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Ten suggestions for female faculty and staff during the pandemic

Padmini Rangamani, a professor in the Department of Mechanical and Aerospace Engineering, is a coauthor of an article in PLOS Computational Biology giving tips for working women to navigate the pandemic. 

When university campuses sent students, staff and faculty members home in March, Padmini Rangamani, a professor at the University of California San Diego, suddenly found herself running her research lab remotely, teaching her classes online, and supervising her two children, ages 10 and 13, who are also learning online. 

To deal with the stress the situation created, Rangamani turned to a support network of fellow female faculty members around the United States. They chatted and texted and eventually decided to write a scholarly article with recommendations for all other female principal investigators in academia. 

The article, “Ten simple rules for women principal investigators during a pandemic,” was published recently in PLOS Computational Biology.  It’s perhaps important to note that despite its title, the article is careful to say that the cardinal rule is that there are no rules. So all 10 points outlined are in fact suggestions. Also despite its title, Rangamani says most of the 10 points outlined in the publication can apply to all caregivers juggling work and caregiving during the pandemic. 

“Without in-person school or daycare, and without after-school programs, there is really no way for caregivers to function at full capacity at work,” Rangamani said. 

In addition,  such concerns have not been discussed openly in the workplace, the authors felt. Their real fear is then that talent nurtured through the years will be lost in one fell swoop--and  their main goal is to try and change this. Rangamani and fellow co-authors want to normalize conversations about juggling work and family obligations. “If you want to say ‘I can’t meet at this time, because I need to be on a Zoom with my kids, that doesn’t mean you’re not serious about your job or not doing your job well,” she said. “We want to reduce this perception bias.”

This is particularly important to maintain equity and diversity within an organization, Rangamani added. “We need to be extremely vigilant to ensure that those who are particularly vulnerable do not exit the system,” she said. Single parents, those who are taking care of elderly parents and relatives, and parents whose children have special services are especially at risk, she added. “The intense pressure of being ‘on’ all the time is simply not realizable right now.” 

While the paper outlines some changes that can be made at a campus-wide or even university system level, Rangamani is focused on a smaller scale: an office or a department for example. It is much easier to get these smaller groups together and have genuine conversations about what the individual needs are and what can be done to get our colleagues through this intensely difficult period without sacrificing quality or fairness.. “There are measures you can take at the grassroots level,” she said. 

In order to normalize these conversations about work-life balance Rangamani hopes that leadership will empower those who hesitate to ask for help to do so. 

Here are the 10 suggestions that the paper outlines to cope during the pandemic: 

  1. Find a peer group of women to provide professional support.
    “The authors are all members of an online group for women PIs in biomedical engineering, which has historically served as a sounding board for professional concerns. We have found that maintaining these connections has been essential over the course of our careers and are even more important during this quarantine period.”
  2. Say no to requests to do anything outside of your main responsibilities
    “If you can’t do them now, you can offer a time when you might be able to do them; the requesting party will need to recognize that your future schedule could go through upheaval as surges of the disease hit different areas and restrictions change. “
  3. Drop something
    “True, your house might not be as clean as you would like, and you may be eating more frozen pizza than you normally would tolerate. Remember that you are not the only person accepting this as your “new normal.” We can’t forget that the goal during a pandemic is survival—if you are keeping yourself physically and mentally healthy, you are more than succeeding.”
  4. When you have energy to do more than the minimum, use it to support women and underrepresented groups
    “We recognize that advocacy of this nature is a privilege, and not everyone is able to do so safely. If you are in the position to support women and underrepresented groups and have the energy, pick a cause and lean into it. Also, recognize that this action can take many forms, some of which may be a better fit for your individual situation.”
  5. Remember, you know yourself best
    “You know the things that have historically helped you relieve stress. Make a list of 10 of them. Some of them may not be an option during quarantine (oh, how some of us miss writing in coffee shops). But for those that are an option, try to do 1 of them every now and then.”
  6. It’s OK to push back
    “Perpetuating the myth that we can all work to the same degree (or better!) than we did a few months ago is very damaging to many women PIs. When you hear statements such as “everyone is writing more grants now” and “since we have more time, let’s have a virtual conference about this topic,” it’s more than OK to push back that this is not your reality, regardless of the reason.”
  7. Remember, you have some flexibility to make your own schedule
    “If there are pockets of time where you find yourself able to focus better than others, do your best to protect them. Block these times on your calendar—both in the near future and in the upcoming months by declining invitations for extraneous responsibilities.”
  8. Whatever help you can get, take it
    “Perhaps your kids are old enough that they can even help with some of your work—1 of the authors tried (unsuccessfully) to engage her son in doing analysis on ImageJ (NIH, Bethesda, Maryland). Another purchased a 3D printer and recruited her daughter to help print parts for an OpenSPIM setup.”
  9. Do your best to remember that others are struggling too—be empathetic and work to build a community
    “We suggest that each situation is approached with empathy, while maintaining your standards and accountability. For example, empathy may mean that when you assign a task to a group member or staff, you ask them whether the timeline is feasible. If it’s not, that may be a sign that in the future you should aim to give them more advance notice. If a pattern of not completing work continues, it is then time to ask for an explanation. Recognize that just as no one is fully aware of your situation, you are not completely aware of your colleague’s situation.” 
  10. Don’t lose your sense of humor
    “We know, there is nothing funny about this situation. Many of us have needed or will need space to grieve deeply. However, our experience is that where you can share a laugh, you should.”

 Rangamani herself does her best to implement some of these suggestions. She prioritizes the well-being of her own research group over other zoom meetings; protects her research time; and does not schedule meetings at lunch time, if she can help it.

“While there is a light at the end of the tunnel in the form of vaccines,” Rangamani also notes, “this global health crisis may be a once-in-a-lifetime opportunity for the academy to take a close look at how we can empower our vulnerable colleagues and make policy changes to change our culture for the better.”

The authors put rule, or rather suggestion, 10 in practice, by including a list of humorous rules and tips in a supplemental file.

“Service expectations are now completely fulfilled by raising scientifically literate humans of our own and science communication by way of family conversations, Facebook and Twitter debates,” they write. 




 

UC San Diego Alumnus at Helm of Company Behind First At-Home COVID Test

Erik Engelson, a UC San Diego bioengineering and microbiology alumnus, is president and CEO of Lucira Health.

In November 2020, Lucira Health received emergency use authorization for the first rapid at-home COVID-19 test from the U.S. Food and Drug Administration. Erik Engelson, a UC San Diego bioengineering and microbiology alumnus, is president and CEO of Lucira Health, which was founded by UC Berkeley bioengineering alumni.

The Lucira COVID-19 All-In-One Test Kit is a molecular test that uses a simple nasal swab to return results in 30 minutes, anywhere, any time. The test is currently available by prescription in select medical centers. Engelson describes the test as a key tool, along with vaccines, in the arsenal required to slow the spread of COVID-19.

The test uses a real-time loop mediated amplification reaction, and works by swirling the self-collected sample swab in a vial that is then placed in the test unit. In 30 minutes or less, the results can be read directly from the test unit’s light-up display. The Lucira test is simple to operate and is completