2020-grads-step-into-the-spotlight

International Symposium on Computer Architecture Honors Scientists for Paper's Lasting Impact

Recent honor marks the record-breaking third time computer science Chair Dean Tullsen has won the Influential Paper Award

The International Symposium on Computer Architecture (ISCA) is honoring a paper by UC San Diego Computer Science and Engineering Department Chair Dean Tullsen — along with Rakesh Kumar, a former student, and Victor Zyuban — with the 2020 Influential Paper Award for its lasting impact.  

San Diego, Calif., June 3, 2020 -- The International Symposium on Computer Architecture (ISCA) is honoring a paper by UC San Diego Computer Science and Engineering Department Chair Dean Tullsen — along with Rakesh Kumar, then a PhD student at UC San Diego and first author on the paper, and Victor Zyuban — with the 2020 Influential Paper Award for its lasting impact. 

Entitled Interconnections in Multi-Core Architectures: Understanding Mechanisms, Overheads and Scaling, the paper examines how interconnections on multiprocessor chips can affect power, performance and design. Prior to this study, the community did not fully understand the significant impact interconnect architectures could have on performance and power usage in this environment. The research also offered new ways to model these issues, findings that proved tremendously helpful for researchers over the years.

The paper was first presented at the 32nd International Symposium on Computer Architecture in June 2005. Fellow authors were Rakesh Kumar, who is now an associate professor of Electrical and Computer Engineering at the University of Illinois, and Victor Zyuban, who spent 15 years at IBM and is now with Apple.

Each year, the Influential Paper Award recognizes one paper from the ISCA conference held 15 years previously with the greatest impact on the field. In addition to this award, the paper has been cited more often than any other from the 2005 conference.

“We are quite honored to receive this Influential Paper Award,” said Tullsen. “ISCA is the flagship conference in computer architecture, making this perhaps the highest distinction for a paper in our field.”

When the study was first presented, dual core architectures were just emerging on the market, and computer scientists were still investigating how they should be designed. While there was a rich literature in the theory of inter-processor and even multicore interconnects, this was the first paper to extensively measure real multicore designs and evaluate the global tradeoffs of interconnect design decisions. A partnership with IBM, and access to the company’s Power processor hardware, were key to the study’s success.

The paper illuminates how the interconnects on chips create unique challenges, which differ significantly from connected chips. To develop the best multi-core design, the core, cache and interconnect architectures must be codeveloped. Designs that provided the best interconnect performance were not optimal in a resource-limited, single-chip processor.

“We pointed out that a naive implementation or what was state-of-the-art then, that kind of interconnection won’t cut it,” said Kumar. “So, people did a lot of innovation subsequently on reducing the overhead of interconnection.”

This is the third time one of Tullsen’s papers has received this award, making him the first to reach that milestone. Simultaneous multithreading: maximizing on-chip parallelism and Exploiting choice: instruction fetch and issue on an implementable simultaneous multithreading processor were honored in 2010 and 2011.

ISCA is the premier forum for computer architecture ideas and research. To safeguard participants, this year’s conference was held virtually.

Joel Conte Named to the Eric and Johanna Reissner Chair for Structural Engineering

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Joel Conte, a professor in the Department of Structural Engineering at UC San Diego, was named to the Eric and Johanna Reissner Chair.
Photos: David Baillot

San Diego, Calif., June 1, 2020 --  Structural engineering professor Joel Conte was named to the Eric and Johanna Reissner Chair in the Department of Structural Engineering at UC San Diego.

Conte is the principal investigator for the operation and maintenance of the world’s largest outdoor shake table located at the UC San Diego Englekirk Structural Engineering Center at the University of California San Diego. The facility, which is also the second  largest shake table in the world overall,  is currently undergoing a major upgrade funded by the National Science Foundation. Once upgraded, the shake table will be able to reproduce all six components of ground motions experienced during earthquakes. Conte is the principal investigator on the $16.3 million upgrade grant. 

“We will be able to reproduce actual earthquake ground motions with the most accuracy of any large shake table in the world,” Conte said.

“This will accelerate the discovery of the knowledge engineers need to design new buildings, bridges, power plants, dams, levees, telecommunication towers, wind turbines, retaining walls, tunnels, and to retrofit older structures vulnerable to earthquakes. It will enhance the resiliency of our communities.”

After the upgrade, the facility will be able to subject the heaviest and tallest test specimens in the world to extreme earthquake forces in near real-world conditions.

In the past 15 years, seismic research carried out at UC San Diego’s outdoor shake table has led to important changes in design codes for commercial and residential structures and new insights into the seismic performance of geotechnical systems, such as foundations, bridge abutments, tunnels and retaining walls. It also has helped validate the use of innovative technologies and design methodologies to make buildings more likely to withstand earthquakes. 

Conte’s research focuses on developing computer models of civil infrastructure that can capture how these systems fail when experiencing extreme seismic forces. By combining structural mechanics and dynamics with probabilistic methods, he and his team are developing risk- and performance-based seismic assessment and design methodologies. Conte calibrates numerical models of structural systems based on measurement data. He then evaluates and validates these models on experimental or field data. These models can be used to predict and diagnose damage in civil structures. Conte also researches shake table dynamics and control.

Funds from the Eric and Johanna Reissner Chair will help support Conte’s teaching and research. 

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As principal investigator for UC San Diego's shake table--the largest outdoor earthquake simulator in the world--Conte conducts research on seismic safety. The shake table is funded by the National Science Foundation. 

“Joel's work in leading the operations and upgrade of our earthquake simulator has been extremely important for the seismic safety research community,” said John McCartney, chair of the Department of Structural Engineering at UC San Diego. “This endowed chair will allow him to continue playing this key role while continuing his own teaching and research.”   

Before joining UC San Diego in 2001, Conte served as associate professor of civil engineering at UCLA and before that at Rice University. He is a member of the American Society of Civil Engineers (ASCE), the Earthquake Engineering Research Institute (EERI), and the International Association for Bridge and Structural Engineering (IABSE). He is also a member of the Chi Epson civil engineering honor society. Conte is a recipient of the Research Initiation Award from the National Science Foundation, a co-recipient of the ASCE Moisseiff Award, and a recipient of the UCSD’s Academic Senate Distinguished Teaching Award.

The Reissner chair is named in honor of Eric Reissner, who served as professor of Applied Mechanics and Engineering Sciences at UC San Diego between 1969 and 1979 before retiring, and his wife, Johanna. 

Reissner was a Guggenheim fellow and received the Timoshenko Medal in 1973, the Theodore von Karman Medal in 1964, and the ASME Medal in 1988. “Dr. Reissner is perhaps best known for the Reissner shear-deformation plate theory, which describes mathematically what happens to a flat surface when a force is applied to it. Engineers use it to analyze the external forces that act on structural surfaces like floors or the skin of airplane wings,” The New York Times wrote in Reissner’s obituary in 1996. 


These flexible feet help robots walk faster

San Diego, Calif., June 1, 2020 -- Roboticists at the University of California San Diego have developed flexible feet that can help robots walk up to 40 percent faster on uneven terrain such as pebbles and wood chips. The work has applications for search-and-rescue missions as well as space exploration.

“Robots need to be able to walk fast and efficiently on natural, uneven terrain so they can go everywhere humans can go, but maybe shouldn’t,” said Emily Lathrop, the paper’s first author and a Ph.D. student at the Jacobs School of Engineering at UC San Diego. 

The researchers will present their findings at the RoboSoft conference which takes place virtually May 15 to July 15, 2020. 

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The soft robotic foot conforms to the surfaces on which it steps, allowing the robot to walk faster. 

“Usually, robots are only able to control motion at specific joints,” said Michael T. Tolley, a professor in the Department of Mechanical and Aerospace Engineering at UC San Diego and senior author of the paper. “In this work, we showed that a robot that can control the stiffness, and hence the shape, of its feet outperforms traditional designs and is able to adapt to a wide variety of terrains.”

The feet are flexible spheres made from a latex membrane filled with coffee grounds. Structures inspired by nature‒ such as plant roots‒ and by man-made solutions‒ such as piles driven into the ground to stabilize slopes‒ are embedded in the coffee grounds.

The feet allow robots to walk faster and grip better because of a mechanism called granular jamming that allows granular media, in this case the coffee grounds, to go back and forth between behaving like a solid and behaving like a liquid. When the feet hit the ground, they firm up, conforming to the ground underneath and providing solid footing. They then unjam and loosen up when transitioning between steps. The support structures help the flexible feet remain stiff while jammed. 

It’s the first time that such feet have been tested on uneven terrain, like gravel and wood chips.  

The feet were installed on a commercially available hexapod robot. Researchers designed and built an on-board system that can generate negative pressure to control the jamming of the feet, as well as positive pressure to unjam the feet between each step.  As a result, the feet can be actively jammed, with a vacuum pump removing air from between the coffee grounds and stiffening the foot. But the feet also can be passively jammed, when the weight of the robot pushes the air out from between the coffee grounds inside, causing them to stiffen. 

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An off-the-shelf six-legged robot equipped with the feet designed by UC San Diego engineers can walk up to 40 percent faster than when not equipped with the feet. 

Researchers tested the robot walking on flat ground, wood chips and pebbles, with and without the feet. They found that passive jamming feet perform best on flat ground but active jamming feet do better on loose rocks. The feet also helped the robot’s legs grip the ground better, increasing its speed. The improvements were particularly significant when the robot walked up sloped, uneven terrain. 

“The natural world is filled with challenging grounds for walking robots---slippery, rocky, and squishy substrates all make walking complicated,” said Nick Gravish, a professor in the UC San Diego Department of Mechanical and Aerospace Engineering and study coauthor. “Feet that can adapt to these different types of ground can help robots improve mobility."

In a companion paper co-authored by Tolley and Gravish with Ph.D. student Shivan Chopra as first author, researchers quantified exactly how much improvement each foot generated. For example, the foot reduced by 62 percent the depth of penetration in the sand on impact; and reduced by 98 percent the force required to pull the foot out when compared to a fully rigid foot. 

Next steps include incorporating soft sensors on the bottom of the feet to allow an electronic control board to identify what kind of ground the robot is about to step on and whether the feet need to be jammed actively or passively. 

Researchers will also keep working to improve design and control algorithms to make the feet more efficient. 

Shear Strengthened Granular Jamming Feet for Improved Performance over Natural Terrain
Emily Lathrop, Nick Gravish and Michael T. Tolley, Department of Mechanical and Aerospace Engineering, UC San Diego

Iman Adibnazari, Department of Electrical and Computer Engineering, UC San Diego 


Premier Innovation Partnership Taps into Talent and Technology at UC San Diego

Making matter out of light: high-power laser simulations point the way

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The study offers a recipe for researchers at the Extreme Light Infrastructure (ELI) high-power laser facility to follow to produce matter from light. Pictured is the L3-HAPLS advanced petawatt laser system at the ELI Beamlines Research Center. Photo courtesy of Lawrence Livermore National Laboratory.

By Becky Ham

San Diego, Calif., May 28, 2020 -- A few minutes into the life of the universe, colliding emissions of light energy created the first particles of matter and antimatter. We are familiar with the reverse process—matter generating energy—which occurs in an atomic bomb, for example, but it has been difficult to recreate that critical transformation of light into matter.

Now, a new set of simulations by a research team led by UC San Diego’s Alexey Arefiev point the way toward making matter from light. The process starts by aiming a high-power laser at a target to generate a magnetic field as strong as that of a neutron star. This field generates gamma ray emissions that collide to produce—for the very briefest instant—pairs of matter and antimatter particles.

The study published May 11 in Physical Review Applied offers a sort of recipe that experimentalists at the Extreme Light Infrastructure (ELI) high-power laser facilities in Eastern Europe could follow to produce real results in one to two years, said Arefiev, an associate professor of mechanical and aerospace engineering.

“Our results put scientists in a position to probe, for the first time, one of the fundamental processes in the universe,” he said.

Harnessing high power

Arefiev, Ph.D. student Tao Wang and their colleagues at the Relativistic Laser-Plasma Simulation Group have been working for years on ways to create intense, directed beams of energy and radiation, work that is supported in part by the National Science Foundation and Air Force Office of Science Research. One way to accomplish this, they noted, would be to aim a high-power laser at a target to create a very strong magnetic field that would throw off intense energy emissions.

High-intensity, ultra-short laser pulses aimed at a dense target can render the target “relativistically transparent,” as the electrons in the laser move at a velocity very close to the speed of light and effectively become heavier, Arefiev explained. This keeps the laser’s electrons from moving to shield the target from the laser’s light. As the laser pushes past these electrons, it generates a magnetic field as strong as the pull on the surface of a neutron star—100 million times stronger than Earth’s magnetic field.

To say this all happens in the blink of an eye is a vast overstatement. The magnetic field exists for 100 femtoseconds. (A femtosecond is 10-15 of a second—a quadrillionth of a second.) But “from the point of the view of the laser, the field is quasi-static,” said Arefiev. “Then again, from the point of view of the laser, our lives are probably longer than the life of the universe.”

A high-power laser in this instance is one in the multi-petawatt range. A petawatt is a million billion watts. For comparison, the Sun delivers about 174 petawatts of solar radiation to the Earth’s entire upper atmosphere. A laser pointer delivers about 0.005 watt to a Power Point slide.

Previous simulations suggested that the laser in question would have to be high powered and aimed at a tiny spot to produce the required intensity to create a strong enough magnetic field. The new simulations suggest that by increasing the size of the focal spot and boosting the laser power to around 4 petawatts, the laser’s intensity could remain fixed and still create the strong magnetic field.

Under these conditions, the simulations show, the laser-accelerated electrons of the magnetic field spur the emission of high-energy gamma rays.

“We did not expect that we didn’t need to go to a crazy intensity, that it’s just sufficient to increase the power and you can get to very interesting things,” said Arefiev.

Particle pairs

One of those interesting things is the production of electron-positron pairs—paired particles of matter and antimatter. These particles can be produced by colliding two gamma-ray beams or colliding one gamma-ray beam with blackbody radiation, an object that absorbs all radiation falling on it. The method produces a lot of them—tens to hundreds of thousands of pairs born out of one collision.

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Alexey Arefiev, an associate professor of mechanical and aerospace engineering at the UC San Diego Jacobs School of Engineering.

Scientists have performed the light-into-matter feat before, notably in one 1997 Stanford experiment, but that method required an extra stream of high-energy electrons, while the new method “is only light used to produce matter,” said Arefiev. He also noted that the Stanford experiment “would produce one particle pair about every 100 shots.”

An experiment that uses only light to create matter more closely mimics conditions during the first minutes of the universe, offering an improved model for researchers looking to learn more about this critical time period. The experiment could also provide more chances to study antimatter particles, which remain a mysterious part of the universe’s composition. For instance, scientists are curious to learn more about why the universe appears to have more matter than antimatter, when the two should exist in equal amounts.

Arefiev and his colleagues were encouraged to do these simulations now because the laser facilities capable of carrying out the actual experiments are now available. “We specifically did the calculations for the lasers that have not been available until recently, but now should be available at these laser facilities,” he said.

In an odd twist, the simulations proposed by the research team could also help the ELI scientists determine whether their lasers are as intense as they think they are. Firing a laser in the multi-petawatt range at a target only five microns in diameter “destroys everything,” said Arefiev. “You shoot and it’s gone, nothing is recoverable, and you can’t actually measure the peak intensity that you produce.”

But if the experiments produce gamma rays and particle pairs as predicted, “this will be a validation that the laser technology can reach such a high intensity,” he added.

Last year, the UC San Diego researchers received a U.S. National Science Foundation grant that allows them to partner with ELI researchers to carry out these experiments. This partnership is critical, Arefiev said, because there are no facilities in the United States with powerful enough lasers, despite a 2018 report from the National Academies of Sciences warning that the U.S. has lost its edge in investing in intense ultrafast laser technology.

Arefiev said the ELI laser facilities will be ready to test their simulations in a couple years. “This is the reason why we wrote this paper, because the laser is operational, so we are not that far away from actually doing this,” he said. “With science, that is what attracts me. Seeing is believing.”

Paper Title: Power scaling for collimated -ray beams generated by structured laser-irradiated targets and its application to two-photon pair production.” Co-authors include Xavier Ribeyre and Emmanuel d’Humières of the University of Bordeaux-CNRS-CEA; Daniel Stutman of the Extreme Light Infrastructure-Nuclear Physics (ELI-NP)/Horia Hulubei National Institute of Physics and Nuclear Engineering and Johns Hopkins University; and Toma Toncian of the Institute for Radiation Physics, Helmholtz-Zentrum Dresden-Rossendorf.

This study was funded by the National Science Foundation (1632777 and 1821944), the Air Force Office of Science Research ( FA9550-17-1-0382), and the French National Research Agency TULIMA Project (ANR-17-CE30-0033-01)

This story originally ran in ThisWeek@UC San Diego

Nanoscale optical pulse limiter facilitated by refractory metallic quantum wells

Comparison of the traditional bulk transmission-mode and the proposed nanoscale reflection-mode pulse limiters. (A and B) Conventional configurations (not to scale) widely used for optical limitation based on Kerr-induced self-defocusing (A) and Kerr-type nonlinear absorption (such as TPA) (B). The former is achieved by inserting a bulk Kerr medium behind the focal plane to accelerate the divergence of an incident Gaussian beam with a high intensity so that only a fraction of the beam is allowed to pass through a preassigned aperture. The latter is performed by placing a bulk Kerr medium ahead of the focal plane to absorb the incident beam’s high-intensity portion. Note that an inhomogeneously distributed bulk Kerr medium, as shown in (B), is desired to maximize the nonlinear absorption. (C) Recently emerging reflective optical limiter (not to scale). To limit the high-intensity transmission, instead of increasing the absorption (B), the reflection of the reflective pulse limiter will be enhanced because of off-resonance above the threshold intensity. (D) Schematic representation of the nanoscale reflective optical limiter (not to scale). The deeply subwavelength optical limiter film can be integrated onto the surface of an existing optical component. Credit: Science Advances, doi: 10.1126/sciadv.aay3456

San Diego, Calif., May 26, 2020 -- In the past several decades, physicists have conducted deep laboratory investigations into nonlinear optics, plasma physics and quantum science using advanced high-intensity, ultrashort-pulse lasers. Increased use of the technology naturally risked damaging the optical detection systems and therefore they proposed a variety of optical limiting mechanisms and devices. Device miniaturization of such designs while maintaining superior integrability and control can, however, become complex. In a new report, Haoliang Qian and a research team in electrical and computer engineering, materials science, chemistry and the Center for Memory and Recording Research at the University of California, San Diego, detailed a reflection-mode pulse limiter. They engineered the device using nanoscale refractory films made of aluminum oxide and sandwiched titanium nitride (Al2O3/TiN/Al2O3) to build the metallic quantum wells (MQWs). The quantum size effect of the MQW provided large and ultra-fast Kerr-type nonlinearities. Functional multilayers containing these MQWs will find new applications in meta-optics, nanophotonics and nonlinear optics, and the results are now published on Science Advances.

An optical limiter can facilitate linear transmission or reflection below a certain incident light intensity or power threshold, and above that threshold, the device can keep the reflected optical power at a tunable value. An appropriate limiter stationed in front of an optical sensor can protect the sensor and extend its working range to conditions more extreme than previously thought possible. Passive optical limiters have a fast response time and are in wide use to limit short optical pulses. The devices are made of materials with one of the following properties – nonlinear optical properties, including nonlinear refraction, nonlinear absorption or nonlinear scattering. Most nonlinear processes are based on the optical Kerr effect (electro-optical feature), giving rise to an ultrafast response time. Researchers therefore study extraordinary Kerr-type nonlinear materials as a critical element for new passive optical limiters to protect against ultrashort optical pulses. Kerr-type passive optical limiters are generally made of macroscale solid or liquid media. Scientists are yet to report on a material or system that provides a strong enough nonlinearity in the nanoscale in order to facilitate a reflection-mode pulse-limiting effect.

Spatio-temporal characterization of pulses. a, Beam profile of SHG generated from the selected unfocused near-IR beam. b, Linewidth of SHG signals from a single-shot autocorrelator. c, Calibration curve of the single-shot autocorrelator. Credit: Science Advances, doi: 10.1126/sciadv.aay3456

In this work, Qian et al. detailed a nanoscale Kerr-type optical limiter based on the durable MQW (metallic quantum wells) material system to generate femtosecond pulses. The device contained refractory materials such as titanium nitride (TiN) and aluminum oxide (Al2O3); ideal for high-intensity nonlinear optical applications developed on a sapphire substrate with atomic level accuracy. In the setup, they quantized the free electrons in the metallic well (TiN) sandwiched between the neighboring dielectric barrier (Al2O3). This experimental arrangement allowed the electronic conduction band of the confined TiN nanofilm to split into subbands. The team noted the first five subbands to be below the Fermi level, providing a wealth of electronic transitions. The transitions contributed to the pulse-limiting effect via the Kerr nonlinearity of the MQW setup and affected a variety of multiphoton absorption processes. The plentiful electronic subbands allowed unprecedented pulse-limiting behavior in the nanoscale refractory thin films.

Multiple electronic subbands in the quantum-sized TiN films enabling extraordinarily high Kerr coefficients. (A) Conduction band diagram of a TiN MQW (left) and the corresponding electronic dispersion of subbands (right). The Fermi level EF (~4.6 eV) is shown as the dashed line. The red arrows indicate the single-photon intersubband transitions between subbands ∣2⟩ and ∣3⟩. (B) Wavelength dependence of the nonlinear optical constant n2 of a 2-nm-thick TiN film, measured by the z-scan technique using 45°-incident p-polarized laser pulses (100-fs pulse width, 1-kHz repetition rate; Astrella, Coherent) with the intensity of ~70 GW/cm2. Note that a minus “−” is used in the imaginary party of the n2. The red arrow corresponds to the calculated transition wavelength shown in (A), while the solid lines are the spline-fitted curves. The fluctuations in multiple measurements at various locations are indicated by the error bars (SD). Inset shows a typical transmission electron microscopy (TEM) cross-section of a TiN MQW thin film. Credit: Science Advances, doi: 10.1126/sciadv.aay3456

Due to the plasmonic effect of the constituent TiN, metallic quantum well samples exhibited a metal-like high reflection at low-intensity illumination. During z-scan measurements used to measure nonlinear optical properties of materials, the team observed a resolved resonant peak associated with the single-photon transition (Kerr nonlinearity) between subbands, which agreed with the calculated band structure. The proposed MQW functioned as a dielectric during high-intensity illumination to form a first-in-study reflection-mode optical limiter, providing a new degree of freedom to design an optimal optical limiting system. The nanoscale thin film MQW for a femtosecond pulse limiter worked in the reflection mode and Qian et al. integrated it on to the surface of an optical component to simplify the optical limiting configuration. They achieved unprecedented tunability for the devices by stacking MQWs as metamaterials and obtained a versatile nanoscale pulse limiter; a crucial element to design compact optical and photonic systems.

Experimental demonstration of the reflection-mode nanoscale femtosecond pulse limiter using TiN-based MQWs. (A) Experimental configuration of the reflection-mode pulse limiter (not to scale). The attenuator is used to vary the incident powers for obtaining pulse-limiting curves. (B) Typical TEM cross section of a 7-unit MQW thin film. The layer on top of the MQWs is a protective layer used only for TEM cross section preparation during the focused ion beam cutting process. (C) Intensity dependence of the measured reflected power for samples with a single unit and 7 units of MQW at the wavelength of 1997 nm (100-fs pulse width, 1-kHz repetition rate, 130-μm beam radius, 45° incidence, and p polarization). The dashed lines show the corresponding linear reflection curves. The onset-of-limiting intensity Ion is defined in the main text. Insets show a zoomed-in TEM cross section of the 7-unit MQW thin film (left) and a dark-field high-resolution TEM image (right) showing the high quality of the grown multilayer. Credit: Science Advances, doi: 10.1126/sciadv.aay3456

Due to metamaterial-enabled engineering the thickness of the nanoscale MQW films provided extraordinary tunability of pulse-limiting performance compared to conventional bulk optical limiters. Additional experiments revealed for the strong Kerr response of MQWs to originate from the single-photon transition between specific subbands. Due to single-photon absorption (1PA) and two-photon absorption (TPA) processes, free electrons above the Fermi sea could be continuously promoted in the setup. Based on the results, Qian et al. believe the observed multiple inter-subband transitions and their broadband Kerr effect in MQW systems to have similar pulse-limiting effects in the near-infrared (NIR) wavelengths.

Physics of optical Kerr nonlinearities of the MQWs. (A and B) Intensity-dependent refractive index nI extracted from the experimentally measured reflectivity and transmissivity [“exp” in (A)] and fitted by the single-photon absorption (1PA) and two-photon absorption (TPA) saturation models [“fit” in (B)]. Inset of (B) shows diagrams representing the Kerr, 1PA, and TPA processes, respectively. The sample used has 7 units of MQW, and the data are taken at the wavelength of 1997 nm. Credit: Science Advances, doi: 10.1126/sciadv.aay3456

In this way, Haoliang Qian and colleagues demonstrated a nanoscale reflection-mode femtosecond pulse-limiting thin film made of refractory materials for the first time in this study. They facilitated the setup using large and ultrafast optical Kerr nonlinearities of the embedded MQWs. The team credited the unprecedented, intensity-dependent Kerr nonlinearities to the electron subbands in the MQW. The work provides a new mechanism to engineer extraordinary optical nonlinearities and novel applications with options for further tunability of nontrivial optical limiting and applications in and integrated photonics.

New Rapid Response Platform Connects Clinicians with Resources and Answers to COVID-19 Questions

January 08, 2004 -- The Integrated Information Solutions Division of SYS Technologies has joined the Jacobs School's Corporate Affiliates Program (CAP). The company provides engineering management and information technology services and solutions primarily to government organizations, but it looking to branch out more into the corporate sector.

Specifically, the Integrated Information Solutions Division (formerly C4ISR Division) delivers solutions that provide customers with timely decision-making and knowledge management systems. This involves collecting, processing, and distributing information in an effective and efficient manner for decision-making support.

SYS Technologies brings a new dimension in analytical thinking for decision analysis to our CAP membership in the interest of cultivating some new research here on campus and recruiting bright engineering students interested in developed enhanced systems for real-time information analysis and knowledge management. The intellectual rigor with which SYS develops decision analysis and visualization tools and the years of experience working with variety of command, control, communications, computers, intelligence (C4I) and surveillance systems complements some compelling research here on campus, said Anne O'Donnell, Jacobs School CAP Director. We look forward to working with their senior engineers in areas siliar with the Jacobs school's high quality graduates. In fact, our CEO, Cliffton Cook, is an alumnus, as well as our Senior Staff Member and Director of Advanced Sciences and Technologies, Dr. John Silva. We hope to take advantage of CAP's recruiting benefits to access the highest quality pool of interns and potential employees in the region. In addition, the division hopes to strengthen its already strong collaborative research relationships with the Jacobs School.

The Corporate Affiliates Program (CAP) is the primary means by which the Jacobs School cultivates relationships with industry. CAP benefits include customized access to students for; research partnerships to ensure a competitive edge; and a voice in the future of engineering education. For more information on CAP, contact Anne O'Donnell at (858) 822-5963 or odonnell@ucsd.edu , or visit the website.

I'm gonna contribute to the revolution of the pharmaceutical world

UC San Diego nanoengineering graduate student knew from day one that biomedical research was his passion

By Alison Caldwell, Bigelow Science Communication Fellow

Qiangzhe “Oliver” Zhang (left) at the annual Research Expo at the UC San Diego Jacobs School of Engineering.

San Diego, Calif., May 20, 2020 -- When Qiangzhe “Oliver” Zhang was still a high school student in China applying to colleges in the United States, UC San Diego’s chemical engineering program at Jacobs School of Engineering was at the top of his list. “I knew they had this very new, very innovative nanoengineering program,” he said. “It’s one of a kind, and that got me really excited.” 

Now, almost eight years later, Oliver Zhang is working at the leading edge of biomedical research under Liangfang Zhang in the Nanomaterials and Nanomedicine Laboratory, developing new technologies that could completely change how scientists combat viruses like HIV and SARS-CoV-2. 

As an undergraduate, Oliver Zhang had a lot of fun meeting other students in the same major. “We were able to form life-long friendships afterward,” he said. “These are really good, brilliant friends that I’m still keeping in close communication with, long after graduation.” 

But when it came to other activities outside of the classroom, Oliver Zhang needed more of a challenge. “I had a hard time figuring out what to do with myself, because I had no idea of what scientific research actually was at that time,” he said. “Luckily, there was a professor in my department who seemed really cool. He was really generous in offering me a lot of advice during our first meeting, knowing that I had zero research experience, and he was able to offer a lot of mentorship on academic life and introduce me to the exciting work happening in his lab.” 

That professor turned out to be Liangfang Zhang, whose lab is focused on creating biomimetic nanotechnologies to solve complex challenges in human disease. After some background reading and a few more conversations, Professor Zhang recruited Oliver Zhang to join his lab as an undergraduate research assistant. “Since then,” Oliver Zhang said, “I’ve been having so much fun, I just can’t stop.”

Within months, Oliver Zhang was deeply embedded in the lab, taking over a project that had been passed down by a PhD student working on “nanosponges” - polymer nanoparticles coated in fragments of cell membrane proteins. These nanosponges can mimic the body’s cells and act as decoys to bind and inactivate harmful pathogens and toxins. As an undergraduate, Oliver Zhang worked to develop these nanosponges for use against pore-forming bacterial toxins.

“In a lot of infectious diseases, bacteria harm us by producing pore-forming toxins that punch holes in the membrane of our cells and kill them,” Oliver Zhang explained. “So we used the same idea in the opposite direction: we put that same membrane onto nanoparticles, so now the toxins are punching holes in the membrane-coated nanoparticles and won’t harm real cells.” 

The team was still just getting started with the application of this technology, and Oliver Zhang was reluctant to leave it behind as he was applying to graduate schools. “I considered Stanford, and Johns Hopkins,” he said, “But after I talked to faculty there, I realized that the research in my current lab is just so exciting and cutting edge that I can’t think of another arena that would fit my interests so well. And I knew that if I stayed in Professor Zhang’s lab, I would be able to get a quick start in graduate school and get more rapidly involved in projects in the field of nanomedicine.

“I was also really excited about working with more of the faculty here at UC San Diego,” Oliver Zhang continued. “During undergrad, I could see that we had a lot of young and hardworking faculty working on multiple different projects that were all really new and exciting. By staying here, I’d be able to meet a lot of new grad students in a variety of fields whose expertise could benefit my research.” 

As a graduate student, Oliver Zhang has expanded his research to include nanosponges made not only from the membranes of red blood cells, as he studied during undergrad, but also using leukocytes - a type of white blood cell. These circulating blood cells can bind to signaling molecules called cytokines. Increased production of cytokines is a hallmark of many different kinds of infections and inflammation, and too many cytokines can lead to overactivation of the immune system. In the lab, Oliver Zhang has been testing using leukocyte-membrane-coated nanosponges to turn down the overheated communication between cells to prevent tissue damage, like that seen in sepsis. 

Other projects Oliver Zhang has worked on include using neutrophil nanosponges to block signaling in rheumatoid arthritis as a potential treatment for the inflammatory joint disease. He also contributed to a major breakthrough using T-cell coated membranes to bind and block HIV viral particles from infecting immune cells, which may provide new hope for treating this difficult-to-tackle virus. 

“What I really like about this work is that it doesn’t involve any therapeutics,” said Oliver Zhang. “It uses the biological principle of how things work: how toxins attack cells, how viruses invade, how cells talk to each other. We’re using it to design something to modulate this communication without using any drugs.”

During his time at UC San Diego, Oliver Zhang has collected a number of first-author publications, and at the time of writing, was gearing up to defend his dissertation in just a few short weeks. Afterward, he plans to continue wrapping up some of his current projects in the lab, and looks forward to continuing his career in the biotech industry working on pharmaceutical research. 

“One thing that really got me interested in nanomedicine in the first place is the idea that for a lot of diseases, it’s not that we don’t have the right drug to treat it - it’s that we can’t get the drug to the right spot. They mostly get lost in circulation,” Oliver Zhang said. “So drug delivery is one thing that nanomedicine can contribute in the future - we can design these particles to directly deliver therapeutics to the right place. There’s a lot of versatility in the way we can manipulate nanomedicine technologies.” 

But the field is not without its challenges. “Because the field is so new, it’s constantly evolving very fast,” said Oliver Zhang. “Overnight, you’ll see a lot of new research work coming out in all of the top journals in nanotech and nanomedicine. So a major challenge is just keeping up with the pace of the field; but I see a lot more opportunities there than anything else.” 

In the future, Oliver Zhang hopes to get involved more on the translational side of nanomedicine. “What I’ve been doing so far has been mostly on developing novel and exciting platforms to treat diseases, and in many cases, we’re still far from applying them into human use. I want to go into industry to narrow the gap between nanomedicine research and clinical use.” 

Even as Oliver Zhang prepares to defend his PhD - via video call, since campus is still closed - he has advice to share for potential Jacobs School of Engineering students: “Get involved in research! There are so many new labs that are flourishing with exciting data in all different fields - immunology, batteries, nanomotors, so many different things that are definitely cutting edge and pretty much the best in the country, or even in the world. As an undergrad, you’re sitting right next to these exciting research fields - you can’t just pass on those opportunities.” 


Oliver Zhang’s first author papers: 

1.    Zhang, Q.; Fang, R. H.; Gao, W.; Zhang, L.* “A biomimetic nanoparticle to ‘lure and kill’ phospholipase A2”, Angewandte Chemie International Edition 2020, doi: 10.1002/anie.202002782.

2.    Zhang, Q.; Gong, H.; Gao, W.; Zhang, L.* “Recent progress in capturing and neutralizing inflammatory cytokines”, CCS Chemistry 2020, in press.

3.    Zhang, Q.; Dehaini, D.; Zhang, Y.; Zhou, J.; Chen, X.; Zhang, L.; Fang, R. H.; Gao, W.; Zhang, L.* “Neutrophil membrane-coated nanoparticles inhibit synovial inflammation and alleviate joint damage in inflammatory arthritis”, Nature Nanotechnology 2018, 13, 1182-1190. 
Highlighted: Nature Nanotechnology 2018, 13, 1098-1099 (News and Views)
            Nature Reviews Rheumatology 2018, 14, 622.
            Science Translational Medicine 2018, 10 (459), eaav0341.

COVID-19: the Jacobs School community engages

San Diego, Calif., updated on May 15, 2020 -- The UC San Diego Jacobs School of Engineering community is stepping up to address many challenges that the COVID-19 pandemic has put before us. This web story highlights is a cross section of projects that Jacobs School faculty, students, staff and alumni have launched in response to COVID-19. Some of these efforts are sure to grow into larger, sustained efforts. Others will morph or conclude as needs and available resources change. Through it all, our commitment to bold innovation for the public good remains. 

Know of a COVID-19 project at the Jacobs School of Engineering?
Reach out to communications director Daniel Kane at: dbkane@eng.ucsd.edu  

June 19, 2020

Understanding COVID-19 through genome analysis

Pavel Pevzner, a professor in the Department of Computer Science and Engineering, has receivd a $300,000 grant from the National Science Foundation through the Early-concept Grants for Exploratory Research (EAGER) mechanism, to study COVID-19. The project is called: Assembling the Immunoglobulin Loci Across Mammalian Species and Across the Human Population.

June 8, 2020

A better way to split ventilators

The COVID crisis has resulted in equipment shortages, including ventilators. Increasing ventilation capacity by sharing them between two or more patients is one option, but it has many risks. Dr. Lonnie Petersen, from the Jacobs School, and Dr. Sidney Merritt, from the School of Medicine, developed a process that would allow use of a ventilator to service two patients at the same time, addressing and solving key safety issues. The research has been accepted for publication by the journal Critical Care. More information: 


June 4, 2020 udpate

A low-power, low-cost wearable to monitor COVID-19 patients

Engineers at the University of California San Diego are developing low-cost, low-power wearable sensors that can measure temperature and respiration--key vital signs used to monitor COVID-19. The devices would transmit data wirelessly to a smartphone, and could be used to monitor patients for viral infections that affect temperature and respiration in real time. The research team plans to develop a device and a manufacturing process in just 12 months. 

May 15, 2020 update

Real-time quantitative detection of protease activity
Patients with severe COVID-19 infections have higher levels of plasmin protease activity in their blood. This enzyme is thought to enhance the virulence and infectivity of SARS-CoV-2 virus by cleaving the viral spike protein. The UC San Diego team developed a sensor that can rapidly quantify protease activity in biological fluids. The new work appears in Nature Scientific Reports and is led by UC San Diego electrical engineering professor Drew Hall and UC San Diego Skaggs School of Pharmacy professor Anthony O’Donoghue. In their new assay, magnetic nanoparticles are immobilized to the surface of a giant magnetoresistive spin-valve sensor using peptides. Cleavage of these peptides by a target protease in a biofluid releases the magnetic nanoparticles resulting in a time-dependent change in the local magnetic field. The team has validated this assay to quantify proteases in urine and is currently modifying this assay to quantify plasmin in blood.  


May 5, 2020 updates

UCSD Privacy-preserving COVID-19 Contact Tracing Apps

Two teams in the Electrical and Computer Engineering (ECE) Department at UC San Diego are developing new cell phone applications for more accurate, private COVID-19 contact tracing. Led by electrical engineering faculty Dinesh Bharadia and Farinaz Koushanfar, the applications use wireless sensing and close integration with health systems, respectively, to monitor an infected person’s social interactions, while preserving the user’s privacy.


 UCSD & TU Darmstadt Privacy-preserving COVID-19 Bluetooth Contact Tracing App

Lead by Professor Farinaz Koushanfar

Prof. Koushanfar in collaboration with Technical University Darmstadt has developed  a novel privacy-preserving Bluetooth-based smart phone app for COVID-19 contact tracing. Contact tracing can be used to record and discover the social exposure of people with close contact to patients tested positive with COVID-19. The resulting app is aimed for integration within the UCSD myHealth website, which is based on the widely used Epic medical platform to perform contact tracing for patients and healthcare professionals. We are also working closely with Qualcomm on learning their Bluetooth measurement data and models for integration within our app. Koushanfar is tightly collaborating with the TU Darmstadt since they have successfully launched the beta testing of their tracing app. The tracing app complies to both privacy regulations of Germany and California.  To download the beta application go to https://tracecorona.net/download-tracecorona/

Meanwhie, BluBLE, an app under development in the Wireless Communications Sensing and Networking Laboratory, which is in the electrical engineering department, provides each user with a customized risk profile to determine their chances of contracting COVID-19. Now available on android and iOS, BluBLE uses infrastructure provided by Google and Apple to launch a novel algorithm that accounts for environmental context, including the exact distance between two people, their activity level (e.g. walking or jogging), whether the interaction took place in an indoor or outdoor environment, and the position of a person’s phone. All of this information is gathered while keeping each user anonymous.

Using voice to detect COVID-19

Researchers at UC San Diego are part of a collaborative, multinational effort to use changes in voice to detect COVID-19. They are gathering voice and coughing audio samples from people who both have and have not tested positive for COVID-19. Then, researchers including those at UC San Diego, are using algorithms and neural networks to pick out differences in the patterns between the two groups, with a goal of being able to detect if someone has the virus simply by them speaking or coughing into their phone or computer microphone. Computer scientists, electrical engineers and mechanical engineers at the Jacobs School are contributing to the analysis of open source data collected by several different companies and institutions, including Voca.ai, Vocalis, Carnegie Mellon University and MIT.  

Shlomo Dubnov, a professor in the Departments of Music and Computer Science and Engineering, is leading UC San Diego’s involvement in the project, and is using tools he and his lab developed to analyze musical sounds. UC San Diego researchers, including mechanical engineering graduate student Tammuz Dubnov and his startup company Zuzor, are also developing and repurposing tools to be able to deploy these detection algorithms over apps and web browsers.

UV-Drone: Mobile Disinfection Platform for Community Facilities with Minimum Human Exposure

Disinfecting areas that have been exposed to COVID-19 using conventional methods of washing and cleaning surfaces with disinfecting liquid and materials, exposes the most disadvantaged workers on the frontlines and increases the risk of exposure and disease contraction for the cleaning crew. Professor Tara Javidi is leveraging her DetecDrone research platform developed at UC San Diego to significantly improve on the process of UV-based disinfection. In addition to providing a cost effective and agile non-contact UV-C sterilization, the researchers envision the first Do It Yourself (DIY) prototype of a drone platform for delivering non-contact mobile UV sterilization unit (UVerizeDrone) for community facilities such as schools, institutions of higher education, offices, daycare centers, businesses and community centers. Javidi is Co-Director of the Center for Machine-Integrated Computing and Security (MICS) at the UC San Diego Jacobs School of Engineering. Learn more on the MICS COVID-19 page.


UC San Diego Team Delivers Protective Equipment to Hospitals in Baja California

The COVID-19 pandemic is impacting the availability of personal protective equipment (PPE) supplies in Baja California, and researchers with UC San Diego are engineering solutions to help. Nadir Weibel, an associate professor in the Department of Computer Science and Engineering and head of the Human-Centered and Ubiquitous Computing Lab, is collaborating with university colleagues, government and industry to develop PPE solutions and to transport ing supplies, like masks and face shields, to hospitals in Baja.

So far, the team in collaboration with the CAICE lab and the Scripps Institution of Oceanography has produced, tested and delivered 3,000 face shields, with around 1,100 masks on the way. The protocols to make this equipment have been published on Earth 2.0, a curated clearinghouse started by UC San Diego faculty and students for COVID-19 information and solutions.

Researchers Awarded NSF Grant to Apply Epidemic Model to COVID-19

Behrouz Touri and Massimo Franceschetti, both on faculty in the Department of Electrical and Computer Engineering Department at UC San Diego, have secured funding from the National Science Foundation to address COVID-19 using the Susceptible Infectious Recovered (SIR) mathematical model. The two researchers are in the early stages of adapting the SIR model to the current pandemic, in the hopes of identifying policies that effectively reduce the number of COVID-19 infections and mortalities, while limiting the cost to the economy. In time, the researchers hope to provide officials and policymakers at the city and regional level with insight into the efficacy of social distancing, stay-at-home orders and other guidelines.

Privacy-preserving COVID-19 Discovery

Several research labs worldwide, both on the industrial and university side, are focused on sequencing the COVID-19 virus and studying its interactions in-vivo and in-vitro. In several cases, sharing the data and models is not possible due to privacy and IP issues, impeding collaboration for achieving a faster discovery. Professor Farinaz Koushanfar’s lab provides one-of-a-kind provable privacy-preserving methodologies, based on verified cryptographic protocols, which enable collaboration among the various entities in an encrypted domain. With this method, the privacy of the IP/content owners is not compromised, while new collaborations and discoveries are uniquely enabled. In particular, multiple research labs will be able to jointly work on the encrypted version of the aggregated data without disclosing their sensitive information to any other research lab. These state-of-the-art technologies provide a secure platform such that the confidentiality of the data during computation is guaranteed. The platform also assured the correctness of the computation; the result is equivalent to running the underlying algorithm on the cleartext (unencrypted) data. The platform will remove several critical obstacles in the global-scale study of COVID-19, and in turn, will accelerate the process of finding new recovery mechanisms. Koushanfar is Co-Director of the Center for Machine-Integrated Computing and Security (MICS) at the UC San Diego Jacobs School of Engineering. Learn more on the MICS COVID-19 page.

Robust AI for Automated and Accelerated Literature and Trend COVID-19 Systemization of Knowledge

Professor Farinaz Koushanfar is leading development of novel robust and safe accelerated methodologies, based on natural language processing (NLP) to systemize knowledge discovery in the COVID-19 domain. While several disparate entities are working in research on the topic, and a multitude of sources are publishing news on a daily basis, their platform is interactive, allowing researchers and public health professionals to follow the many updates. NLP-based methods are useful for automated knowledge discovery but suffer from the existence of unreliable sources, data poisoning and fake news. This effort focuses on making the automated knowledge search systematic, safe and robust, while we simultaneously address scalability through new hardware/software/algorithm co-design. Koushanfar is Co-Director of the Center for Machine-Integrated Computing and Security (MICS) at the UC San Diego Jacobs School of Engineering. Learn more on the MICS COVID-19 page.

A Controlled Response to COVID-19

Electrical engineering rofessors Massimo Franceschetti and Behrouz Touri are proposing a generalization of Susceptible Infectious Recovered (SIR) model for inhomogeneous population. Using tools from optimal control and nonlinear control and based on the proposed mean-field model, they are working to find the optimal-cost containment policy to meet the local health-care provider's care capacity.

May 4, 2020 update

Protecting medical staff during procedures and providing non-invasive respiratory support

Researchers have desgined and build a large enclosure that extracts exhaled aerosols and droplets from COVID-19 patients, providing health care workers with a safety barrier. The vaccum exhaused isolation locker, or VEIL, is currently being used on five patients. "We hope that the properties of the VEIL will increase the number of options for non-invasive respiratory support for COVID19 patients without increasing the risk of viral contagion," researchers write. They've made 20 of the devices so far and plan to manufacture 90 more as soon as possible. The team includes Dr. Timothy Morris, a pulmonologist at UC San Diego, James Friend, a professor the Department of Mechanical and Aerospace Engineering at UC San Diego, his PhD student Gopesh Tivawala and other physicians and researchers at the Jacobs School of Engineering, the UC San Diego School of Medicine and the Qualcomm Institute. More information: http://friend.ucsd.edu/veil/

Friend, Tivawala and colleagues also partnered with Dr. Alexander Girgis, a UC San Diego anesthesiologist, to build a device that protects medical staff from aerosols and droplets from COVID-19 patients during intubation and extubation. The team built about 20 of the devices. You can watch a demonstration of how the device is used here: http://friend.ucsd.edu/madbox/ 

April 20, 2020 update

Plant-based COVID-19 Vaccine
Nanoengineers at UC San Diego received NSF funding for their work to develop a COVID-19 vaccine that is based on a plant virus. The team’s goal is to use plants to create a stable, easy to manufacture vaccine that can be shipped around the globe. It will be packaged in slow-release microneedle patches that patients can wear on the arm to painlessly self-administer the vaccine in a single dose. The work is being led by nanoengineering professors Nicole Steinmetz and Jon Pokorski. Read the full story.

Earth2.0 / COVID Collective Response System
The UC San Diego community is part of the new, interdisciplinary Earth2.0 initiative, which focuses on leveraging emerging digital technologies to harness, coordinate and empower citizen-centric activities that can quickly surface problems and crowd source innovations, resource management or development. The Earth2.0 / COVID Collective Response System supports front-line clinicians and researchers who need help answering questions, performing tasks or locating resources in real-time by engaging a local network of experts ranging from clinical researchers, to scientists and engineers (faculty, staff and students) to help provide solutions. UC San Diego researchers include computer science professor Nadir Weibel, who is also with the Design Lab; computer science professor and Contextual Robotics Institute Director Henrik Christensen; and Qualcomm Institute Director and electrical engineering professor Ramesh Rao.  You can read the story here

April 17,2020 update

UC San Diego Researchers Optimize Microbiome Tool for Computer GPUs​
Researchers at UC San Diego have been applying their high-performance computing expertise by porting the popular UniFrac microbiome tool to graphic processing units (GPUs) in a bid to increase the acceleration and accuracy of scientific discovery, including urgently needed COVID-19 research.  Learn more.


April 13, 2020 update

IBM and UC San Diego to pivot AI for Healthy Living collaboration to take on COVID-19 pandemic
UC San Diego and IBM are building on the existing AI for Healthy Living (AIHL) collaboration in order to help tackle the COVID-19 pandemic. AI for Healthy Living is a multi-year partnership leveraging a unique, pre-existing cohort of adults in a senior living facility to study healthy aging and the human microbiome as part of IBM's AI Horizons Network of university partners. “In this challenging time, we are pleased to be leveraging our existing work and momentum with IBM through the AI for Healthy Living collaboration in order to address COVID-19,” said Rob Knight, UC San Diego professor of pediatrics, computer science, and bioengineering and Co-Director of the IBM-UCSD Artificial Intelligence Center for Healthy Living. Knight is also Director of the UC San Diego Center for Microbiome Innovation.  

April 2, 2020 updates
Engineers and doctors team up to retrofit and 3D-print ventilators 

A team of engineers and physicians at UC San Diego is working to turn emergency hand-held ventilators into devices that can work autonomously for long periods of time, without human input. Ventilators are medical devices that push air in and out of a patient’s lungs when they are unable to breathe on their own. One of the primary symptoms of COVID-19 is difficulty breathing; approximately 1 percent of people who contract the virus require ventilation to support their recovery — sometimes for weeks. Read the full storyWatch the video. Read the story in STAT

Researchers work on early warning system for COVID-19
To better understand early signs of coronavirus and the virus' spread, physicians around the country and data scientists at UC San Diego are working together to use a wearable device to monitor more than 12,000 people, including thousands of healthcare workers. The effort has started at hospitals in the San Francisco Bay Area and at the University of West Virginia. The team includes bioengineer Ben Smarr, and computer scientists Rob Knight and Ilkay Altintas. Read the full story. An early press report ran in the San Francisco ChronicleRead the KPBS story. Read the US News story

Crowdsourcing SARS-CoV-2 info
A crowdsourced research effort based at the University of California San Diego School of Medicine, has expanded its capabilities to now allow citizen-scientists around the world to help collect crucial information about SARS-CoV-2, the novel coronavirus causing a COVID-19 pandemic. “We are now positioned to collect data that will help drive epidemiological studies of where the virus is and isn’t, and help researchers determine who is at greatest risk, who is already immune, how the virus is transmitted and how it spreads through a population,” said UC San Diego professor Rob Knight, co-founder of The Microsetta Initiative. Knight is Director of the Center for Microbiome Innovation at the UC San Diego Jacobs School of Engineering and holds appointments in the departments of Bioengineering and Computer Science and Engineering. Read the story in This Week @ UC San Diego.   

A smart scale to detect COVID-19
​A smart scale installed below patients’ beds can detect sleep duration, cough, heartbeats and respiration. A team of engineers and physicians who developed the device are hoping it will be able to detect respiratory and cardiac changes that occur before patients develop COVID-19 related pneumonia. Hundreds of devices have been manufactured and they are currently in patients’ homes throughout San Diego County. The effort is led by bioengineering professor Dr. Kevin King, who is also a practicing cardiologist with UC San Diego Health, and bioengineering professor Todd Coleman.

COVID-19 sequencing analysis in real time
Bioinformatics researcher (and computer science teaching professor) Niema Moshiri created an automated tool that analyzes in real time genomic coronavirus open-source datasets from the Global Initiative on Sharing All Influenza Data (GISAID).  The tool outputs results in a way that is more user-friendly for public health and biology researchers. Some of the information that can be extracted from analysis includes the virus' most likely evolutionary history; information about the common ancestors of viral samples; and information about how recent each version of the virus is in given clusters of patients. This could help health officials determine effective policies to contain the virus and to potentially design therapeutics. Moshiri received a $200,000 RAPID grant from the National Science Foundation for the work, with computer science professor Tajana Rosing. The tool can be found here on Github.  Read Moshiri's related article in The Conversation, which also appeared in many US newspapers, including the San Francisco Chronicle

UV light- and heat-based decontamination system
Nanoengineering professor Jesse Jokerst is part of a team at UC San Diego developing a process to decontaminate N95 masks with UV light and heat so they can be safely reused. The work, which is still in the experimental stages, aims to address the shortage of protective masks for health care workers.

Imaging medical masks at the nanoscale
Nanotechnology researchers led by Prof. Shirley Meng are evaluating the effectiveness of improvised medical masks using scanning electron microscope (SEM) technology available at UC San Diego’s Nano3, which is a nanofabrication cleanroom facility that is part of the Qualcomm Institute. This technique can image structures whose dimensions are much smaller than the novel Coronavirus, providing researchers a means to accurately gage the effectiveness of various personal protection equipment materials.  

Qualcomm Institute Prototyping Lab
Researchers and engineers at UC San Diego's Qualcomm Institute Prototyping Lab are evaluating the use of 3D printing technologies and rapid prototyping techniques to create safe and effective medical equipment and gear, such as ventilator components and face shields. Teams are also exploring the possibility of using 3D printers to produce large quantities of the nasal swabs needed for COVID-19 testing. Read the full story.

Non-invasive Spleen Ultrasound Treatment for COVID-19 Patients
Based on established results that show stimulation of the vagus nerve (the longest cranial nerve in the body) can produce anti-inflammatory effects that can help prevent sepsis-related mortality, UC San Diego researchers affiliated with the Qualcomm Institute are developing and testing Focused Ultrasound Spleen Stimulation, or FUSS, as a potential treatment for the hospitalized COVID-19 patient. FUSS engages the vagus cholinergic anti-inflammatory reflex to potentially aid the body’s response to the virus. The project is a collaboration between Qualcomm Institute and UC San Diego Health researcher Dr. Imanuel Lerman and bioengineering professor Todd Coleman and electrical engineering professor Truong Nguyen from the Jacobs School. 

Folding SARS-CoV-2
The Pacific Research Platform, a National Science Foundation-supported project, overseen by Larry Smarr, the Harry E. Gruber Professor in Computer Science and Engineering, has lent its distributed computing and storage powers to help in the fight against COVID-19. Within the last two weeks, more than half of the distributed system’s 600 GPUs have been made available to the global Folding@home effort to study the dynamics of how viral proteins interact with human receptors. Smarr says this shows how quickly the system’s resources are able to be repurposed to support an urgent and critical need such as combating the novel coronavirus.

Sharing mass spectrometry data
UC San Diego researchers created an open-data community resource for sharing of mass spectrometry data and (re)analysis results for all experiments pertinent to the global SARS-CoV-2 pandemic. The resource, called CoronaMassKB, is designed for the rapid exchange of data and results among the global community of scientists working towards understanding the biology of SARS-CoV-2/COVID19 with the goal of accelerating the emergence of effective responses to this global pandemic. The project is led by computer science professor Nuno Bandeira.  

Crowd-Sourcing Pandemic Management
Michael Barrow, a PhD candidate in the research group of computer science professor Ryan Kastner, is leading efforts to mitigate shortages in ventilators and critical care specialists. He and his team are developing a universal control system to help produce high-quality, safe DIY ventilators. (This effort is related to the ventilator projects listed above being led by mechanical and aerospace engineering professors James Friend and Lonnie Petersen.) They are also developing a telemedicine platform that allows specialists to focus on the patients who need them most while less-trained clinicians can monitor more stable patients and query as necessary.  

Using robots to combat COVID-19
Can robots be effective tools in combating the COVID-19 pandemic? A group of leaders in the field of robotics, including Henrik Christensen, director of UC San Diego’s Contextual Robotics Institute, say yes, and outline a number of examples in an editorial in Science Robotics. They say robots can be used for clinical care such as telemedicine and decontamination; logistics such as delivery and handling of contaminated waste; and reconnaissance such as monitoring compliance with voluntary quarantines. Read the full story. Read coverage in Wired. Read news coverage in The Washington Post

SEDS students join ventilator challenge
Students from the Students for the Exploration and Development of Space (SEDS) organization are turning their attention to a challenge to design a low-cost, simple, easy-to-use and easy-to-build ventilator that can serve COVID patients, in an emergency timeframe. What SEDS brings to the table is experience with High Oxygen Environment safety, and 3D-printing and fluid system experience. A UC San Diego emergency medicine resident is providing medical input. More information on the Code Life Ventilator Challenge. More information on SEDS at UC San Diego.

Jacobs School Alumni Projects


Fluxergy, a medical diagnostic company based in Irvine, California, that designs and builds rapid point-of-care diagnostic testing devices, collaborated with UC San Diego Health faculty to test a system to diagnose COVID-19 in under an hour.  On March 30 they submitted an Emergency Use Authorization (EUA) to the U.S. Food and Drug Administration (FDA) in the hopes that their device can be deployed in medical settings within the next few weeks, making it possible for healthcare systems to test for the virus in under an hour, at the point-of-care. Most of the team behind Fluxergy met as engineering students at the Jacobs School of Engineering, where they were members of the Formula Society of Automotive Engineers (SAE) team, now known as Triton Racing, as undergraduates. Learn more about Fluxergy: https://fluxergy.com/ Read the April 9 story in This Week @ UC San Diego.

Nanome, a company founded by Jacobs School of Engineering alumni and that spent its earliest days in the Qualcomm Institute Innovation Space (QIIS), is providing researchers with a virtual reality platform to visualize and study the novel coronavirus. Nanome develops open-access virtual reality software that creates a shared virtual space for researchers to collaborate with one another and interact with 3D models of molecules. Currently, Nanome’s team is working with collaborators from around the world to use their virtual reality software to examine the protein structures that allow the novel coronavirus to attach to healthy cells. Learn more: https://nanome.ai/

flashPub—a QIIS-incubated company on a mission to make scientific publishing smarter, smaller and faster—is organizing a global campaign of researchers to model outbreak scenarios at the city scale. The group will be rapidly publishing the modeling results and organizing data into an interactive map. Their goal is to predict when a city is going to hit a tipping point of hospitalizations in order to inform preparation and resource allocation decisions. Learn more: https://www.flashpub.io/

Know of a COVID-19 project at the Jacobs School of Engineering?
Reach out to communications director Daniel Kane at: dbkane@eng.ucsd.edu


eCOVID platform provides remote patient monitoring

Goto Flickr

San Diego, Calif., May 19, 2020 -- Engineers at the University of California San Diego have developed a remote monitoring platform for patients who have tested positive for COVID-19 but aren’t in need of hospitalization. The system is being tested by patients in a clinical trial at UC San Diego Health. It is intended to help health care teams prioritize more critical patients, while also providing data on which symptoms are most indicative of healing or further progression of COVID-19.

Currently at UC San Diego Health, patients who test positive for the virus but aren’t in need of hospitalization are sent home to recover, with care team members calling patients daily to monitor  symptoms and determine whether additional interventions are necessary.

However, not all health systems have the resources and capacity to support such an effort.  

With the eCOVID remote monitoring platform, that process is automated. Patients use a wearable Engineers at the University of California San Diego have developed a remote monitoring platform for patients who have tested positive for COVID-19 but aren’t in need of hospitalization. The system is being tested by patients in a clinical trial at UC San Diego Health.device to continuously monitor vital signs such as heart rate and oxygen saturation levels, as well as activity and sleep levels. They also complete a daily questionnaire about their symptoms, such as fatigue, cough and shortness of breath, using the eCOVID app.

This information is automatically transmitted to a secure dashboard that health care providers can monitor; the app and dashboard are interactive – providing guidance and alerts to both the care team and patients, as well as receiving feedback from the care team. This can reduce anxiety for patients who are healing as expected, and allows the health care team members to focus more attention on patients in greater need.  

Goto Flickr
Professor Sujit Dey, director of the UC San Diego Center for Wireless Communications, and lead of this remote monitoring platform.

“We wanted to jump in and help in a real translational way,” said Sujit Dey, professor of Electrical and Computer Engineering at UC San Diego, director of the UC San Diego Center for Wireless Communications, and lead of this remote monitoring platform. “We looked to see what technology we had in our arsenal that we could repurpose to help the COVID-19 patients and the health care workers treating them.”

The technology behind the eCOVID app derives from a similar virtual system Dey and colleagues developed to monitor and provide personalized care for hypertensive patients, using machine learning to better understand which health behaviors were most impactful to personalized blood pressure levels. The information was used to provide behavioral guidance.

A team of engineers worked with physicians at UC San Diego Health to repurpose this system to one capable of alleviating some of the additional workload health care personnel face with the COVID-19 pandemic, while also contributing to positive patient outcomes and a global understanding of the virus.

"The eCOVID app provides us with concrete information daily regarding each patient’s clinical status, allowing us to prioritize who needs to be personally contacted that day,” said Dr. Michele Ritter, an infectious diseases specialist at UC San Diego Health and director of the COVID-19 telemedicine clinic, who collaborated with the engineering team on the eCovid app. “It also gives patients peace of mind knowing that they are being monitored and can quickly convey any changes in their status to our COVID team."

In a second phase of the project, Dey plans to use machine learning algorithms and data from the patients’ vital signs, health behavior and self-reported symptoms to try and understand if changes in certain vital signs and behaviors can indicate an expected change in symptoms and a patient’s condition. This could lead to more predictive and effective care. They’ll also try to determine if certain symptoms are more indicative of a severe case of infection than others.  This could result in more personalized care, and even preemptive hospitalization before the situation becomes dire, which could improve patient outcomes and give hospital systems time to prepare and allocate resources.

The app can be scaled to other health systems as well, which may not have the resources to conduct daily check-in calls.

“If done properly and in collaboration with physicians, virtual monitoring platforms such as the eCOVID system can provide great benefits for health care systems,” said Dey. “Not only for COVID-19, but for many ongoing and common health issues, being able to monitor a patient’s status continuously and engage with them by providing personalized guidance and care is an ideal solution.”

Engineers develop low-cost, high-accuracy GPS-like system for flexible medical robots

San Diego, Calif., May 18, 2020 -- Roboticists at the University of California San Diego have developed an affordable, easy to use system to track the location of flexible surgical robots inside the human body. The system performs as well as current state of the art methods, but is much less expensive. Many current methods also require exposure to radiation, while this system does not. 

The system was developed by Tania Morimoto, a professor of mechanical engineering at the Jacobs School of Engineering at UC San Diego, and mechanical engineering Ph.D. student Connor Watson. Their findings are published in the April 2020 issue of IEEE Robotics and Automation Letters. 

“Continuum medical robots work really well in highly constrained environments inside the body,” Morimoto said. “They’re inherently safer and more compliant than rigid tools. But it becomes a lot harder to track their location and their shape inside the body. And so if we are able track them more easily that would be a great benefit both to patients and surgeons.”

The researchers embedded a magnet in the tip of a flexible robot that can be used in delicate places inside the body, such as arterial passages in the brain. “We worked with a growing robot, which is a robot made of a very thin nylon that we invert, almost like a sock, and pressurize with a fluid which causes the robot to grow,” Watson said.  Because the robot is soft and moves by growing, it has very little impact on its surroundings, making it ideal for use in medical settings.

The researchers then used existing magnet localization methods, which work very much like GPS, to develop a computer model that predicts the robot’s location. GPS satellites ping smartphones and based on how long it takes for the signal to arrive, the GPS receiver in the smartphone can determine where the cell phone is. Similarly, researchers know how strong the magnetic field should be around the magnet embedded in the robot. They rely on four sensors that are carefully spaced around the area where the robot operates to measure the magnetic field strength. Based on how strong the field is, they are able to determine where the tip of the robot is.

The whole system, including the robot, magnets and magnet localization setup, costs around $100. 

Morimoto and Watson went a step further. They then trained a neural network to learn the difference between what the sensors were reading and what the model said the sensors should be reading. As a result, they improved localization accuracy to track the tip of the robot.

“Ideally we are hoping that our localization tools can help improve  these kinds of growing robot technologies. We want to push this research forward so that we can test our system in a clinical setting and eventually translate it into clinical use,” Morimoto said.  

Permanent Magnet-Based Localization for Growing Robots in Medical Applications

Connor Watson and Tania Morimoto, Department of Mechanical and Aerospace Engineering, UC San Diego

IEEE Robotics and Automation Letters: https://bit.ly/MorimotoICRA2020paper


New wearable sensor tracks Vitamin C levels in sweat

Non-Invasive tech could support dietary adherence, detect nutritional deficiencies

By Alison Caldwell, Bigelow Science Communication Fellow

San Diego, Calif., May 18, 2020 -- A team at the University of California San Diego has developed a wearable, non invasive Vitamin C sensor that could provide a new, highly personalized option for users to track their daily nutritional intake and dietary adherence. The study was published in the May 18, 2020 issue of ACS Sensors.

“Wearable sensors have traditionally been focused on their use in tracking physical activity, or for monitoring disease pathologies, like in diabetes,” said first-author Juliane Sempionatto, a PhD Candidate in nanoengineering in Joseph Wang’s lab at the UC San Diego Jacobs School of Engineering. “This is the first demonstration of using an enzyme-based approach to track changes in the level of a necessary vitamin, and opens a new frontier in the wearable device arena.”

“Wearable sensors have rarely been considered for precision nutrition,” said Joseph Wang, a professor of nanoengineering and director of the Center of Wearable Sensors at UC San Diego.

Why vitamin C is important

Vitamin C is an essential dietary component, as it cannot be synthesized by the human body and must be obtained through our food or via vitamin supplements. The vitamin is important for supporting immune health and collagen production, a vital player in wound healing, as well as improving iron absorption from plant-based foods. Ongoing research is examining whether or not the vitamin’s role as an antioxidant might support its use in treating diseases like cancer and heart disease.

Most pressingly, the vitamin is being studied in several clinical trials for its potential in supporting recovery from COVID-19, the disease caused by the novel SARS-CoV-2 virus. A handful of past studies have linked high doses of vitamin C, alongside other treatments, to reduced mortality rates in patients with sepsis and, in one study, acute respiratory distress syndrome (ARDS) - both common conditions seen in serious cases where patients with COVID-19 require intensive care and intubation.

If vitamin C does help patients recover from the disease, such a wearable sensor might aid doctors and recovering patients in tracking their vitamin C levels during treatment and recovery, providing an opportunity for healthcare providers to precisely tune vitamin supplementation to match a patient’s needs.

The wearable device

The sensor stretches without tearing.

The new wearable device consists of an adhesive patch that can be applied to a user’s skin, containing a system to stimulate sweating and an electrode sensor designed to quickly detect vitamin C levels in sweat. To do so, the device includes flexible electrodes containing the enzyme ascorbate oxidase. When vitamin C is present, the enzyme converts it to dehydroascrobic acid and the resulting consumption of oxygen generates a current that is measured by the device.

In vitro testing and testing in four human subjects who had consumed vitamin C supplements and vitamin C-containing fruit juices showed that the device was highly sensitive to detecting changes in the levels and dynamics of the vitamin when tracked across two hours. The researchers also tested the electrode detector’s ability to detect temporal vitamin C changes in tears and saliva, demonstrating its cross-functionality. Differences observed in the vitamin C dynamics across different human subjects indicates that the device has promise for personal nutrition applications.

“Ultimately, this sort of device would be valuable for supporting behavioral changes around diet and nutrition,” said Sempionatto. “A user could track not just vitamin C, but other nutrients - a multivitamin patch, if you will. This is a field that will keep growing fast.” The UC San Diego  team is closely collaborating with a major global nutrition company DSM towards the use of wearable sensors for personal nutrition.

The sensor is paired with a board that can trasmit data wirelessly.  

“Despite the rapid development of wearable biosensors, the potential of these devices to guide personalized nutrition has not yet been reported,” said Wang. “I hope that the new epidermal patch will facilitate the use of wearable sensors for non-invasive nutrition status assessments and tracking of nutrient uptake toward detecting and correcting nutritional deficiencies, assessing adherence to vitamin intake, and supporting dietary behavior change.”

With the pressing need to develop new treatments for COVID-19, the team is also looking for ways to quickly get this technology into a clinical setting, in the event that vitamin C does prove to be a helpful treatment for the disease.


Computer Scientists Win Test of Time Award for Paper that Changed the Auto Industry

San Diego, Calif., May 18, 2020 -- UC San Diego computer scientist Stefan Savage and his colleagues first gave the automotive industry a wake-up call when they published research demonstrating the ability to hack a car’s computer system in 2010.

This research, and the resulting academic paper, was honored with the Test of Time Award at this year’s IEEE Symposium on Security and Privacy for its broad and lasting impact.

“This effort alerted the automotive sector that security needed to become a top priority,” Savage said. “When we showed up it was not considered a critical function by any automaker or the U.S. Department of Transportation. All of that changed remarkably quickly as a result of our work.”

In the decade since the paper was first published, it has spawned new automotive security standards and organizations, government programs focused on vehicular cybersecurity, dozens of automotive security startups, countless follow-on research efforts and, most importantly, a pervasive focus on product security by major automakers around the globe.

Identifying Security Risks in Cars

In the 2010 paper, titled Experimental Security Analysis of a Modern Automobile, Savage and colleagues at UC San Diego and the University of Washington demonstrated the ability to hack an automobile and control everything from the brakes to the windshield wipers.

With their eye-opening results in hand, and prior to publishing them, one of the first things the researchers did was reach out directly to the automotive industry. Their goal was to alert industry to the vulnerabilities and form lasting partnerships that would ultimately enhance the safety, security, and privacy of millions of cars on the road.

“We observed that this was an industry-wide issue and not specific to a particular manufacturer,” said Tadayoshi Kohno, a paper coauthor who is now a professor at the University of Washington. 

Collaboration Spawns Change

The idea for the project began percolating when Kohno, who was completing his doctorate degree at UC San Diego at the time, and Savage struck up a casual conversation about potential security threats after seeing an OnStar advertisement. After Kohno moved to the University of Washington, he and Savage decided the time was ripe to explore the issue further.

From there the team, which included several students and faculty, came together. They soon purchased two cars and started investigating. For many of the team members who were students at the time, the collaborative nature of the project still influences their research philosophy and style.

Stephen Checkoway, now an assistant professor at Oberlin College, was the lead graduate student researcher from UC San Diego on the project. He was involved in most of the technical aspects, from reverse-engineering the automotive computers’ firmware to building tools to developing and testing exploits. His experience is one he remembers fondly.

“This was an extremely collaborative effort. No task was performed by an individual researcher alone. This was the key to our success. I count myself lucky to have had the opportunity to be on the team. Collaborative research has been my preferred method of research ever since,” Checkoway said.

Karl Koscher, now a research scientist with the University of Washington’s Security and Privacy Research Lab, was the lead graduate student on the project from the university. “It’s extremely gratifying to see lessons learned from our work are now baked into car manufacturers’ next-generation platforms, just now rolling off the assembly line."

The team also included Brian Kantor, a longtime staff member in the Department of Computer Science and Engineering at UC San Diego who died unexpectedly in November 2019. Kantor played an important role, mentoring and teaching the students the basics of hardware engineering. Hovav Shacham, Shwetak Patel, Alexei Czeskis, Franziska Roesner, Damon McCoy and Danny Anderson rounded out the team.

Research that Stands the Test of Time

Many of Savage’s collaborative research efforts have had lasting impacts that are recognized by the field. Last year, he and his colleagues were honored with another Test of Time Award from the ACM Conference on Computer and Communications Security for a 2009 paper titled "Hey You Get Off of My Cloud: Exploring Information Leakage in Third-party Compute Clouds." In 2017, Savage was part of a team that won yet another Test of Time Award from the USENIX Security Symposium for their 2001 "Inferring Internet Denial of Service” paper.

“All three of these papers reflect a notion of being open to investigating interesting problems and working as a team,” Savage said, “UC San Diego has always been a place that’s very welcoming to people who work well on teams – and I am one of those.” 

The 2020 award was presented at the 41st annual IEEE Symposium on Security and Privacy, which is an all-digital conference this year. The symposium is the premier forum for presenting developments in computer security and electronic privacy, and for bringing together researchers and practitioners in the field.

For more information about this collaboration between UC San Diego and the University of Washington, please read a recent blog posted by the university’s Paul G. Allen School of Computer Science and Engineering.

A low-power, low-cost wearable to monitor COVID-19 patients

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Near-zero-power temperature sensor runs on 113 picowatts of power. Photos by David Baillot/UC San Diego Jacobs School of Engineering

The device could be used to monitor COVID-19 patients and those at risk for coronavirus

San Diego, Calif., May 18, 2020 --Engineers at the University of California San Diego are developing low-cost, low-power wearable sensors that can measure temperature and respiration--key vital signs used to monitor COVID-19. The devices would transmit data wirelessly to a smartphone, and could be used to monitor patients for viral infections that affect temperature and respiration in real time. The research team plans to develop a device and a manufacturing process in just 12 months. 

The effort is led by Patrick Mercier, a professor in the Department of Electrical and Computer Engineering at UC San Diego, and has been funded through a Rapid Response Research (RAPID) grant from the National Science Foundation. 

“We desperately need a way to quantitatively triage individuals who are at high risk of carrying COVID-19, based on more than just their self-reported symptoms,” Mercier said. “In addition, those who are infected and are quarantining at home have no way of knowing how they are progressing in their recovery and/or if their symptoms are sufficient to warrant hospitalization before it may be too late. All of this is true not just for COVID-19, but for any future viral infection that may take the world by storm.”

Mercier’s research group specializes in low-power sensors; Mercier is the current world record holder for the lowest-powered temperature sensor ever built: only about 100 picowatts, which is about 100,000 times lower than even the most basic digital watch. Since the power level is so low, Mercier’s group will be exploring some novel forms of energy harvesting to power such devices without a battery. 

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The sensor would be connected to electrodes and a small electronic board. 

Since no battery is required, the researchers plan to scale up manufacturing while keeping costs under 10 cents per unit. 

Currently, temperature sensors are often bulky, power hungry and, importantly, only measure spot temperatures infrequently. In addition, respiration, including shortness of breath and lung function, is measured via manual spot processes that quantify how much air a person inhales and exhales and how quickly. The process relies on bulky devices which can’t be easily miniaturized. 

Mercier proposes to combine his group’s temperature sensing work together with a way to electrically monitor respiration function in a convenient manner without having to make a person breathe into a device. This will allow continuous, real-time monitoring of symptoms.  

The wearable’s low power capacity could be achieved through various technologies that Mercier’s research group has explored, including WiFi, custom Bluetooth, magnetic fields and wake-up radios.  Mercier holds several world records for low power wireless communications devices as well and plans to use those technologies for this project. 

“This is actually a revolutionary idea that can help enable entirely new classes of wearable devices that do not require batteries, and thus has broader impacts beyond just this project,” Mercier said.

The chip and sensor would transmit date to a smartwatch or smartphone. Data analysis would show local and national infection rate. 
Ronald Graham -- Click Here to visit JSOE Flickr


Undergraduate engineers design neonatal ECMO simulation

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A team of mechanical engineering students designed a neonatal ECMO simulation for their senior design project. 

San Diego, Calif., May 11, 2020 -- In collaboration with physicians and surgeons at Rady Children’s Hospital- San Diego, a team of undergraduate mechanical engineering students developed a neonatal simulation system for a critical and rare surgical procedure called ECMO. They developed this realistic simulation system- believed to be the first for neonatal patients—for their senior design project. 

ECMO—extracorporeal membrane oxygenation-- is a rare procedure used when a patient’s heart or lungs aren’t able to function. Doctors use a machine to circulate and oxygenate the patient’s blood by pumping it through an external system of tubes and filters outside of their body, through an artificial lung, and back into the body. 

ECMO is used for patients recovering from heart or lung surgery; for people whose heart or lungs aren’t functioning; or for infants experiencing respiratory or cardiac distress. The procedure is rare, particularly for children—at Rady Children’s, it’s only performed a handful of times per year. However, it has been used more often during the COVID-19 pandemic as a means to give patient’s lungs time and capacity to heal. 

“ECMO is done very rarely on children and infants, which makes it higher risk; both because it’s so rare that it can be difficult to train for, and because they’re physically smaller so it’s harder to put the cannulas into the artery and vein,” said Guinevere Berg, an engineering student on the team. 

Since the procedure is so rare yet so complex, physicians rely on simulations to properly train to perform the operation. Existing simulations aren’t always very realistic, with mock arteries strapped outside of mannequins, and high-end ones can cost several thousand dollars, precluding some clinics from having sufficient training opportunities.

The parts required for the students’ design cost $70, and most of them are reusable for multiple simulations.

 “They have one pediatric ECMO simulation at Rady now, but they don’t have one at every hospital because they tend to be really expensive and difficult to make. There are currently no neonatal sized simulators,” said Samantha Landis, another team member. “Our goal was to create an ECMO simulation system for a neonatal infant and to reduce the cost, so we can spread this method to other hospitals, especially lower resourced hospitals.”

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The neonatal ECMO simulation, with the interior components shown outside of the mannequin.

The students developed low cost, easy to replicate artificial arteries and musculature that are placed in a 3D-printed holder inside the neck of an off-the-shelf neonatal-sized mannequin. They placed artificially created skin over the neck, where doctors make an incision during the simulated procedure to insert a tube into the arteries. The students also developed a pump system to circulate the blood in the mannequin’s vasculature, which existing simulators don’t have. They even went so far as to devise a new formulation for mock blood to make it feel, look and smell more realistic. Many current simulators use a bag with saline solution and red food dye hung on an IV pole to mimic blood circulating in the body.

“We added a pump with different size tubings and fittings, so that arteries had a different pressure than blood flowing through than veins,” said student Rahaf Alharbi.

They used glycerin, water, coloring and iron capsules to develop a substance that would flow, feel and smell more like blood.

Student Yichen Cai said they also devised a way to tension the muscles, so that they’d react and retract as they do in vivo when a physician is making the incision to insert a tube into the artery. 

A team of surgeons, doctors, nurses and technicians at Rady Children’s tested their simulator, and were pleased. They plan to present it at an ECMO conference later this year, including a manual the students created detailing where to source and how to make the required components. The total cost of their simulator was $70, and it can be easily scaled up to a larger size for a pediatric or adult ECMO simulator. 

“The Rady ECMO team is very thankful for this opportunity,” said project sponsor Dr. Denise Suttner, clinical director of the neonatal intensive care unit at Rady Children's Hospital and director of the San Diego Regional ECMO Program. “The simulation is very impressive and has added great value to our educational offerings.” 

The students said this hands-on project was also valuable to them for several reasons. 

“I think a lot of our prior practice stemmed from theoretical knowledge, and in the beginning of the project we were kind of stressed out because we couldn’t find any literature, any studies or any equations to help us with this. But when we realized we can move to other methods that designers really use, it helped us a lot,” said Alharbi.

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The students met with Rady physicians and surgeons frequently to ensure the design met their needs, and are pictured here after a Rady team tested their completed ECMO simulation.

“It ended up being almost entirely qualitative, not quantitative, which is very different from a lot of engineering courses,” Berg added. “The main measure of success was ‘Does this feel real to surgeons?’”  

Knowing that their project could one day help physicians and patients was a motivating factor, too.

“We combined an engineering approach along with a human-centered design approach to solve a real world problem,” said team member Reem Mohanty. “I think our team’s interdisciplinary application of design thinking and engineering tools was a unique and creative idea. The course gave us an avenue to potentially make a difference in people’s lives and that really motivated us to give our best.”

UC San Diego Team Delivers Protective Equipment to Hospitals in Baja California


San Diego, Calif., May 11, 2020-- The COVID-19 pandemic is impacting the availability of personal protective equipment (PPE) supplies in Baja California, and researchers with UC San Diego’s Department of Computer Science and Engineering are developing solutions to help.

Nadir Weibel, an associate professor in the department and head of the Human-Centered and Ubiquitous Computing Lab, is collaborating with university colleagues, government and industry to develop PPE solutions and to transport  supplies, like masks and face shields, to hospitals in Baja.

So far, the team has produced and tested 3,000 face shields and 1,100 masks. The protocols to make this equipment have been published on Earth2.0’s COVID-19 Rapid Response, an online portal that supports information sharing, rapid science and innovative solutions curated by UC San Diego’s Weibel, Eliah Aronoff-Spencer, Linda Hill, and many other faculty and students.

Scaling Up Production and Distribution 

After engineering an initial batch of masks and face masks, Weibel and Earth 2.0 partner Linda Hill, a clinical professor in UC San Diego’s Department of Family Medicine and Public Health, began developing a PPE pipeline to Mexico, working closely with the San Diego Mayor’s Office of International Affairs, the State of Baja Economic Development Authority and others.

Hospitals in Baja California aren’t the only group that could benefit. “There might be others who need it, like populations that typically have less access to this kind of protection: refugees, homeless people, small community clinics, nursing homes,” Weibel pointed out. 

The group’s next goal is to partner with industry in Baja to scale up their efforts and fully implement their project. They are supplying their instructions and specifications to create the safe and effective PPE in both English and Spanish, so local manufacturers can lend a hand.

“We will act as technical know-how liaisons for potential industry partners and manufacturers in Baja who are interested in producing these supplies at scale,” Weibel said. 

Developing DIY Solutions

Weibel and colleagues had been looking for ways to support COVID-19 care and prevention since the earliest days of the pandemic.

“We started to research existing solutions,” said Weibel. “A physician at the University of Florida had designed a mask using surgical wrap, a material that keeps surgical equipment sterile, and that solution really intrigued us.”

While surgical wrap protects instruments from viruses and other potential contaminants and is relatively plentiful, making it great DIY mask material, the initial design was too labor-intensive to scale up.

Working with UC San Diego’s Simulation Training Center and others, Weibel and his team began refining it. The researchers, including computer science PhD student Tommy Sharkey and undergraduate Shiv Patel, iterated several mask designs, using surgical wrap and other easy-to-find materials.

Developing these designs was just the first step – they also had to be validated. Weibel’s team worked closely with infectious disease, emergency room and other UC San Diego physicians to get feedback. They’ve also been testing prototypes on a PortaCount, a device that measures the numbers of particles going through the mask.

“We have been able to produce a surgical mask that has better protection than any other DIY masks out there,” said Weibel.

Weibel’s group has also been working with Qualcomm Institute’s Prototyping Lab and Scripps Institution of Oceanography’s CAICE Lab to produce mask components. The UC San Diego chapter of Delta Epsilon Mu, led by Ann Nguyen, an undergraduate research assistant in the Human-Centered and Ubiquitous Computing Lab, is helping assemble them. The computer science department has provided much-needed funding.


COVID-19: What is obvious and clear for us may not be for a lot of people

A nanoengineering grad student at UC San Diego finds ways to talk to loved ones.

Juliane Sempionatto is a Ph.D. student at Jacobs School of Engineering at UC San Diego.

San Diego, Calif., May 7, 2020 -- This is my fifth year away from my family. If anyone knows about being out of reach from loved ones, it’s me. But unfortunately, with our current situation, it is likely you, too.

The community of international students at UC San Diego have all experienced “family distancing” for a while. We have done our best to keep our friends and family safe overseas. But last time I checked in on my family during this COVID-19 pandemic, I was terrified.

I come from a simple family. Last week, I called my mother. I asked how they were dealing with the lockdowns and such, and she said everything was good. I could hear my little nephew, who lives with my parents, playing with my father in the background. Then I learned that he was away from school because he had a cold and high fever. “Wait…what?” I said, as my mother tried to calm me down, explaining how he did not have the coronavirus because he wasn’t having difficulty breathing.

Let me explain my shock: My father has diabetes and hypertension, and my grandmother is over 70 years old and lives with them. My mother apparently had no clue about the risk they were all exposed to. I had to explain to her that in most people the symptoms are very mild, especially among kids. From that day on, my nephew would only get better, but just because he has no respiratory symptoms does not mean he is not a vector. I told her to keep him as far away as possible from his grandpa and asked her to teach him “the right way” to sneeze. It was very painful to be away at that moment. I knew my father and grandmother’s health were at high risk. At the same time, I know how difficult it is to control a child. Without actually being there with them, I felt I could not do anything more to help.

I had to be selective about what to share with my family. I started looking for information about COVID-19 that made it easier to understand—things like videos and pictures, for example, or information and tips that were clear and persuasive. We tend to assume that all people have access to the same information we do, because it is all over the news and social media. But what we need to keep in mind is that what is obvious and clear for us may not be for a lot of people, including our families. I’ve learned to make sure people really understand what is happening before judging or chastising them. They just might not have gotten the right message yet.

This is a common theme in academia, where many of us focus intently on one specific subject or discipline until we know it inside and out, while it may remain completely obscure and unknown to the majority of people. As a nanoengineering researcher, for example, I am very accustomed to extremely small scales. So I can readily envision what I read about with regards to the virus. I can imagine how, when we sneeze, our saliva comes out in the form of tiny droplets, each less than 100 micrometers in diameter—about the width of a strand of human hair—and how they can travel up to 8 meters (26 feet) away from us. And in each of these tiny saliva droplets, there can be as many as 200 million individual virus particles, almost one virus for each of us in the U.S., all of it covering everything around us. So, I tell my friends and family to wipe clean all surfaces they come in contact with. That includes desks, computer keyboards and mouses, cell phones, and eyeglasses. There could even be 200 million viruses just hanging out on our hands as we scroll down our screens, so we should all go wash our hands right now! (But wait… stay a little bit more, I’m almost done.)

My personal experience throughout this COVID-19 pandemic has taught me to be aware of current developments, to learn everything I can, and to be a proactive and helpful player in conveying this information to others, so I am able to keep others informed and safe. As a member of the scientific community, I see it as my duty to communicate technical information accurately and in a way more people can understand. 

So throughout all of this, just keep in mind that all of us—the whole of humanity—are all isolated cells of the same body, and that body is sick and needs us to fight the disease together! 

So, let’s all go wash our hands now. This story originally ran in Triton Magazine. 

Juliane Sempionatto is a Ph.D. student at Jacobs School of Engineering at UC San Diego. Her research focuses on the development of wearable biosensors for medical and healthcare applications. She hopes to graduate with a Ph.D. in nanoengineering in 2021.  


UC San Diego's Earth 2.0 COVID-19 Response Platform Connects Clinicians with Resources, Engineers and Answers

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San Diego, Calif., April 20, 2020 -- Everything about the COVID-19 pandemic is new: the virus’s transmission to humans, the stay-at-home orders, the challenges many caregivers are facing. With so much in flux, providers are often being asked to find solutions. In response, a group of UC San Diego faculty, with the help of hundreds of students, has stepped up to create an online portal called Earth 2.0 COVID-19 Rapid Response.

A collaboration between UC San Diego School of MedicineQualcomm Institute, the Department of Computer Science and Engineering in the Jacobs School of Engineering and many others, the portal gives direct caregivers a simple way to ask urgent questions and receive rapid responses from expert teams, providing timely solutions during this quickly changing crisis.

Earth 2.0’s first live component is CoRESPOND, an emergency response Q&A resource for healthcare workers. The Earth 2.0 COVID Rapid Response platform will also include OASIS, a crowd-sourced information and resource-sharing platform, and HomeBound, an app to manage COVID-19 symptoms at home and a living data system to drive learning and innovation.

Earth 2.0 Brings a Collaborative Response to COVID-19 

Earth 2.0 was first envisioned several years ago to solve global-scale problems through crowd-sourced innovation. When the COVID-19 pandemic emerged, the platform was immediately retasked to help manage the pressing crisis and the Earth 2.0 COVID Rapid Response platform was born.

“We wanted to reformulate the Earth platform so that any researcher or health worker could email or text our system and get answers,” said Eliah Aronoff-Spencer, a physician-scientist with UC San Diego School of Medicine and the Qualcomm Institute. Aronoff-Spencer also directs the UC San Diego Design Lab Center for Health.

Aronoff-Spencer and Nadir Weibel, an associate professor in the Department of Computer Science and Engineering and head of the Human-Centered and Ubiquitous Computing Lab, quickly pulled together several customer service, communication and collaboration platforms, including Freshdesk, Google Docs, Github, GrabCAD and Slack. From there, the team, which also includes Linda Hill, a clinical professor in the Department of Family Medicine and Public Health, and Andrew Baird, a professor in the Department of Surgery, created CoRESPOND, an emergency response Q&A resource for frontline healthcare workers.

CoRESPOND is the first live component of the Earth 2.0 COVID Rapid Response platform, which will also include OASIS, a crowd-sourced information and resource-sharing platform, and HomeBound, an app to manage COVID-19 symptoms at home and a living data system to drive learning and innovation.

Finding Answers in the Midst of a Crisis 

CoRESPOND gives healthcare workers ready access to information they don’t have time to research on their own. Through the portal, workers simply email or text their queries to covid-help@ucsd.edu, and the system goes to work to find an answer.

Each email triggers a problem ticket, which is then categorized and forwarded to a system moderator, who immediately assembles a team of relevant experts. The platform uses Slack to enable and stimulate discussion among ad hoc research groups who reply to moderators with possible answers.

CoRESPOND then leverages uPuban online authoring system, to publish open access solutions that can be continuously updated and made available worldwide. The answers are further vetted for quality and accuracy before being emailed – all within as short a time-frame as possible.

“In two or three days, we created a ticketing system and an ad hoc response group, as well as an editorial structure to make sure the responses were valid,” said Aronoff-Spencer. “We have been getting most responses back to people on the frontline in 24 hours or less.”

Since launching, the platform has received and answered numerous questions on everything from how long a person is contagious to how to make a face shield. Each question activates a network of around 200 knowledge experts and several hundred students who provide the legwork, searching for answers, validating the results, and sending that information back to the requester.

“We have people triaging the tickets and communicating back directly with the frontline workers,” said Weibel. “We have infectious disease and primary care physicians, supply chain people trying to figure out where to find masks and other important items, a whole team of experts.”

Some questions are easier than others as knowledge about the virus grows and changes, but all answers end up in a solutions portal where the information is accessible for future use.

“We get questions like ‘do people create antibodies when they're recovering?’” said Hill. “The teams will research what we call the gray literature, as well as the medical literature, and develop a response. The field is changing in real time. We have told our teams these are living documents, like a wiki, and we have the capacity to continuously update the platform and keep it current.”

The bottom line for the entire team is making sure they always provide relevant, accurate information that will be useful. Anyone can join Earth 2.0 and add their expertise to the system, and are encouraged to contribute, whether it’s clinical experience, engineering know-how or current supply-chain information.

“It’s not just an information exchange, it's a quality information exchange,” said Aronoff-Spencer. “For instance, we have to do more than come up with an alternative PPE [personal protective equipment]. We have to come up with an alternative PPE that meets specific requirements, and we can track those specifications.”

In addition to Aronoff-Spencer, Weibel, Hill and Baird, other members of the Earth 2.0 COVID-19 Rapid Response leadership team include Henrik Christensen, a professor of computer science and director of the Institute for Contextual RoboticsDr. Doug Ziedonis, UC San Diego associate vice chancellor for Health Sciences, Ramesh Rao, director of the Qualcomm Institute, Don Norman, director of the Design Lab, Nikhil Jain, VP and lead on the Qualcomm Toq smart watch, and Nicolas DiTada.

Story written by Josh Baxt

The heart of experimentation beats outside the classroom anyway...

Andy Zhao

Adrift in his research, grad student Andy Zhao, MA ’17, finds hope in teaching a virtual quarter.

San Diego, Calif., May 5, 2020 -- Working from home as an experimental scientist is a bit… impossible. My lab mates and I synthesize new materials destined for next-generation lasers, magnets, and batteries. We work with custom-built, expensive equipment with special power supplies and materials that are toxic, carcinogenic, and corrosive. These things don’t exactly fit nicely into graduate student apartments, or really any home outside the Stark family.

As I shelter in place with my family, hundreds of miles from UC San Diego, it has been nice to take a step back to process and write up results in the backlog. But I already feel the dread of not having any new data, no new progress toward my PhD. I wonder if my research problems I need to solve before graduation are important anymore given the global pandemic and financial crisis.

I will confess here and now, however, to myself and my advisor, that I haven’t done any of the processing or writing up of backlogged results I just mentioned. The day after Governor Newsom ordered the state-wide shelter-in-place, I spent about 3 hours on Instagram watching people do pushups and draw oranges, 2 hours napping, an hour blind-taste-testing 2 percent vs. whole milk (objectively confirming that 2 percent milk is garbage), another hour thinking about how the first person to milk a cow probably had no friends. My giant research elephants have sheltered-in-place nicely at home with me, constantly guilt-tripping me with a reminder that I have work to do. But I still haven’t found the courage to confront my elephants. Instead, I keep asking myself, “How could I possibly be expected to go to school on a day like this?”


Where I currently fail to find meaning and motivation in my own research, I hope to find it in teaching. This spring quarter I will present MAE 170: Experimental Techniques to undergrads in mechanical and aerospace engineering and bioengineering. Despite teaching this lab class remotely, I have this strange excitement for the challenge to teach these experiments at home with Arduino, an open-source, affordable electronic prototyping platform that allows users to create interactive electronic objects. It’s like buying a baby C-3PO off Amazon, and then programming it to do your bidding. 

The lab class is traditionally taught with all the bells and whistles provided for the students: well-managed lab stations with computers, power supplies, LabVIEW data acquisition boards, voltmeters, resistors, BNC connectors… everything ready and set out in front of the student. This time around, the experiments will be recorded on video and the data provided to students. Students will still analyze the data and write technical lab reports to sharpen their communication skills, but they won’t have a chance to get the crucial hands-on experience by acquiring that data themselves. But I’m still hopeful that we can salvage some of this element, as a major part of the class revolves around programming Arduinos, which students can buy for about $30, to run their own experiments at home. If they can’t buy a physical Arduino, they can still build circuits and code Arduinos in an online, virtual environment as well.

At the end of the day, teaching an experimental lab class remotely like this is not ideal, but we’re making the most of the situation, and there is a subtle lesson worth learning: A real experiment grapples with a question that no one knows the answer to. All the required equipment and understanding cannot come prepackaged, waiting for you on a lab bench. Real experimentation relies on ingenuity, cobbling together parts from here and there to make it work – something that can be ingrained into students as they are home alone, hacking together something with some cheap Arudinos and makeshift components. A great experiment doesn’t require the latest, most expensive equipment. It just takes more personal time, care, attention, willpower, and sacrifice than any reasonable person would trade away; anyone willing to barter those away can do Science in my book.

In the 1800s, when capital-S “Science” seemed to be reserved for the likes of Lord Kelvin and his society of noble friends, strapped with enough disposable income and castle space to run weird-ass experiments. But the heart of science was also carried out by people like Gregor Mendel, a monk who spent decades tenderly growing peas, meticulously measuring them, trying to figure out how traits are inherited across generations, in essence creating the science of genetics. Anyone can cook. 

So while I spend this quarter trying to teach students how to run experiments over Zoom (which will be its own giant experiment), my goal will be to spark an interest in my students to create personal tools to measure things that interest them. Things like the amount of force inflicted by a finger flick; their bread’s temperature during fermentation and how it affects flavor; the difference in reaction time between their left and right hand; or the frequency range of their voice. So while I can’t provide my students the actual experience of performing the class experiments, I can try my best to encourage them to take the lab’s lessons and use them in the course of their lives, as the heart of experimentation beats outside the classroom anyway. I will teach them the tools they need to conduct real-life scientific experimentation on their own. I will guide them to more clearly report their methods and findings. And by doing all this, I hope my students can help reignite my own passion for research, which has flickered, but not quite extinguished, amidst this crisis.

Andy Zhao, MA ’17 is teaching UC San Diego undergraduates remotely while he shelters-in-place with his family in Fremont, Calif. He spends his free-time raising a 100 year old sourdough starter named Sandy, descended from Il Dandy’s bread and pizza dough starter, Gino; he spends his not-free-paid-like-a-grad-student-time studying how heat moves in liquids, with applications in molten salt energy storage and water desalination. Andy hopes to graduate with a PhD in Materials Science and Engineering in 2021. 

This story originally ran in Triton Magazine.

UC San Diego Researchers Optimize Microbiome Tool for Computer GPUs

Microbiome analyses including COVID-19 research made significantly faster

An ordination plot of unweighted UniFrac distances over 113,721 samples. AGP: American Gut Project. EMP: Earth Microbiome Project. Credit: Rob Knight, Daniel McDonald, UC San Diego

San Diego, Calif., April 17, 2020 -- Researchers at the University of California San Diego have been applying their high-performance computing expertise by porting the popular UniFrac microbiome tool to graphic processing units (GPUs) in a bid to increase the acceleration and accuracy of scientific discovery, including urgently needed COVID-19 research.

“Our initial results exceeded our most optimistic expectations,” said Igor Sfiligoi, lead scientific software developer for high-throughput computing at the San Diego Supercomputer Center (SDSC) at UC San Diego. “As a test we selected a computational challenge that we previously measured as requiring some 900 hours of time using server class CPUs, or about 13,000 CPU core hours. We found that it could be finished in just 8 hours on a single NVIDIA Tesla V100 GPU, or about 30 minutes if using 16 GPUs, which could reduce analysis runtimes by several orders of magnitude. A workstation-class NVIDIA RTX 2080TI would finish it in about 12 hours.”

“The new executable will also be of tremendous value for exploratory work, as the moderate-sized EMP dataset that used to require 13 hours on a server class CPU can now be run in just over one hour on a laptop containing a mobile NVIDIA GTX 1050 GPU,” added Sfiligoi.

Sfiligoi has been collaborating with Rob Knight, founding director of the Center for Microbiome Innovation, and a professor of Pediatrics, Bioengineering, and Computer Science & Engineering at UC San Diego, and Daniel McDonald, scientific director of the American Gut Project. Microbiomes are the combined genetic material of the microorganisms in a particular environment, including the human body.

“This work did not initially begin as part of the COVID-19 response,” said Sfiligoi. “We started the discussion about such a speed-up well before, but UniFrac is an essential part of the COVID-19 research pipeline.”

UniFrac compares microbiomes to one another using an evolutionary tree that relates the DNA sequences to each other. “UniFrac played a key role in the Human Microbiome Project, allowing us to understand how microbes are related across our bodies, and in the Earth Microbiome Project, allowing us to understand how microbes are related across our planet,” said Knight. “We are using it to understand how a person’s microbiome might make them more or less susceptible to COVID-19, and what microbes in environments ranging from health care facilities to sewage to ocean spray make the environment more or less hospitable to SARS-CoV-2, the coronavirus that causes COVID-19.”

Knight noted that Sfiligoi had sped up the latest version of the algorithm, published less than two years ago in Nature Methods, which itself already represented a dramatic speed improvement over previous implementations.

“As microbial sequence data increase exponentially, from dozens of sequences to billions, we have to re-implement all the algorithms,” he said. “This latest step really shows how optimizing the research infrastructure can dramatically reduce time-to-result while preserving the accuracy of the findings and enabling completely new scales of questions to be asked.”

Specifically, Sfiligoi used OpenACC, a user-driven, directive-based parallel programming model to port the existing Striped UniFrac implementation to GPUs because this allows a single codebase for both CPU and GPU code. Additional speedup was obtained by carefully exploiting cache locality. Also explored was the use of lower-precision floating point math to effectively exploit consumer-grade GPUs typically found in desktop and laptop computers.

UniFrac was originally designed and always implemented using higher precision floating point math, often called fp64 code path. The higher-precision floating point math was used to maximize reliability of the results. After implementing the lower-precision floating point math, usually called fp32 code path, researchers observed nearly identical results, but with significantly shorter compute times.

“We saw a 3x speed-up in the fp32 code path for gaming GPUs such as the 2080 Ti and the mobile 1050, and we believe that precision should be adequate for the vast majority of studies,” explained Sfiligoi.

Moreover, the code changes introduced to speed up GPU computation also significantly sped up the execution on CPU resources. The computational challenge mentioned above can now be completed in about 200 hours on the same server-class CPU, a 4x speedup, according to the researchers.

“Making computation available on GPU-enabled personal devices, even laptops, eliminates a large barrier within the resource infrastructure for many scientists,” said Sfiligoi.

More about Sfiligoi’s recent groundbreaking research on GPU cloudbursting can be found here.

This work was sponsored by the U.S. National Science Foundation (NSF) under grants OAC-1826967, OAC-1541349, and CNS-1730158; and by the U.S. National Institutes of Health (NIH) under grant DP1-AT010885. Compute resources from both the Knight Lab and the Pacific Research Platform (PRP) were used in assessing the executable speeds.

Grit and Resolve

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San Diego, Calif., May 5, 2020 -- I never thought we would face so much headwind as a school. Despite the challenges, we are maintaining the forward momentum that we have spent more than six years building together. The health and safety of our students, staff and faculty is my number one priority. This is the foundation of our momentum.

I am profoundly grateful for the grit and resolve of everyone inside and outside the Jacobs School of Engineering who is empowering us to pivot, adapt, and at times, thrive. There has never been a more important time to strengthen engineering and computer science education and research for the public good.

Going for 25+ faculty hires this year

We have hired 18 world-class faculty to the Jacobs School so far this year, and we’ll have more new professors to announce shortly. This is already the most diverse group of faculty we’ve hired into the Jacobs School in a single year. Thank you to everyone who is working so hard on these recruitments.

Franklin Antonio Hall

Great news! Bioengineering professor emeritus Shu Chien, his wife KC Chien M.D., and Peter Farrell, founder of ResMed, have joined forces to strengthen connections between engineering and medicine at the Jacobs School. We will name a research collaboratory in our new building, Franklin Antonio Hall, in their honor. Thank you Shu, KC, and Peter for your incredible generosity and leadership. Your gifts come at an exciting time for the building project: the foundation is being poured and construction continues on schedule. Join me in watching progress via our construction cam.   

COVID-19 research response

So many labs have stepped up. Student, faculty and staff expertise and creativity is pouring into COVID-19 projects. Thank you. Many of these projects at the Jacobs School are already in various stages of efficacy testing, FDA approval, license negotiation and manufacture. There are also bold new projects I'm following closely, and I will update you as soon as I’m able.

Artificial Intelligence / Machine Learning curriculum

As we physically distance, the creativity that our faculty, students and staff are putting into remote and asynchronous lecture and lab courses is breathtaking. At the same time, we continue to revitalize our educational offerings. In the 2020-21 academic year, we will have Artificial Intelligence / Machine Learning courses in all of our engineering majors, through the new AI Tools for Engineering Practice curriculum.

An open line of communication

Advice, collaboration and support from all our constituents is more important than ever. In this time of COVID-19, I have tripled my efforts to connect with constituents; work connections; empower educators and students; engage staff; and accelerate research. You have an open line of communication to me: DeanPisano@eng.ucsd.edu

Take care and stay safe. We are all in this together. 

~Albert P. Pisano, Dean

UC San Diego Jacobs School of Engineering


Green method could enable hospitals to produce hydrogen peroxide in house

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The researchers' H-cell setup for developing their hydrogen peroxide production method.

San Diego, Calif., May 1, 2020 -- A team of researchers has developed a portable, more environmentally friendly method to produce hydrogen peroxide. It could enable hospitals to make their own supply of the disinfectant on demand and at lower cost.

The work, a collaboration between the University of California San Diego, Columbia University, Brookhaven National Laboratory, the University of Calgary, and the University of California, Irvine, is detailed in a paper published in Nature Communications.

Hydrogen peroxide has recently made headlines as researchers and medical centers around the country have been testing its viability in decontaminating N95 masks to deal with shortages amid the COVID-19 pandemic.

While results so far are promising, some researchers worry that the chemical’s poor shelf life could make such decontamination efforts costly.

The main problem is that hydrogen peroxide is not stable; it starts breaking down into water and oxygen even before the bottle has been opened. It breaks down even more rapidly once it is exposed to air or light.

“You maybe only have just a couple of months to use it before it expires, so you would have to order batches more frequently to keep a fresh supply,” said UC San Diego nanoengineering professor Zheng Chen. “And because it decomposes so quickly, shipping and storing it become very expensive.”

Chen and colleagues developed a quick, simple and inexpensive method to generate hydrogen peroxide in house using just a small flask, air, an off-the-shelf electrolyte, a catalyst and electricity.

“Our goal is to create a portable setup that can be simply plugged in so that hospitals, and even households, have a way to generate hydrogen peroxide on demand,” Chen said. “No need to ship it, no need to store it, and no rush to use it all before it expires. This could save up to 50 to 70% in costs.”

Another advantage is that the method is less toxic than industrial processes.

The method is based on a chemical reaction in which one molecule of oxygen combines with two electrons and two protons in an acidic electrolyte solution to produce hydrogen peroxide. This type of reaction is known as the two-electron oxygen reduction reaction, and it is user-friendly because it can produce dilute hydrogen peroxide with the desired concentration on demand. “In the next step, we will develop electrocatalysts suitable for other electrolyte solutions to further increase the range of its applications,” said UC San Diego chemical engineering graduate student Qiaowan Chang.

The key to making this reaction happen is a special catalyst that the team developed. It is made up of carbon nanotubes that have been partially oxidized, meaning oxygen atoms have been attached to the surface. The oxygen atoms are bound to tiny clusters of three to four palladium atoms. These bonds between the palladium clusters and oxygen atoms are what enable the reaction to occur with a high selectivity and activity due to its optimal binding energy of the key intermediate during the reaction.

Columbia University chemical engineering professor Jingguang Chen said, “The coordination between oxygen-modified Pd cluster and the oxygen-containing functional groups on carbon nanotubes is the key to enhancing its catalytic performance.”

The team originally developed this method to make battery recycling processes greener. Hydrogen peroxide is one of the chemicals used to extract and recover metals like copper, nickel, cobalt and magnesium from used lithium-ion batteries. Similarly, it also makes the activation of hydrocarbon molecules more efficient, which is a critical step in many industrial chemical processes.

“We had been working on this project for about one and a half years. As we were wrapping things up, the COVID-19 pandemic hit,” Chen said. Seeing news reports about the use of hydrogen peroxide vapor to disinfect N95 masks for reuse motivated the team to pivot directions.

“We saw that there was a more pressing need for efforts to help health care workers who may not have sufficient protection while caring for patients suffering from the new coronavirus,” he said.

The work is at the proof-of-concept stage. Moving forward, the team will work on optimizing and scaling up the method for potential use in hospitals. Future studies include modifying the method so that it can be done using a neutral electrolyte (basically a salt solution) instead of an acidic one, which would be better for household and clinical applications, Chen said. Part of this continuing work is currently supported by UC San Diego’s Sustainable Power and Energy Center.

Paper title: “Promoting H2O2 Production via 2-Electron Oxygen Reduction by Coordinating Partially Oxidized Pd with Defect Carbon.” Co-authors include Qiaowan Chang, Pu Zhang and Hongpeng Gao, UC San Diego; Amir Hassan Bagherzadeh Mostaghimi and Samira Siahrostami, University of Calgary; Xueru Zhao, Brookhaven National Laboratory; Steven R. Denny, Ji Hoon Lee and Jingguang G. Chen, Columbia University; and Ying Zhang, Central South University, China.

This work was supported in part by the ACS Petroleum Research Fund (59989-DNI5), the U.S. Department of Energy (DE-FG02-13ER16381) and the UC San Diego Jacobs School of Engineering.

Article by Liezel Labios

The Software that's Saving Corals

San Diego, Calif., April 27, 2020 -- A powerful visual analytics platform is translating photographs of coral reefs into navigable 3D maps that allow researchers to delve into the depths of these critically important and delicate ecosystems. Developed by Vid Petrovic, a computer scientist and software engineer with the Cultural Heritage Engineering Initiative at the UC San Diego Qualcomm Institute, the platform, called Viscore, is being used by researchers at Scripps Institution of Oceanography to study coral reefs around the world.

A 100 Island Challenge team member from Scripps Institution of Oceanography captures imagery of a coral reef.

Transforming Reefs into Virtual Maps
The 100 Island Challenge brings together researchers from Scripps Institution of Oceanography and the Qualcomm Institute (QI) to study the structure and health of coral reefs, and understand how they respond to climate change and inform their management. The project uses Viscore to digitally recreate plots from 100 reefs across the tropical Pacific, Caribbean and Indian Oceans.
Historically, researchers have relied on static, 2D representations of their study sites, such as photographs and measurements taken by divers in the field, to examine coral reefs from the laboratory. A number of factors—location, weather, water temperature, depth and finite reserves of breathing gas—can impact the amount of data that divers collect. Now, with Viscore, marine scientists at Scripps Oceanography can spend unlimited “dive time” exploring coral reefs—virtually.
“This is the kind of data that scientists haven’t had access to before. So it’s really exciting to see what sort of a difference it makes,” said Petrovic.

A 3D model of a coral reef plot near Kaho'olawe, southwest of Maui, imaged in 2016. The box highlights a 10 x 10m study region, with dots marking sample points used for coral cover estimation.

The process of creating a coral reef’s “digital twin” begins with thousands of overlapping images captured by Scripps Oceanography divers. Through a technique called structure-from-motion, researchers transform these images into hundreds of million or even billions of 3D points. These dense point-clouds are the first step in making a reef’s “digital twin,” capturing its unique geometry and color in lifelike resolution. With more than one thousand coral reef plots—some dating back nearly a decade—surveyed over years, the 100 Island Challenge has created what Falko Kuester, director of QI’s Cultural Heritage Engineering Initiative (CHEI) and a professor with the Department of Structural Engineering, calls a “data tsunami.”
“While we often hear about big-data science, this truly is an example of ‘Ocean Exploration in a Sea of Data,’” said Kuester.

Vid Petrovic studies a coral reef plot in CHEI’s Wide Angle Virtual Environment (WAVE), a room-scale immersive virtual reality environment that allows researchers to explore study sites and travel across space and time. 

This is where Viscore comes in, transforming billions of data points into vivid, lifelike models that can be experienced, explored and analyzed in UC San Diego’s walk-in virtual reality environments the WAVE and SunCAVE.  The immersive virtual reality systems can instantaneously transport researchers through time and space, giving them the power to revisit their study sites from hundreds of miles away.
Petrovic likens the experience of swimming through a virtual reef to “taking a patch of rainforest and being able to see all the life that’s there.” Researchers can inspect these rich ecosystems in detail, identifying coral species and tracking shifts in populations. With each passing year, these records provide a historical archive of coral reefs, one that can help marine scientists determine how corals respond to short-term disturbances, like storms, or to longer-term shifts, such as warming ocean temperatures.

“Viscore facilitates the creation of ‘digital twins’ allowing us to measure, classify, and annotate, as well as quantify change over time,” said Dominique Rissolo, a QI research scientist involved in the project. “This has resulted in observations of ecological processes that would otherwise not be possible.”

(Experience the fascinating coral reef visualizations created with Viscore on the project’s YouTube channel.)

“The tools developed by our colleagues at QI have been invaluable for visualizing coral reefs,” said Brian Zgliczynski, project coordinator for the 100 Island Challenge at Scripps Oceanography. “For instance, we can observe how corals respond to disturbances including storms and variations in sea temperature. While these events can negatively impact the structure and function of coral reefs, we have documented a number of cases where corals can recover and bounce back. This is incredible and is changing our understanding of how coral reefs will respond to a changing world.”

Time series showing change in a coral reef from Palmyra Atoll in the Pacific Ocean.

A New Way to Look at the World

The 100 Island Challenge has fostered a thriving partnership between CHEI’s engineering team, led by Kuester, and the team of marine specialists working under marine ecologist Stuart Sandin at Scripps Oceanography. Each has learned from the other; Petrovic has refined his approach and adjusted Viscore’s algorithms based on feedback from his Scripps Oceanography colleagues, while his counterparts have made note of new measurements they’d like to collect and add to the archive. Petrovic, CHEI’s remote imaging expert Eric Lo and Scripps Oceanography doctoral student Hugh Runyan are also in the process of developing machine learning techniques to automate the otherwise painstaking work of identifying individual coral species.

Beyond the 100 Island Challenge, Viscore supports efforts to explore and document vulnerable historical and cultural sites across the globe, including heritage sites in Mexico, Puerto Rico and Italy, and the marine ecosystem off the coast of Bermuda. Viscore has transported researchers to shipwrecks, underwater caves and ancient Maya ruins, has aided in digitally preserving indigenous archaeological sites and historically significant buildings, and has enabled the assessment of at-risk national and international infrastructure and life-lines in the face of extreme events.

The platform is featured in multimedia art installations, as well; one recent piece, “Hearing Seascapes,” blends visuals of coral reefs and an original score composed by Lei Liang, QI’s Research Artist in Residence.

“While serving as a fundamental research tool, Viscore is enabling scientifically anchored story-telling, allowing scientists and the ultimate stake holder, the public, to explore and experience the beauty of the environment that surrounds us, and with a bit of luck help create the empathy and stewards needed to preserve it,” said Kuester. “Just imagine what would be possible if we had the resources to create a global coral reef atlas, allowing anyone anywhere to join in the adventure of discovery, life-long-learning and stewardship of this precious resource.”

To donate to the 100 Island Challenge and support coral reef research, contact Adrienne Bolli at abolli@eng.ucsd.edu.

New SPEC video

Students harness their knowledge for ventilator challenge

San Diego, Calif., April 28, 2020 -- Inspire: meaning both to breathe in, and to be filled with the urge to take action. The definitions went hand-in-hand for two groups of engineering students at UC San Diego, who spent their spring break harnessing their knowledge to contribute to the ventilator shortage the world is facing with the COVID-19 pandemic. 

“We realized that we actually do have the engineering skills to try and make a meaningful difference,” said Anjulie Agrusa, a bioengineering PhD student at the UC San Diego Jacobs School of Engineering, who worked with two fellow bioengineering PhD candidates to form a multidisciplinary, international team for the Code Life Ventilator Challenge. 

Their task? To design a low-cost, simple, easy-to-use and easy-to-build ventilator that could serve COVID-19 patients. In eight days. 

Agrusa and bioengineering PhD students Sydnee Hyman and Nicholas Harrington spent their spring break designing a pressure-controlled ventilator based on technology used in scuba diving regulators. They worked with a retired electrical engineer and a retired video game developer in Canada that they met through the challenge, who added prototyping and user interface skills to the team, respectively. They also worked closely with a physician in Sacramento who provided input on what capabilities the ventilator needed to have, particularly for serving COVID patients.

“I think that was a call to action for all of us: that realization that we actually do know how to solve this problem-- or at least how to try to solve it,” said Agrusa. “UC San Diego prepared us really, really well to be equipped for something like this. It was a really cool experience to know that you actually have the tools to make a difference.”

None of the three students actually had a background in ventilator technology; Agrusa does computational work to better understand the electrical waves in our gastrointestinal tract; Hyman studies rotator cuff disease and therapies to treat it; and Harrington’s research focuses on developing home health devices to reduce the rate of rehospitalization due to heart failure.

But they did know how to problem solve. They knew how to think critically. They had software engineering skills, knew how to model, design, build and test medical device prototypes, and understood the importance of stakeholder feedback.

“We were given these skills, we were given these first principles in school, and we’re at a point in our careers where we actually know how to try and solve this problem,” Agrusa said. “All of us felt that we couldn't just sit there and have a spring break without trying to help solve this problem.”

Their solution

More than 1,000 teams participated in the ventilator challenge, which laid out specific criteria that all submitted designs needed to meet. 

“One of the primary design specifications was that the ventilator had to be pressure-controlled as opposed to flow-controlled,” Hyman explained. “That’s a distinction that makes it a lot trickier to design for and is important to be able to regulate pressure well for COVID patients specifically, because of all the acute respiratory distress that they experience. That creates a lot of changes to the lung physiology that provide more ventilation challenges.”

After delving deep into the world of breathing devices, the students learned that a key issue of designing a ventilator is the extremely precise modulation of very low pressures at very low flows-- the actuators and sensors used to accomplish this in state-of-the-art ventilators are very expensive and hard to manufacture. 

“So we decided to think about what's out there that currently works for people to breathe on that works at low pressures, and we thought about scuba regulators,” said Hyman.

When you inhale using a scuba pressure regulator, a diaphragm in the device gets depressed, creating a negative pressure and allowing air to flow in. The students learned that the same effect can also be achieved in a regulator by pushing what’s called a purge button, used to get water out of the device. 

“If you press that button, it depresses the diaphragm and allows air to go through,” said Agrusa. “Because COVID patients, or any patient that needs to be on a ventilator, cannot produce that negative pressure in their lungs since they can't inhale themselves, you force air in by creating a pressure gradient yourself. The way that we did this was by pressing the purge button on the scuba regulator a very specific amount, to let a very specific amount of air flow through.”

The students used an Arduino computer board  to precisely control the concentration of oxygen entering the lungs each time the button is pressed. On their ventilator, this is adjusted by a physician based on the individual patient’s needs, through an easy-to-manipulate user interface. The whole system is controlled by a servo motor.

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A CAD design of the graduate students' scuba regulator and actuating apparatus.

 A panel of engineers and judges reviewed all the submissions, and selected three designs as most promising. Those were made open source in an attempt to get the ventilators where they’re most needed as soon as possible. 

The team said the process was an empowering learning experience. 

“This was all new to us,” Harrington said. “Even from the ground up, as to what exactly a ventilator is and what it does, we didn’t really know the specifics before….So it was interesting to learn about how to balance the different requirements of having a high pressure supply, but then needing to use low pressure to not hurt the patient. The interplay there was interesting.”

For Hyman, the learning also included agile project management. 

“Managing a whole multidisciplinary team, virtually, in a very short timeframe with the design specifications which got updated as the challenge continued… that for me I think was the biggest learning opportunity.”

Undergraduates also shoot for the stars

The team of bioengineering graduate students wasn’t the only one to lend their skills to the cause. Undergraduate engineers from the rocket team of Students for the Exploration and Development of Space group also chose to put their engineering know-how to use.

“At the end of the day, a ventilator is there to deliver a specific volume at a specific pressure, which is exactly what mechanical engineering prepares you to do,” said Scott Hall, a mechanical engineering student and member of SEDS’ rocket team.

Hall, who had a job offer rescinded due to COVID-19 related financial woes, was looking for something to fill his time in quarantine that could also add to his resume, when the Agorize ventilator challenge crossed his path.

“That  sounded like a great way to spend time meaningfully in quarantine. I ran it past the rocket team, and everyone got super excited. Then I told them the deadline, which was in a week, and we were like ok, well that’s a crazy short deadline, but let’s at least still try.”

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The team of undergraduate students working on their SEDS rocket.

Hall was joined by Tristan Kinney, Shannon Lin, Patrick Finn, and Harker Russell. The students worked through their spring break to understand the engineering behind ventilators, and started creating a design of their own that would be inexpensive and easy to manufacture, per the hackathon criteria. 

They soon realized that they wouldn’t be able to have their design completed in time for the contest deadline, but decided to keep pursuing the goal anyway. 

“We’re still working on it. Everyone agreed that we want to build something that could help people, even if it’s not within this particular challenge timeframe,” Hall said.

The students-- three mechanical engineers and one bioengineer-- are working on the ventilator design remotely, since the state is under shelter-at-home orders. Luckily, they’re still able to piecemeal together a prototype. 

“What’s nice about SEDS is that we’re all big nerds,” Hall said. “We have our own 3D printers at home, so all of us will be able to 3D print parts and leave them on someone else’s doorstep. So the plan from quarantine is to put this thing together through 3D printing, and buy any other parts we need online from McMaster.”

While the team plans to see their design through to completion, Hall said they all feel that it’s been an invaluable learning experience and use of their spring break and quarantine time, regardless of the outcome. 

“I think so far in my undergraduate career there've been six or seven projects that have really taught me how to be an engineer, and this is one of them,” he said. “This is the way you learn engineering--by doing stuff like this. Taking on crazy projects and trying to make it work.”


Creating an Early Alert System for COVID-19



Researchers combine power of wearable device and big data analytics to track spread and early signs of infection-including among healthcare workers

San Diego, Calif., April 2, 2020 -- To better understand early signs of coronavirus and the virus' spread, physicians around the country and data scientists at UC San Diego are working together to use a wearable device to monitor more than 30,000 people, including thousands of healthcare workers. The research started at hospitals in the San Francisco Bay Area, and has now expanded nationwide. 

The wearable tracks temperature, heart rate, respiration and activity. Based on early data analysis, the researchers seem able to predict whether someone is getting sick; whether it's going to be mild or severe; and potentially whether the illness is specifically COVID-19 Now, the researchers want to broaden the number of subjects to make sure they are capturing a representative sample of the U.S. population. 

Ben Smarr, a professor of data science and bioengineering at UC San Diego, leads the data analysis effort on the project.

“Our first push is to get as many people involved as possible,” said Benjamin Smarr, who leads the data analysis effort and is a professor of data science and bioengineering at the Jacobs School of Engineering at UC San Diego. “If enough people are involved we can cover the whole country.”

Initial data analysis has also shown that some patients who tested positive for COVID-19 and recovered have long-lasting side effects. Data has also shownCOVID-19 symptoms differ widely from one person to the next.

“It really shows you need as much information as possible - heart rate or temperature on their own wouldn’t get you the whole picture, so involving a wearable that can collect multiple data streams is key,” Smarr said. 

Early analysis also suggests that some “asymptomatic” cases may in fact simply go unnoticed by people, but can actually be detected by sensors.
"The sensors successfully reveal when someone is physiologically ill, but these signals in the data don't always line up with when that person reports symptoms, which is sometimes earlier but sometimes much later." said Smarr. "Those cases where people report symptoms after their physiology shows illness are important, because a big concern is knowing when people are sick while they don't yet know it themselves. This suggests some of those cases may be able to be detected in the physiology, even as the person is not feeling sick.”

The difference is a key insight into one of the major challenges COVID-19 poses to public health - identifying contagious individuals before they become noticeably sick. “It highlights how important participation is in helping to understand this illness - tech alone won’t get us there,” concludes Smarr.

Rob Knight, from the UC San Diego School of Medicine and Jacobs School of Engineering, will lead an effort to collect samples to supplement data.

Subjects don't necessarily have to use a wearable device to participate. They can simply enter their symptoms on a web form, such as those provided by UC San Diego’s own reportyoursymptoms.ucsd.edu/survey, as well as https://www.covidnearyou.org/#!/ and https://quantifiedflu.org. Researchers then access the data and conduct analysis. 

Subjects in the study also have an option to take part in sample collection led by professor Rob Knight, from the UC San Diego School of Medicine and the Jacobs School of Engineering. Samples could include swabs, stools and blood that will confirm infection and immunities mailed to researchers. The research team is also trying to secure and distribute tests that can determine whether someone has developed antibodies against COVID-19. 

The researchers are mindful of privacy concerns. When people opt in to the study, they make their data available for three months to UC San Francisco. It is then anonymized before large-scale analysis starts at UC San Diego. 

The ultimate goal is to develop the equivalent of a weather map for COVID-19 spread and severity, based on developing algorithms for sickness prediction and early alert. This will be done with the help of Ilkay Altintas, the chief data science officer at the San Diego Supercomputer Center and a fellow at the Halicioglu Data Science Institute at UC San Diego. She and her team have developed tools to gather data about wildfires and predict where the blazes are headed. They hope to do the same with the virus. Algorithms will be released publicly and anyone providing data would have the option to contribute to these efforts.

Ilkay Altintas, chief data officer at the San Diego Supercomputer Center, and her team will work on developing algorithms for sickness prediction and early alert.

“This will be the deepest data dive into an illness that has been attempted and carried out,” said Smarr.

The wearable device is a ring provided by Oura, a Finnish startup. More than 10,000 Oura ring users have signed up to provide data and fill out questionnaires for this study. While not an FDA registered  healthcare device, the ring monitors a range of signals, including continuous temperature, heart rate, respiration rate and activity. Initial analysis suggests that a destabilization of temperature happens a couple of days before coronavirus symptoms manifest. The Oura ring detects this pattern. The app also reports daily temperature changes, which can be a signal for healthcare workers to check their temperature with a thermometer and stay home if it’s elevated. Oura has provided the device free of charge to 2,000 healthcare workers at the UCSF Medical Center and Zuckerberg San Francisco General Hospital.

The study will help healthcare workers stay home from work sooner and get treatment sooner, Dr. Ashley Mason, an assistant professor of psychiatry  at UC San Francisco who developed the project and is the lead investigator, told the San Francisco Chronicle. “[The virus] is expected back in the fall and we need to have tools ready.”

An image provided by Oura, showing someone wearing one of the rings the company makes.

Mason is a sleep clinician and had been using the Oura ring to look at temperature data for treatment-resistant depression. Smarr was helping her think about how to analyze the data. After UC San Francisco shut down all non-essential work, Mason realized the same stream of temperature data could be used to monitor sickness. She and Smarr quickly worked together with Oura to design a study and run it by UC San Francisco’s Institutional Review Board.

As part of the study, Santa Clara Valley Medical Center will also receive rings for 1,000 healthcare workers. The hospital, located in San Jose, the third largest city in California, is in one of the areas most severely affected by COVID-19. 

Our healthcare workers are probably the worst hit,” said Dr. Marco Lee, a neurosurgeon at Santa Clara Valley and a clinical professor of neurosurgery at Stanford University, who first brought the idea of using the device there. “We want them to feel that we are supporting them and providing them with tools so they may get an early warning.”

Lee also said he hopes that the study will help gather crucial data about the coronavirus and how it manifests itself. “We don’t know what the study will show,” Lee said. “But this is a unique situation and we suddenly have a device where we can monitor a group that is very susceptible to infection.”

Ultimately, said Smarr, the researchers hope to use the data to predict the virus’ spread and set up an early alert system. 




Making recombinant-protein drugs cheaper

San Diego, Calif., April 23, 2020 -- The mammalian cell lines that are engineered to produce high-value recombinant-protein drugs also produce unwanted proteins that push up the overall cost to manufacture these drugs. These same proteins can also lower drug quality. In a new paper in Nature Communications, researchers from the University of California San Diego and the Technical University of Denmark showed that their genome-editing techniques could eliminate up to 70 percent of the contaminating protein by mass in recombinant-protein drugs produced by the workhorses of mammalian cells -- Chinese Hamster Ovary (CHO) cells.

With the team’s CRISPR-Cas mediated gene editing approach, the researchers demonstrate a significant decrease in purification demands across the mammalian cell lines they investigated. This work could lead to both lower production costs and higher quality drugs.

Recombinant proteins currently account for the majority of the top drugs by sales, including drugs for treating complex diseases ranging from arthritis to cancer and even combating infectious diseases such as COVID-19 by neutralizing antibodies. However, the cost of these drugs puts them out of reach of much of the world population. The high cost is due in part to the fact that they are produced in cultured cells in the laboratory. One of the major costs is purification of these drugs, which can account for up to 80 percent of the manufacturing costs.

In an international collaboration, researchers at the University of California San Diego and the Technical University of Denmark recently demonstrated the potential to protect the quality of recombinant protein drugs while substantially increasing their purity prior to purification, as reported in the study entitled “Multiplex secretome engineering enhances recombinant protein production and purity” published in April 2020 in the journal Nature Communications.

“Cells, such as Chinese hamster ovary (CHO) cells, are cultured and used to produce many leading drugs,” explained Nathan E. Lewis, Associate Professor of Pediatrics and Bioengineering at the University of California San Diego, and Co-Director of the CHO Systems Biology Center at UC San Diego (http://cho.ucsd.edu). “However, in addition to the medications we want, the cells also produce and secrete at least hundreds of their own proteins into the broth. The problem is that some of these proteins can degrade the quality of the drugs or could elicit negative side effects in a patient. That’s why there are such strict rules for purification, since we want the safest and most effective medications possible.”

Making recombinant-protein drugs cheaper
Cleaning up CHO cells for improved drug production involves an interdisciplinary research approach. By cleaning up mammalian cell lines that produce recombinant-protein drugs, researchers forge a path to purer, cheaper drugs that treat cancer, arthritis and other complex diseases.

These host cell proteins (HCPs) that are secreted are carefully removed from every batch of drug, but before they are removed, they can degrade the quality and potency of the drugs. The various steps of purification can remove or further damage the drugs.

“Already at an early stage of our research program, we wondered how many of these secreted contaminating host cell proteins could be removed,” recounted Director Bjorn Voldborg, Head of the CHO Core facility at the Center of Biosustainability at the Technical University of Denmark.

In 2012 the Novo Nordisk Foundation awarded a large grant, which has funded ground-breaking work in genomics, systems biology and large scale genome editing for research and technology development of CHO cells at the Center for Biosustainability at the Danish Technical University (DTU) and the University of California San Diego. This funded the first publicly accessible genome sequences for CHO cells, and has provided a unique opportunity to combine synthetic and systems biology to rationally engineer CHO cells for biopharmaceutical production.

“Host cell proteins can be problematic if they pose a significant metabolic demand, degrade product quality, or are maintained throughout downstream purification,” explained Stefan Kol, lead author on the study who performed this research while at DTU. “We hypothesized that with multiple rounds of CRISPR-Cas mediated gene editing, we could decrease host cell protein levels in a stepwise fashion. At this point, we did not expect to make a large impact on HCP secretion considering that there are thousands of individual HCPs that have been previously identified.”

This work builds on promising computational work published earlier in 2020.

Researchers at UC San Diego had developed a computational model of recombinant protein production in CHO cells, published earlier this year in Nature Communications (http://dx.doi.org/10.1038/s41467-019-13867-y). Jahir Gutierrez, a former bioengineering Ph.D. student at UC San Diego used this model to quantify the metabolic cost of producing each host cell protein in the CHO secretome, and with the help of Austin Chiang, a project scientist in the Department of Pediatrics at UC San Diego, showed that a relatively small number of secreted proteins account for the majority of the cell energy and resources. Thus the idea to eliminate the dominant contaminating proteins had the potential to free up a non-negligible amount of cellular resources and protect drug quality. The authors identified and removed 14 contaminating host-cell proteins in CHO cells. In doing this they eliminated up to 70 percent of the contaminating protein by mass and demonstrated a significant decrease in purification demands.

These modifications can be combined with additional advantageous genetic modifications being identified by the team in an effort to obtain higher quality medications at lower costs.

Article cited: Kol, S., Ley, D., Wulff, T., Decker, M., Arnsdorf, J., Schoffelen, S., Hansen, A.H., Gutierrez, J.M., Chiang, A.W.T., Masson, H.O., Palsson, B.O., Voldborg, B.G., Pedersen, L.E., Kildegaard, H.F., Lee, G.M., Lewis, N.E. Multiplex secretome engineering enhances recombinant protein production and purity. Nature Communications, in press (2020). DOI: 10.1038/s41467-020-15866-w

This study was supported by the Novo Nordisk Foundation (NNF10CC1016517), the National Institutes of Health (R35 GM119850), and a fellowship from the Government of Mexico (CONACYT) and the University of California Institute for Mexico and the United States (UC-MEXUS).

A patent based on this work has been filed with authors B.O. Palsson, B.G. Voldborg, and  L.E. Pedersen as inventor. The International Patent Application No. is EP20160166789. All other authors declare no competing interests.

Marrying molecular farming and advanced manufacturing to develop a COVID-19 vaccine

Researcher examines plants grown in the lab
Nicole Steinmetz

San Diego, Calif., April 20, 2020 -- Nanoengineers at the University of California San Diego are working on a COVID-19 vaccine using an unconventional candidate: a plant virus.

The team’s goal is to use plants to create a stable, easy to manufacture vaccine that can be shipped around the globe. It will be packaged in slow-release microneedle patches that patients can wear on the arm to painlessly self-administer the vaccine in a single dose.

The project, led by UC San Diego nanoengineering professors Nicole Steinmetz and Jon Pokorski, received a Rapid Response Research (RAPID) grant from the National Science Foundation. The grant funds research proposals that have the potential to immediately address urgent challenges, such as the novel coronavirus pandemic.

“To really make an impact, we are making a vaccine that’s stable at room temperature and above so it can be shipped—without refrigeration—throughout the world and be distributed to resource-poor areas,” said Steinmetz, who is the director of the Center for NanoImmunoEngineering at UC San Diego.

The Steinmetz lab will work on vaccine development, while the Pokorski lab will work on vaccine delivery devices in the form of slow-release microneedle patches that are inexpensive and also easy to manufacture and ship worldwide.

Researcher poses in front of lab equipment
Jon Pokorski

“People can just self-apply these patches, so no need for doctor’s visits. Our goal is to reduce the barriers to vaccination around the world,” said Pokorski, a faculty member of the Center for NanoImmunoEngineering. 

To create the vaccine, the team is using a plant virus that infects legumes and engineering it to look like the novel Coronavirus (SARS-CoV-2). Molecular signatures called peptides that are specific to SARS-CoV-2 will be woven onto the surface of the plant virus so it can stimulate an immune response.

The beauty of this approach is that the plant virus is non-infectious in humans, said Steinmetz, whose lab specializes in engineering plant viruses to treat plant and human health. Also, plant viruses are easy to produce in large scales because they can be grown on plants via a technique called molecular farming.

And since plant viruses are extremely stable up to high temperatures, the team’s vaccine is compatible with the methods that will be used to fabricate the microneedle patches.

The methods, called melt extrusion and injection molding, are polymer processing techniques that are used to mass-produce plastic products like Legos and disposable cutlery. They involve melting polymer materials at 100 degrees Celsius. This is too hot for most biological materials, but not for the plant virus-based vaccine, making it easy to manufacture into vaccine patches.

Pokorski’s lab will customize the methods so they can be first scaled down to do quick, inexpensive pilot studies on the vaccine patches. “These methods are usually performed at kilogram scales, and trying to make that much vaccine to do a pilot study would be incredibly expensive,” Pokorski said. “Once we find something that works, we could easily scale it up because these methods are widely used in manufacturing.”

“By synergistically combining our labs’ areas of expertise in plant virus-based vaccine design and biomedical device manufacturing, we hope to really move this research forward to rapidly generate a scalable solution for the current pandemic,” Steinmetz said.

Engineering student leaders honored by Gordon Center

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San Diego, Calif., April 20, 2020 -- The Gordon Engineering Leadership Center at UC San Diego recently announced the 2020 winners of its Engineering Leadership Awards.

The Engineering Leadership Awards recognize undergraduate and graduate engineering students who have demonstrated excellence in leadership, technical ability, communication, and teamwork. The recipients are chosen through a competitive selection process based on these four criteria. Since 2009, the Gordon Center has awarded almost 100 engineering leaders. A full list of award winners is available online.

This year 38 highly competitive applicants applied for the Engineering Leadership Awards. The selection committee, composed of industry partners and UC San Diego alumni, selected four exceptional students to receive the award. These four students clearly demonstrated a commitment to dedicating the time and hard work required to serve as ethical leaders within the field of engineering. Three of these recipients were also part of the Gordon Center’s Gordon Scholars Program: Olivia Dippo, Varun Govil, and Vesal Razavimaleki.

The Gordon Center was established in 2009 with the generous support of the Bernard and Sophia Gordon Foundation and exists to educate and equip engineering leaders to positively impact society. The Gordon Center is commonly recognized for its Gordon Scholars Program, a year long application-based program offered to Jacobs School of Engineering students. Scholars attend classes and workshops that focus on leadership, communication, and team building skills. The program offers personal development training, individual and team coaching, mentoring, and connections with industry. Additionally, Gordon Center rewards outstanding students through its Engineering Leadership Awards.

2020 Graduate Engineering Leadership Award Winners

Two graduate students were awarded and received a $10,000 prize.

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Isaac Cabrera

Isaac Cabrera

Graduate; Mechanical and Aerospace Engineering 

Cabrera has been involved in a number of diverse research projects and has held several leadership roles during his time as an undergraduate, as well as while he pursues his PhD. His proudest accomplishment to date has been his involvement with Project Lim(b)itless, where he serves as the lead engineer and project manager. Project Lim(b)itless enables amputees to receive prosthetic care remotely and at a lower cost than existing options. He has done various research at UC San Diego, MIT, and the University of Oxford.



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Olivia Dippo

Olivia Dippo

Graduate; Materials Science and Engineering

Gordon Scholar, 2019-2020

Dippo is currently working towards her PhD in Materials Science and Engineering. In addition to her extensive research experience, she holds roles as a teaching assistant, research team leader, the chair of a mentoring organization, and is a current Gordon Scholar. Dippo participates in several outreach opportunities, where she has taught classes for high school students and volunteered with an organization that introduces young girls to STEM. She has received the ASM International Abe Hurlich Award, Charles Lee Powell Foundation Fellowship, and American Ceramic Society Travel Scholarship.

2020 Undergraduate Engineering Leadership Award Winners

Two undergraduate students were awarded and received a $5,000 prize.

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Varun Govil

Varun Govil

Undergraduate; Bioengineering

Gordon Scholar 2018-2019

Govil has an affinity for medically focused innovation and bioengineering theory. He led 11 undergraduate students in a project called Epinoma, developing a new platform that screens for liver cancer. Govil is also the director and co-founder of Verde Lux, a subdivision of a national nonprofit called SendForC. For more than a year, he has conducted clinical research at UC San Diego. Govil was a Gordon Scholar and is also the founder and project development lead for Scrybe, a company that enables real-time handwriting transcription onto any surface.


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Vesal Razavimaleki

Vesal Razavimaleki

Undergraduate; Electrical and Computer Engineering

Gordon Scholar 2019–2020  

Razavimalekil has been heavily involved in UC San Diego's chapter of Students for the Exploration and Development of Space. He currently serves as the director of Electrical Engineering and has also been project manager and electronics lead for SEDS’ Pythia CubeSat team, as well as electronics lead for the Vulcan II Rocket. Razavimaleki developed additional leadership skills through his involvement with student-founded company paq wearables and his PowerShare project for IDEAHack 2019.

The Gordon Engineering Leadership Center will be accepting Gordon Scholar applications for the 2020-2021 program in the fall of 2020. Undergraduates and graduate engineering students committed to further developing their leadership and management skills for the betterment of society should consider applying. Follow the Gordon Center's Facebook, Instagram, and LinkedIn for updates.


'Decoy' nanoparticles can block HIV and prevent infection

Cloaking nanoparticles in cell membranes draws HIV away from immune cells


San Diego, Calif., April 20, 2020 -- Flipping the standard viral drug targeting approach on its head, engineers at the University of California San Diego have developed a promising new “nanosponge” method for preventing HIV from proliferating in the body: coating polymer nanoparticles with the membranes of T helper cells and turning them into decoys to intercept viral particles and block them from binding and infiltrating the body’s actual immune cells. 

This technique, developed in the Nanomaterials and Nanomedicine Lab led by nanoengineering professor Liangfang Zhang, could be applied to many different kinds of viruses, opening the door for promising new therapies against difficult-to-combat viruses. Zhang is a professor in the Department of NanoEngineering at the UC San Diego Jacobs School of Engineering. 

This HIV work first appeared in the journal Advanced Materials in November 2018 in a paper entitled: T-Cell-Mimicking Nanoparticles Can Neutralize HIV Infectivity. The work is ongoing. 

“The key innovation here is that we’re standing on the other side of the big problem with HIV,” said Weiwei Gao, a chemical engineer and associate project scientist in the Zhang Lab at the UC San Diego Jacobs School of Engineering. “The traditional drug development approach requires that we figure out how to block critical protein or signaling pathways in the virus so that it can’t attack the body. The problem is that there are so many pathways and so much redundancy in these viruses, it’s really difficult to find one pathway that’s truly critical.

“Our approach comes from the other side: look at the virus target,” he continued. “The nanoparticles are wrapped with the membranes of cells that the virus targets. Therefore, they can act as a decoy of the cell to intercept the viral attack.”

The HIV virus typically targets cells called CD4+ T cells; also called T helper cells, in the healthy body, these cells help detect foreign pathogens and target them for attack and removal. The HIV virus finds and binds to the surface of these T cells using the CD4 receptor, then injects their genetic material into the T cells and uses the T cell machinery to replicate itself. Eventually, after enough new HIV virus has been made, the viral particles burst out of the cell and search for other T cells to attack.

Part of why HIV is so devastating is that attacking and killing T cells severely damages the immune system, making it harder for the body to fight off secondary infections. And the virus mutates quickly, changing its genetic code and making it difficult to target with traditional antiviral and drug discovery methods.

In the 2018 Advanced Materials study, the researchers coated nanoparticles with the isolated cell membranes of CD4+ T cells. When added to T cells in a dish and exposed to viruses, these nanoparticles, called TNPs, acted like a sort of sponge, soaking up the virus and protecting the T cells from being infected. They found that the HIV virus was just as likely to bind to a TNP as it is to bind to a T cell -- but since there’s no cellular machinery inside these nanoparticles, the virus can’t inject or replicate itself, and it is rendered harmless.

Just like with CD4+ T cells, the nanoparticles bind with HIV virus through the gp120 protein on the surface of the virus. When TNPs were added to the T cell mixture at a concentration of 3 mg/mL, the team saw a reduction of infection of over 80 percent, when compared to cells that had not been treated with TNPs. They take this as promising evidence that these nanoparticles could be infused into the bloodstream in patients to soak up the HIV infection, knocking down their infection levels and ultimately clearing it out of the system.

“There is another potential application of using TNPs to treat HIV. Immune cells in the body that are infected with HIV but are not actively producing new virus become viral reservoirs,” said Gao. “Finding ways to destroy such reservoirs is a major challenge facing HIV researchers. But these reservoir cells may also express gp120, so TNPs can be used as vehicles to precisely deliver antivirals to these cells and kill them.”

The work was inspired by earlier projects in Zhang’s lab focused on red blood cells. “Our work has been focused on using nanoparticles for drug delivery,” Gao said, “but nanoparticles don’t circulate for long in the body. We had the idea: to make it harder for the body to recognize the nanoparticles as foreign, what if we disguise them as red blood cells? Red blood cells are naturally long circulating, so if we can mimic them with nanoparticles, we should see a similar circulation pattern.” The team’s work on the red blood cell cloaking technology first appeared in the academic literature in 2011 in the PNAS paper Erythrocyte membrane-camouflaged polymeric nanoparticles as a biomimetic delivery platform.

Gao says this approach can likely be applied to a wide variety of pathogens. “Lots of bacteria also like to attack red blood cells,” he said. “So maybe these nanoparticles can act as a decoy to block the toxins from the bacteria. Or they could act as decoys to react to other toxins, like nerve agents, that target red blood cells.”

There are a number of obstacles still in their path before these TNPs can be used in human patients. For example, they have not yet been able to test their TNPs in living animal models.

“Because HIV is a human disease, it’s difficult to replicate it in animal models,” Gao said. “So we’re working closely with Dr. Stephen Spector, the Chief of the Division of Pediatric Infectious Diseases at UC San Diego Health, on that issue, to figure out the best approach for testing this in vivo.

“Our study is really proof of concept,” Gao continued. “The disease development changes at different stages of the disease, and the virus works differently inside the body, with different levels of infectivity and activity. It will be critical to work with doctors and researchers who are very familiar with HIV pathology to optimize the treatment regime based on what’s known about the disease to be sure that the nanoparticles are the most effective for treatment.”

Still, this work represents the first step in an exciting new direction for HIV treatment, and Gao sees the field as full of possibilities. “This technology is very adaptable, both for existing pathogens and for new, emerging diseases,” he said. “This platform can overcome drug resistance, and can be easily adapted to use other cell membranes or load other drugs or treatments into the nanoparticle core. It’s very modular, and doesn’t require custom designs for each compound, which may help treatment development in the future.” 

This work was supported by the Defense Threat Reduction Agency Joint Science and Technology Office for Chemical and Biological Defense under Grant No. HDTRA1–14-1-0064 and by the National Institute of Neurological Disorders and Stroke under Award R01NS104015.  

Alison Caldwell, PhD, Bigelow Science Communication Fellow, UC San Diego

Engineering telemedicine app, universal control system for ventilators for COVID-19 care

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San Diego, Calif., April 20, 2020 -- Engineers in the Department of Computer Science and Engineering at UC San Diego have partnered with physicians at the Mayo Clinic to create a telemedicine app to help critical care specialists provide the best possible care, even when resources are stretched thin.
The team is also working on a universal control system that would work with any DIY ventilator.

Michael Barrow, a Ph.D. candidate with Professor Ryan Kastner’s research group in the Computer Science and Engineering Department is leading an effort at UC San Diego and working closely with Dr. Shanglei Liu, a general surgeon at Mayo Clinic and the project’s clinical primary investigator. 

The team is also exploring how clinicians can address the potential need to simultaneously ventilate many patients. In addition to UC San Diego and Mayo Clinic, collaborators at MIT, Scuola Superiore Sant' Anna Pisa in Italy and several private companies have joined the project. 

Technology to Multiply Expertise 

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Michael Barrow is a Ph.D. student in the research group of computer science professor Ryan Kastner. 

“We can’t 3D-print doctors and nurses,” Barrow said, “however, we can increase their patient care capabilities through 21st century telecommunications.”

He and his team are developing a telemedicine platform, called TV CV19, designed to enhance hospital-wide communications in a crisis and help medical specialists care for more patients. Clinicians with the most acute care experience can focus on the sickest patients while having a telecommunications conduit to advise their colleagues. This way, technology can multiply expertise. Acute care specialists can’t possibly monitor all patients, but their knowledge can easily be shared with other clinicians.

“It creates an efficient network of communication for clinicians,” said Barrow. “At the top, you have the experts, whose attention is going to be focused on complex decisions for the sickest patients. The platform gives them the ability to selectively allocate their attention where it’s needed most. This empowers front line practitioners of all backgrounds with the real-time expertise on how to care for their critically ill patients. It also reduces exposure to infected individuals to prevent the spread of COVID.”

The goal is to quickly provide key decision-making information, such as vital signs, lung compliance and even a live video feed of patients. With this platform, specialists can view alerts and respond in real time, providing specific tasks for bedside clinicians. 

“This way, we can have others monitor the patients who are more or less stable,” said Barrow. “They still need to be ventilated, but their condition isn't changing. This frees up decision-makers to look at the cases where patients really need their expertise right now.”

 Evaluating DIY Ventilators 

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A prototype of the universal ventilator control system designed by Barrow and colleagues. 

Clinicians may also be forced to grapple with a ventilator shortage as the numbers of patients who need care surge. Some companies are shifting production, from cars for example, to meet the need. But in the short term, open source ventilator-building instructions have appeared on the internet.



Barrow and colleagues analyzed some of these designs and found them wanting. The most common flaw is the lack of precise controls, difficulty adapting to local materials, lengthy building times and overly complex designs. These flaws would make it difficult to use these devices with real patients.

Ventilator control is particularly important. As a patient’s lungs stiffen from coronavirus infection, ventilator pressure must be adjusted to avoid additional damage. The team has developed an experimental universal control system—built with a mobile phone and other off-the-shelf components—which will allow operators to adjust these ventilators and protect patients. 

"Right now, we are adapting our universal controller software to support as many makeshift ventilator designs as we can,” Barrow said. “We are also working with our clinical collaborators to improve the usability of our case management interface.” 

From there, the group will work to ensure regulatory compliance before potentially delivering their research into the hands of healthcare providers. 



New Rapid Response Platform Connects Clinicians with Resources and Answers to COVID-19 Questions


San Diego, Calif., April 20, 2020-- Everything about the COVID-19 pandemic is new: the virus’s transmission to humans, the stay-at-home orders, the challenges many responders are facing. With so much in flux, providers are being asked to find new solutions. In response, a group of UC San Diego faculty, with the help of hundreds of students and community volunteers, has stepped up to create an online portal called Earth 2.0 COVID-19 Rapid Response

The portal's first live component is CoRESPOND, a just-in-time research and innovation system that offers doctors, nurses, researchers and other responders a simple way to ask urgent questions and receive rapid responses from expert teams, providing timely solutions during this quickly changing crisis. The Earth 2.0 COVID-19 Rapid Response platform will also include OASIS, a crowd-sourced information and resource-sharing platform, and HomeBound, an app to manage COVID-19 symptoms at home and a living data system to drive learning and innovation. The platform is a collaboration between the UC San Diego School of Medicine, the Qualcomm Institute, the Department of Computer Science and Engineering in the Jacobs School of Engineering and many others. 

Earth 2.0 Brings a Collaborative Response to COVID-19

Earth 2.0 was envisioned several years ago to solve global-scale problems through crowd-sourced innovation. When the COVID-19 pandemic emerged, the platform was immediately retasked to help manage the pressing crisis and the Earth 2.0 COVID-19 Rapid Response platform was born.

“We wanted to reformulate the Earth platform so that researchers or healthcare workers could reach out and get answers, resources or even DIY inventions. Anyone can join the platform and add their expertise to the system, whether it’s clinical experience, engineering know-how or current supply-chain information,” said Eliah Aronoff-Spencer, a physician-scientist with UC San Diego School of Medicine and the Qualcomm Institute. Aronoff-Spencer also directs the UC San Diego Design Lab Center for Health.

Aronoff-Spencer and Nadir Weibel, an associate professor in the Department of Computer Science and Engineering and head of the Human-Centered and Ubiquitous Computing Lab, quickly pulled together several customer service, communication and collaboration platforms, including Freshdesk, Google Docs, Github, GrabCAD and Slack. From there, the team, which also includes Linda Hill, a clinical professor in the Department of Family Medicine and Public Health, and Andrew Baird, a professor in the Department of Surgery, created CoRESPOND.

Finding Answers in the Midst of a Crisis

CoRESPOND gives workers responding to COVID-19 ready access to information they dont have time to research on their own. Through the portal, workers simply email their queries to covid-help@ucsd.edu, and the system goes to work to find an answer.

Each email triggers a problem ticket, which is then categorized and forwarded to a system moderator, who immediately assembles a team of relevant experts. The platform uses Slack to enable and stimulate discussion among ad hoc research groups who reply to moderators with possible answers.

CoRESPOND then leverages uPub, an online authoring system, to publish open access solutions that can be continuously updated and made available worldwide. The answers are further vetted for quality and accuracy before being emailed – all within as short a time-frame as possible.

“In two or three days, we created a ticketing system and an ad hoc response and innovation network, as well as an editorial structure to make sure the solutions were valid,” said Aronoff-Spencer. “We have been getting most responses back to people on the frontline in 24 hours or less.”

Since launching, the platform has received and answered numerous questions, matched needs to resources and even developed new innovations in protective equipment. Questions have ranged from how long a person is contagious to how to make a face shield. Each query activates a network of more than 200 knowledge experts and several hundred students who provide the legwork, searching for answers, building innovations, validating the results, and sending that information back to the requester.

We have people triaging the tickets and communicating back directly with the frontline workers,” said Weibel. We have infectious disease and primary care physicians, supply chain people trying to figure out where to find masks and other important items, a whole team of experts.”

Some questions are easier than others as knowledge about the virus grows and changes, but all answers end up in a solutions portal where the information is accessible for future use.

We get questions like do people create antibodies when they're recovering?’” said Hill. The teams will research what we call the gray literature, as well as the medical literature, and develop a response. The field is changing in real time. We have told our teams these are living documents, like a wiki, and we have the capacity to continuously update the platform and keep it current.”

The bottom line for the entire team is making sure they always provide relevant, accurate information that will be useful. The team encourages everyone to join Earth 2.0 and contribute their expertise to the system.

“It’s not just an information exchange, it's a quality information exchange,” said Aronoff-Spencer. “For instance, we have to do more than come up with an alternative PPE [personal protective equipment]. We have to come up with an alternative PPE that can actually be built in the places it is needed, meets specific requirements, and we can track those specifications.”

In addition to Aronoff-Spencer, Weibel, Hill and Baird, other members of the Earth 2.0 COVID-19 Rapid Response leadership team include: Sandra Brown, UC San Diego Vice Chancellor for Research and a distinguished professor of psychology and psychiatry, Doug Ziedonis, UC San Diego Associate Vice Chancellor for Health Sciences, Ramesh Rao, director of the Qualcomm Institute, Henrik Christensen, a professor of computer science and director of the Institute for Contextual Robotics, Don Norman, director of the Design Lab, Nikhil Jain, VP and lead on the Qualcomm Toq smart watch, and Nicolas DiTada, chief technical officer at InSTEDD.

Incoming President of Quiz Bowl Club Represents Campus in 'Jeopardy!' College Championship


San Diego, Calif., April 16, 2020 -- UC San Diego was one of 15 schools represented in the 2020 Jeopardy College Championship, thanks to Alistair Gray, a second year computer science and linguistics double major. 

“I couldn’t believe it, honestly,” Gray said of learning he was selected to compete in the annual Jeopardy college tournament with a $100,000 prize. “Even though it’s always been a dream, it’s not the kind of dream that you think is ever going to happen.”

Gray, a native of Sunnyvale, Calif., always loved trivia but didn’t watch Jeopardy much as a child. That changed when he got to UC San Diego and the Revelle Atlantis dorm. 

“Our whole suite would watch Jeopardy together and yell answers at the screen, which was very fun,” he said. “You know James Holzhauer? We caught his whole run, we were rooting for him the whole way. He was a bit of a hero among us.”

Gray, who was heavily involved in his high school’s Quiz Bowl team, is now the incoming president of the Quiz Bowl Club at UC San Diego. He’s also a member of the Acapella Choir, and a tutor in the Department of Computer Science and Engineering. 

He decided to study computer science after being exposed to it early on, growing up in the Bay area. 

“You just get exposed to coding at a young age and I really liked it, so I kept doing it.”

His interest in linguistics was piqued when reading The Lord of the Rings series. 

“I enjoy learning languages, and enjoyed the part of Lord of the Rings where Tolkien is just talking about his invented languages, as I dabbled with inventing languages myself. So it was a side interest that blossomed into another major.”

In addition to English, Gray learned French in school and taught himself Latin. He’s trying to learn a bunch of other languages as well, including Japanese, Chinese and Esperanto. 

The Jeopardy Experience

The College Championship was filmed on Feb. 3 and 4, and Gray’s episode aired on April 8. Though he didn’t move on to the semifinals, Gray said it was a great experience. The best part? Meeting his fellow contestants. 

“We’re all still in touch; we’re talking about it constantly now that they’re airing our episodes and sharing the social media posts about us and such. They're all great people, really smart and really, really kind. Honestly, they were the best part of the process, meeting all these amazing wonderful people.”

One other amazing person he got to meet was, of course, Alex Trebek.

“Oh, wow. He acts exactly the same way he does on TV. It's so funny seeing the contrast between him and everyone else. He's very sweet. Before the games and during commercial breaks, he takes questions from the audience and he's very funny too, although you don't really see that on TV. A very dry wit.”

While his Quiz Bowl skills came in handy when preparing for the competition, Gray did put in extra time training, by re-watching all the old episodes from previous college tournaments to see what topics were asked about; buffing up on pop culture; and practicing his buzzer speed and wagering skills. 

His advice for anyone else with a dream to make it on Jeopardy? Just go for it!

“Well, join your school’s Quiz Bowl program—just do it.” Gray said. “It’s not hard to just try to go for things. Then, who knows; they could work out. I never thought that I would actually get it; I always thought I didn't have a TV personality or whatever, but then they chose me. And if I hadn't just done it, then it never would have happened.”

Undergraduates simplify intubation tool for senior design project

San Diego, Calif., April 16, 2020 --A team of UC San Diego undergraduate engineers helped design a simple, all-in-one tool to perform endotracheal intubations, which could simplify the steps clinicians need to take when performing the time-sensitive, complex procedure. The mechanical engineering students took on the challenge as their senior design project, with direction from project sponsor Dr. Taylor Graber of the Department of Anesthesiology at the UC San Diego School of Medicine. 

“Our device essentially combines multiple devices into one that can be used using only one hand,” said David Ivison, a mechanical engineering student and team member. “This could save time as well as ensure that the anesthesiologist's attention stays on the airway. This can help ensure patient safety and save lives by reducing procedural time and lowering risk to the patient.” 

Endotracheal intubation is most often performed when a patient isn’t able to breathe on their own, either due to trauma or in preparation for a significant surgery. During an intubation, an anesthesiologist inserts a tube into a patient’s mouth and down into their trachea, clearing the airway. Intubation allows the patient to be hooked up to a ventilator to keep them breathing during a procedure, or, as we’re seeing during the COVID-19 pandemic, if a patient is unable to breathe on their own for other reasons.

Currently, anesthesiologists need to use several separate devices over the course of the intubation procedure, which is often completed in less than a minute. Having to transition between these different tools is not optimal, since intubation is a critical procedure performed at a time when a patient is not breathing, and yet their organs are still using up their body’s oxygen stores. Dr. Graber, an anesthesiologist in residency at the UC San Diego School of Medicine with a background in biomedical engineering, tasked the team of four students with developing and iterating on a design for a tool he thought could make the process simpler.

The students spent winter quarter working with Dr. Graber to design a device that combines two previously separate tools required for intubation-- the laryngotracheal cannula and endotracheal tube stylet-- into one streamlined device which could simplify the procedure.  A provisional patent for the design has been filed in collaboration with the UC San Diego Office of Innovation and Commercialization. Dr. Graber hopes to obtain investment funding in the future to be able to manufacture the prototype, and then work toward FDA approval for patient trials. 

.The students' final design.

An intubation currently requires several separate devices: an endotracheal tube, the actual plastic tube connecting the lungs to the oxygen source; a laryngoscope, a device used to move the tongue and soft tissues and provide direct visualization of the vocal cords and trachea with or without a small lens or camera; a stylet, the malleable metal device that goes inside the endotracheal tube, guiding it down the trachea; and the laryngotracheal cannula, which is used to spray lidocaine into the trachea to numb the soft tissues and mucosal surfaces of the airway.

The student’s device, which combines the laryngotracheal cannula and endotracheal tube stylet, simplifies the steps anesthesiologists have to perform. After using a laryngoscope to get a view of where the tube will be inserted, anesthesiologists simply insert the unified device, consisting of the combination laryngotracheal stylet and cannula housed inside of the endotracheal tube, which can be easily guided through the airway and vocal cords into the trachea and spray the lidocaine out of its tip to reduce the noxious stimulus of intubation. The combination device is then removed from the interior of the endotracheal tube, where the tube is left in place in the trachea, providing a conduit for oxygen and mechanical ventilation from a ventilator.

Ivison said that he and the team learned a lot through the project and the senior design course, and not just about the technical skills required to design a complicated device for medical use. 

“This class essentially taught students what a real-world project would be like. Projects don't only need knowledge in engineering standards. Real projects need project management skills, budget management skills, and social skills in order to keep sponsors and supervisors or professors up to date as well as ensure that they are on board with progress.” 

Team Members: David Ivison, Ascher Ramsay, Jiahao Sun, Daniel Lee

Economic Impact of COVID-19 will Make the Fight Against Climate Change Harder

Credit: claffra. The shock of the novel coronavirus may be expected to catalyze serious solutions to other shared global problems, such as of climate change, but prospects appear bleak.

Bending the Keeling Curve remains bleak, but technological advances provide hope for the planet 

San Diego, Calif., April 15, 2020 -- Measures to slow the spread of the coronavirus have reduced the demand for fuel and slashed oil prices. Global emissions of carbon dioxide (CO2), the chief long-term cause of climate warming, have slid perhaps by one-fifth and pollution is down, but can we expect COVID-19 to create lasting change in reversing global warming?

“I doubt it,” said David Victor, professor of international relations at the University of California San Diego School of Global Policy and Strategy. “While the pandemic might alter societies permanently, the same market forces that drive our dependence on fossil fuels are still in play and may even be reinforced with the economic fallout of COVID-19.”

Victor is a Co-director of the UC San Diego Deep Decarbonization Initiative, which is led through a collaboration between the UC San Diego School of Global Policy and Strategy and the UC San Diego Jacobs School of Engineering. 

Hard economic times may not bode well for societies to get serious about climate change

While energy markets try to stabilize during the economic free-fall COVID-19 has caused, the atmosphere is catching its breath. The results are visible, as evidenced by images that went viral last week of Delhi, India that showed before and after shots of city streets with improved air quality.

However, the greenery has come at a huge, unacceptable cost, Victor noted. And though shock of the novel coronavirus may be expected to catalyze serious solutions to other shared global problems, such as of climate change, prospects appear bleak. 

“Just by looking around today—with everyone stuck at home for the moment and holding meetings on Zoom—it is easy to envision a future with a lot less travel,” Victor said. “But history suggests that when incomes start growing again and the constraint of locality is lifted then people will spend, again, on mobility. The higher the incomes, the more the money and the more the emissions, at least historically.”

Furthermore, Victor points out that hard economic times are usually bad times to mobilize support for aspirational missions such as mitigating climate change which still has abstract benefits to many members of the public.

“The best polling data show that the public wants clean energy, to be sure, but they also want cheap energy,” Victor notes. “When pocketbooks are empty, every extra costs looks expensive.”

The oil industry is hurting, but likely to make a comeback

The sharp declines in the demand for oil recently spurred OPEC and allies led by Russia to approve the biggest-ever cut to the world’s oil supply to arrest the price decline.

With the economic shake up, what changes can we expect from the industry? According to Victor, it will rebound; however, it will likely look a lot different.

“Pecking orders will change a lot,” Victor noted in a recent piece for the Brookings Institution on forecasting the future of energy. “In oil, American shale suppliers will be hammered while the core of OPEC – Saudi Arabia and Abu Dhabi, plus perhaps Russia – will have more control. In electricity, reliable firms will remain on top. Consolidation of weak into stronger, bigger firms is likely across the industry.  We could even see some large, financially sound state-connected firms take over parts of the industry—for example, Chinese state-owned enterprises that could buy distressed assets on the cheap.” 

Victor worries, in particular, that all the economic distress caused by the global pandemic will hit small firms and entrepreneurs really hard. “Much of what could really transform the global energy system has been coming from smaller firms that have the flexibility to back radically new ideas, which is much of what we need in effort to reduce emissions.”

Political obstacles notwithstanding, deep decarbonization is within reach

Today, energy sources that do not emit are more expensive; however, in the decades to come, innovation could make severe cuts in emissions, also known as “deep decarbonization,” achievable at reasonable costs. Victor and collaborators including Michael Davidson, an assistant professor of energy systems who holds a joint appointment with the School of Global Policy and Strategy and the Jacobs School of Engineering, lay out what decarbonization can look like in a new Foreign Affairs article authored by the researchers. At the Jacobs School of Engineering, Davidson is part of the Department of Mechanical and Aerospace Engineering.

“Deep Decarbonization translates into reshaping about 10 sectors in the global economy—including electric power, transportation and parts of agriculture—by reinforcing positive change where it is already happening and investing heavily wherever it isn’t,” they write.

This work is a major driver for Victor and Davidson who both are involved with UC San Diego’s Deep Decarbonization Initiative. Victor co-leads the interdisciplinary effort focused on helping the world cut emissions of warming gases given the very real technology, economic and political constraints that exist. Davidson is a key researcher involved in the program. 

They note that the power sector offers the most promising avenue for weaning off greenhouse gas emitting energy sources for various reasons.

The impact of electricity use on emissions depends on how clean the energy was that was used to generate it; however, “electrifying” the economy by designing more processes to run on electricity rather than the direct combustion of fuels—is essential.

“This is because, compared with trying to reduce emissions in millions of places where they might occur, it is far easier and more efficient to reduce emissions at a modest number of power plants before distributing the clean electricity by wire,” the authors write.

Investments in tech and state support are key ingredients to a greener future

In sectors such as transportation, steel, cement and plastics, companies can be expected to continue to resist profound change unless they are convinced that decarbonization represents an opportunity to increase value and revenue.

Key in these efforts is governments and businesses coming together now to change that. Not simply with bold-sounding international agreements and marginal tweaks such as mild carbon taxes, but also with a comprehensive industrial policy—there will be little hope of reaching net-zero emissions before it’s too late,” Victor and Davidson noted.

They added, the world needs new technology, and that means more much R&D and a lot of practical experience in testing and deploying new technologies and business strategies at scale.

“Setting bold goals can help,” they write. “But new technological facts on the ground—sped along by active industrial policy and international cooperation—are what will transform the politics and make deep decarbonization a reality.”

Victor and Davidson will speak on COVID-19’s impacts to energy systems and climate change policies on May 14 at noon, as part of the School of Global Policy and Strategy COVID-19’s webinar series. Visit the event website for more information and to register.

Part 2: Treating Cancer with Plant Viruses: A Conversation with Nicole Steinmetz

IBM and UC San Diego to pivot AI for Healthy Living collaboration to take on COVID-19 pandemic

San Diego, Calif., April. 13, 2020 -- The University of California San Diego and IBM are building on the existing AI for Healthy Living (AIHL) collaboration in order to help tackle the COVID-19 pandemic.

AI for Healthy Living is a multi-year partnership leveraging a unique, pre-existing cohort of adults in a senior living facility to study healthy aging and the human microbiome as part of IBM's AI Horizons Network of university partners.

“In this challenging time, we are pleased to be leveraging our existing work and momentum with IBM through the AI for Healthy Living collaboration in order to address COVID-19,” said Rob Knight, UC San Diego professor of pediatrics, computer science, and bioengineering and Co-Director of the IBM-UCSD Artificial Intelligence Center for Healthy Living. Knight is also Director of the UC San Diego Center for Microbiome Innovation.

“Industry-academic collaborations offer powerful opportunities to address far more difficult challenges than we can take on alone,” said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. “Our collaboration with IBM is both agile and deep. The insights we gain from the pivot to COVID-19 are sure to improve our understanding of this pandemic in ways that wouldn’t otherwise be possible.”

The pivot on the AI for Healthy Living (AIHL) collaboration will involve applying machine learning techniques to decode the biology behind the SARS-CoV-2 virus as fast as possible by collecting and analyzing samples.

“Through this collaboration with UC San Diego, our scientists will leverage our leading edge AutoAI technologies to rapidly generate, explore, and optimize a breadth of high performance models for COVID-19 specific bioinformatics data,” said Dr. Lisa Amini of IBM. Lisa is the Director of IBM's AI Horizons Network, Lab Director of IBM Research Cambridge, and leads IBM Research's global AI Automation and Scaling research theme.

AutoAI automates data preparation, model development, feature engineering and other key aspects of AI creation.

The team will also use the IBM Functional Genomics Platform and access to sequences of COVID-19 patient samples and healthy individuals to assemble additional molecular data on already-collected samples.

In addition, the researchers will use natural language processing (NLP) to extract insights from COVID-19 related literature and study infection and death rates.

In February 2020, researchers participating in the AI for Healthy Living collaboration published research showing that human age can be predicted based on your microbes. This new understanding of how microbiomes change as humans age sets the stage for future research on the role microbes play in accelerating or decelerating the aging process and influencing age-related diseases.

“There is so much we can potentially learn by folding COVID-19 into our research roadmap. Our goal is to help people live longer as well as healthier and happier,” said Dilip Jeste M.D., Distinguished Professor of Psychiatry & Neurosciences at UC San Diego, and Co-Director of the IBM-UCSD Artificial Intelligence Center for Healthy Living.  


3D printed corals provide more fertile ground for algae growth

Close-up of coral reef structures at the microscopic level
Left: Close-up of coral reef microstructures consisting of a coral skeleton (white) and coral tissue (orange-yellow). Right: SEM image of 3D printed coral skeleton. Images courtesy of Nature Communications

San Diego, Calif., Apr. 9, 2020 -- Researchers at the University of California San Diego and the University of Cambridge have 3D printed coral-inspired structures that are capable of growing dense populations of microscopic algae. The work, published Apr. 9 in Nature Communications, could lead to the development of compact, more efficient bioreactors for producing algae-based biofuels. It could also help researchers develop new techniques to repair and restore coral reefs.

In tests, the printed coral structures grew a commercial strain of microalgae, Marinichlorella kaistiae, up to 100 times more densely than natural corals.

“Corals are one of the most efficient organisms at using, capturing and converting light to generate energy. And they do so in extreme environments, where light is highly fluctuating and there’s limited space to grow. Our goal here was to use corals as inspiration to develop more productive techniques for growing microalgae as a form of sustainable energy,” said first author Daniel Wangpraseurt, a marine scientist at the University of Cambridge.

To build the coral structures, Wangpraseurt teamed up with UC San Diego nanoengineering professor Shaochen Chen, whose lab specializes in a rapid, 3D bioprinting technology capable of reproducing detailed structures that mimic the complex designs and functions of living tissues. Chen’s method can print structures with micrometer-scale resolution in just minutes.

This is critical for replicating structures with live cells, Chen said.

“Most of these cells will die if we were to use traditional extrusion-based or inkjet 3D printing processes because these methods take hours. It would be like keeping a fish out of the water; the cells that we work with won’t survive if kept too long out of their culture media. Our process is high throughput and offers really fast printing speeds, so it’s compatible with human cells, animal cells, and even algae cells in this case,” he said.

The 3D printed corals are built to capture and scatter light more efficiently than natural corals. They consist of cup-shaped, artificial skeletons that support coral-like tissue. The skeleton is made up of a biocompatible polymer gel, called PEGDA, embedded with cellulose nanocrystals. The coral tissue consists of a gelatin-based polymer hydrogel, called GelMA, mixed with living algae cells and cellulose nanocrystals.

Microscopic view of microalgae growing on 3D printed coral structure
Microalgae growing on the 3D printed coral structure.

On the surface are tiny cylindrical structures that act as coral tentacles, which increase the surface area for absorbing light. Nanocrystals embedded in the skeleton and coral tissue, along with the corals’ cup shape, also improve light absorption and enable more light to be focused onto algae cells so that they photosynthesize more efficiently.

In future studies, Chen and Wangpraseurt will build on this work to better understand the symbiosis between algae and corals. Their ultimate goal is to apply their findings to help coral reef restoration projects.


Paper title: “Bionic 3D printed corals.” Co-authors include Shangting You, Farooq Azam, Olga Gaidarenko, Mark Hildebrand and Dimitri Deheyn, UC San Diego; Gianni Jacucci, Alison G. Smith, Matthew P. Davey, Alyssa Smith and Silvia Vignolini, University of Cambridge; and Michael Kühl, University of Copenhagen, Denmark and University of Technology Sydney, Australia.

This study was funded by the European Union’s Horizon 2020 research and innovation programme (702911-BioMIC-FUEL), the European Research Council (ERC-2014-STG H20202 639088), the David Phillips Fellowship, the National Institutes of Health (R21HD090662 and R01EB021857), the National Science Foundation (1907434), the Carlsberg Foundation and the Villum Foundation (00023073).

Call for Citizen Scientists to Contribute to COVID-19 Studies

Rob Knight, director of the Center for Microbiome Innovation, and Daniel McDonald, scientific director of The Microsetta Initiative.

San Diego, Calif., April 9, 2020 -- The Microsetta Initiative, a crowdsourced research effort based at the University of California San Diego School of Medicine, has expanded its capabilities to now allow citizen-scientists around the world to help collect crucial information about SARS-CoV-2, the novel coronavirus causing a COVID-19 pandemic.

“We are now positioned to collect data that will help drive epidemiological studies of where the virus is and isn’t, and help researchers determine who is at greatest risk, who is already immune, how the virus is transmitted and how it spreads through a population,” said Rob Knight, professor and director of the Center for Microbiome Innovation at the UC San Diego Jacobs School of Engineering. Knight is co-founder of The Microsetta Initiative, which is run by his research lab at UC San Diego School of Medicine under Scientific Director Daniel McDonald.

Knight also holds appointments in the departments of Bioengineering and Computer Science and Engineering at the UC San Diego Jacobs School of Engineering.  

NOTE: The Microsetta Initiative and its subsidiaries, including the American Gut Project, are research enterprises, and do not provide clinical diagnostic information or medical advice to participants.

The Microsetta Initiative’s original goal is to improve our understanding of human microbiomes—which types of bacteria live where in our bodies, how many of each and how they are influenced by diet, lifestyle and disease. To do this, citizen-scientists around the world contribute $99 to receive a kit to collect fecal, nasal, oral or skin swabs and instructions to mail them back.

Assembling new sample collection kits for citizen scientists to contribute to studies of SARS-CoV-2. Pictured at center is Daniel McDonald, scientific director of The Microsetta Initiative at UC San Diego School of Medicine.

Once Knight and McDonald’s team processes the sample, participants receive a report that details what is living in their guts (based on a fecal specimen) or other body sites they sampled. The anonymized data contributed by participants drive hundreds of research studies around the world on the many ways bacteria and other microbes are influenced by our environments, health, diet and habits, and how those microbes in turn influence our health.

In order to now collect valuable research data on SARS-CoV-2, the team has tweaked the Microsetta kits in two key ways:

How You Can Participate in the Microsetta Initiative

Your help is needed to participate as a citizen-scientist in the Microsetta Initiative. Please visit microsetta.ucsd.edu for more information on how you can become involved.

1) Preserving viral RNA: Instead of including dry swabs appropriate for collecting microbial DNA, the kits mailed out to participants will now include 95 percent ethanol, which preserves viral RNA, the genetic material used by SARS-CoV-2. (Live viruses cannot survive in ethanol.) This information will help researchers better understand how the virus spreads and the environmental and lifestyle factors that might increase a person’s risk for contracting and transmitting the virus.

Microsetta’s ability to pivot to RNA collection was driven by collaboration with several other UC San Diego School of Medicine faculty members, including Karsten Zengler, Jack Gilbert, Gene Yeo, and Dr. Victor Nizet. Rapid collaboration among labs, departments and neighboring institutions has been enabled by a new group and Slack channel created by Yeo called San Diego COVID Research Enterprise Network (SCREEN), which now includes more than 800 San Diego researchers.

2) Collecting blood samples: The kits will also include lancets—small devices that allow for easy blood sample collection by finger-stick, similar to at-home glucose tests used routinely by persons with diabetes. Only a couple of drops of blood will be drawn. The team will store the donated blood samples for future studies. For example, the samples may be used to determine who has already been exposed to SARS-CoV-2 and has developed immunity in the form of antibodies. Many research groups around the world are currently developing ways to detect these antibodies (serological tests).

A sample Microsetta Initiative kit

When the team realized they would need a lot of lancets in order to be able to collect blood for serological studies, they turned to Anne O’Donnell, UC San Diego’s senior executive director for Corporate Relations, for help. She reached out to her many contacts in the San Diego and global biopharma industry. Within hours, BD (Becton, Dickinson and Company), a global medical technology company with a large presence in San Diego, offered 20,000 lancets.

Ranjeet Banerjee, worldwide president of Medication Management Solutions at BD, said the lancet offer was inspired by BD’s commitment to public/private partnership that address critical community needs, both scientific and global.

“Adding lancets to collect blood samples was an idea we had late in the afternoon of Saturday, March 21,” said Mohit Jain, an associate professor of pharmacology at UC San Diego School of Medicine, who is working with Knight and team. “By the very next afternoon, BD was delivering caseloads to my lab. The collaboration, speed and efficiency of everyone involved, the willingness to cut through red tape, is unprecedented and moving.”

Thanks to procurement and logistical support from Netherlands-based DaklaPack and FedEx, the Microsetta team now has kits with ethanol and lancets available for order. Any unused lancets will be donated to UC San Diego Health or other local health providers, if needed to support patient care.

To participate, go to microsetta.ucsd.edu.

UC San Diego researchers move closer to producing heparin in the lab

San Diego, Calif., April. 09, 2020 -- In a recent study published in the Proceedings of the National Academy of Sciences, University of California San Diego researchers moved one step closer to the ability to make heparin in cultured cells. Heparin is a potent anti-coagulant and the most prescribed drug in hospitals, yet cell-culture-based production of heparin is currently not possible.  

In particular, the researchers found a critical gene in heparin biosynthesis: ZNF263 (zinc-finger protein 263).  The researchers believe this gene regulator is a key discovery on the way to industrial heparin production. The idea would be to control this regulator in industrial cell lines using genetic engineering, paving the way for safe industrial production of heparin in well-controlled cell culture.

Heparin is currently produced by extracting the drug from pig intestines, which is a concern for safety, sustainability, and security reasons. Millions of pigs are needed each year to meet our needs, and most manufacturing is done outside the USA. Furthermore, ten years ago, contaminants from the pig preparations led to dozens of deaths. Thus, there is a need to develop sustainable recombinant production. The work in PNAS provides new insights on exactly how cells control synthesis of heparin.

Heparin regulation

Heparin is a special subtype of a more general class of carbohydrates, called heparan sulfates, that are produced by a wide range of cells, both in the human body, as well as in cell culture. Yet, heparin is exclusively produced in a special type of blood cells called mast cells. To this day, heparin cannot be successfully produced in cell culture. Researchers at UC San Diego reasoned that heparin synthesis must be under the control of certain gene regulators (called transcription factors), whose tissue-specific occurrence might give mast cells the unique ability to produce heparin.

Since regulators for heparin were not known, a research team led by UC San Diego professors Jeffrey Esko and Nathan Lewis used bioinformatic software to scan the genes encoding enzymes involved in heparin production and specifically look for sequence elements that could represent binding sites for transcription factors. The existence of such a binding site could indicate that the respective gene is regulated by a corresponding gene regulator protein, i.e. a transcription factor.

“One DNA sequence that stood out the most is preferred by a transcription factor called ZNF263 (zinc-finger protein 263),” explains UC San Diego professor Nathan E. Lewis, who holds appointments in the UC San Diego School of Medicine’s Department of Pediatrics and in the UC San Diego Jacobs School of Engineering’s Department of Bioengineering. “While some research has been done on this gene regulator, this is the first major regulator involved in heparin synthesis,” said Lewis. He is also Co-Director of the CHO Systems Biology Center at the UC San Diego Jacobs School of Engineering.

Using the gene-editing technology, CRISPR/Cas9, the UC San Diego researchers mutated ZNF263 in a human cell line that normally does not produce heparin. They found that the heparan sulfate that this cell line would normally produce was now chemically altered and showed a reactivity that was closer to heparin.

Experiments further showed that ZNF263 represses key genes involved in heparin production. Interestingly, analysis of gene expression data from human white blood cells showed suppression of ZNF263 in mast cells (which produce heparin in vivo) and basophils, which are related to mast cells. The researchers report that ZNF263 appears to be an active repressor of heparin biosynthesis throughout most cell types, and mast cells are enabled to produce heparin because ZNF263 is suppressed in these cells.

This finding could have important relevance in biotechnology. Cell lines used in industry (such as CHO cells that normally are unable to produce heparin) could be genetically modified to inactivate ZNF263 which could enable them to produce heparin, like mast cells do.

Philipp Spahn, a project scientist in Nathan Lewis’ lab in the Departments of Pediatrics and Bioengineering at UC San Diego, described further directions the team is pursuing: “Our bioinformatic analysis revealed several additional potential gene regulators which can also contribute to heparin production and are now exciting objects of further study.”

This work was led by Ryan Weiss and Philipp Spahn. Ryan Weiss is a postdoc in professor Jeffrey Esko's lab in the Department of Cellular and Molecular Medicine at the UC San Diego School of Medicine where he is Co-Director of the Glycobiology Research and Training Center. Philipp Spahn is a project scientist in Nathan Lewis’ lab in the Department of Pediatrics at the UC San Diego School of Medicine and in the Bioengineering Department at the UC San Diego Jacobs School of Engineering.

Weiss, R.J.*, Spahn, P.N.*, Chiang, A.W.T., Li, J., Kellman, B.P., Benner, C., Glass, C.K., Gordts, P.L.S.M., Lewis, N.E.‡, Esko, J.D.‡ ZNF263 is a transcriptional regulator of heparin and heparan sulfate biosynthesis, Proc. Nat. Acad. Sci. USA.

Support was provided by the NIH (R01 GM33063, to J.D.E.; R21 CA199292, to J.D.E. and N.E.L.; R35 GM119850, to N.E.L; and R21 HD089067, to P.L.S.M.G.), the Fondation Leducq (to C.K.G and P.L.S.M.G.), a fellowship award to R.J.W. (K12HL141956), and the Novo Nordisk Foundation Center for Biosustainability at the Technical University of Denmark (NNF10CC1016517; N.E.L.).

Competing interest statement
The University of California San Diego and J.D.E. have a financial interest in TEGA Therapeutics, Inc. The terms of this arrangement have been reviewed and approved by the University of California San Diego in accordance with its conflict of interest policies.  

Bioengineers inducted into prestigious biomedical institution

San Diego, Calif., April 8, 2020 --  Two researchers at the Jacobs School of Engineering were inducted into the College of Fellows of the American Institute for Medical and Biological Engineering (AIMBE). Professors Christian Metallo from the Department of Bioengineering and Rob Knight from the Departments of Computer Science, Bioengineering and Pediatrics were inducted along with 156 colleagues who make up the AIMBE College of Fellows Class of 2020.

The College of Fellows is comprised of the top 2 percent of medical and biological engineers in the country, including the most accomplished and distinguished engineering and medical school chairs, research directors, professors, innovators and successful entrepreneurs. AIMBE Fellows are recognized for their contributions in teaching, research and innovation. 

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Rob Knight

Knight was recognized for his development of state-of-the-art computational and experimental techniques to probe the microbiome. As co-founder of the Earth Microbiome Project and American Gut Project, Knight’s research aims to understand the role of the microbiome in diseases ranging from obesity to mental illness. He develops new data visualization methods to handle large amounts of microbial data from spatially and temporally mapping microbial communities on scales from a human body to our planet. 

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Christian Metallo

Metallo was honored for the development and application of metabolic flux analysis technologies to better understand the biochemical pathways that drive cancer and neuropathy. His research focuses on metabolism within cells and tissues to understand how dysregulation of nutrient processing drives disease. His research could lead to new targets for therapeutic drugs designed to stop cancer cell growth and mitigate neuropathy or macular disease.

AIMBE’s mission is to recognize excellence in, and advocate for, the fields of medical and biological engineering in order to advance society. Since 1991, AIMBE‘s College of Fellows has led the way for technological growth and advancement in the fields of medical and biological engineering. Fellows have helped revolutionize medicine and related fields in order to enhance and extend the lives of people all over the world. They have also successfully advocated public policies that have enabled researchers and business-makers to further the interests of engineers, teachers, scientists, clinical practitioners, and ultimately, patients.

Thanks to 'flexoskeletons,' these insect-inspired robots are faster and cheaper to make

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Ph.D. student James Jiang, the paper's first author, shows one of the flexoskeletons developed with the researchers' 3D printing method. 

San Diego, Calif., April 8, 2020 -- Engineers at the University of California San Diego have developed a new method that doesn’t require any special equipment and works in just minutes to create soft, flexible, 3D-printed robots. 

The innovation comes from rethinking the way soft robots are built: instead of figuring out how to add soft materials to a rigid robot body, the UC San Diego researchers started with a soft body and added rigid features to key components. The structures were inspired by insect exoskeletons, which have both soft and rigid parts--the researchers called their creations “flexoskeletons.” 

The new method allows for the construction of soft components for robots in a small fraction of the time previously needed and for a small fraction of the cost. 

“We hope that these flexoskeletons will lead to the creation of a new class of soft, bioinspired robots,” said Nick Gravish, a mechanical engineering professor at the Jacobs School of Engineering at UC San Diego and the paper’s senior author. “We want to make soft robots easier to build for researchers all over the world.” 

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The printed parts are easily swappable. 

The new method makes it possible to build large groups of flexoskeleton robots with little manual assembly as well as assemble a library of Lego-like components so that robot parts can be easily swapped.

The flexoskeletons are made from 3D printing a rigid material on a thin sheet that acts as a flexible base. They are printed with various features that increase rigidity in specific areas--again inspired by insect exoskeletons, which combine softness and rigidity for movement and support.

Researchers detail their work in the April 7 issue of the journal Soft Robotics.The team plans to make their designs available to researchers at other institutions as well as high schools. 

One flexoskeleton component takes 10 minutes to print and costs less than $1. Flexoskeleton printing can be done on most low-cost commercially available printers. Printing and assembling a whole robot takes under 2 hours. 

Researchers surveyed a range of materials until they found the right flexible surface to print the flexoskeletons on--that turned out to be a sheet of polycarbonate. Careful observation of insect behavior led them to add features to increase rigidity. 

The ultimate  goal is to create an assembly line that prints whole flexoskeleton robots without any need for hand assembly. A swarm of these small robots could do as much work as one massive robot on its own--or more. 

In 1989, iRobot cofounder Rodney Brooks, then at the MIT Artificial Intelligence Lab, advocated for space missions that would consist of “large numbers of mass produced simple autonomous robots that are small by today's standards.” He and coauthor Anita Flynn titled the paper “Fast, cheap and out of control: a robot invasion of the solar system.”  The paper was seminal for Gravish, who hopes this study is one step further in that direction--but for the entire field of robotics, not just space. 


Company founded by engineering alumni advances 1-hour COVID test

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The Fluxergy diagnostic testing system has been able to provide COVID-19 test results in under an hour at the point of care.

By Alison Caldwell, PhD, Bigelow Science Communication Fellow

San Diego, Calif., April 7, 2020 -- As businesses are forced to close their doors and communities hunker down to ride out the coronavirus pandemic, many people in the tech and engineering industries are looking for ways to help.

One such group includes the engineers behind Fluxergy, a medical diagnostic company based in Irvine, California, that designs and builds rapid point-of-care diagnostic testing devices. Over the last several weeks and in collaboration with UC San Diego Health faculty, they’ve been testing a system to diagnose COVID-19 in under an hour. 

On March 30, 2020, they submitted an Emergency Use Authorization (EUA) to the U.S. Food and Drug Administration (FDA) in the hopes that their device can be deployed in medical settings within the next few weeks, making it possible for healthcare systems to test for the virus in under an hour, at the point-of-care. Currently, most COVID-19 tests are sent from the hospital or testing location to an outside lab to be analyzed, often taking hours or days for patients to get a result. During Fluxergy’s validation testing on patient samples with UC San Diego Health, they were able to provide results in an hour or less. 

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Tej Patel, co-founder of Fluxergy, as an undergraduate engineer and member of the Formula SAE race car team at UC San Diego.

Most of the team behind Fluxergy met as engineering students at the UC San Diego Jacobs School of Engineering, where Tej Patel, Fluxergy co-founder and president, and others were members of the Formula Society of Automotive Engineers (SAE) team as undergraduates. 

Years later, over dinner one night with his wife Priya Bhat-Patel, while discussing coursework for her PhD in global public health, Patel started thinking about the challenges of accessible diagnostic testing in low resource settings. 

“I thought, ‘Hey, figuring out how to bring those kinds of lab tests to those areas seems like a straightforward problem to solve,’” said Patel. “It was a mistake to think that it was easy, but seven years later, we’re finally ready to launch the product.”  

Patel and co-founder Ryan Revilla, also a UC San Diego engineering alumnus, started out tinkering in Revilla’s garage, funding the project with their own money and testing it in Patel’s kitchen. “It was a fun side project,” said Patel. “It felt good to be working on something that could help people.” 

Eventually, they connected with the co-founder of Kingston Technology, John Tu, who was very excited by their technology and the way it could be applied in healthcare. “Kingston Technology’s focus on manufactured computer products has been an asset for us from the get-go,” said Patel. “The manufacturability of the project has been a key component from the start.” 

With Tu’s support, they’ve been building a lightweight, portable diagnostic system. About the size of a shoebox, the device includes disposable test cards that use printed circuit board and microfluidics technology to rapidly perform any number of diagnostic tests. The goal was to create a system that could be easily transported and used at the point of care, providing important diagnostic results even in regions with little access to laboratory testing resources. 

They first began collaborating with UC San Diego Health faculty while working on a system to test a patient’s HIV viral load; they’re also working with UC Davis on commercial veterinary medicine applications for the device. They were getting close to officially launching the product when the COVID-19 pandemic began, and they rapidly changed their focus to address the global testing need.

“Our system is perfect for addressing many of the issues with current COVID-19 testing technologies,” said Patel. “Ordinary lab testing technologies require a many-step process, with different hoops you have to jump through to get it done. In the case of COVID-19, when it can take weeks to get results back, being able to do the testing in under an hour in the doctor’s office is a game changer.” 

For the last several weeks, they’ve been testing their coronavirus assay with Dr. Davey Smith, a professor of medicine at UC San Diego Health and a translational research virologist. So far, the initial tests have been promising, and with EUA approval, they’ll be set to start sending the devices to other hospitals and medical facilities.

“This could be huge for situations like drive-through testing,” said Eric Mendonsa, the director of sales and marketing at Fluxergy. “Someone could drive up and provide their sample, then pull over and wait for the result. Right now, there are so many essential businesses that are still operating, and it’s important to know if folks in our community are getting sick or might be at risk of spreading the virus to others quickly.”

While each device can only run one test at a time, the device’s small footprint makes it easy for many of them to be set up side-by-side for higher through-put testing. The device is also unique in that it can test against many modalities at once. While it currently uses a traditional PCR approach to test for COVID-19 infection, they are also working on adapting the testing cartridge to include a serological test that could determine if a person has already had the virus and recovered. 

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Steve Lee, a UC San Diego engineering alumnus and member of the Formula SAE team, is now the director of Product Development for Fluxergy.

“Who’s been exposed without realizing it, or who’s been sick and recovered – that’s important information, too,” said Patel. “It’s especially important for healthcare workers, since they’re still going in and treating these patients every day, and need to know if they’ve already been exposed.”

In addition to collaborating with UC San Diego Health, the team is also working on identifying other health systems that might be able to use this device if it’s approved for this application. 

Because of their connection to Kingston Technology, if demand increases, Fluxergy is confident that they’ll be able to rapidly scale up manufacturing of the system. “We’re aiming to be able to run several hundred thousand, or even millions, of test cards each month, if that’s the kind of demand we see from users,” said Patel.

But the goal isn’t just to have the system usable during this current crisis. “COVID-19 is here now, but it’s really about setting the infrastructure to have this in place for things that may happen in the future,” said Patel. “Unfortunately, this probably isn’t the last time we’ll face a situation like this. Our hope is to build better public health infrastructure so we can be better prepared to respond to situations like these in the future.” 

UC San Diego battery pioneer Shirley Meng earns Faraday Medal from Royal Society of Chemistry

San Diego, Calif., April 6, 2020 -- Congratulations to UC San Diego nanoengineering professor Shirley Meng, who has earned the 2020 Faraday Medal from the Royal Society of Chemistry. Meng is a leader in materials characterization and synthesis, including development of novel battery technologies that are driving a low-carbon, more sustainable future.

As the faculty leader of the Laboratory for Energy Storage and Conversion at the UC San Diego Jacobs School of Engineering, Meng leads a research team that is pioneering smaller, more efficient batteries that can harness wind and solar energy to fuel items like electric vehicles and the stations used to charge them.

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UC San Diego nanoengineering professor Shirley Meng

“It is an extraordinary time with COVID-19 crisis, yet my team continues to push the frontiers of energy storage technologies during this difficult time. The physical distancing leaves us a bit more time to plan for the next big wave in breakthroughs of energy storage technologies,” said Meng. “I believe that the uptake for renewable energy is unstoppable. The ability for us to store electrons with batteries indeed makes renewable energy sources reliable and economically viable.”

The Faraday Medal is awarded annually by the Electrochemistry Group of the Royal Society of Chemistry to an electrochemist working outside the UK and Ireland in recognition of their outstanding original contributions and innovation as a mid career researcher in any field of electrochemistry. Meng is scheduled to deliver the Faraday Medal lecture at Electrochem 2020 in Nottingham, UK in September 2020.

Meng is the founding director of the Sustainable Power and Energy Center at the UC San Diego Jacobs School of Engineering and the inaugural director of the UC San Diego Institute for Materials Discovery and Design. Meng is also the inaugural holder of the Zable Endowed Chair in Energy Technologies in the UC San Diego Jacobs School of Engineering.

Meng has authored or co-authored more than 200 peer-reviewed journal articles, two book chapters and four issued patents. She is the recipient of a number of awards, including a National Science Foundation CAREER Award, the UC San Diego Chancellor’s Interdisciplinary Collaboratories Award, the Charles W. Tobias Award from the Electrochemical Society and the International Battery Association Research Award.

Meng received her doctorate in advanced materials for micro and nano systems from the Singapore-MIT Alliance in 2005, after which she worked as a postdoctoral research fellow and became a research scientist at MIT. She joined the UC San Diego faculty in 2009.


WiFi-Boosting 'Smart Surface' Could Help Remote Workers and Students

Student holds a WiFi-boosting "smart surface" (made of printed circuit boards) up against a wall.
Manideep Dunna, a UC San Diego electrical and computer engineering Ph.D. student, holds a prototype "smart surface" that can be stuck on the wall to improve WiFi connectivity in the home and office.

San Diego, Calif., Apr. 2, 2020 -- Frustrated with spotty WiFi connection? Engineers at the University of California San Diego have developed a “smart surface” that could make signal available in dead spots—and also make the existing connection twice as fast.

“You can stick this on your wall like a painting to improve WiFi connectivity in your home or office,” said Dinesh Bharadia, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering.

The technology could benefit both employees who are working remotely and students who are receiving remote instruction. It could also reduce interference from your neighbors’ WiFi networks, which would make working or learning from home easier for everyone, Bharadia said.

In indoor tests, the smart surface extended WiFi range from 30 meters (98 feet) to 45 meters (147 feet). It also doubled the data rate in areas already receiving signal.

“You can use this with off-the-shelf WiFi devices. You don’t need specialized equipment to make it work,” Bharadia said. And the technology is low enough power that it could last for a year on a coin cell battery, researchers said.

“The surface gives the improved signal advantage of a large array but without having to modify the access point or any of the devices,” said UC San Diego electrical and computer engineering professor Daniel Sievenpiper, who is a collaborator on the study.

The smart surface is a 10 centimeter × 30 centimeter printed circuit board containing 48 small antennas. These antennas combine and reflect incoming WiFi signals from a router or access point to create an entirely new path for signals to travel. This new path, or data stream, is just as strong as the original one coming from the router or access point.

“The key feature of this technology is that it creates a second data stream that goes to your phone or other WiFi-connected device. So not only can you get connectivity in areas that don’t have it, you also get double the data rate in areas where you already have connectivity,” Bharadia said.

This is made possible by innovative hardware and algorithms that the team developed. Each antenna is programmed to adjust the phase of the incoming signal, or radio wave, that it receives so that all the waves reflected off the surface have the same phase at the receiver. These waves then merge to make a single amplified radio wave.

“Initially, the antennas are hit with incoming signals of different phases, so you get a reflected signal that’s weak, or no signal at all. It’s like adding 1 and -1. But by changing any -1 phases to +1, we boost the signal strength,” said Manideep Dunna, a UC San Diego electrical and computer engineering Ph.D. student in Bharadia’s lab.

Researchers envision this setup will be inexpensive to deploy. Mass producing the printed circuit boards could cost as little as $5 each, Dunna said.

In future studies, the team will explore if combining multiple smart surfaces can further improve data rate. “Could adding one more triple the data rate? And could another one quadruple it? That would be interesting to find out,” Bharadia said.

The team is also working on making the smart surface flexible.

Paper title: “ScatterMIMO: Enabling Virtual MIMO with Smart Surfaces.” Co-authors include Chi Zhang, UC San Diego.

Discovery of new biomarker in blood could lead to early test for Alzheimer's disease

San Diego, Calif., Mar. 31, 2020 -- Researchers at the University of California San Diego discovered that high blood levels of RNA produced by the PHGDH gene could serve as a biomarker for early detection of Alzheimer’s disease. The work could lead to the development of a blood test to identify individuals who will develop the disease years before they show symptoms.

The team published their findings in Current Biology.

The PHGDH gene produces RNA and proteins that are critical for brain development and function in infants, children and adolescents. As people get older, the gene typically ramps down its production of these RNAs and proteins. The new study, led by Sheng Zhong, a professor of bioengineering at the UC San Diego Jacobs School of Engineering in collaboration with Dr. Edward Koo, a professor of neuroscience at the UC San Diego School of Medicine, suggests that overproduction of a type of RNA, called extracellular RNA (exRNA), by the PHGDH gene in the elderly could provide an early warning sign of Alzheimer’s disease.

“Several known changes associated with Alzheimer’s disease usually show up around the time of clinical diagnosis, which is a little too late. We had a hunch that there is a molecular predictor that would show up years before, and that’s what motivated this study,” Zhong said.

The discovery was made possible thanks to a technique developed by Zhong and colleagues that is sensitive enough to sequence tens of thousands of exRNAs in less than one drop of blood. The method, dubbed SILVER-SEQ, was used to analyze the exRNA profiles in blood samples of 35 elderly individuals 70 years and older who were monitored up to 15 years prior to death. The subjects consisted of 15 patients with Alzheimer’s disease; 11 “converters,” which are subjects who were initially healthy then later developed Alzheimer’s; and 9 healthy controls. Clinical diagnoses were confirmed by analysis of post-mortem brain tissue.

The results showed a steep increase in PHGDH exRNA production in all converters approximately two years before they were clinically diagnosed with Alzheimer’s. PHGDH exRNA levels were on average higher in Alzheimer’s patients. They did not exhibit an increasing trend in the controls, except for in one control that became classified as a converter.

The researchers note some uncertainty regarding the anomalous converter. Since the subject died sometime during the 15-year monitoring, it is unclear whether that individual would have indeed developed Alzheimer’s if he or she lived longer, Zhong said.

The team acknowledges additional limitations of the study. “This is a retrospective study based on clinical follow-ups from the past, not a randomized clinical trial on a larger sample size. So we are not yet calling this a verified blood test for Alzheimer’s disease,” said co-first author Zixu Zhou, a bioengineering alumnus from Zhong’s lab who is now at Genemo Inc., a startup founded by Zhong. “Nevertheless, our data, which were from clinically collected samples, strongly support the discovery of a biomarker for predicting the development of Alzheimer’s disease.”

In addition to randomized trials, future studies will include testing if the PHGDH biomarker can be used to identify patients who will respond to drugs for Alzheimer’s disease.

The team is also open to collaborating with Alzheimer’s research groups that might be interested in testing and validating this biomarker.

“If our results can be replicated by other centers and expanded to more cases, then it suggests that there are biomarkers outside of the brain that are altered before clinical disease onset and that these changes also predict the possible onset or development of Alzheimer’s disease,” Koo said. “If this PDGDH signal is shown to be accurate, it can be quite informative for diagnosis and even treatment response for Alzheimer’s research.” 

This study was performed in collaboration with Genemo Inc.

Paper title: “Presymptomatic Increase of an Extracellular RNA in Blood Plasma Associates with the Development of Alzheimer’s Disease.” Co-authors include Zhangming Yan*, UC San Diego; Qiuyang Wu*, Genemo Inc.; and Zhen Chen, Beckman Research Institute.

*These authors contributed equally

UC San Diego Engineers and Doctors Team Up to Retrofit and Build Ventilators

This post features ongoing research and will be updated with new developments.

Students, staff and faculty address one of the key challenges of COVID-19 outbreak
By Alison Caldwell

March 26, 2020

San Diego, Calif. -- Even as university campuses close across the nation in an effort to slow the spread of the novel coronavirus, a team of engineers and physicians at the University of California San Diego is rapidly developing simple, ready-to-use ventilators to be deployed if the need arises.

The project kick-started several weeks ago when news started to trickle in that communities in Northern Italy with widespread COVID-19 were in dire straits.

“One of the biggest things we heard was that there weren’t enough ventilators to treat all of the patients coming into the hospitals,” said James Friend, a professor in the Department of Mechanical and Aerospace Engineering and the Department of Surgery at UC San Diego. “It’s clear that if we’re not careful, we might end up in the same situation.”

Ventilators are medical devices that push air in and out of a patient’s lungs when they are unable to breathe on their own. One of the primary symptoms of COVID-19 is difficulty in breathing; approximately 1 percent of people who contract the virus require ventilation to support their recovery—sometimes for weeks.

The situation in Italy spurred Dr. Lonnie Petersen, an assistant professor in the Department of Mechanical and Aerospace Engineering at UC San Diego and an adjunct with UC San Diego Health, to reach out to her medical and engineering colleagues, proposing a new collaboration to quickly produce simple ventilators that could be easily built and readily used to support patients in a crisis.

“We immediately had a lot of support from staff and faculty, all working to get this project off the ground,” Lonnie Petersen said. “Our community is taking this threat very seriously and acting accordingly.”

The first step was to seek consensus with anesthetists and respiratory therapists about minimum requirements for a ventilator. The next was to determine whether engineers could reasonably produce them, and how quickly. Lonnie Petersen coordianted efforts with  Dr. Casper Petersen, a postdoctoral researcher at the UC San Diego School of Medicine. 

Within days, a team of researchers from the Friend and Petersen labs, including graduate students Aditya Vasan, William Connacher, Jeremy Sieker and Reiley Weekes, began building devices using premade parts and 3D printers. Their first goal was to convert an existing manual ventilator model to automatic, able to provide breathing assistance without human intervention.

Engineering students and faculty are developing a simple device using 3D-printed parts and off-the-shelf components to convert an existing manual ventilator system into an automatic one.

The existing manual design features a mask fitted over a patient’s face and a bag that can be squeezed by hand to push air into the patient’s lungs. The team is designing a machine that can do the squeezing instead, freeing doctors and nurses to address other concerns.

“We’re 3D-printing parts that can be attached to a motor to compress the bag of the manual ventilator,” said Ph.D. student Vasan. “This allows us to control the speed and volume of the compressions to help patients breathe.”

The advantage of 3D printing is that it can be used to quickly produce customized parts. Devices can be made on a small scale much faster than by traditional manufacturing methods.

“As long as the correct materials are used, 3D printing can be used to produce a wide variety of tools in the fight against COVID-19,” said Shaochen Chen, a professor of nanoengineering at the Jacobs School of Engineering. “It’s not good for, say, entire N95 masks, but it can be used for producing testing swabs or even face shields for healthcare workers.”

Meanwhile, Lonnie Petersen’s team is awaiting a few more parts to build a more sophisticated ventilator using an electric pump. “Our aim is to have functional devices as soon as possible,” she said. “Once we’ve got the bare bones system up and running, we can start adding layers of sophistication and automation. Those additional layers will include advanced regulation of air pressure and flow to allow for a more disease-specific and patient-tailored respiratory support.”

The first ventilators will be simple, but the goal is to have something readily at hand when the need arises.

San Diego-based Kratos Defense & Security Solutions, Inc., which develops fields systems, platforms and products for national security and communications needs, contributed $100,000 to help fund the ventilator project.

“We are pleased to provide greatly needed charitable support to UC San Diego at this unprecedented time in history,” said Kratos CEO Eric M. DeMarco.  

The researchers are also receiving $144,000 in support from US Office of Naval Research (ONR).

“We humbly thank everyone involved in this project. The support from Kratos and ONR came through incredibly quickly. I believe the outstanding effort of everyone involved will save lives,” said Friend.  

A broader goal and volunteers needed

“We are preparing for a shortage of both ventilators and specialized staff to run them,” said Lonnie Petersen. “The questions quickly became ‘How can we tweak the ventilators that are available to support multiple patients? How can we create more ventilators that are easier for staff to use?’”

Other projects include collecting and inventorying oxygen supplies in preparation for increased demand by local hospitals; converting other air pressure machines, such as CPAPs and Bi-PAPs into ventilators; and adapting existing ventilators to serve more patients.

Dr. Sidney Merritt displays an in-house pressure measurement device, currently in testing for use on a system designed to split a single ventilator to serve up to four patients.

The team hopes to have functional prototypes within a few days and are ready to test them in simulators, in collaboration with anesthesiologists, before potentially applying to patients.

“Normally, the production timeline on something like this would be months, or even years,” said Lonnie Petersen. “By building on existing technology and taking multiple steps at once, we aim to reduce that timeline to weeks.”

While grappling with challenges in locating parts that can’t be 3D-printed and obtaining them from outside vendors, the biggest roadblock right now is gathering enough people to assemble the devices.

The UC San Diego campus is largely closed and empty, due to efforts to minimize coronavirus exposure and slow the spread of COVID-19. The graduate student team continues work, thanks to a special exception granted by the Dean of the Jacobs School of Engineering.

“This is a team effort,” said Lonnie Petersen. “And we can use the assistance of other engineers. We would love to hear from students, staff, and faculty with hands-on engineering experience who can help us with this project.”

San Diego-based Kratos Defense & Security Solutions, Inc., which develops fields systems, platforms and products for national security and communications needs, contributed $100,000 to help fund the ventilator project.

“We are pleased to provide greatly needed charitable support to UC San Diego at this unprecedented time in history,” said Kratos CEO Eric M. DeMarco.  

The researchers are also receiving $144,000 in support from US Office of Naval Research (ONR).

Qualified volunteers should email: UCSDVentilatorEngHelp@gmail.com

Splitting ventilators

Meanwhile, Petersen’s colleague Dr. Sidney Merritt, an associate clinical professor of anesthesiology at UC San Diego Health, is working with a team that includes U.S. Navy and Lockheed Martin personnel to develop a 3D-printable system for splitting a ventilator designed for one patient so that it can be used by up to four patients at a time.

“We found a file online that showed us how it could be done,” said Merritt. “We’ve been working with the Navy and others to print them in different materials and test them on a ventilator, and, so far, it works. We were able to get enough pressure on each line that it should be adequate for serving four patients at a time.”

The challenge now is finding valves that can regulate the pressure for each patient on the system and monitor individual air pressure for each one, allowing for the fine control needed to support each patient’s specific needs. “As soon as we have the valves worked out, we’ll be just a couple days out from getting them set up and running,” said Merritt.

Using 3D-printed parts, Dr. Sidney Merritt and a team at the U.S. Navy and Lockheed Martin are developing a system to convert ventilators designed for a single patient to be used by up to four patients at a time.

“This situation is going to be very severe,” she continued. “We need to have every tool available to us, so we are ready to treat patients because we still don’t know how many people will get sick.”

“We want to help as many patients as possible,” said Dr. Casper Petersen, an assistant project scientist in the Department of Orthopedic Surgery at UC San Diego Health. “Having something simple in hand is better than nothing at all in situations where existing respirator demand exceeds supply. Our colleagues around the world have made us aware that we may face a situation where patients need ventilator support for weeks. This is a unique medical emergency situation.”

Despite obstacles, the team said it has been overwhelmed by support and advocacy from colleagues and university leadership. For example, the Institute on Global Conflict and Cooperation at UC San Diego has contributed $10,000 to assist in the development of prototypes.

“The UC San Diego family is really pulling together on this one,” said Lonnie Petersen. “From the dean, through chairs, faculty and students, regardless of who we’ve spoken to, everyone has gone above and beyond to help with this project as much as they can. It’s really bringing the community together. Everyone is moving in the same direction. While the work may be preparing for something unpleasant, it’s very good to be working in such a supportive environment.”

Members of the team:

Jacobs School of Engineering: Professors James Friend and Lonnie Petersen, and their students, Aditya Vasan, William Connacher, Jeremy Sieker and Reiley Weekes, as well as Professor Tania Morimoto.

UC San Diego Health: Dr. Casper Petersen, Dr. Daniel Lee; Dr. Preetham Suresh; Dr. William Mazzei; Dr. Matthew Follansbee; Dr. Micheal Vanietti; Dr. Hemal Patel; Theodore Vallejos.

Qualcomm Institute: Mark Stambaugh of the Qualcomm Institute.


UC San Diego Jacobs School of Engineering jumped to #9 in U.S. News and World Report Rankings of Best Engineering Schools

San Diego, Calif., March 20, 2020 -- The University of California San Diego Jacobs School of Engineering jumped to the #9 spot in the influential U.S. News and World Report Rankings of Best Engineering Schools. This is up from #11 last year and #17 four years ago. It’s the first time the UC San Diego Jacobs School of Engineering has broken into the top 10 of this closely watched ranking.

“This is not a time for a celebration because our priority right now is dealing with COVID-19. But I want to recognize the many people here at UC San Diego whose excellence is reflected in this ranking. They are part of our strong UC San Diego community that is committed to working so hard right now to confront COVID-19 on campus and in our region,” said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering.

The UC San Diego Jacobs School of Engineering educates engineers and computer scientists who develop the innovative ideas and capabilities critical to the success of the San Diego region, the state of California, and the nation.
UC San Diego Jacobs School of Engineering jumped to #9 in U.S. News and World Report Rankings of Best Engineering Schools
US News Rankings: Jacobs School of Engineering

The Jacobs School ranks #1 in the nation among public engineering schools for research expenditures per faculty member. The Jacobs School performed $212 million in research during the 2018-2019 fiscal year, up from $188 million last year.

Many Jacobs School departments ranked highly in program-specific rankings this year, including the following.

The biomedical / bioengineering graduate program at the Jacobs School ranks #4 in the nation. Bioengineering at UC San Diego has been ranked first by the National Research Council since its founding 50 years ago. Learn more about bioengineering at UC San Diego here.  

Computer engineering at the Jacobs School ranks #14 in the nation. The computer engineering graduate program is a collaboration between the Department of Computer Science and Engineering, and the Department of Electrical and Computer Engineering.

Electrical / electronic / communications engineering ranks #14

Mechanical engineering ranks #17

Aerospace / aeronautical / astronautical engineering ranks #18

Computer science programs were not ranked this year by U.S. News. But the Department of Computer Science and Engineering (CSE) ranks 11th in computer systems; 13th in programming languages; 14th in computer science theory; and #16 in the nation overall, according to the US News and World Report Ranking of Best Engineering Schools published March 2018.     

How Robots Can Help Combat COVID-19: Science Robotics Editorial

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Henrik Christensen, a professor of computer science at UC San Diego, is one of authors of an editorial in Science Robotics that looks at how robots could help in a pandemic. 

San Diego, Calif., March 25, 2020 -- Can robots be effective tools in combating the COVID-19 pandemic? A group of leaders in the field of robotics, including Henrik Christensen, director of UC San Diego’s Contextual Robotics Institute, say yes, and outline a number of examples in an editorial in the March 25 issue of Science Robotics. They say robots can be used for  clinical care such as telemedicine and decontamination; logistics such as delivery and handling of contaminated waste; and reconnaissance such as monitoring compliance with voluntary quarantines.

“Already, we have seen robots being deployed for disinfection, delivering medications and food, measuring vital signs, and assisting border controls,” the researchers write.

Christensen, who is a professor in the Department of Computer Science and Engineering at UC San Diego, particularly highlighted the role that robots can play in disinfection, cleaning and telepresence.

Other co-authors include Marcia McNutt, president of the National Research Council and president of the National Academy of Sciences, as well as a number of other robotics experts from international and U.S. universities. 

“For disease prevention, robot-controlled noncontact ultraviolet (UV) surface disinfection has already been used because COVID-19 spreads not only from person to person via close contact respiratory droplet transfer but also via contaminated surfaces,” the researchers write.

“Opportunities lie in intelligent navigation and detection of high-risk, high-touch areas, combined with other preventative measures,” the researchers add. “New generations of large, small, micro-, and swarm  robots that are able to continuously work and clean (i.e., not only removing dust but also truly sanitizing/sterilizing all surfaces) could be developed.”

In terms of telepresence, “the deployment of social robots can present unique opportunities for continued social interactions and adherence to treatment regimes without fear of spreading more disease,” researchers write. “However, this is a challenging area of development because social interactions require building and maintaining complex models of people, including their knowledge, beliefs, emotions, as well as the context and environment of interaction.”

“COVID-19 may become the tipping point of how future organizations operate,” researchers add. “Rather than cancelling large international exhibitions and conferences, new forms of gathering—virtual rather than in-person attendance—may increase. Virtual attendees may become accustomed to remote engagement via a variety of local robotic avatars and controls.”

“Overall, the impact of COVID-19 may drive sustained research in robotics to address risks of infectious diseases,” researchers  go on. “Without a sustainable approach to research and evaluation, history will repeat itself, and technology will not be ready ready to assist for the next incident.”


Making cell modeling more realistic

San Diego, Calif., Mar. 17, 2020 -- Researchers at the University of California San Diego have developed a computational tool that makes modeling and simulation of complex cellular processes more true to life. 

The tool, dubbed GAMer 2, simplifies the process of using realistic cell geometries in mathematical models. The UC San Diego team details the work in a paper published in Biophysical Journal.

“This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Our hope is that this tool will open a new frontier for biophysical simulations with realism enhanced by geometries derived from experimental images,” said first author Christopher T. Lee, a Hartwell Foundation postdoctoral fellow at UC San Diego.

Lee worked on this project co-advised by Padmini Rangamani, a professor of mechanical and aerospace engineering at the UC San Diego Jacobs School of Engineering, and Michael Holst, a professor of mathematics and physics at UC San Diego. This interdisciplinary project also involved UC San Diego chemistry professors Rommie Amaro and J. Andrew McCammon.

Researchers have typically used idealized geometries to develop mathematical models of cell signaling dynamics. That’s because they have lacked tools capable of converting structural information from cell imaging datasets to simulation compatible formats.

UC San Diego researchers are bridging this gap with their GAMer 2 tool. It is a mesh generation library that converts structural and biological datasets into geometric meshes, such as those commonly used in graphics and mathematics, Lee explained. 

Here is a video of a model of the subcellular structures in a mouse heart reconstructed using GAMer2. Shown are the mitochondria (magenta), sarcoplasmic reticulum (yellow) and t-tubule (green). The floating glass beads diffusing around the structures represent calcium ions searching for their targets to initiate the contraction for a heartbeat.

This work has uniquely benefitted from the broad expertise and cross-talk between researchers from the Jacobs School of Engineering and Division of Physical Sciences at UC San Diego, the team said. 

GAMer 2 is available under an open source license here: https://github.com/ctlee/gamer.

Paper title: “An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries.” 

This work is supported by the National Institutes of Health, Air Force Office of Scientific Research, and the National Science Foundation

Undergraduate students bring Intranet to rural Ghanaian school

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The Schoolhouse Ghana student team with Godfreds Foundation co-founder Fredrick Benneh Frimpong, third from right. The students, from left to right: Matthew Chen, Vanshika Agrawal, Neve Foresti, Sohyun Lee, Cristina Barney, and Cynthia Butarbutar. Photo courtesy of Global Ties.

San Diego, Calif., March 12, 2020 -- A few years ago, a photo went viral of a Ghanaian schoolteacher who drew detailed computer screens and software systems on his blackboard every morning so that his students—who didn’t have access to computers—could have a shot at passing the computer literacy portion of their exams. Now, a team of UC San Diego students has partnered with a school in Ghana that faces a similar challenge, and created a more effective and scalable solution.

The team of undergraduates, who are part of the Global Ties program at the UC San Diego Jacobs School of Engineering, developed a self-sustaining and scalable computer server and intranet system. The system will allow teachers to download Internet pages and educational materials that students can access anytime at school—even when there is no Internet.

It will be installed at the Semanhyiya American School (SAS) in the rural village of Senase, Ghana this summer. The Global Ties Schoolhouse Ghana team partnered with the nonprofit Godfreds Foundation, which runs SAS, to ensure the system met the school’s needs.

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The Global Ties students partnered with the nonprofit Godfreds Foundation and its Semanhyiya American School in the rural village of Senase, Ghana, to develop an intranet server that would meet the school’s needs. Photo courtesy of SAS.

In Ghana, all students take a national test in ninth grade, which includes a section on computer literacy. Students who don’t pass this test aren’t able to progress past ninth grade.

While the rural school has one shared computer lab for all the students—who don’t have computers at home—the WiFi is spotty at best, and prohibitively expensive. This means the students often aren’t able to access the materials their teachers would have liked, and struggle to complete their computer curriculum.

“The goal is to provide these students with access to the technology that we have access to thanks to the internet,” said Cristina Barney, a bioengineering student and the Schoolhouse Ghana undergraduate advisor. “We can’t change the reliability or cost of the internet in Ghana or in that school location. We can’t do much about that, so we saw an opportunity to change the perspective and maybe instead of trying to have better internet, have a system that can work around the problem.”

Compounding the lack of internet is the reality that textbooks are very expensive, so each student isn’t able to have a copy of the books used. Having reliable access to the internet will allow teachers to add more resources from digital versions of textbooks, as well as from different media including videos and interactive websites, to their toolbox.

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Students in the school’s one computer lab, where access to internet is spotty and prohibitively expensive. Photo courtesy of SAS.

The Schoolhouse Ghana team got a boost recently when the project was accepted into the Clinton Global Initiative-University (CGIU), the higher education program of the Clinton Foundation. Through CGIU, the project will receive mentorship from leaders with experience completing similar social innovation projects, and a completion plan template with timetables to finish small portions of the project, to ensure the entire system is complete and ready for installation by the summer.

Barney and Neve Foresti, a cognitive science student with minors in sociology and visual arts speculative design and the current Schoolhouse Ghana project team lead, were accepted to participate in the CGIU conference in Edinburgh, Scotland in April. They’ll have an opportunity to meet student teams from around the world tackling other social innovation challenges, and participate in leadership development, mentorship, skills training, and partnership building workshops.

The system the UC San Diego students developed includes a rugged computer server, an intranet, web crawler, and a network-attached storage platform. All told, it will allow teachers to download and store the webpages they want when there is WiFi; the students will then be able to access them regardless of internet availability. Students can also practice emailing one another; use internet-based software programs; and access the vast depths of knowledge available online, even when there is no WiFi.

“We want to have a working server that has at least four main components: email, data storage, a working interface webpage for students, and a working web crawler—the crawler is what downloads all the pages into the actual interface,” said Barney. “But thinking ahead about a more long-term solution, we want to be able to create a standardized manual to recreate this for other schools that need it.”

Another key component of the project is its relevance for SAS teachers, said Foresti.

“A really big part of this system is that it’s being worked into the curriculum,” Foresti said. “We have the curriculum of the school, and we’re building this system and the website with that curriculum in mind in terms of the computer literacy skills the students will be expected to learn.”

In addition to the software skills required to create the intranet and web crawler, the students also had some hardware constraints to consider.

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Students in Ghana must pass a national test in ninth grade in order to progress further with their education. The exam includes a section on computer literacy.

“We built a rugged case and cooling system for the server because it’s in a place with a very hot climate that’s very dusty in the summers, so we needed something that will be able to filter out the dust and have a robust cooling system that doesn’t require a lot of maintenance,” Barney said. “You could apply a really cool water cooling system to a server, but if it breaks, that’s a problem. So we had to create something new.”

The student team is designing the system to be as self-sustaining as possible, and is working with The Godfred’s Foundation to provide training for SAS teachers and administrators to ensure they’re able to maintain the system.

"We are honored to have been chosen by the UC San Diego Global Ties team to support our goal of providing the children of Senase with educational opportunities as good or better than those found in Accra and other large cities in Ghana,” said Mike Allison, co-founder of The Godfreds Foundation. “Access to computer technology will allow our students to succeed on the national exam and continue their journey for a better future through education."

Global Ties is part of the Jacobs School of Engineering and its Experience Engineering Initiative, which aims to give every engineering and computer science undergraduate student at UC San Diego a hands-on or experiential engineering course or lab each and every year. Global Ties partners interdisciplinary teams of UC San Diego students with nonprofits and NGOs to co-create solutions to socially urgent problems in San Diego and the developing world.

This story originally ran in ThisWeek@UCSanDiego.

Pathways toward realizing the promise of all-solid-state batteries

San Diego, Calif., Mar. 13, 2020 -- When it comes to batteries, there are always areas for improvement: the race is on to develop batteries that are cheaper, safer, longer lasting, more energy dense, and easily recyclable. 

In a review article published in the March 2020 issue of Nature Nanotechnology, nanoengineers at the University of California San Diego offer a research roadmap that includes four challenges that need to be addressed in order to advance a promising class of batteries—all-solid-state batteries—to commercialization. This article summarizes the team’s work to tackle these challenges over the past three years, which have been reported in several peer-reviewed articles published in various journals.

Unlike today’s rechargeable lithium ion batteries, which contain liquid electrolytes that are often flammable, batteries with solid electrolytes offer the possibility of greater safety, in addition to a whole range of benefits including higher energy density.  

In the Nature Nanotechnology review article, the researchers focus on inorganic solid electrolytes such as ceramic oxides or sulfide glasses. Inorganic solid electrolytes are a relatively new class of solid electrolytes for all-solid-state batteries (in contrast to organic solid electrolytes which are more extensively researched.)

Roadmap: inorganic electrolytes for all-solid-state batteries

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Illustration of various recycling methods with reference to direct battery recycling method proposed in solid state batteries. Image courtesy of Nature Nanotechnology

The following is an outline of the roadmap that the researchers describe in their review article:

1) Creating stable solid electrolyte chemical interfaces 
2) New tools for in operando diagnosis and characterization 
3) Scalable and cost-effective manufacturability
4) Batteries designed for recyclability

“It’s critical that we step back and think about how to address these challenges simultaneously because they are all interrelated,” said Shirley Meng, a nanoengineering professor at the UC San Diego Jacobs School of Engineering. “If we are going to make good on the promise of all-solid-state batteries, we must find solutions that address all these challenges at the same time.” 

As director of the UC San Diego Sustainable Power and Energy Center and director of the UC San Diego Institute for Materials Discovery and Design, Meng is a key member of a cluster of researchers at the forefront of all solid-state battery research and development at UC San Diego. 

Creating stable solid electrolyte chemical interfaces 

Solid-state electrolytes have come a long way since their early days, when the first electrolytes discovered had exhibited conductivity values too low for practical applications. Today’s advanced solid-state electrolytes show conductivities exceeding even those of conventional liquid electrolytes used in today’s batteries (greater than 10 mS cm-1). Ionic conductivity refers to how fast lithium ions can move within the electrolyte.

Unfortunately, most highly conductive solid electrolytes reported are often electrochemically unstable and face problems when applied against electrode materials used in batteries.

“At this point, we should shift our focus away from chasing higher ionic conductivity. Instead, we should focus on stability between solid state electrolytes and electrodes,” said Meng. 

If ionic conductivity is analogous to how fast a car can be driven, then interface stability refers to how hard it is to get through rush hour traffic. It doesn’t matter how fast your car can go if you’re stuck in traffic on your way to work.

Researchers at UC San Diego recently addressed this interface stability bottleneck, demonstrating how to stabilize the electrode-electrolyte interface and improve battery performance using solid electrolytes with moderate ionic conductivities but exhibit stable interfaces.

Related interface stability papers from UC San Diego:

New tools for in operando diagnosis and characterization 

Why do batteries fail? Why does short circuit occur? The process of understanding what goes on inside a battery requires characterization down to the nanoscale, ideally in real time. For all-solid-state batteries, this is immensely challenging. 

Battery characterization typically relies on using probes such as X-rays, or electron or optical microscopy. In commercial lithium ion batteries, the liquid electrolytes used are transparent, allowing observation of various phenomena at the respective electrodes. In some cases, this liquid can also be washed away to provide a cleaner surface for higher resolution characterization.

“We have a much easier time observing today’s lithium ion batteries. But in all-solid-state batteries, everything is solid or buried. If you try the same techniques for all-solid-state batteries, it’s like trying to see through a brick wall,” said Darren H. S. Tan, a nanoengineering Ph.D. candidate at the UC San Diego Jacobs School of Engineering. 

In addition, solid electrolytes and lithium metal used in solid-state batteries can be sensitive to electron beam damage. This means that standard electron microscopy techniques used to study batteries would damage the materials of interest before they can be observed and characterized. 

One way UC San Diego researchers are overcoming these challenges is using cryogenic methods to keep battery materials cool, mitigating their decomposition under the electron microscope probe. 

Another tool used to overcome the obstacles of characterizing solid electrolyte interfaces is X-ray tomography. This is similar to what humans undergo during their health checkups. The approach was used in a recent paper reporting on the observation—without opening or disrupting the battery itself—of lithium dendrites buried within the solid electrolyte. 

Related characterization papers from UC San Diego:

Scalable and cost-effective manufacturability

Breakthroughs in battery research often don’t mean much if they are not scalable. This includes advances for all-solid-state batteries. If this class of batteries is to enter the market within the next few years, the battery community needs ways to manufacture and handle their sensitive component materials cost effectively and at large scales.

Over the past few decades, researchers have developed—in the lab—various solid electrolyte materials that exhibit chemical properties that are ideal for batteries. Unfortunately, many of these promising materials are either too costly or too difficult to scale up for high-volume manufacturing. For example, many become highly brittle when made thin enough for roll-to-roll manufacturing, which demands thicknesses of under 30 micrometers. 

Additionally, methods to produce solid electrolytes at larger scales are not well established. For instance, most synthesis protocols require multiple energetic processes that include multiple milling, thermal annealing and solution processing steps. 

To overcome such limitations, researchers at UC San Diego are merging multiple fields of expertise. They are combining ceramics used in traditional material sciences with polymers used in organic chemistry to develop flexible and stable solid electrolytes that are compatible with scalable manufacturing processes. To address problems of material synthesis, the team also reports how solid electrolyte materials can be scalably produced using single-step fabrication without the need for additional annealing steps.

Related scalable manufacturing papers from UC San Diego:

Batteries designed for recyclability

Spent batteries contain valuable and limited-abundance materials such as lithium and cobalt that can be reused. 

When they reach the end of their life cycles, these batteries need to go somewhere, or else they will simply be accumulated over time as waste. 

Today’s recycling methods, however, are often expensive, energy and time intensive, and include toxic chemicals for processing. Moreover, these methods only recover a small fraction of the battery materials due to low rates of recycling of electrolytes, lithium salts, separator, additives and packaging materials. In large part, this is because today’s batteries have not been designed with cost-effective recyclability in mind from the start. 

UC San Diego researchers are at the forefront of efforts to design reusability and recyclability into tomorrow’s all-solid-state batteries. 

“Cost-effective reusability and recyclability must be baked into the future advances that are needed to develop all-solid-state batteries that provide high energy densities of 500 watt-hours per kg or better,” said UC San Diego nanoengineering professor Zheng Chen. “It’s critical that we don’t make the same recyclability mistakes that were made with lithium ion batteries.”

Batteries also need to be designed with their full life-cycle in mind. This means designing batteries that are meant to remain in use well after they drop below the 60 to 80 percent of their original capacity that often marks the end of the useful life of a battery. This can be done by exploring secondary uses for batteries such as stationary storage or for emergency power, extending their lifespans before they finally hit the recycling centers.

All-solid-state batteries with organic electrolytes offer great promise as a future battery technology that will deliver high energy density, safety, long life times and recyclability. But turning these possibilities into realities will require strategic research efforts that consider how the remaining challenges, including recyclability, are interrelated. 


Paper title
From Nanoscale Interface Characterization to Sustainable Energy Storage Using All Solid-State Batteries,” in the March 2020 issue of Nature Nanotechnology

Darren H. S. Tan, Abhik Banerjee, Zheng Chen, and Ying. Shirley Meng from the Department of NanoEngineering, Program of Chemical Engineering, and Sustainable Power & Energy Center (SPEC) University of California San Diego Jacobs School of Engineering. 

This work was financially supported by the LG Chem through the Battery Innovation Contest (BIC) program as well as the Energy & Biosciences Institute through the EBI-Shell program. Z.C. acknowledges funding from the US Department of Energy via ReCell Center and the start-up fund support from the Jacob School of Engineering at University of California San Diego. Y.S.M. acknowledges the funding support from Zable Endowed Chair Fund.

'Spillway' for electrons could keep lithium metal batteries from catching fire

Battery separator coated on one side with a thin layer of carbon nanotubes
UC San Diego nanoengineers developed a separator that could make lithium metal batteries fail safely so that they do not rapidly overheat, catch fire or explode. Photos by David Baillot/UC San Diego Jacobs School of Engineering

San Diego, Calif., Mar. 12, 2020 -- Nanoengineers at the University of California San Diego developed a safety feature that prevents lithium metal batteries from rapidly heating up and catching fire in case of an internal short circuit.

The team made a clever tweak to the part of the battery called the separator, which serves as a barrier between the anode and cathode, so that it slows down the flow of energy (and thus heat) that builds up inside the battery when it short circuits.

The researchers, led by UC San Diego nanoengineering professor Ping Liu and his Ph.D. student Matthew Gonzalez, detail their work in a paper published in Advanced Materials.

“We’re not trying to stop battery failure from happening. We’re making it much safer so that when it does fail, the battery doesn’t catastrophically catch on fire or explode,” said Gonzalez, who is the paper’s first author.

Lithium metal batteries fail because of the growth of needle-like structures called dendrites on the anode after repeated charging. Over time, dendrites grow long enough to pierce through the separator and create a bridge between the anode and cathode, causing an internal short circuit. When that happens, the flow of electrons between the two electrodes gets out of control, causing the battery to instantly overheat and stop working.

Researcher casts a black layer of carbon nanotubes on a glass slide
To make the new separator, a slurry of polymer gel is casted onto a glass slide, followed by a layer of carbon nanotubes.

The separator that the UC San Diego team developed essentially softens this blow. One side is covered by a thin, partially conductive web of carbon nanotubes that intercepts any dendrites that form. When a dendrite punctures the separator and hits this web, electrons now have a pathway through which they can slowly drain out rather than rush straight towards the cathode all at once.

Gonzalez compared the new battery separator to a spillway at a dam.

“When a dam starts to fail, a spillway is opened up to let some of the water trickle out in a controlled fashion so that when the dam does break and spill out, there’s not a lot of water left to cause a flood,” he said. “That’s the idea with our separator. We are draining out the charge much, much slower and prevent a ‘flood’ of electrons to the cathode. When a dendrite gets intercepted by the separator’s conductive layer, the battery can begin to self-discharge so that when the battery does short, there’s not enough energy left to be dangerous.”

Researcher peels off a battery separator from a glass slide
Matthew Gonzalez, a UC San Diego nanoengineering Ph.D. student, fabricates the new battery separator.

Other battery research efforts focus on building separators out of materials that are strong enough to block dendrites from breaking through. But a problem with this approach is that it just prolongs the inevitable, Gonzalez said. These separators still need to have pores that let ions flow through in order for the battery to work. As a consequence, when the dendrites eventually make it through, the short circuit will be even worse.

Rather than block dendrites, the UC San Diego team sought to mitigate their effects.

A battery separator being peeled off a glass slide

In tests, lithium metal batteries equipped with the new separator showed signs of gradual failure over 20 to 30 cycles. Meanwhile, batteries with a normal (and slightly thicker) separator experienced abrupt failure in a single cycle.

“In a real use case scenario, you wouldn’t have any advance warning that the battery is going to fail. It could be fine one second, then catch on fire or short out completely the next. It’s unpredictable,” Gonzalez said. “But with our separator, you would get advance warning that the battery is getting a little bit worse, a little bit worse, a little bit worse, each time you charge it.”

While this study focused on lithium metal batteries, the researchers say the separator can also work in lithium ion and other battery chemistries. The team will be working on optimizing the separator for commercial use. A provisional patent has been filed by UC San Diego.

Paper title: “Draining Over Blocking: Nano-Composite Janus Separators for Mitigating Internal Shorting of Lithium Batteries.” Co-authors include Qizhang Yan, John Holoubek, Zhaohui Wu, Hongyao Zhou, Nicholas Patterson, Victoria Petrova and Haodong Liu, UC San Diego.

New record set for cryptographic challenge

portrait of Nadia Heninger
Nadia Heninger is a professor of computer science and engineering at the Jacobs School at UC San Diego. 

San Diego, Calif., March 11, 2020 -- An international team of computer scientists has set a new record for integer factorization, one of the most important computational problems underlying the security of nearly all public-key cryptography currently used today.  

Public-key cryptography is used for a number of applications including encrypting sensitive and confidential data and digital signatures.  In public-key cryptography, keys that protect data come in pairs, one public, and one private. The security of the encryption or digital signature relies on the assumption that it’s impossible to compute the private key from the public key.

One of the most commonly used public-key cryptographic algorithms for both encryption and digital signatures is the RSA cryptosystem, invented in 1977.  It’s named for its inventors Rivest, Shamir, and Adleman. Its security is based on the fact that it is believed to be difficult to factor large integers of a specific form.

To encourage research into integer factorization, the "RSA Factoring Challenges" were created in 1991. These challenges consisted of challenge integers of varying sizes, named for the number of integer digits. 

The team of computer scientists from France and the United States set a new record by factoring the largest integer of this form to date, the RSA-250 cryptographic challenge. This integer is the product of two prime numbers, each with 125 decimal digits. In total, it took 2700 years of running powerful computer cores to carry out the computation, which was done on tens of thousands of machines around the world over the course of a few months. 

The key broken with this record computation is smaller than keys that would typically be used in practice by modern cryptographic applications: it has 829 binary bits, where current practice dictates that RSA keys should be at least 2048 binary bits long. Researchers use these types of computations to choose key strength recommendations that will remain secure for the foreseeable future.

“Achieving computational records regularly is necessary to update cryptographic security parameters and key size recommendations,” said Nadia Heninger, a professor of computer science at the University of California San Diego, and a member of the research team. 

The same team set the previous integer factoring record back in December 2019, when they factored the RSA-240 challenge, a 795-bit integer.

The researchers carried out this computation using CADO-NFS, which is free software developed by the team at INRIA Nancy.  They used a number of computer clusters, including research group, university, and national research clusters in France, Germany, and UC San Diego. 

The team was composed of Aurore Guillevic, Paul Zimmermann, and Emmanuel Thomé of Inria Nancy, France; Pierrick Gaudry of CNRS Nancy, France; Nadia Heninger of the University of California San Diego; and Fabrice Boudot of the University of Limoges, France.


Microbial DNA in Patient Blood May be Tell-Tale Sign of Cancer

Detecting cancer at its earliest stages from a simple blood draw is the goal of several companies currently developing “liquid biopsies” to detect circulating human tumor DNA. Now UC San Diego researchers have demonstrated they can determine who has cancer, and what type, based on a readout of microbial DNA found in their blood. Photo credit: MacDill Air Force Base

From a simple blood draw, microbial DNA may reveal who has cancer and which type, even at early stages

San Diego, Calif., March 11, 2020 -- When Gregory Poore was a freshman in college, his otherwise healthy grandmother was shocked to learn that she had late-stage pancreatic cancer. The condition was diagnosed in late December. She died in January.

“She had virtually no warning signs or symptoms,” Poore said. “No one could say why her cancer wasn’t detected earlier or why it was resistant to the treatment they tried.”

As Poore came to learn through his college studies, cancer has traditionally been considered a disease of the human genome — mutations in our genes allow cells to avoid death, proliferate and form tumors.

But when Poore saw a 2017 study in Science that showed how microbes invaded a majority of pancreatic cancers and were able to break down the main chemotherapy drug given to these patients, he was intrigued by the idea that bacteria and viruses might play a bigger role in cancer than anyone had previously considered.

Poore is currently an MD/PhD student at University of California San Diego School of Medicine, where he’s conducting his graduate thesis work in the lab of Rob Knight, PhD, professor and director of the Center for Microbiome Innovation.

Together with an interdisciplinary group of collaborators, Poore and Knight have developed a novel method to identify who has cancer, and often which type, by simply analyzing patterns of microbial DNA — bacterial and viral — present in their blood.

The study, published March 11, 2020 in Nature, may change how cancer is viewed, and diagnosed.

“Almost all previous cancer research efforts have assumed tumors are sterile environments, and ignored the complex interplay human cancer cells may have with the bacteria, viruses and other microbes that live in and on our bodies,” Knight said.

“The number of microbial genes in our bodies vastly outnumbers the number of human genes, so it shouldn’t be surprising that they give us important clues to our health.”

Cancer-associated microbial patterns

The researchers first looked at microbial data available from The Cancer Genome Atlas, a database of the National Cancer Institute containing genomic and other information from thousands of patient tumors. To the team’s knowledge, it was the largest effort ever undertaken to identify microbial DNA in human sequencing data.

From 18,116 tumor samples, representing 10,481 patients with 33 different cancer types, emerged distinct microbial signatures, or patterns, associated with specific cancer types. Some were expected, such as the association between human papillomavirus (HPV) and cervical, head and neck cancers, and the association between Fusobacterium species and gastrointestinal cancers. But the team also identified previously unknown microbial signatures that strongly discriminated between cancer types. For example, the presence of Faecalibacterium species distinguished colon cancer from other cancers.

Armed with the microbiome profiles of thousands of cancer samples, the researchers then trained and tested hundreds of machine learning models to associate certain microbial patterns with the presence of specific cancers. The machine learning models were able to identify a patient’s cancer type using only the microbial data from his or her blood.

The researchers then removed high-grade (stage III and IV) cancers from the dataset and found that many cancer types were still distinguishable at earlier stages when relying solely on blood-derived microbial data. The results held up even when the team performed the most stringent bioinformatics decontamination on the samples, which removed more than 90 percent of the microbial data.

Applying the microbial DNA test

To determine if these microbial patterns could be useful in the real world, Knight, Poore and team analyzed blood-derived plasma samples from 59 consenting patients with prostate cancer, 25 with lung cancer and 16 with melanoma, provided by collaborators at Moores Cancer Center at UC San Diego Health. Employing new tools they developed to minimize contamination, the researchers developed a readout of microbial signatures for each cancer patient sample and compared them to each other and to plasma samples from 69 healthy, HIV-negative volunteers, provided by the HIV Neurobehavioral Research Center at UC San Diego School of Medicine.

The team’s machine learning models were able to distinguish most people with cancer from those without. For example, the models could correctly identify a person with lung cancer with 86 percent sensitivity and a person without lung disease with 100 percent specificity. They could often tell which participants had which of the three cancer types. For example, the models could correctly distinguish between a person with prostate cancer and a person with lung cancer with 81 percent sensitivity.

“The ability, in a single tube of blood, to have a comprehensive profile of the tumor’s DNA (nature) as well as the DNA of the patient’s microbiota (nurture), so to speak, is an important step forward in better understanding host-environment interactions in cancer,” said co-author Sandip Pravin Patel, MD, a medical oncologist and co-leader of experimental therapeutics at Moores Cancer Center at UC San Diego Health.

“With this approach, there is the potential to monitor these changes over time, not only as a diagnostic, but for long-term therapeutic monitoring. This could have major implications for the care of cancer patients, and in the early detection of cancer, if these results continue to hold up in further testing.”

Comparison to current cancer diagnostics

According to Patel, diagnosis of most cancers currently requires surgical biopsy or removal of a sample from the suspected cancer site and analysis of the sample by experts who look for molecular markers associated with certain cancers. This approach can be invasive, time-consuming and costly.

Several companies are now developing “liquid biopsies”— methods to quickly diagnose specific cancers using a simple blood draw and technologies that allow them to detect cancer-specific human gene mutations in circulating DNA shed by tumors. This approach can already be used to monitor progression of tumors for some types of already-diagnosed cancers, but is not yet approved by the U.S. Food and Drug Administration (FDA) for diagnostic use.

“While there has been amazing progress in the area of liquid biopsy and early cancer detection, current liquid biopsies aren’t yet able to reliably distinguish normal genetic variation from true early cancer, and they can’t pick up cancers where human genomic alterations aren’t known or aren’t detectable,” said Patel, who also serves as the deputy director of the San Diego Center for Precision Immunotherapy.

That’s why there’s often a risk that current liquid biopsies will return false-negative results in the setting of low disease burden. “It’s hard to find one very rare human gene mutation in a rare cell shed from a tumor,” Patel said. “They’re easy to overlook and you might be told you don’t have cancer, when you really do.”

According to the researchers, one advantage of cancer detection based on microbial DNA, compared to circulating human tumor DNA, is its diversity among different body sites. Human DNA, in contrast, is essentially the same throughout the body. By not relying on rare human DNA changes, the study suggests that blood-based microbial DNA readouts may be able to accurately detect the presence and type of cancers at earlier stages than current liquid biopsy tests, as well as for cancers that lack genetic mutations detectable by those platforms.

Limitations and cautions

The researchers are quick to point out that there’s still the possibility blood-based microbial DNA readouts could miss signs of cancer and return a false-negative result. But they expect their new approach will become more accurate as they refine their machine learning models with more data.

And while false negatives may be less common with the microbial DNA approach, false positives — hearing you have cancer when you don’t — are still a risk.

Patel said that just because a cancer is detected early, it doesn’t mean it always requires immediate treatment. Some DNA changes are non-cancerous, changes related to aging, harmless or self-resolve. You would never know about them without the test. That’s why more screening and more cancer diagnoses might not always be a good thing, Patel said, and should be determined by expert clinicians.

The team also cautioned that even if a microbial readout indicates cancer, the patient would likely require additional tests to confirm the diagnosis, determine the stage of the tumor and identify its exact location.

Looking ahead

Knight said many challenges still lay ahead as his team further develops these initial observations into an FDA-approved diagnostic test for cancer. Most of all, they need to validate their findings in a much larger and more diverse patient population, an expensive undertaking. They need to define what a “healthy” blood-based microbial readout might look like among many, diverse people. They’d also like to determine whether the microbial signatures they can detect in human blood are coming from live microbes, dead microbes or dead microbes that have burst open, dispersing their contents — an insight that might help them refine and improve their approach.

In the future, blood-based microbial DNA readouts might be used to detect a variety of different cancers.

To advance blood-based microbial DNA readouts through the next steps toward regulatory approval, commercialization and clinical application of a diagnostic test, Knight and Poore have filed patent applications and they founded a spinout company called Micronoma, with co-author Sandrine Miller-Montgomery, PhD, professor of practice in the Jacobs School of Engineering and executive director of the Center for Microbiome Innovation at UC San Diego.

The latest study may prompt important shifts in the field of cancer biology, Poore said.

“For example, it’s common practice for microbiologists to use many contamination controls in their experiments, but these have historically been rarely used in cancer studies,” he said. “We hope this study will encourage future cancer researchers to be ‘microbially conscious.’”

The researchers also suggest cancer diagnostics may only be the beginning for the newly discovered cancer-associated blood microbiome.

“This new understanding of the way microbial populations shift with cancer could open a completely new therapeutic avenue,” Miller-Montgomery said. “We now know the microbes are there, but what are they doing? And could we manipulate or mimic these microbes to treat cancer?”

Additional co-authors include: Qiyun Zhu, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Se Jin Song, Jad Kanbar, Robert Heaton, Rana McKay, Austin D. Swafford, UC San Diego; Evguenia Kopylova, formerly of UC San Diego, now at Clarity Genomics; and Jessica Metcalf, formerly of UC San Diego, now at Colorado State University, Fort Collins.

This research was funded, in part, by National Institutes of Health (grants and contracts 5T32GM007198-42, 5T32GM007198-43, R00AA020235, R01DA026334, P30MH062513, P01DA012065, P50DA026306, HHSN261201400008C and HHSN261201500003I) and the UC San Diego Chancellor’s Microbiome and Microbial Sciences Initiative.

Disclosures: Gregory Poore and Rob Knight have jointly filed U.S. Provisional Patent Application Serial No. 62/754,696 and International Application No. PCT/US19/59647 on the basis of this work. Poore, Knight and Sandrine Miller-Montgomery have started a company to commercialize the intellectual property. Knight is a member of the scientific advisory board for GenCirq, Inc., holds an equity interest in GenCirq, and can receive reimbursements for expenses up to $5,000 per year from the company. Knight, Miller-Montgomery and Austin D. Swafford are directors at the Center for Microbiome Innovation at UC San Diego, which receives industry research funding for various microbiome initiatives, but no industry funding was provided for this cancer microbiome project. Evguenia Kopylova is employed by Clarity Genomics, but the company did not provide funding for this study.


Treating Cancer with Plant Viruses: A Conversation with Nicole Steinmetz

Computer scientists receive $1 million DARPA grant to address information onslaught

Tajana Rosing

San Diego, Calif., March 9, 2020 -- By 2025, computers and other instruments will generate more than 175 zettabytes of data. For context, there are a billion terabytes in a zettabyte. If you’re wondering how all that information will be analyzed, you’re not alone. At present, only one percent of data produced worldwide is ever evaluated.

To help solve this problem, the Defense Advanced Research Projects Agency (DARPA) has awarded a $1 million grant to professors Tajana RosingSanjoy Dasgupta in the Department of Computer Science and Engineering and  professor Tara Javidi in the Department of Electrical and Computer Engineering to explore how hyperdimensional computing (HD) can help address this informational onslaught. The project is called HyDREA (Hyperdimensional Computing: Robust, Efficient and Accurate).

HD computing seeks to better replicate human brain power in silico. The “hyper” part comes from much larger data sizes. Instead of 32 or 64 bits, data can contain 10,000 bits or more.

“Let's imagine I have a 32-bit number,” said Rosing. “Today, each 32-bit number would have to be stored separately. But with hyperdimensional computing, I can combine the information into a single, 10,000-bit vector, which could, for example, represent all photos of a cat or all photos of a dog.”

Brains have similar mechanisms. Sensory data enters at relatively low dimensionality, but the mind expands those representations as it processes them. Data that started at a million bits can be enlarged to 200 million bits.

The 18-month HyDREA project will have to overcome a long list of technical challenges. Current memory isn’t really designed to handle these large datasets. In addition, the team will need to develop new ways to process data and handle large dimensionality without losing speed.

“One issue is encoding the data, or taking whatever data we're currently collecting that's in 32- or 64-bit numbers, and figuring out the right way to map it into high dimensional space,” said Rosing. “This encoding process takes the majority of the time, and we are looking at how we could make it run a lot faster.”

They also want to identify the best applications for HD computing. At present, no one fully understands all the possible HD applications, though that challenge is a bit downstream.

“If I have multiple nodes that can do hyperdimensional computing, how should they communicate the data?” asked Rosing. “Should they communicate the hypervectors? Should they communicate something we learned from the hypervectors? What happens if some data gets blocked? Do we lose a lot of accuracy?” These are just a few of the questions that the project seeks to address.

Overall, the team will have to develop new coding and decoding strategies, fast HD algorithms and efficient hardware. On this last point, the HyDREA team is collaborating with Northrop Grumman to test HD computing on the aerospace company’s stochastic computing chip.

“At the end of the project we'll hopefully have a couple of hardware implementations that will show the power of HD,” said Rosing. “We want to show that HD computing can be made a thousand times more efficient and faster than current machine learning without losing accuracy.”

UC San Diego's Qualcomm Institute Names Shirley Meng Associate Director

Shirley Meng, QI Associate Director

San Diego, Calif., March 10, 2020 --The Qualcomm Institute (QI) at UC San Diego has appointed nanoengineering professor Shirley Meng as its associate director. Meng will play a critical role in developing strategies that further enhance QI’s mission to accelerate technology-driven innovation and to educate current and future generations of innovators. She will succeed Rajesh Gupta, director of the Halıcıoğlu Data Science Institute at UC San Diego, who served as associate director since 2009. 

“We are delighted and honored to have Shirley Meng join the QI leadership team,” said Ramesh Rao, director of the Qualcomm Institute. “Professor Meng is a world-renowned researcher with a proven record of building strong collaborations that spur innovation. She is also a tireless educator whose dedication to the student experience here at UC San Diego is well known and will be critical as QI increases its engagement with students.”   

Meng, who joined the UC San Diego faculty in 2009, is a leader in developing novel battery technologies that are driving a low-carbon, more sustainable future. As the principal investigator of the Laboratory for Energy Storage and Conversion, she leads a research team that is pioneering smaller, more efficient batteries that can harness wind and solar energy to fuel items like electric vehicles and the stations used to charge them. 

Meng joins QI as it celebrates its twentieth year of promoting innovation and collaboration in the areas of culture, energy, the environment and health. QI, the University of California San Diego division of the California Institute for Telecommunications and Information Technology, is an interdisciplinary research and education institute. It was founded to promote discovery and innovation and educate new generations who can translate scientific discoveries into new applications, industries, businesses and jobs in California. 

In her new position, Meng will play a critical role in developing the strategic vision for the institute’s future. Meng has a long history with QI going back to her earliest days on campus. She is a supporter and frequent user of QI’s Nano3 nanofabrication facilities, where she and her students design and develop new nano-materials and nano-structures for advanced energy storage and conversion applications. She also serves on the Nano3 Faculty Oversight Committee.

“I am honored to accept this role. QI is the incubator for the best talents and transformative ideas, and has always promoted interdisciplinary research between science, technology, policy and society,” Meng said.

Meng received her doctorate in advanced materials for micro and nano systems from the Singapore-MIT Alliance in 2005, after which she worked as a postdoctoral research fellow and became a research scientist at MIT. 

She is the founding director of the Sustainable Power and Energy Center at the UC San Diego Jacobs School of Engineering and the inaugural director of the UC San Diego Institute for Materials Discovery and Design. Meng is also the inaugural holder of the Zable Endowed Chair in Energy Technologies in the UC San Diego Jacobs School of Engineering. 

Meng has authored or co-authored more than 190 peer-reviewed journal articles, one book chapter and four patents. She is the recipient of a number of awards, including a National Science Foundation CAREER Award, the UC San Diego Chancellor’s Interdisciplinary Collaboratories Award, the Charles W. Tobias Award from the Electrochemical Society and the International Battery Association Research Award.

UC San Diego synthetic biologists redesign the way bacteria 'talk' to each other

An innovative bacterial communication system, regulated by a safe biological compound, achieves precise control of single and multiple bacterial populations.

San Diego, Calif., March. 4, 2004 --

Bioengineers at the University of California San Diego have redesigned how harmless E. coli bacteria “talk” to each other. The new genetic circuit could become a useful new tool for synthetic biologists who, as a field, are looking for ways to better control the bacteria they engineer to perform all sorts of tasks, including drug delivery, bioproduction of valuable compounds, and environmental sensing.

What’s new about the UC San Diego control strategy of the E. coli that serve as workhorses of synthetic biology? The bacterial cells within a population are engineered to be unable to communicate with each other through chemical signals unless one particular external molecule is present.

This work is published in the March 4, 2020 issue of the journal Nature Communications.

“We hope that this system can increase control and safety of synthetic genetic circuits, and therefore facilitate their transition to real life applications,” said Arianna Miano, a UC San Diego bioengineering PhD student and the first author on the Nature Communications paper.

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“We hope that this system can increase control and safety of synthetic genetic circuits, and therefore facilitate their transition to real life applications,” said Arianna Miano, a UC San Diego bioengineering PhD student and the first author on the Nature Communications paper. Miano also wrote a blog post for Nature, which is available here.

This work is from the UC San Diego lab led by Jeff Hasty, who is a professor of bioengineering at the Jacobs School of Engineering, and of biology in the Division of Biological Sciences.

Traditionally, synthetic biologists use native bacterial communication systems, known as quorum sensing, to control the bacterial communities they use for tasks such as targeted drug delivery.

Quorum sensing in bacteria is based on the production, diffusion and reception of small signaling molecules between bacterial cells within a population. The majority of these systems rely on the internal resources of each cell for the production of the signaling molecule.

One of the challenges of quorum sensing systems is that they are hard to externally regulate. To address this issue, the UC San Diego researchers created an “inducible quorum sensing system.” It is designed to give synthetic biologists better control of bacterial communication systems -- and thus better control of the useful tasks these bacterial communities are performing.

Inspired by a genetic circuit found in the photosynthetic bacterium Rhodopseudomonas palustris and first described in the academic literature in 2008, the UC San Diego researchers created a quorum sensing system that only functions when the bacterial are provided with a plant-derived compound called p-coumaric acid. This compound is found in most fruits and vegetables. 

“The bacteria coordinate differently according to how much of the p-coumaric acid we provide in the media,” said Miano. “If we give no p-coumaric acid, the bacteria can't communicate with each other, but when we provide them with medium concentrations they are able to signal and share information on the size of their colony.”

“If we give them too much, they over-produce signaling molecules which tricks them into behaving as if they were always part of a large population,” said Miano.

The UC San Diego bioengineers demonstrated their inducible quorum sensing circuit, which can control bacterial cell coordination in time and space, by co-expressing it with a lysis gene.

The choice to demonstrate via a lysis gene builds on previous projects from the Hasty lab at UC San Diego, including research demonstrating how bacteria lysis could be used to deliver cancer-killing drugs around a tumor.

In the new work, the UC San Diego researchers demonstrated how the inducible quorum sensing could greatly expand control over this cargo delivery platform, compared to currently available native quorum sensing systems.

In particular, the researchers used low and medium concentrations of p-coumaric acid to cause populations of bacteria with both the new inducible quorum sensing circuit and the lysis gene to switch between no delivery and steady oscillations of cargo delivery.

Using a lysis gene and traditional quorum sensing system, the cargo would only be delivered when the bacteria reached a high enough concentration.

“We have just scratched the surface of the potential of this communication system. We are excited to see the applications that will follow by coupling it to the expression of different genes,” said Miano.

The researchers also demonstrated that subjecting bacteria to high concentrations of p-coumaric acid wiped out all the cells by forcing them to constantly produce the lysis proteins, independent of population size. (See video below)


Paper title: “Inducible cell-to-cell signaling for tunable dynamics in microbial communities,” in the March 4 2020 issue of Nature Communications.

Authors: Arianna Miano, Michael J. Liao, and Jeff Hasty at the University of California San Diego.

Funding: This work was supported by the National Science Foundation (NSF) award MCB1616997.

Scientists Design Way to Use Harmless Bacteria to Detect Heavy Metals in Drinking Water

(L-R)  Gregoire Thouvenin and Nicholas Csicsery in the UCSD Biodynamics Lab run by bioengineering and biology professor Jeff Hasty at UC San Diego.

San Diego, Calif., February 27, 2020 -- When it comes to testing drinking water for dangerous contaminants, such as heavy metals like lead or cadmium, continuous testing directly from faucets people drink from is important. Yet, very little of this kind of water testing is done. A team from UC San Diego and the campus spinout Quantitative BioSciences is working to improve the situation.

Natalie Cookson (UC San Diego bioengineering Ph.D. ‘08) is the CEO Quantitative BioSciences, a startup which spun out of the Hasty lab at UC San Diego.

“Water might be fine to drink, fine to drink, fine to drink...and then it’s not,” said UC San Diego bioengineering alumna Natalie Cookson (‘08) as she explained the value of continuous monitoring of drinking water, as compared to sporadic water monitoring.

She hopes this work will produce affordable water testing systems that can be installed at the faucets that people actually drink from. The water that was leaving the treatment plant in Flint Michigan, for example, didn’t have dangerously high levels of lead. But by the time that same water poured from faucets of Flint residents, lead was in the water.

A team from UC San Diego and Quantitative BioSciences has a new approach to continuous monitoring of heavy metal contamination in drinking water using bacteria as sensors of contamination. The team recently published their advances in the journal Proceedings of the National Academy of Science (PNAS).

“Our top priority is to do work we feel proud of and will have an impact,” said Cookson.

While some options for residential water testing of heavy metals do exist, there are technical, cost and logistical limitations that are getting in the way of widespread, continuous monitoring of tap water inside homes, schools and farms. The San Diego team is looking to remove these barriers.

E. coli as the water testers

The new water monitoring approach relies on harmless strains of E. coli bacteria to actually detect heavy metal contaminants. While E. coli makes headlines in connection with food poisoning, harmless strains of the microbe are used in labs around the world for many different research purposes.

They are the lab rats of the bacterial world.

“Ok E. coli,” said Nick Csicsery. “If arsenic is there and you know it, let us know.”

Sometimes the E. coli knew and sometimes they didn’t, “depending on the metal,” explained Csicsery. He recently earned his bioengineering Ph.D. in the Hasty lab at UC San Diego and has joined Quantitative BioSciences, where he’s working on developing synthetic biology-based monitoring techniques.

UC San Diego bioengineers Nicholas Csicsery, Lizzy Stasiowski, Gregoire Thouvenin in the UCSD Biodynamics Lab run by bioengineering and biology professor Jeff Hasty at UC San Diego.

How do these microbes “let us know” about the presence of a dangerous heavy metal in the water?

The answer is that bacterial genomes react to contaminants in ways that humans have learned to recognize.

“We have access to the code of life that surrounds us,” said Gregoire Thouvenin, a UC San Diego bioengineering Ph.D. student and another of the co-first authors on the PNAS paper. “When you’re studying microbes, you dig deeper and you realize they are more connected to everything else than you initially thought.”

In this case, harnessing these connections required researchers from many fields including bioengineering, synthetic biology, microfluidics, mathematics and data science to combine forces. The result is a system that monitors water for two weeks and recognizes when contaminants in the water change the genetic behavior of 2,000 different strains of bacteria.

E. coli hotel

In this bacteria-driven water testing system, each strain of bacteria lives inside its own small chamber, and all 2,000 strains are lined up in the same chip made of a hard translucent material. There are tiny channels that deliver water, contaminants and food to each of the chambers in a controlled way.

2000-strain microfluidic device loaded with blue dye. Each teal-colored splotch corresponds to a single growth chamber for light-producing E. coli. Fluorescence values are extracted from each teal colored splotch (they are lightbulb shaped if you look carefully) to monitor the unique response of each E. coli strain to environmental inputs. The design allows each chamber to be continuously fed with growth media while waste flows away. Growth media can be spiked with water samples to be tested for heavy metal detection.

These 2,000 bacterial strains each have a bit of genetic material inserted into a small circular piece of its DNA (a plasmid) that enables a fluorescence output to “highlight” the activity of a specific gene. When a water contaminant interacts with the inserted gene, the bacteria light up.

With their microfluidics setup, the researchers can record which strains light up when. This pattern of blinking is recorded and fed into an artificial intelligence system. The outcome is an automated ability to identify when the bacteria encounter specific heavy metal contaminants in the water, based on the pattern of lights being produced by the bacteria. Bioengineering Ph.D. student Garrett Graham led the data science and artificial intelligence part of the project. (He graduated and is working as a climate data analyst at the North Carolina Institute for Climate Studies.)

The idea is for the systems to be installed in places where people actually drink water, in order to identify contaminated water.

While the researchers chose heavy-metal identification in order to demonstrate the power and flexibility of their system, the artificial intelligence components of it could be trained to identify other contaminants as well.

The art and science of making

One of the big advances for this project was figuring out how to design, build and run the system for inserting, housing, feeding and keeping track of the 2,000 different strains of bacteria over the course of two weeks.

Lizzy Stasiowski and Nick Csicsery led the design and fabrication of the system which allows for all 2,000 E. coli strains to be loaded into the system at once.

This project merged the art and science of “making” with synthetic biology, genomic analysis and machine learning, to create a system poised to do good in the world.

“One of my favorite things about this project is how versatile it can be. Our system allows you to monitor dynamic changes in gene expression for thousands of bacterial strains simultaneously to any environmental change. It’s a project that’s relevant for both industry and academia,” said Stasiowski.

She recently finished her bioengineering Ph.D. at UC San Diego and is a Vertex Pharmaceuticals Fellow in San Diego working on instrumentation research and development.

“While I find the focus on heavy metals interesting in terms of a careful proof of concept, I am most excited about the technology as a screening tool for researchers and companies that focus on synthetic biology,” said Jeff Hasty, a UC San Diego professor of bioengineering and biology who is the senior author on the PNAS paper. “The technology is well-positioned for the discovery of genes that respond to complex signals that are found in environmental and medical applications.”

Used as a screening tool, the platform’s unique combination of microfluidics and artificial intelligence could help shed new light on the mechanisms that enable cells to interpret and react to changing environments, and enable the testing of synthetic strains designed to interact with the environment in new ways. Existing screening techniques rarely have both the temporal resolution and throughput needed to do so. Hence the platform has the potential to be of great value to both synthetic biologists (who design and implement new functions in living cells) and systems biologists (who build comprehensive models of all reactions occuring in a cell).

Thouvenin waxed a bit more philosophical. “Living things around us are malleable and they’ve been beautifully shaped and crafted by evolution over millions of years. And now we have access to that, both in terms of understanding it, repurposing it, and ultimately optimizing it for a changing world.”

PNAS Paper citation: "Genome-scale transcriptional dynamics and environmental biosensing," by Garrett Graham a,1, Nicholas Csicsery a,1, Elizabeth Stasiowski a,1, Gregoire Thouvenin a,1, William H. Mather b, Michael Ferry b, Scott Cookson b, and Jeff Hasty a,b,c,d,2

Affiliations key:

a Department of Bioengineering, University of California San Diego, La Jolla, CA 92093; b Quantitative BioSciences, Inc., San Diego, CA 92121; c Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093; and d BioCircuits Institute, University of California San Diego, La Jolla, CA 92093

 Funding: This work was supported by the Defense Advanced Research Projects Agency.

Competing interest statement from PNAS paper: William H. Mather, Michael Ferry, Scott Cookson, and Jeff Hasty have a financial interest in Quantitative BioSciences. Quantitative BioSciences has an exclusive license to IP stemming from this work, which is owned by the University of California San Diego.

Light-shrinking device enables detection of ultra-tiny substances

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Illustration of the multilayered periodic plasmonic structure supporting exceptional points (EPs). Image courtesy of Kanté lab/Nature Physics

San Diego, Calif., Feb. 25, 2020 -- Engineers at the University of California San Diego and the University of California Berkeley have created light-based technology that can detect biological substances with a molecular mass more than two orders of magnitude smaller than previously possible. The advance was made possible by building a device that shrinks light while exploiting mathematical singularities known as exceptional points (EPs).

The research, published in Nature Physics, could lead to the development of ultra-sensitive devices that can quickly detect pathogens in human blood and considerably reduce the time needed for patients to get results from blood tests.

“Our goal is to overcome the fundamental limitations of optical devices and uncover new physical principles that can enable what was previously thought impossible or very challenging,” said Boubacar Kanté, associate professor of electrical engineering and computer sciences and faculty scientist at Lawrence Berkeley National Laboratory, who led the work while a professor of electrical and computer engineering at UC San Diego. “What I’m really excited about is the ability to implement such singularities at such a small scale. The results are both fundamentally exciting and practically important.”

The wavelength of light is much larger than the size of most biologically relevant substances. For light to strongly interact with these small substances, its wavelength must be reduced.

The researchers used plasmons, which are small fluids of electronic waves that can move back and forth in metallic nanostructures.

The group placed two plasmonic nano-antenna arrays on top of each other with each array producing plasmon resonances that control light waves of a certain frequency. The researchers then “coupled” the nano-antenna arrays, pushing the two waves to come together until they finally resonated at the same frequency and, most critically, lost energy at the same rate—a moment known as the exceptional point. This marked the first time researchers have used EPs for plasmons.

When an external substance comes into contact with the EP and disturbs the synchronized rates of lost energy, the device detects the substance with higher sensitivity.

"While many methods have been explored to make biosensors more sensitive, using the EP of coupled plasmonic nano-antenna arrays to raise sensitivity is a unique approach. It alters the basic relation between the signal and the target concentration (or copy number) from a simple linear relation to a square-root equation, which is key to the superb sensitivity of the design," said Yu-Hwa Lo, electrical and computer engineering professor at the UC San Diego Jacobs School of Engineering and co-author on the study.

The device detected anti-Immunoglobulin G in blood, the most common antibody in human blood to fight infection, at a molecular weight 267 times lighter than in previous reports using plasmonic arrays.

Adding additional plasmonic arrays to the original device could also further boost the sensitivity at the EP, Kanté said.


Paper title: "Symmetry-breaking-induced plasmonic exceptional points and nanoscale sensing." Co-authors include Jun-Hee Park, Abdoulaye Ndao, Wei Cai, Liyi Hsu, Ashok Kodigala and Thomas Lepetit.

This research was supported by the National Science Foundation Career Award (ECCS-1554021), the Office of Naval Research Young Investigator Award (N00014-17-1-2671) and the ONR JTO MRI Award (N00014-17-1-2442). The work was partially supported by the DARPA DSO-NLM Program (no. HR00111820038) and the US Department of Energy (grant DE-EE0007341). The work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) at UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which is supported by the National Science Foundation (grant ECCS-1542148). 

Researchers Develop Framework that Improves Firefox Security

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A snippet of the RLBox code

Computer scientists develop a technique to protect browsers from buggy third-party libraries

San Diego, Calif., Feb. 25, 2020 -- Researchers from the University of California San Diego, University of Texas at Austin, Stanford University and Mozilla have developed a new framework to improve web browser security. The framework, called RLBox, has been integrated into Firefox to complement Firefox’s other security-hardening efforts.

RLBox increases browser security by separating third-party libraries that are vulnerable to attacks from the rest of the browser to contain potential damage—a practice called sandboxing. The study will be published in the proceedings of the USENIX Security Symposium in March.

Browsers, like Firefox, rely on third-party libraries to support media decoding (e.g., rendering images or playing audio files) among many other functionalities. These libraries are often written in low-level programming languages, like C, and highly optimized for performance.

"Unfortunately, bugs in C code are often security vulnerabilities—security vulnerabilities that attackers are really good at exploiting," noted senior author Deian Stefan, an assistant professor with UC San Diego’s Department of Computer Science and Engineering.

RLBox allows browsers to continue to use off-the-shelf, highly tuned libraries without worrying about the security impact of these libraries. "By isolating libraries we can ensure that attackers can’t exploit bugs in these libraries to compromise the rest of the browser," said the lead PhD student on the project, Shravan Narayan.

A key piece of RLBox is the underlying sandboxing mechanism, which keeps a buggy library from interfering with the rest of the browser. The study investigates various sandboxing techniques with different trade-offs. But the team ultimately partnered with the engineering team at San Francisco-based Fastly to adopt a sandboxing technique based on WebAssembly, a new intermediate language designed with sandboxing in mind. The team believes that WebAssembly will be a key part of future secure browsers and secure systems more broadly. The WebAssembly sandboxing effort is detailed in a recent Mozilla Hacks blog post.

“Unfortunately, it’s not enough to put a library in a sandbox, you need to carefully check all the data that comes out of the sandbox—otherwise a sophisticated attacker can trick the browser into doing the wrong thing and render the sandboxing effort useless, " said Stefan. RLBox eliminates these classes of attacks by tagging everything that crosses the boundary and ensuring that all such tagged data is validated before it is used.

RLBox has been integrated into Mozilla’s Firefox and will be shipping to Linux users in Firefox 74 and Mac users in Firefox 75, with plans to implement in other platforms.

"This is a big deal," says Bobby Holley, principal engineer at Mozilla. "Security is a top priority for us, and it’s just too easy to make dangerous mistakes in C/C++. We’re writing a lot of new code in Rust, but Firefox is a huge codebase with millions of lines of C/C++ that aren’t going away any time soon. RLBox makes it quick and easy to isolate existing chunks of code at a granularity that hasn’t been possible with the process-level sandboxing used in browsers today."


In the study, the team isolated half a dozen libraries using RLBox. To start, Firefox will ship with their sandboxed Graphite font shaping library. Mozilla plans to apply the sandboxing more broadly in the future, ultimately making millions of users’ browsers more secure.

Other authors included: Craig Disselkoen and Sorin Lerner at UC San Diego; Hovav Shacham at  UC San Diego and UT Austin; Nathan Froyd and Eric Rahm at Mozilla; and Tal Garfinkel at Stanford University.fi9r

Barrett Romasko: structural engineer

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Ronald Graham -- Click Here to visit JSOE FlickrB

By Daniel Li

San Diego, Calif., Feb. 25, 2020 -- Barrett Romasko’s path in college has been full of exploration. Romasko, a senior majoring in structural engineering with a focus on aerospace structures, applied to UC San Diego without knowing much about the different applications of structural engineering, assuming it only involved civil engineering structures. His willingness to seek out new opportunities — through on-campus activities, classes, and internships — has been a contributing factor in helping him figure out his interests and goals for the future. 

On campus, Romasko is heavily involved in the UC San Diego Society of Civil and Structural Engineers (SCSE), which has three technical project teams that students can join to get hands-on structural engineering experience: steel bridge, concrete canoe, and seismic design. Romasko has been part of the steel bridge project team since his sophomore year –he was the team’s welding lead his junior year and is currently the project manager. 

The steel bridge project challenges students to design, fabricate, and construct a scaled model bridge that stays competitive in terms of the lightest weight, greatest stiffness, and fastest construction speed. The students start preparing their bridge each fall and bring it to the annual Pacific Southwest Conference each year to see how it stacks up to the competition.

“We start the design process in fall quarter, which generally consists of using a lot of design software and analysis,” Romasko said. “Winter quarter is dedicated to fabrication, so the team takes the design to a machining space and manufactures each component of the bridge. The last stage is construction, which is when we practice assembling each member of the bridge according to the regulations that we received in preparation for the competition.”

According to Romasko, the hardest part of the competition is getting all the components fabricated by the competition in April. That was compounded this year, as the team had to find a new location to fabricate their bridge, as the location they’d been using for 18 years was no longer available. Romasko and his co-project manager got to work and were able to come up with a solution.

Despite unexpected challenges, Romasko has enjoyed working on the steel bridge project the past three years. His favorite parts about steel bridge: the teamwork and hands-on learning aspect.

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Members of the steel bridge team.

“I really like steel bridge because you get to apply what you learn in class to a real project and work with so many cool, motivated people,” Romasko said. “You also start to understand important industry concepts such as fabrication and tolerancing.”

Romasko encourages students to get involved in student groups as early as possible, and stresses the importance of finding organizations that are not only career focused, but also fun. 

“Joining the steel bridge project has introduced me to so many new people that I wouldn’t have met otherwise,” he said. “It has been a good way for me to make friends who share like-minded interests.”

In addition to their hands-on technical projects, SCSE organizes two main community outreach events each year: Seismic Outreach and Esperanza International. 

“Seismic outreach consists of us going to schools to teach elementary and middle school students about how to design for seismic safety and teach them about earthquakes,” Romasko said. “The goal is to get these students more interested in STEM fields. We also have another event where we go down to Rosarito in Mexico with an organization called Esperanza International, and put our engineering skills to use as we help build houses for the less fortunate.”

In addition to his involvement in SCSE, Romasko is a research assistant in Professor Machel Morrison’s lab, where he works on projects related to metallography and mechanics of materials. He’s also nabbed several internships over the summers, working at the Naval Surface Warfare Center in 2018 and General Atomics in 2019. 

“Internships are valuable because you can get direct experience in the industry,” Romasko said. “The internships that I have done really allowed me to see what I could do with my major and what I don’t want to do with my major. For example, at General Atomics, I was a manufacturing engineering intern; after the summer, I realized that although it was a great learning experience, I wouldn’t want to do it as a career. I feel that it is important for everyone to explore different areas to find what they’re most passionate about, and even more importantly, to find what they aren’t passionate about.”

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The steel bridge team with their bridge. 

Romasko came to UC San Diego thinking that he was going to follow the civil structures route in the structural engineering department, but during his internship at the Naval Surface Warfare Center, he realized that aerospace structures were more interesting to him. Without that internship, Romasko said he fears he would never have changed to the aerospace structures focus.

Romasko is returning to UC San Diego to complete a master’s degree in structural engineering this fall. In the future, he hopes to work abroad for a couple years, either in Australia, Europe, or New Zealand.

“I would love to work outside of the United States for two to three years doing something related to aerospace structures,” Romasko said. “One of my dream companies to work at is Virgin Galactic, which specializes in developing commercial spacecraft.”

This wearable device camouflages its wearer no matter the weather

San Diego, Calif., March 2, 2020 -- Researchers at the University of California San Diego developed a wearable technology that can hide its wearer from heat-detecting sensors such as night vision goggles, even when the ambient temperature changes--a feat that current state of the art technology cannot match.  The technology can adapt to temperature changes in just a few minutes, while keeping the wearer comfortable.

The device, which is at the proof-of-concept stage, has a surface that quickly cools down or heats up to match ambient temperatures, camouflaging the wearer’s body heat. The surface can go from 10 to 38 degrees Celsius (50 to 100.5 degrees Fahrenheit) in less than a minute. Meanwhile, the inside remains at the same temperature as human skin, making it comfortable for the wearer. The wireless device can be embedded into fabric, such as an armband. A more advanced version could be worn as a jacket.

To build the device, the team turned to a phase-changing material that’s similar to wax but with more complex properties. The melting point of the material is 30 degrees Celsius (roughly 86 degrees F), the same temperature as the surface temperature of human skin. If the temperature on the outside of the device is higher than that, the material will melt and stabilize, insulating the wearer; if colder, it will slowly solidify, still acting as an insulating layer.

The team, led by UC San Diego mechanical and aerospace engineering professor Renkun Chen, detailed their work in a recent issue of the journal Advanced Functional Materials

At the technology’s core are materials that can create heating or cooling effects when the ambient temperature changes, and flexible electronics that can be embedded into clothing. The outside layer of the device is driven by a technology that Chen and colleagues detailed in a paper in Science Advances in May 2019. It is made of thermoelectric alloys—materials that use electricity to create a temperature difference—sandwiched between stretchy elastomer sheets. It is powered by a battery and controlled by a wireless circuit board. The device physically cools or heats to a temperature that the wearer chooses.

Current state of the art heat camouflage technology consists of a surface coating that changes how much heat clothing emits at the surface. The coating absorbs the heat from the wearer’s body and reflects only enough energy to match the ambient temperature. However, the coating only works at a predetermined temperature. If the ambient temperature rises or falls, it no longer works.

The researchers’ biggest challenge now is to scale up the technology. Their goal is to create a jacket with the technology built-in, but under current conditions, the garment would weigh 2 kilograms (about 4.5 lbs.), be about 5 millimeters thick and only function for one hour. The team will be looking to find lighter, thinner materials so the garment could weigh two or three times less.

The work was supported by the Advanced Research Project Agency and by a UC San Diego start up grant. It work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) at UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which is supported by the National Science Foundation.

An Adaptive and Wearable Thermal Camouflage Device

Sahngki Hong and Renkun Chen, University of California San Diego

Sunmi Shin, National University of Singapore

Controlling CAR T cells with light selectively destroys skin tumors in mice

San Diego, Calif., Feb. 19, 2020 -- Bioengineers at the University of California San Diego have developed a control system that could make CAR T-cell therapy safer and more powerful when treating cancer. By programming CAR T cells to switch on when exposed to blue light, the researchers controlled the cells to destroy skin tumors in mice without harming healthy tissue.

In tests in mice, administering the engineered CAR T cells and stimulating the skin tumor sites with blue LED light reduced tumor size by eight to ninefold. The results were observed in nine out of ten mice tested. Engineered CAR T cells on their own did not inhibit tumor growth.  

The work is published Feb. 19 in Science Advances.

Chimeric antigen receptor (CAR) T-cell therapy is a promising new approach to treat cancer. It involves collecting a patient’s T cells and genetically engineering them to express special receptors on their surface that can recognize an antigen on targeted cancer cells. The engineered T cells are then infused back into the patient to find and attack cells that have the targeted antigen on their surface.

While this approach has worked well for some types of blood cancer and lymphoma, it so far has not worked well against solid tumors. One reason is because many targeted cancer antigens are also expressed on healthy cells. 

“It is very difficult to identify an ideal antigen for solid tumors with high specificity so that CAR T cells only target these diseased tumor sites without attacking normal organs and tissues,” said Peter Yingxiao Wang, a professor of bioengineering at the UC San Diego Jacobs School of Engineering and the senior author of the study. “Thus, there is a great need to engineer CAR T cells that can be controlled with high precision in space and time.”

To create such cells, Wang and his team installed an on-switch that would allow them to activate the CAR T cells at a specific site in the body. The switch uses two engineered proteins located inside the CAR T cell that bind when exposed to one-second pulses of blue light. Once bound together, the proteins trigger expression of the antigen-targeting receptor. 

Since light cannot penetrate deeply in the body, Wang envisions that this approach could be used to treat solid tumors near the surface of the skin. For future studies, Wang is looking to collaborate with clinicians to test the approach on patients with melanoma.

Paper title: “Engineering Light-controllable CAR T Cells for Cancer Immunotherapy.” Co-authors include Ziliang Huang*, Yiqian Wu*, Molly Allen, Yijia Pan, Phillip Kyriakakis, Shaoying Lu, Ya-Ju Chang, Xin Wang and Shu Chien, UC San Diego.


*These authors contributed equally to this work.

This work is supported by the National Institutes of Health and UC San Diego. 

Electrical engineering student wins prestigious aerospace defense award

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Tanish Jain, center, and Shlok Misra, right, accept their award at a USAIRE meeting in Paris. Photos courtesy of USAIRE

San Diego, Calif., Feb. 19, 2020 -- Tanish Jain, an electrical engineering undergraduate student at UC San Diego, earned second place in the USAIRE Student Award competition for a 10-page paper on the aerospace defense capabilities and strategies of Israel and India, two burgeoning powers in an increasingly multipolar world.

Jain and his research partner, Shlok Misra, a friend from high school and an aeronautical science major at Embry-Riddle Aeronautical University in Daytona Beach, were one of five finalist teams honored by the Association of United States and European Aerospace Industries Representatives (USAIRE) at their annual meeting in Paris in November.

Jain is involved in machine learning research and is interested in how ML can be applied to defense technologies, while Misra researches aviation safety and human factors in aviation. Their combination of interests motivated them to participate in the USAIRE competition.

“Since the topic of the paper was in line with our interests and related to our research areas, we thought it would be interesting to explore it,” Jain said. “At the time, we didn’t really think we would win, and just thought it was an exciting topic to research and write about over the summer.

“We looked at India and Israel specifically because they are emerging defense powers that have similar geopolitical situations, and we’re seeing how they could be a model for other countries in general to navigate the space of a newly protectionist, multipolar world; where do they source equipment from, how do their domestic industries deal with changing geopolitics?”

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Misra and Jain with their 2nd place plaques. 

In addition to being flown to Paris to attend the USAIRE meeting, they also received scholarship funds, two additional tickets to Paris, several aircraft display models, and a visit to the AAR aviation services facility in Miami.

At UC San Diego, Jain studies electrical and computer engineering with a focus on machine learning and controls.

This summer, he’ll be conducting research on ML-enabled drones to augment human vision and senses in Professor Tara Javidi’s lab, before working toward his master’s degree—location TBD!

On campus, he’s the Project Director for Project in a Box, a student organization that aims to promote hands-on engineering skills that can complement theoretical classes through supporting project development, workshops, and developing self-contained project kits for students from elementary school through college.

Jain is also testing his entrepreneurial skills, working with five other students on a startup called SoleInTech to help people with Parkinson’s disease walk more steadily and monitor the progression of their condition more effectively. The shoe insole they’re developing uses ML to conduct gait analysis as the user walks to detect changes in the progression of their Parkinson’s, and provides vibrational feedback to help the user walk more steadily. The idea was generated during the UC San Diego Department of Electrical and Computer Engineering’s Design Competition in 2019, which was focused on creating solutions for people with Parkinson’s disease. The team of six students has followed through with their concept, and is working in UC San Diego student startup center The Basement to further develop their prototype so it’s ready for more patient trials. 

Ultrasound device improves charge time and run time in lithium batteries

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This ultrasound-emitting device is an integral part of the battery.
Full photo gallery

 The device brings lithium metal batteries one step closer to commercial viability

San Diego, Calif., Jan. 27, 2020 -- Researchers at the University of California San Diego developed an ultrasound-emitting device that brings lithium metal batteries, or LMBs, one step closer to commercial viability. Although the research team focused on LMBs, the device can be used in any battery, regardless of chemistry. 

The device that the researchers developed is an integral part of the battery and works by emitting ultrasound waves to create a circulating current in the electrolyte liquid found between the anode and cathode. This prevents the formation of lithium metal growths, called dendrites, during charging that lead to decreased performance and short circuits in LMBs.

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The device is made from off-the-shelf smartphone components. 

The device is made from off-the-shelf smartphone components, which generate sound waves at extremely high frequencies—ranging from 100 million to 10 billion hertz. In phones, these devices are used mainly to filter the wireless cellular signal and identify and filter voice calls and data. Researchers used them instead to generate a flow within the battery’s electrolyte.

“Advances in smartphone technology are truly what allowed us to use ultrasound to improve battery technology,” said James Friend, a professor of mechanical and aerospace engineering at the Jacobs School of Engineering at UC San Diego and the study’s corresponding author.

Currently, LMBs have not been considered a viable option to power everything from electric vehicles to electronics because their lifespan is too short. But these batteries also have twice the capacity of today’s best lithium ion batteries. For example, lithium metal-powered electric vehicles would have twice the range of lithium ion powered vehicles, for the same battery weight.

Researchers showed that a lithium metal battery equipped with the device could be charged and discharged for 250 cycles and a lithium ion battery for more than 2000 cycles. The batteries were charged from zero to 100 percent in 10 minutes for each cycle.

“This work allows for fast-charging and high energy batteries all in one,” said Ping Liu, professor of nanoengineering at the Jacobs School and the paper’s other senior author. “It is exciting and effective.”

The team details their work in the Feb. 18 issue of the journal Advanced Materials

Goto FlickrPh.D. student An Huang holds a lithium metal battery equipped with the device. 

Most battery research efforts focus on finding the perfect chemistry to develop batteries that last longer and charge faster, Liu said. By contrast, the UC San Diego team sought to solve a fundamental issue: the fact that in traditional metal batteries, the electrolyte liquid between the cathode and anode is static. As a result, when the battery charges, the lithium ion in the electrolyte is depleted, making it more likely that lithium will deposit unevenly on the anode.  This in turn causes the development of needle-like structures called dendrites that can grow unchecked from the anode towards the cathode, causing the battery to short circuit and even catch fire. Rapid charging speeds this phenomenon up.

By propagating ultrasound waves through the battery, the device causes the electrolyte to flow, replenishing the lithium in the electrolyte and making it more likely that the lithium will form uniform, dense deposits on the anode during charging.

The most difficult part of the process was designing the device, said An Huang, the paper’s first author and a Ph.D. student in materials science at UC San Diego. The challenge was working at extremely small scales, understanding the physical phenomena involved and finding an effective way to integrate the device inside the battery.

“Our next step will be to integrate this technology into commercial lithium ion batteries,” said Haodong Liu, the paper’s co-author and a nanoengineering postdoctoral researcher at the Jacobs School.

The technology has been licensed from UC San Diego by Matter Labs, a technology development firm based in Ventura, Calif. The license is not exclusive.

The work was funded by the U.S. Department of Energy and the Accelerating Innovation to Market team at UC San Diego.  It is protected by patents: US#16/331,741-- “Acoustic wave based dendrite prevention for rechargeable batteries” and provisional# 2019-415 -- “Chemistry-agnostic prevention of ion depletion and dendrite prevention in liquid electrolyte”.

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All study coauthors. From left: Professor Ping Liu, postdoctoral researcher Haodong Liu, Ph.D. student An Huang and Professor James Friend, all from UC San Diego. 

Advanced Materials paper: Enabling rapid charging lithium metal batteries via surface acoustic wave-drive electrolyte flow

An Huang and James Friend, Department of Mechanical and Aerospace Engineering, UC San Diego

Ping Liu and Haodong Liu, Department of NanoEngineering, UC San Diego


New chip brings ultra-low power Wi-Fi connectivity to IoT devices

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A set of ultra-low power Wi-Fi radios integrated in small chips, each measuring 1.5 square millimeters in area (grain of rice shown for scale). Photos by David Baillot/UC San Diego Jacobs School of Engineering

San Diego, Calif., Feb. 17, 2020 -- More portable, fully wireless smart home setups. Lower power wearables. Batteryless smart devices. These could all be made possible thanks to a new ultra-low power Wi-Fi radio developed by electrical engineers at the University of California San Diego.

The device, which is housed in a chip smaller than a grain of rice, enables Internet of Things (IoT) devices to communicate with existing Wi-Fi networks using 5,000 times less power than today’s Wi-Fi radios. It consumes just 28 microwatts of power. And it does so while transmitting data at a rate of 2 megabits per second (a connection fast enough to stream music and most YouTube videos) over a range of up to 21 meters.

The team will present their work at the ISSCC 2020 conference Feb. 16 to 20 in San Francisco.

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UC San Diego electrical and computer engineering professor Dinesh Bharadia holds a PCB onto which the Wi-Fi radio is mounted (component underneath the black blob).

“You can connect your phone, your smart devices, even small cameras or various sensors to this chip, and it can directly send data from these devices to a Wi-Fi access point near you. You don’t need to buy anything else. And it could last for years on a single coin cell battery,” said Dinesh Bharadia, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering.

Commercial Wi-Fi radios typically consume hundreds of milliwatts to connect IoT devices with Wi-Fi transceivers. As a result, Wi-Fi compatible devices need either large batteries, frequent recharging or other external power sources to run.

“This Wi-Fi radio is low enough power that we can now start thinking about new application spaces where you no longer need to plug IoT devices into the wall. This could unleash smaller, fully wireless IoT setups,” said UC San Diego electrical and computer engineering professor Patrick Mercier, who co-led the work with Bharadia.

Think a portable Google Home device that you can take around the house and can last for years instead of just hours when unplugged.

“It could also allow you to connect devices that are not currently connected—things that cannot meet the power demands of current Wi-Fi radios, like a smoke alarm—and not have a huge burden on battery replacement,” Mercier said.

The Wi-Fi radio runs on extremely low power by transmitting data via a technique called backscattering. It takes incoming Wi-Fi signals from a nearby device (like a smartphone) or Wi-Fi access point, modifies the signals and encodes its own data onto them, and then reflects the new signals onto a different Wi-Fi channel to another device or access point.

Goto FlickrIllustration of the backscattering process.

This work builds on low-power Wi-Fi radio technology that Bharadia helped develop as a Ph.D. student at Stanford. In this project, he teamed up with Mercier to develop an even lower-power Wi-Fi radio. They accomplished this by building in a component called a wake-up receiver. This “wakes up” the Wi-Fi radio only when it needs to communicate with Wi-Fi signals, so it can stay in low-power sleep mode the rest of the time, during which it consumes only 3 microwatts of power.

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Bharadia (center), with graduate student researchers Rohit Kumar (left) and Manideep Dunna (right), displaying a setup in which the Wi-Fi radio would be backscattering between two Wi-Fi compatible devices.

The UC San Diego team’s improvements to the technology also feature a custom integrated circuit for backscattering data, which makes the whole system smaller and more efficient, and thus enables their Wi-Fi radio to operate over longer communication range (21 meters). This is a practical distance for operating in a smart home environment, the researchers said.

“Here, we demonstrate the first pragmatic chip design that can actually be deployed in a small, low-power device,” Mercier said.

Paper title: “A 28µW IoT Tag that can Communicate with Commodity WiFi Transceivers via a Single-Side-Band QPSK Backscatter Communication Technique.” The student researchers include Po-Han Peter Wang, Chi Zhang, Hongsen Yang and Manideep Dunna, UC San Diego.

Building a new generation of software programming languages

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Computer scientist Nadia Polikarpova is Earning National Accolades for Her Research and Forging New Collaborations

San Diego, Calif., Feb 13, 2020 --Nadia Polikarpova is a computer scientist who thinks outside the box. As an assistant professor in the Department of Computer Science and Engineering, her innovative approaches to automating software programming languages are earning her national recognition.

Polikarpova is a recent recipient of the National Science Foundation CAREER Award for work to help software developers increase productivity and reduce the number of mistakes in their code. She is also a 2020 recipient of the Sloan Research Fellowship. Each year, the Alfred P. Sloan Foundation awards two-year fellowships to just over 100 early-career scientists and scholars who demonstrate a unique potential to make a substantial contribution to their fields.

“I want to automate programming,” Polikarpova explained. “Today, software is crafted meticulously, involving a large amount of human effort. The problem with that is humans make mistakes. We routinely hear about private information being leaked or power outages being caused by software errors. Just like assembly lines made it possible to produce cars faster and more reliably, I want to give programmers the tools to build software faster and with fewer errors.”

Polikarpova’s ongoing projects include Lifty, a programming language that makes web applications more secure; Resyn, a tool that automatically generates resource-efficient programs; and Hoogle+, a website that helps programmers solve data manipulation tasks by combining functions from standard libraries.

Computer science meets phonology

One of her most recent efforts has Polikarpova and her team collaborating with Professor Eric Baković, chair of UC San Diego’s Department of Linguistics. On the surface it might not seem like the work of a computer scientist and a linguist share much common ground, but as it turns out Polikarpova’s research is well suited to solving some of Baković’s more complex phonology problems.

Phonology focuses on how sounds are put together to make language. Sounds aren’t organized arbitrarily into words; they follow certain patterns. The variations in how words are pronounced can be quite complex. Consider the word begged, which sounds like it ends in a “d.” On the other hand, sipped sounds like it ends in a “t.”

Some of these patterns can be quite complex, and analyzing them manually is time-consuming and prone to errors. Baković and colleagues wondered: Could computers help?

“We are looking at a particular set of complex language patterns that some phonologists have claimed are too computationally complex to actually be phonological patterns, that they are somehow unlearnable,” said Baković. “We started thinking, this is where the linguistics stops and computer science begins. We need to collaborate with people who understand these things more than we do.”

While looking for collaborators, one of Baković’s students reached out to a programming languages group and Polikarpova was intrigued.

“The phonologists wanted to use our expertise to automatically analyze the language data and then come up with rules that explain the processes that are happening in languages,” she said. “I'm happy they reached out to us; it was an unusual problem for me to think about.”

The team is currently developing an initial prototype that could solve some basic, textbook phonology problems. Once this is fully accomplished, the tool will process more complicated patterns and realistic data.

“We’re at the stage of figuring out how we can teach a computer phonology, but we're not looking at the outer realms of complexity here,” said Baković. “We're just figuring out, okay, where do we start?”

This project allows Polikarpova and her team her to delve into a completely different research area, which is rewarding for everyone.

“If someone is looking to collaborate with you, who is very different from you, just take the opportunity,” she says.

Listen to Polikarpova talk about her efforts to create new programming languages in this UCTV video.



Your AI stylist will see you now

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A flow chart showing how Complete the Look works. 

Computer scientists help teach an AI-powered tool a sense of style
San Diego, Calif., Feb. 13, 2020 -- Do you ever wonder what shoes or purse you should wear with your outfit? Well, have no fear: AI is here to help. Computer scientists at UC San Diego, in collaboration with Pinterest, developed “Complete the Look,” an AI-powered tool that recommends accessories and other fashion items to match your outfit based on just one photo.

Most recommendation systems for clothing are based on pictures of individual pieces of clothing or accessories (think product pictures on Amazon). But they lack important information, such as the season, the person’s body type and the clothes they usually wear--the kind of information that can be extracted from real-life images (think selfies). Most systems also focus on whether items are similar, as opposed to whether they are compatible.

To train the Complete the Look tool, computer science Ph.D. student Wang-Cheng Kang used data from Pinterest’s Shop the Look service, which finds clothing items for sale similar to those displayed in any given picture. Kang was an intern with the company at the time. The process was a little bit like helping the AI solve a puzzle. First researchers divided the images into pieces: clothes, shoes, accessories, and so on. Then they taught the AI which pieces are compatible to make a complete puzzle.

To test the tool’s performance, researchers had the AI solve more of these puzzles, this time without help. Complete the Look was able to identify compatible items 86.5 to 75.3 percent of the time for fashion and 80 percent of the time for home decor--better than all other similar computer tools.

In addition, researchers wanted to know how well Complete the Look did when compared to a real person. So they asked four fashion experts to complete the same compatibility task. They did not fare better than the tool.

Complete the Look still needs to be refined further before fashionistas--and the rest of us--can start using it. But in one aspect at least, it’s met the goal researchers set out to achieve. “The model appears to have learned a complex notion of style,” researchers write.

Kang is part of the research group led by computer science professor Julian McAuley, whose work focuses on better understanding how people behave and express opinions in online communities, including Amazon, Yelp, Reddit and Facebook. One application of his work is improving recommendation algorithms that power the likes of Amazon and Netflix.

Complete the Look: Scene-based Complementary Product Recommendation

Wang-Cheng Kang, Julian McAuley, UC San Diego 

Eric Kim, Charles Rosenberg, Pinterest

Jure Leskovec Pinterest and Stanford University

CVPR conference, 2019



Structural engineering students showcase construction engineering skills

San Diego, Calif., Feb. 12, 2020 -- Structural engineering undergraduate students put their construction engineering skills to the test at the Associated Schools of Construction Region 6 and 7 competition in Reno, Nevada from February 5-8. The group of 14 students competed in two categories this year: Heavy Civil, sponsored by Granite Construction; and Design-Build, sponsored by Swinerton Builders.

This is the second year UC San Diego students participated in the Heavy Civil challenge, but the first time they competed in the Design-Build Challenge, both of which are structured like hackathons.

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Students on the Heavy Civil team, with John McCartney (left), professor and chair of the Department of Structural Engineering, and the faculty mentor for the competition. 

“We are given a set of heavy civil project plans and specifications,” said Skye Yang, a structural engineering student and captain of the Heavy Civil project team. “Without internet access, in the duration of 15+ hours, we are required to prepare a bid package that details the price breakdown for the whole project. Then, we present our bid to a panel of judges.”

Yang said the students trained with estimators from Flatiron Construction for the past seven months to ramp up their skills.  

“We learned about the bidding process of a construction project, topics ranging from plan reading, understanding how something is built, to preparing a construction schedule. We also learned how to price each construction activity.”

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The Design-Build team with Professor McCartney. 

Ammar Salem, a structural engineering student and captain of the Design-Build team, said his team of six students plus two alternates was trained by Clark Construction starting in July, meeting once a week at 5am!

“We learned all about the design-build contract process and the role the general contractor has in making sure the project is successful,” he said. “We used UC San Diego's new college as a real-life example of how the design-build process works.”

Come competition time in Reno, the Design-Build team was tasked with completing a request for proposal.

“In 15 hours we were asked to complete a schedule of construction, cost estimate, schematic design, multiple narratives detailing how we would handle certain circumstances, and countless other things,” Salem said. “We were up against 14 other schools on the west coast, and the goal is to win the project, meaning that the judges are comparing all of the schools as if they are separate companies and they are trying to see who should get the job, like in a real life scenario.”

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The Design-Build team with the judges during their presentation.

In addition to learning the skills necessary to be a construction management professional, Yang said many of the students also enjoyed getting to network and learn from professionals and practice their interview skills.

“The competition event itself gave students from both of our teams a lot of exposure to construction industry professionals,” she said. “Many of us were offered interviews and internships from the competition. The process of preparing for the competition was also very beneficial to everyone from both teams-- back at UC San Diego, having an understanding of the construction process really helped us to better visualize the problems we were solving in class, and having this knowledge also gives us a head start when we take on internships positions during the summer."

Lim(b)itless in India: UC San Diego Students Travel Abroad to Empower Amputees

The Project Lim(b)itless app creates a 3D digital model of an amputee's residual limb through a process called photogrammetry, an imaging technique Lin has used to map historical sites around the world.

San Diego, Calif., Feb. 6, 2020 -- In November 2019, 10 UC San Diego students filed into a bustling amputee clinic in Jaipur, India. On one side of the room, men and women, some bearing crutches, watched as their new limbs took shape under the staff’s careful hands. For many of them, a prosthetic limb represented the chance to regain their mobility, independence and livelihoods.

The students’ visit to the Jaipur Foot clinic—a non-profit known around the world for providing affordable, prosthetic limbs and other mobility aids to those in need—marked more than a year of painstaking work to develop technology connecting amputees directly to prosthetists. The work is part of Project Lim(b)itless, an initiative founded by Albert Lin, a recent amputee and researcher at the Qualcomm Institute (QI) at UC San Diego.

With Lin’s guidance, and led by graduate student Isaac Cabrera, the students created a cellphone app that gives amputees the power to scan their residual limb, send an autonomously-generated 3D model to a prosthetist, and have a custom-built prosthetic delivered right to them. The project has the potential to help organizations like Jaipur Foot reach many more amputees, especially those without the means to travel.

In new territory

Days earlier, the students touched down west of Jaipur in the rural town of Jaisalmer, India. Jet-lagged and exhausted, they rallied together, donned matching team T-shirts and accompanied Lin and Qualcomm Institute Director Ramesh Rao to the November 2019 INK Conference, where Lin presented Project Lim(b)itless. As he spoke to the rapt crowd, Lin wore a bright red, 3D-printed limb created just for him by the students days earlier through the Project Lim(b)itless app.

The students of Project Lim(b)itless pose with Albert Lin and a 3D-printed prosthetic limb in the desert dunes outside Jaisalmer, India.

Cabrera, a Ph.D. candidate and co-leader of the Project Lim(b)itless student team, remembers being thrilled. It had been his dream to bring the team’s students to India, where nearly a million citizens are amputees. He wanted them to witness how their efforts could help people.

“I was incredibly inspired by how motivated, disciplined and determined my students were,” said Cabrera. “They each worked hundreds of hours, including many late nights and weekends, all because they believe that this project has the potential to change the world.”

At Rao’s invitation, Cabrera had shared Project Lim(b)itless at an annual awards ceremony for the Mahatma Ghandi Memorial Scholarship earlier that fall. His request touched many in the audience and Project Lim(b)itless raised enough money to cover travel funds for the entire student team.

Soon, the students were networking with high-profile individuals, like the Vice President of Google India, and celebrating Lin’s successful presentation at INK. Kaela Wong, a Mechanical Engineering undergraduate and Cabrera’s co-leader, recalls an especially bright moment as Lin danced through the night on the 3D-printed leg she and her teammates had designed.

“It was proof of the power of undergraduate students—everyone in the audience and on the dance floor with Albert was so impressed and moved by our dedication to the project and the amount of progress we have achieved as undergraduates,” she said.

The work begins

Project Lim(b)itless’ student team was born out of the determination of a handful students wanting to make a difference. Inspired by a recent class on 3D-printing, Cabrera, Wong and a few classmates had started their own project designing a prosthetic limb that could be 3D-printed with cost-effective materials. They began working with Lin, who had been involved in an off-roading vehicle accident that ultimately led to the amputation of his right leg below the knee in 2016. At the time of the accident, Lin had been thriving as an engineer, QI innovator and National Geographic explorer. Active and adventurous, he used his background in research to search for hidden markers of civilization buried deep underground, and surfed, ran or rock-climbed during his time off.

he team poses in Jaisalmer. Albert Lin, project lead, stands far left. Ramesh Rao, director of the UC San Diego Qualcomm Institute, stands third from the left, background.

After the loss of his lower leg, Lin struggled with overcoming phantom limb pain and adjusting to life as an amputee. As he learned to use a prosthetic, he began to consider the lives of other amputees around the world. His false limb would allow him to rejoin his old life; what of those who couldn’t?

“I feel this guilt for having access to a prosthetic that lets me have a full life when so many others don’t. So, in a way, I know I have this responsibility to take on the barriers to democratizing that access,” said Lin, founder of the QI Center for Human Frontiers.

Of the approximately 40 million amputees worldwide, only a fraction have access to a prosthetic limb. Multiple office visits, travel fees, and material and labor costs can drive prices into the tens of thousands of dollars.

Lin planned to use an engineering approach to devise a way to lower the cost of prosthetic limbs and remove the need for an amputee (the most immobile population he notes) to travel to a prosthetist for care. He suspected that 3D-printing and nearly-ubiquitous cellphone technology might be the key. In coming across Cabrera and Wong, he’d found the team with the intense drive, curiosity and background needed to make Project Lim(b)itless a reality.

"I have never encountered such a dedicated group of individuals. These students put in countless hours of problem-solving and innovating, purely out of the desire to help others," said Lin. "What's more, they self-organized in a way that describes the best in engineering leadership."

3D-printing the road to India

The Project Lim(b)itless team has continued to expand. Soon after meeting Lin, Cabrera and Wong set about recruiting other students from diverse engineering backgrounds to strengthen their team. Together, these dedicated students helped Lin repurpose photogrammetry—an imaging technique Lin has used to map historical sites in Mexico, China and Guatemala—to create a 3D model of someone’s limb using a cell phone app.

All an amputee needs to do is snap photographs of their limb from different angles, and let the app recreate it digitally. The amputee can then electronically deliver the virtual model of their limb to a prosthetist, who will use cutting-edge software to design a comfortable, custom-fitted prosthesis. With 3D printing added in, a prosthesis takes fewer hours of human labor to produce, and the price drops significantly.

Albert Lin sits beside a patient at the Jaipur Foot amputee clinic.

In India, the Project Lim(b)itless team had an opportunity to put their workflow to the test. Rao and Lin established a formal partnership with Jaipur Foot, with the promise to send 100 3D-scans of residual limbs as a reference for prosthetics. It is the first step in a new experiment, one that will support Jaipur Foot’s ongoing efforts to reach remote patients and give students a chance to learn through real, person-to-person interactions outside the classroom.

“The trip to India was an inspiration to those of us involved in designing students’ educational experiences,” said Rao. “Project Lim(b)itless exemplifies experiential learning in an interdisciplinary setting. As the Qualcomm Institute extends its mission to education, we seek to nurture such opportunities for UC San Diego students on a large scale. We welcome engagement with partners on and off campus who may wish to join hands with us to enable more such educational initiatives.”

Near the close of their trip, Rao and Cabrera visited partners at the Webel-Fujisoft-Vara Center of Excellence (COE) in Calcutta. As an initiative of the West Bengal government, the COE offers services, training and access to high-end laboratories, including ones equipped with state-of-the-art 3D printers, to promote local talent and benefit the community. In the future, Cabrera says, Project Lim(b)itless and the COE plan to 3D-print prosthetics right in Calcutta and distribute them through a network of high-tech kiosks run by Sahaj Retail Limited, allowing them to reach amputees from the bustling city of Jaipur to more isolated villages.

In their own words, here are the team’s favorite moments or takeaways from their travels:

Eric Ngo, B.S. Mathematics – Computer ScienceI learned a lot from this whole trip, mostly about what I want to do in life. I had always struggled with the thought of going into industry or going into a Ph.D. program as a computer science student. But after seeing how passionate many of these people were at the conference, it inspired me to continue forward with humanitarian work.

Connie Gean, B.S. Bioengineering 2019Even though we were in a foreign country that most of us had never been to before, we were able to connect to the people at the conference and the people at Jaipur Foot. Humans have a way of communicating and supporting each other that can surpass barriers of culture and language, and I feel so grateful to have been a part of this experience.

Patricia Castillo, B.S. BioengineeringMy absolute favorite moment of the trip was when we went to Jaipur Foot and saw Albert walk and jump on his new leg that [the clinic staff] made [for him]. I think it really made an impact on me because it was the first time I could actually see the impact our project could have on amputees everywhere.

Joseph Martin, B.S. Mechanical EngineeringI have to say my favorite general takeaway was from the cumulative small moments bonding with the team. You learn a lot about people’s tolerances and how they deal with the pressure, and how to work through the confusion with them while maintaining a sense of humor to pull each other through.

Samantha Fong, B.S. Mechanical EngineeringWhile our team had some ideas as to what the experience was going to be like, there was no way to account for exactly what it was going to be like... There were many times it was difficult to come up with a response or have a plan of action, but one of the best things about working with a team is that when you yourself do not have an answer or solution, you can fall back on your team to help you out.

Sebastian Troncoso, B.S. Biochemistry 2019My heritage is Chilean, but I was born in Mexico City and spent my childhood moving to different countries (Chile, Peru, Mexico City, and the U.S.). People in South America have a common bond through language, so it feels like being home. India, on the other hand, was a different culture beyond the language difference. People value education very much, the sense of being with your family is strong, and [the drive] to strive for success flows among the people we met.

Victor Bourgin, Master’s in Machine Learning and Machine Intelligence (University of Cambridge)I was born in Austria, raised in Slovakia, Czech Republic and Belgium, I studied in the U.K. and in the U.S., so I was accustomed to traveling and discovering new cultures. But little could I imagine how exciting and rewarding this 3-day trip would be. It was amazing to hear inspiring talks from people who are bringing transformative projects to life.

Zhaoliang Zheng, graduate student in Mechanical and Aerospace EngineeringMy favorite moment was when I was in Jaipur Foot. I was so astonished those [amputees] regained mobility because of Jaipur Foot and I was shocked that Jaipur Foot would be able to make such a cheap and robust residual limb in such a short time (approximately within one day).

The students of Project Lim(b)itless would like to thank the late Professor Joanna McKittrick for her invaluable mentorship and support. An expert engineer and compassionate advisor, she advocated for engaging women and minority students in the STEM fields and extended her kindness to the Project Lim(b)itless team, guiding it from its inception. A more detailed recounting of her life, research and contributions can be found at the Jacobs School of Engineering website.

Unlock The Secrets Of Your Gut! New Research Project Offers 800 Participants Opportunity To Map Their Gut Health Free Of Charge


WHITE PLAINS, N.Y. and SAN DIEGO, Feb. 6, 2020 /PRNewswire/ -- The Microsetta Initiative, a research project led by a team at the University of California, San Diego in partnership with Danone Nutricia Research — the research and innovation division of Danone North America's global parent company, Danone S.A. — is recruiting hundreds of U.S. citizen scientists to map their gut microbiome. Participants in the program will have the opportunity to get their microbiome sequenced, at no personal charge, and will receive a free report. This is the first phase of an unprecedented program to map the gut microbiome of people around the world. 

The gut microbiome — the trillions of bacteria living in the gut — is considered  the next frontier in health and wellbeing.  This research program, known as "The Human Diets & Microbiome Initiative" (THDMI) aims to discover the best diets and foods on the planet that can nourish the Gutties of the world using the latest sequencing technology, such as shotgun metagenomic sequencing. This technique enables THDMI scientists to comprehensively sample the genes of all organisms present in the gut microbiome, evaluate bacterial diversity and detect the abundance of microbes in the gut. Shotgun metagenomics will also provide means to study unculturable microorganisms that are otherwise difficult or impossible to analyze.

"Today, the gut is increasingly recognized as a cornerstone of health. Unfortunately, our modern lifestyles are impacting our gut and eroding the foundation of our wellness. Our diets are too often lacking in foods that feed our gut microbiomes such as fruits, vegetables, and fermented foods that provide key nutrients and substances like fibers, probiotics, and prebiotics," said Miguel Freitas, PhD, Vice President of Scientific Affairs for Danone North America. "As a leader in fermented foods and probiotics, our global parent company and the team at Danone Nutricia Research are deeply committed to gaining an even deeper understanding of gut health. This research has the potential to transform the lives of millions of people, and is consistent with our global ambition to bring health through food to as many people as possible."

Professor Rob Knight, Faculty Director of the Center for Microbiome Innovation at University of California, San Diego and the leader of the Microsetta Initiative added: "With the support of citizen scientists and the structure of the Microsetta Initiative, THDMI is employing cutting-edge metagenomic techniques and using the latest shotgun sequencing technology to map the gut microbiome, providing a deeper level of analysis than is typically performed for this type of project. In addition, THDMI will enable us to gain a deeper understanding of the relationship between the diets and gut health of thousands of people around the world. This project is unlike anything of its kind in terms of the breadth of our research, especially when integrated with the Earth Microbiome Project, which will add an environment angle to this project— it's very exciting!"

With the help of an animated character called Gutty, representing the gut microbiome, the initiative  will recruit hundreds of citizen scientists across the United States. After the U.S., the study will be extended to other countries to create a global map of the gut microbiome across diverse ethnicities and diets.

To take part in this exciting citizen science initiative, participants will test their microbiome and complete a questionnaire about their diet and lifestyle. Each participant will learn how their gut microbiome compares to other people, and most importantly, how diet and lifestyle may shape their gut microbiome.

THDMI is a unique opportunity for people to become citizen scientists and meet their Gutty free of charge! Learn more and sign up today at www.thdmi.org.   

About Danone North America
Danone North America is purpose-driven company with a portfolio of dairy and plant-based foods. As the world's largest Certified B Corporation®, Danone North America is committed to the creation of both economic and social value, while nurturing natural ecosystems through sustainable agriculture. Our portfolio of brands includes: Activia®, DanActive®, Danimals®, Dannon®, Good PlantsTM, Horizon Organic®, International Delight®, Light + Fit®, Oikos®, Silk®, So Delicious® Dairy Free, STōK®, Two GoodTM, Vega®, Wallaby® Organic and YoCrunch®. With more than 6,000 employees and 13 production locations across the U.S., our mission is to bring health through food to as many people as possible. For more information, visit www.danonenorthamerica.com. For more information on Danone North America's B Corp™ status, visit: https://bcorporation.net/directory/danone-north-america.

About Danone Nutricia Research
Danone S.A. is a multinational food and beverage corporation headquartered in Paris, France, with four different product categories: Essential Dairy and Plant-based Products, Waters, Early Life Nutrition, and Advanced Medical Nutrition, and employs over 110,000 people worldwide. Danone Nutricia Research, the Research and Innovation organisation within Danone, is at the heart of Danone's strategy: innovating to bring health through food to as many people as possible.

Worldwide Danone Nutricia Research builds bridges between science and food according to our company vision "One Planet, One Health". Our teams of 1,700 R&I employees work from 2 main research centers in France & Netherlands & 6 specialised centers (France, Spain, Russia, USA, Singapore and China) and in 55 Business units. They partner with recognized scientific communities, suppliers and innovators and through these collaborations, create unique consumer experiences and bring health and well-being at every stage in life.

SOURCE Danone North America

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What's for Dinner? AI Can Help

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San Diego, Calif., Feb. 5, 2020 -- Research from computer scientists at the University of California San Diego could eventually lead to AI-generated recipes—customized to your personal taste. The study breaks new ground in natural language processing, which studies how AI understands and generates human (natural) language. The research was published on arXiv.org.

“You can imagine various applications like dialogue systems, question answering systems and recommender systems, which is a lot of what my lab builds,” said associate professor Julian McAuley from the UC San Diego Department of Computer Science and Engineering. “Our research is all about improving these models by personalizing them. Whenever you're dealing with text where there might be subjectivity or people having different writing styles or individuals liking or disliking some content, these natural language generation systems can potentially perform a lot better.”

In the study, the team pulled 180,000 recipes and 700,000 user reviews from Food.com to teach the neural network how to create recipes. The goal was to give the system enough data to produce personalized recipes based on individual likes and dislikes.

After that, the researchers would submit a recipe name, short ingredient list and calorie information, which the model extrapolated into a complete recipe. For example, the team asked the AI for a low-calorie pomberrytini recipe with pomegranate-blueberry juice, cranberry juice and vodka. The network produced several recipes, including:

Combine all ingredients except for the ice in a blender or food processor. Process to make a smooth paste and then add the remaining vodka and blend until smooth. Pour into a chilled glass and garnish with a little lemon and fresh mint.

The AI added lemon and mint based on the reviewer’s previous recipes – a nice touch.

McAuley and colleagues chose to study natural language processing with recipes because they were easy to access and would challenge the system.

“Recipes are interesting because they're a form of semi-structured texts where it's not just a bag of words the way some natural language models are,” said McAuley. “Potentially, there’s a lot of structured data – constraints on which ingredients are allowed or quantities or perhaps a nutritional profile. The model has to learn which combinations, and orders, of ingredients make sense together.”

The personalization serves two roles. In addition to providing recipes that are better suited to specific individuals, it helps teach the system.

“It should improve the quality of the text because we're helping the model along a bit,” said McAuley, “giving it some historical records of how an individual’s recipes typically look.”

While McAuley would love to generate an entire recipe without inputting any ingredients, the technology is not quite there. He looks forward to a time when this approach could help people navigate food preparation based on personal preferences, lifestyle, health issues and other factors.

“This is a prototype now, but maybe you could imagine building this into a system where you could say: I want more ingredients like this one,” said McAuley. “Or, I have an allergy, or I like this recipe, but can you give me a version that includes this ingredient or does not include this other ingredient? Or it's just a healthier version of the recipe.”

Generating Personalized Recipes from Historical User Preferences

Other authors included: UC San Diego Computer Science and Engineering PhD students Bodhisattwa Prasad Majumder, Shuyang Li and Jianmo Ni

Five Outstanding Engineering Honor Awards to be Presented by the San Diego County Engineers Council

Integrating robots in public and private spaces for the common good

Hee Rin Lee presents a demo during the 2018 Contextual Robotics Forum at UC San Diego.

San Diego, Calif., Feb. 5, 2020 -- UC San Diego alumna Hee Rin Lee, now an assistant professor in MSU’s Department of Media and Information, explores how we can integrate robots into our lives for social good, whether it be in a retirement community or a bustling factory. The roots of her research go back to her time in the lab of computer science professor Laurel Riek here at the Jacobs School of Engineering at UC San Diego. 

Robotic inspirations

Lee first moved to the United States from South Korea a decade ago to attend graduate school. As she tried to fit into American society, Lee encountered many different experiences that amounted to culture shock in her new home. Her need for cultural adjustment led to her interest in implementing robots in human spaces. Lee stated that there is a parallel: Robots have to undergo a form of culture shock when integrating into human life, just as Lee did.

Lee wanted to not only bridge this divide, but to also improve human experiences with robots once this divide is crossed, while at the same time addressing the need for social intervention.

Robots currently used in factories, for example, are segregated to their own section of the workspace. Lee said they are focused on efficiency. To her, there are greater possibilities for the establishment of robots in the workforce than separation and improved workflow. There is a lack of interaction with humans when addressing the presence of robots. 

“Those people were engineers, which means when you’re trained in school, what you’re learning is how to talk to machines,” Lee said. “You’re not really getting into this space, how you interview people and analyze data.”

Lee wants to take the interaction of robots and humans a step further, with a focus on the positive social impact robots can have on humans. Through working with elders with dementia, nurses in hospitals and factory workers, Lee plans to assist humans with the implementation of robots to aid with their own needs.

Personalized robotic elder care

Lee’s goal is to help those who are marginalized in society. This first came to fruition through her work with elders. She sought to personalize care below the surface of what gets recorded on the medical charts. These human-friendly robots would not be focused on disabilities or the typical stereotypes related to aging, but on what support the elders in her study felt they needed in their everyday lives.

During her work as a postdoctoral researcher at UC San Diego, Lee went about creating individualized prototypes for robots that could suit elders’ specific needs. She began by interviewing the elders, not for their medical condition or what they needed assistance with, but to learn about them as unique individuals who have lived fulfilling lives.

“That became my focus,” Lee said. “How can I reflect those groups? What are their actual issues? How can we design a robot to support them from their perspective?”

The elders created situational maps to highlight their needs. Lee then worked closely with the elders to design the robots and created customized prototypes. The elders in the study tested and used the prototypes, and Lee reworked the design based on their feedback.

The concept of using robots to assist aging citizens is not uncharted territory. Lee discussed the previous ventures many robotists have had into assisted living and in improving the lives of older adults with machines.

“It becomes really interesting research, because they were so interested in robots but they didn’t really think about how elders would feel about this,” Lee said. “Robotists’ understanding of aging and older adults’ understanding of aging is completely different.”

AI implications in nursing

Lee’s most recent work took place in the sterilized white walls of the common hospital. She and her research partner, Angelique Taylor, one of Riek's Ph.D. students at UC San Diego, noticed a power hierarchy between physicians and nurse practitioners in the medical space, where they were concerned with errors in patient care.

Lee and Taylor developed a group tracking algorithm that nurses can use to keep track of errors they find made by their cohorts, in order to ensure there is no cross contamination of germs in the workplace. The technology has broader implications in team communication and improving everyday workflow.

During her work, Lee said she observed a shortage of nurses at the hospital. So, the team also devised ways for the algorithm to be used in critical situations, providing a “robot crash cart” as a backup service. They brainstormed a set choreography that would help to ensure the right amount of people were present at the right time, with the “robot crash cart” making up for any shortages in staff.
“Throughout our design process, we want to test our technology with nurses to ensure their needs are being met when they work alongside our robots, as well as use robots as a means of speaking up for nurses in situations that make them uncomfortable or when doctors/physicians do not take their concerns seriously,” Taylor said.

“These situations lead to patient safety risks, which can lead to patient deaths.”

Robotic ventures into factories and education

An avenue of social assistance Lee has already scoped out, but wants to investigate further, is the factory work environment. Lee visited a factory that was already using a robot to carry out certain duties. These duties included carrying packages and making sure materials arrived where they needed to be. Lee found an issue: the removal of jobs from older workers to make room for this robotic innovation. 

Lee aims to educate workers who know little about the robot and its capabilities, while coming up with a solution to use the robot without interfering with the current factory workflow. She is also interested in creating an educational program that teaches youth about AI, with a focus on what people most want to learn about the advanced technology.

Lee plans to continue researching robotics, as it relates to how machines can fit into human spaces to better human society.

This story originally appeared on the website of Michigan State University.

Jacobs School faculty, student, staff honored with Inclusive Excellence Awards

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Ariana Mirian, Veronica Abreu, and Daniela Valdez-Jasso.

San Diego, Calif., Feb. 4, 2020 -- Three members of the Jacobs School of Engineering community were awarded 2020 Inclusive Excellence Awards for their outstanding contributions toward increasing diversity at all levels at UC San Diego. The 25th annual UC San Diego Inclusive Excellence Awards recognizes faculty, staff, students, departments and organizations who have made outstanding contributions in support of UC San Diego’s commitment to inclusive excellence and diversity. A review committee comprised of representatives from the Executive Vice Chancellor and all Vice Chancellor Areas evaluated nominations and recommended award recipients.

“I wish to extend my sincerest congratulations to the recipients of the 2019 Inclusive Excellence Award,” said Becky Petit, Vice Chancellor of Equity, Diversity and Inclusion. “Their individual and collective contributions help create a welcoming environment for living, learning, and working—an environment where all faculty, staff, and students can make their best contributions.”

Daniela Valdez-Jasso, a professor of bioengineering, is the 2020 faculty recipient of the Inclusive Excellence Award; Ariana Mirian, a computer science graduate student, is the student recipient; Veronica Abreau, a computer science and engineering undergraduate affairs manager, was selected from within academic affairs.

Learn more about the Jacobs School recipients and their work for a more inclusive campus below.

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Daniela Valdez-Jasso, professor of bioengineering and the faculty recipient of the 2020 Inclusive Excellence Award.  

Daniela Valdez-Jasso, Professor of Bioengineering

Daniela Valdez-Jasso, who uses math and physics to computationally model the effect of heart and lung diseases on various tissues, was honored for her commitment to creating and sustaining a more diverse student body. Valdez-Jasso serves as the faculty advisor for the UC San Diego chapter of the Society of Hispanic Professional Engineers, and worked with the Center for Research on Educational Equity, Assessment & Teaching Excellence (CREATE) to support the restarted chapter of the Society for Advancement of Chicanos and Native Americans in Science (SACNAS). She will also serve as faculty advisor to this group of students.

In addition, Valdez-Jasso is an avid supporter of students in the Society of Women Engineers, and is involved in the Fleet Science Center’s BeWise program for high school girls, bringing a group of students to campus each year to tour her lab and learn more about bioengineering.

“I feel responsible, in some sense,” she said. “Bioengineering is still a new field and I think it’s really hard to know what it entails, unless you’re already in the field and know what it is all about. I feel like it’s part of my duty to really teach and show people what we do as bioengineers.”

While Valdez-Jasso views this outreach as a responsibility, connecting with and encouraging current and prospective students is one of the perks of the job.

“For me this is one of the fun things—it’s rewarding,” she said. “I love interacting with students and seeing them get all excited, partly because I really like what I do, and I really want others to get involved in the field and have fun with us.”

She focuses her efforts, in particular, on girls and Hispanic students, because she didn’t see enough people like her during her journey to becoming a professor, and wants to not only encourage these students to choose paths in STEM, but to not lose any parts of their identity in the process.

“I was really discouraged, a lot, for being in science and being bubbly and very social,” Valdez-Jasso said. “I want to make sure we don’t keep having scientists with the same type of personalities, because I think we need people who also have other interests and are different. I like to be a little bit of an ambassador in that sense. The other thing is it saddens me to see that UC San Diego is a university in San Diego yet the population of students is not really representative of the city’s population. I really like to reach out to a lot of the Hispanic communities and make sure they know that we’re here, this is their school and they should apply to UC San Diego.”

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Ariana Mirian, center, is a computer science Ph.D, student and the student recipient of the 2020 Inclusive Excellence Award.

Ariana Mirian, Ph.D. Student (Computer Science and Engineering)

In January 2018, Ph.D. student Ariana Mirian and two peers launched the CSE Diversity, Equity, and Inclusion (DEI) committee, a grassroots organization that provides a platform for students, faculty and staff interested in enacting change. From a team of three, the committee has grown to include between 30 and 40 regular members. Mirian counts its formation as one of her proudest achievements.

Mirian is being honored with an Inclusive Excellence Award for actively working to make her community welcoming to people from all backgrounds.

“I’ve experienced first-hand how it feels when you don't belong — when you double guess every action, and truly don’t feel like you can be yourself,” said Mirian. “I’ve also experienced what a difference it can make to be in an environment where you feel like you truly belong. I’ve been able to grow and flourish in ways I never imagined before, and much of that is because I can be me.”

The CSE DEI committee fosters initiatives like the CSE Celebration of Diversity, a day-long event that had its inaugural year in 2019. The free event features a keynote speaker and workshops on resources for the LGBTQ+ community, more inclusive designs and tactics for handling microaggressions. Mirian is also active in Graduate Women in Computing (GradWIC), which offers resources for women in her field of study.

Within both organizations, Mirian considers herself part of a team that works hard to create an environment where others can succeed and pursue their own projects. She says she was “absolutely shocked” to hear that she’d received the award.

“To me, receiving this award is truly a testament to the amazing work my colleagues do in the department,” she said.

This year, Mirian looks forward to watching both the CSE DEI committee and GradWIC grow as they tackle the 2020 CSE Celebration of Diversity and a series of collaborative wellness workshops, respectively.

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Veronica Abreu, undergraduate affairs manager at the Computer Science and Engineering Department, and the academic affairs recipient of the 2020 Inclusive Excellence Award.

Veronica Abreu, Undergraduate Affairs Manager at CSE

Within the CSE DEI committee, Veronica Abreu acts as a culture subcommittee co-lead, focusing on the committee’s forward momentum and devoting time to learning about social justice issues. She describes realizing that she felt “very frustrated” with perceived imbalances of power in society, and decided to channel it into action.

With the help of a colleague, Abreu established a training workshop for advisors in her department. The training prepared staff to identify microaggressions, a term defined by Merriam-Webster as “a comment or action that subtly and often unconsciously or unintentionally expresses a prejudiced attitude toward a member of a marginalized group."

The reaction to the workshop was overwhelmingly positive among Abreu’s peers, especially for members of more underrepresented communities.

“I am proud to have worked on creating a workshop… it helps bring awareness to issues and situations that some people do not even realize still happen today or maybe do not realize how they hurt members of our community,” said Abreu.

Abreu discovered that she was a recipient of an Inclusive Excellence Award via email. Like Mirian, she’d had no idea that she’d been nominated.

“I was very shocked but honored that my work would be recognized by people outside of my immediate circle,” said Abreu. “Those close to me are quick to support me and validate my work, but it was an entirely different feeling to have the larger community essentially say ‘we see you’ and ‘you have earned this.’”

The award and an outpouring of support and congratulations has inspired Abreu to keep moving forward. In the future, she looks forward to continuing to push herself to create space for difficult and complex dialogues, and raise awareness about causes in social justice.

Algae Shown to Improve Gastrointestinal Health

Volunteers in the first study of green algae on human digestion consumed daily spoonfuls of Chlamydomonas reinhardtii algae.
Credit: Frank Fields, UC San Diego

Project is the first to test green algae on symptoms related to human digestion

San Diego, Calif., Feb. 3, 2020 -- A widespread, fast-growing plant called Chlamydomonas reinhardtii is famous in scientific laboratories due to its position as the world’s most exhaustively studied algae.

For decades, the green, single-celled organism, which primarily grows in wet soil, has served as a model species for research topics spanning from algae-based biofuels to plant evolution. While other species of algae have been used as dietary nutraceuticals that provide beneficial oils, vitamins, proteins, carbohydrates, antioxidants and fiber, the benefits of consuming C. reinhardtii were previously unexplored.

Researchers at the University of California San Diego recently completed the first study examining the effects of consuming C. reinhardtii and demonstrated that the algae improves human gastrointestinal issues associated with irritable bowel syndrome (IBS) such as diarrhea, gas and bloating. Results of the project are published in the Journal of Functional Foods.

“People have been looking at this algae for decades, but this is the first study to show what many of us have suspected—it’s good for you,” said principal investigator and algae expert Stephen Mayfield, a distinguished professor in UC San Diego’s Division of Biological Sciences and co-director of the Food and Fuel for the 21st Century Program (FF21). “This is exciting because it demonstrates a clear benefit: If you have IBS-like symptoms, this is good for you.”

For the human digestion study, algae were grown in a large stainless steel fermentation tank, similar to fermentation tanks seen at beer breweries. A smaller bench-top fermentation tank, or bioreactor, is pictured.
Credit: Frank Fields, UC San Diego

For years researchers in Mayfield’s laboratory have been exploring C. reinhardtii as a cost-competitive and sustainable source of valuable plant-based products, specifically pharmaceuticals and biofuels. Now, working with several collaborators, including UC San Diego’s John Chang (School of Medicine), Rob Knight (School of Medicine, Jacobs School of Engineering and Center for Microbiome Innovation) and the San Diego-based startup Triton Algae Innovations, they turned their attention towards investigating the algae as a nutritious food additive for improving human health.

The C. reinhardtii biomass used in the study, which was grown by Triton Algae Innovations, was subject to rigorous safety testing and designated as “Generally Recognized As Safe” by the U.S. Food and Drug Administration, green-lighting the use of the organism in a human study.

Preliminary data in mouse studies demonstrated that consuming C. reinhardtii significantly reduced the rate of weight loss in mice with acute colitis, which is generally linked to inflammation of the digestive tract. Building off these results, the researchers set out to test for a similar effect when the algae was consumed by human volunteers, including those with and without symptoms associated with IBS. Volunteers consumed daily spoonfuls of powdered C. reinhardtii biomass and reported their gastrointestinal health for one month. Of the hundreds of interested participants in the project, data from 51 volunteers met the study’s requirements for inclusion in the final data analyses.

Results showed that participants who suffered from a history of frequent gastrointestinal symptoms reported significantly less bowel discomfort and diarrhea, significantly less gas or bloating and more regular bowel movements.

“The benefits of consuming this species of algae were immediately obvious when examining the data from both mice and humans who suffered from gastrointestinal symptoms,” said Frank Fields, a research scientist in Mayfield’s lab and lead author of the paper. “I hope that this study helps destigmatize the thought of incorporating algae and algae-based products into your diet—it is a fantastic source of nutrition and we have now shown that this species of algae has additional benefits to animal and human health.”

Volunteers also were provided with stool sampling kits and sent samples to the American Gut Project, a citizen science effort led by Knight and his lab, to assess any changes in their microbiomes. The results indicated that the gut microbiome composition remained diverse, which is typical of healthier individuals, and that no significant changes to the composition of their gut microbiome occurred during the study as a result of consuming the algae.

The researchers say much more testing with larger groups of participants across longer time periods is needed. At this point, they are unclear about how the algae works to improve gastrointestinal health. The scientists believe the benefits could be traced to a bioactive molecule in algae or perhaps a change in gene expression of gut bacteria caused by algae consumption.


Still, the observed results in human volunteers led them to conclude in the paper that “the addition of C. reinhardtii into the diet will not only add nutritional value but may also function to relieve some gastrointestinal symptoms of certain individuals.”

The full coauthor list includes Frank Fields, Franck Lejzerowicz, Dave Schroeder, Soo Ngoi, Miller Tran, Daniel McDonald, Lingjing Jiang, John Chang, Rob Knight and Stephen Mayfield. Collaborators included the California Center for Algae Biotechnology, American Gut Project, Center for Microbiome Innovation and Jacobs School of Engineering.

The project was partially supported by the U.S. Department of Energy (DE-EE0008246).

Triton Algae Innovations provided the C. reinhardtii biomass and the funding necessary to conduct the mouse feeding trial and to sequence stool samples.

Assessing 'stickiness' of tumor cells could improve cancer prognosis

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Microfluidic device sorts and separates less “sticky” cancer cells from their more sticky counterparts in the same tumor. Photos by David Baillot/UC San Diego Jacobs School of Engineering

San Diego, Calif., Feb. 3, 2020 -- A team of researchers led by the University of California San Diego has created a device that measures how “sticky” cancer cells are, which could improve prognostic evaluation of patient tumors. The device is built with a microfluidic chamber that sorts cells by their physical ability to adhere to their environment.

Researchers found that weakly adherent cells migrated and invaded other tissues more than the strongly adherent cells from the same tumor. Also, the genes that identify these weakly adherent cells make patients’ tumors five times more likely to reoccur within five years.

The team reported their findings in a study published in Cancer Research.

Their work addresses a longstanding problem in the field of cancer research: it has been difficult to find biological markers to universally identify and select the most aggressive cells in tumors.  This study may provide a much-needed physical marker that identifies highly metastatic cells within a heterogeneous tumor cell population.

“This new device could be the first step to better assess how likely tumor recurrence is,” said Adam Engler, bioengineering professor at the UC San Diego Jacobs School of Engineering and senior author of the study. “Patients with few of these aggressive cells lying dormant in their surrounding tissue may be less likely to see a tumor reoccur 5, 10, or 20 years later.” Engler noted that by knowing a patient’s risk, follow-up treatments could be better tailored to the individual.

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Pranjali Beri, UC San Diego bioengineering Ph.D. student and first author of the study, collecting different populations of cancer cells based on their stickiness.

The device that Engler’s team built consists of a microfluidic chamber coated with an adhesive protein. Cancer cells are placed in the chamber and after they adhere, a fluid is pushed through to detach cells. The faster the fluid moves, the higher the shear stress that the cells experience. The team can isolate cells that detach at specific shear stresses and analyze them. Cells collected at lower shear stress are weakly adherent, while those collected at higher shear stresses are strongly adherent.

Their analysis led the team to another critical finding: weakly adherent cells have a unique genetic signature that identifies them and enables them to migrate and invade faster. Comparing this signature to thousands of patients in the Cancer Genome Atlas (TCGA) database, researchers found that patients with tumors high in this "weakly adherent signature” experienced tumor recurrence earlier and more frequently.

Building on these findings, Engler and his team hope to “prime” tumors with weakly adherent cells to see if they indeed metastasize faster and more frequently. 

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Fluid is pushed through to detach cancer cells from the microfluidic chamber. Slower fluid flow pushes out less sticky cancer cells, which can be collected separately from the more sticky cells.

“If our mouse model shows that these cells indeed reduce cancer-free survival times, it will pave the way for substantial prognostic studies in humans with these types of solid tumors,” said first author Pranjali Beri, a bioengineering Ph.D. student in Engler’s lab. Beri also noted that nearly any solid tumor should exhibit this physical marker, and the team has so far tested cells from breast, prostate, and lung tumors.

In the future, the team hopes that clinicians will use this microfluidic device to examine tumor biopsies to estimate the likelihood of metastasis and adjust treatment at earlier disease stages.

Engler’s clinical collaborator, Dr. Anne Wallace, director of the Comprehensive Breast Health Center at UC San Diego Health who will provide patient samples for follow-up studies, concurred and confirmed this approach. “Many cancers that we see in the clinic, such as ductal carcinoma in situ or DCIS, remain dormant for years. It is nearly impossible for us to predict which fraction of that population will reoccur,” she noted. The team’s device could be the first to address these hard to predict recurrences.


Paper title: “Cell adhesiveness serves as a biophysical marker for metastatic potential.” Co-authors include Anna Popravko, Benjamin Yeoman, Aditya Kumar, Kevin Chen, Enio Hodzic, Alyssa Chiang, Afsheen Banisadr, Jesse K. Placone, Hannah Carter and Stephanie I. Fraley, UC San Diego; and Parag Katira, San Diego State University.

This work was supported by the National Institutes of Health (grants R01CA206880, R21CA217735, T32AR060712, and F32HL126406), National Science Foundation (grant 1651855, 1763132, and 1763139), Army Research Office (W911NF-17-1-0413), and American Cancer Society (15–172–45-IRG).

Microsized bacterial bait could provide new treatment for infections

San Diego, Calif., Jan. 31, 2020 -- Micromotors that swim to infected sites in the body to lure, trap and destroy bacteria could offer a more efficient form of treatment against pathogens. Nanoengineers at the University of California San Diego have developed a “microtrap” that zips around in an acidic environment (like that found in the stomach) and serves as a toxic bait for E. coli bacteria.

The proof-of-concept work addresses a common medical issue that most drugs get diluted in body fluids before they can do their job. It would be more efficient if the drug and its target were brought together so that less medicine is wasted, said Joseph Wang, a professor of nanoengineering at UC San Diego and the study’s senior author. By creating a self-propelling chemical trap to corner and destroy pathogens, Wang and his team present a new way to make medications, as well as environmental decontaminants, more effective.

Researchers published their findings in the journal Angwandte Chemie.

The micromotor is made up of an onion-like structure, consisting of a magnesium metal core partially enclosed in several polymer layers. The exposed part of the magnesium core reacts with acid to produce hydrogen bubbles to propel the micromotor forward. Once the magnesium core is fully dissolved, a hollow structure remains.

This hollowed-out micromotor acts as a trap for E. coli. Its exposed inner layers are made of an acid-soluble polymer containing the amino acid serine, which lures the bacteria inside. After these layers dissolve and bacteria accumulate in the micromotor, the remaining polymer layers then dissolve and release silver ions, which kill the bacteria.

The micromotors were tested in an acidic solution containing a suspension of E. coli bacteria. They were four times more effective at killing bacteria than micromotors loaded with silver ions alone.

The researchers report in the paper that this is a “first step towards chemical communication between synthetic microswimmers and motile microorganisms. Such a novel concept can be readily expanded to a multitude of important applications ranging from food safety, healthcare, or environmental remediation.”


Paper title: “Onion-like Multifunctional Microtrap Vehicles for Atraction-Trapping-Destruction of Biological Threats.” Co-authors include Fernando Soto, Daniel Kupor, Miguel Angel Lopez-Ramirez, Fanan Wei, Emil Karshalev, Songsong Tang and Farshad Tehrani, UC San Diego.

This work was supported by the Defense Threat Reduction Agency Joint Science and Technology Office for Chemical and Biological Defense (grant HDTRA1-14-1-0064).

Machine learning technique speeds up crystal structure determination

San Diego, Calif., Jan. 30, 2020 -- Nanoengineers at the University of California San Diego have developed a computer-based method that could make it less labor-intensive to determine the crystal structures of various materials and molecules, including alloys, proteins and pharmaceuticals. The method uses a machine learning algorithm, similar to the type used in facial recognition and self-driving cars, to independently analyze electron diffraction patterns, and do so with at least 95% accuracy.

The work is published in the Jan. 31 issue of Science.

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Illustration of the inner workings of a convolutional neural network that computes the probability that the input diffraction pattern belongs to a given class (e.g. Bravais lattice or space group).

A team led by UC San Diego nanoengineering professor Kenneth Vecchio and his Ph.D. student Kevin Kaufmann, who is the first author of the paper, developed the new approach. Their method involves using a scanning electron microscope (SEM) to collect electron backscatter diffraction (EBSD) patterns.  Compared to other electron diffraction techniques, such as those in transmission electron microscopy (TEM), SEM-based EBSD can be performed on large samples and analyzed at multiple length scales. This provides local sub-micron information mapped to centimeter scales.  For example, a modern EBSD system enables determination of fine-scale grain structures, crystal orientations, relative residual stress or strain, and other information in a single scan of the sample.

However, the drawback of commercial EBSD systems is the software’s inability to determine the atomic structure of the crystalline lattices present within the material being analyzed. This means a user of the commercial software must select up to five crystal structures presumed to be in the sample and then the software attempts to find probable matches to the diffraction pattern. The complex nature of the diffraction pattern often causes the software to find false structure matches in the user selected list. As a result, the accuracy of the existing software’s determination of the lattice type is dependent on the operator’s experience and prior knowledge of their sample.

The method that Vecchio’s team developed does this all autonomously, as the deep neural network independently analyzes each diffraction pattern to determine the crystal lattice, out of all possible lattice structure types, with a high degree of accuracy (greater than 95%).

A wide range of research areas including pharmacology, structural biology, and geology are expected to benefit from using similar automated algorithms to reduce the amount of time required for crystal structural identification, researchers said.

Paper title: “Crystal symmetry determination in electron diffraction using machine learning.” Co-authors include Chaoyi Zhu*, Alexander S. Rosengarten*, Daniel Maryanovsky, Tyler J. Harrington and Eduardo Marin.

*These authors contributed equally to this work

Passion drives True Tritons to service

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San Diego, Calif., Jan. 30, 2020 -- From creating scholarships and providing leadership, to student mentoring and preserving the arts, four shining examples of Triton passion and commitment will be honored Feb. 7 at UC San Diego’s True Triton Celebration to be held in the Great Hall on campus.

The True Triton alumni honorees—Janet “Jan” Fisher ’76 , Sheri Jamieson ’73, William “Bill” Proffer ’76, MS ’78 and Leo Spiegel ’83—will be celebrated alongside the next generation of inspiring leaders, as we recognize their role as UC San Diego volunteer champions. Proffer earned both bachelor and master’s degrees in applied mechanics and engineering science in what is now the Jacobs School’s Department of Mechanical and Aerospace Engineering.

“Look no further than Jan, Sheri, Bill and Leo to see changemakers in action,” said Chancellor Pradeep K. Khosla. “They engage in and advocate for causes personal to them, mentor students and other alumni who need their learned expertise, and invest in their university because they recognize UC San Diego as a force for human progress. True Tritons know that individual ripples work together to become waves of change. Together, our power is strengthened and amplified to help solve real-world problems.”

The True Triton alumni honorees will be celebrated alongside the next generation of inspiring leaders, as we recognize their role as UC San Diego volunteer champions.


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Janet “Jan” Fisher ’76 is a passionate and dedicated volunteer at UC San Diego. She’s been an active participant with the L.A. alumni chapter and the Black Alumni Council for many years. As a strong supporter of higher education, she has funded the William C. and Anita Fisher Scholarship to benefit black students, and considers volunteering at UC San Diego an important facet of her life.



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Sheri Jamieson ’73 is a devoted volunteer, fundraiser and philanthropist at UC San Diego. She was one of the early members of the UC San Diego Cancer Center Board and later became one of its founding donors. In addition, she founded and served as president of the University Art Gallery Board, created the Dean’s Advisory Council of Arts and Humanities and chaired the opening of the Sulpizio Cardiovascular Center.



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William “Bill” Proffer ’76, MS ’78 is a volunteer champion who has devoted countless hours mentoring engineering students at Jacobs School of Engineering, and shares his scientific and technical expertise with student entrepreneurs at The Basement. He serves as a judge and hosts poster workshops at the Jacobs School of Engineering Research Expo and has participated as an executive member on the UC San Diego Alumni Board of Directors. He is the chief systems engineer at Leidos.



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Leo Spiegel ’83 is a longtime contributor at UC San Diego. He serves as a Trustee of the UC San Diego Foundation where he is the chair of the Trustee Recruitment and Engagement Committee and is a member of the International Leadership Committee, Campaign for UC San Diego. He is also a member of the Dean's Advisory Council at the Rady School of Management.




The awards will be presented during the Triton Leaders Conference + Celebration, Feb. 7-8, a two-day campus experience featuring dynamic sessions and motivating speakers. Attendees will learn how to elevate their passions to action, with sessions on innovation, leadership, diversity and inclusion, volunteerism and more. New this year, is the Triton Women Who Lead Forum, a special luncheon featuring a panel of inspiring women who lead on campus, in their communities and beyond. For more information or to register, visit the Triton Leaders event page.

This story originally ran in ThisWeek@UCSanDiego

UC San Diego startup selected as finalist in UC Pitch contest

Goto FlickrJingpei Lu, Shelly Bae, Monal Parmar, Jason Bunk, Rohit Ghosh, and Lyn Scott, members of the EVT team, pose at Scripps Beach a short walk from UC San Diego’s campus. Photo courtesy of EVT.

San Diego, Calif., Jan. 30, 2020 -- A startup founded by a UC San Diego electrical and computer engineering graduate student is one of five finalists in the 2020 UC Pitch Startup Showcase held Jan. 29 and 30 in tandem with the Global Corporate Venturing and Innovation Summit in Monterey, Calif.

Educational Vision Technologies, founded by Monal Parmar, a UC San Diego electrical engineering master’s student and electrical engineering undergraduate alumnus, uses technology to help students study more efficiently. Specifically, EVT uses computer vision and machine learning algorithms to autonomously generate interactive notes and video from course lectures, without any extra work required on the part of the professor or lecturer.

During the UC Startup Pitch contest, Parmar will have five minutes to wow a room full of thousands of venture capitalists, and three judges who are also investors. The winning startup moves on to Extreme Tech Challenges’ regional round, and a shot at up to $10 million in funding.

“The biggest value I think is in just attending the conference,” said Parmar. “Presenting at it is crazy—there are 800 corporate VCs attending and the keynote is the president of Samsung Electronics, so for an early stage startup to present at the same conference as the president of Samsung, that’s a crazy opportunity.”

Though Parmar and the EVT team have racked up a slew of awards and funding—including wins at UC San Diego’s Basement Demo Day, Triton Entrepreneur Night, and Ignite’s pitch competition, as well as participation in the Institute for the Global Entrepreneur’s I-Corps program, funded by the National Science Foundation—they were still surprised when they learned they were a finalist at the UC-wide competition.

“It’s amazing that we were selected,” Parmar said. “I was totally stunned because the UC system is so vast and this competition includes alumni, faculty and students, so for us to get selected, that meant a lot. The UC system doesn’t joke when they say they want to support students, faculty, and alumni to create companies that will make an impact on society.”

After the competition and conference wraps up on Thursday, Parmar heads to Arizona State University the next day to compete in the Innovation Open competition. EVT is one of 28 startups selected from universities across the country vying for two $100,000 grand prizes. EVT is one of only three startups at Innovation Open from California, and the only startup selected from the University of California.

Widening the Lens

With a camera installed in the back of a classroom and some patent-pending algorithms and computer vision technology behind the scenes, students gain valuable study resources and a digital version of their course that enables efficient learning. The EVT system allows students to easily find specific portions of content using scrollable time-stamped notes, text transcripts, and keyword-searchable videos on a single web platform.

“EVT autonomously creates notes from a lecture, so students don’t have to write every single thing down and can focus more on understanding,” Parmar said. “It also enables them to study more efficiently outside of class through the ability to click on a word and be taken to the point in the lecture when the professor wrote that on the board or talked about it.”

The tool can also be used for lectures given with a traditional chalkboard or dry erase board, as well as for lectures using slides.

EVT’s pilot program targeted higher education settings, with successful trials at UC San Diego and the University of San Diego—with an electrical engineering course having an average of 58 percent of students logging in every week.

Parmar said the company has spent the past six months growing its team from four to 11 employees—most of whom are also UC San Diego alumni—and working on ensuring the product is scalable and fully automated. They’ve also branched out from focusing only on higher education to creating solutions for learning more broadly, focusing on corporate clients wanting to improve the effectiveness and cost for creating employee training and presentations.

“Learning occurs everywhere—we created a solution which optimizes learning in a higher ed setting, but a lot of issues in higher education also exist in other learning environments like corporations, conferences, and K-12 education,” Parmar said. “In addition to our higher ed offering, this year we’ve generalized our product to better fit a corporate market to expand into new areas and solve new challenges.”

Visit the EVT website to learn more.

This story originally ran in the ThisWeek@UCSanDiego newsletter.

Finalists announced for 2020 UC Startup Pitch Showcase

Land, Sea & Air

This story originally ran in the winter 2020 edition of Triton Magazine

San Diego, Calif., Jan. 29, 2020 --Student engineering clubs push the limits and their vehicles—here’s the fastest, deepest and highest-flying out there.


Custom-made and built from scratch, these Formula One-style race cars are designed, manufactured and driven entirely by undergrads. They’re no slouch either—110 horsepower brings these hot rods from 0 to 60 in 3.5 seconds. And while professional racers can cost millions, these students do it with roughly $50,000, thanks to the support of sponsors.

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Triton Racing members show off their speed machine with advisors Carlos Coimbra and Rob Shanahan (front, from left) and Albert P. Pisano, dean of the Jacobs School of Engineering (center).

About 35 students each year, split between five subsystems—Aerodynamics, Chassis, Electrical, Powertrain and Suspension.


Over the past two decades, the team has built 14 cars. For their 2019 car, the team decreased the wheel diameter, went with a narrower track width between the two tires and built a lower-slung chassis. Their car weighed 50 pounds less than previous machines, and had a lower center of gravity, just 11 inches off the ground—a lean, mean speed machine.


The Formula Society of Automotive Engineers’ (SAE) engineering design competition tests cars for acceleration, braking, speed (a 1-mile autocross race) and endurance (a 14-mile course). Of the 90+ universities that compete, many teams don’t make it to the endurance challenge, and only 30 percent of those actually complete it.


Triton Racing zoomed into eighth place out of 80 teams in the 2017 and 2018 competitions, making them the top-performing SAE team in the state of California.


Nadia Casper, Triton Racing president: “It’s always a matter of making sure our five subsystems work together properly, functionally and efficiently to create a race car that is fast, lightweight and can handle corners.”


“Over four years on the team, I’ve gai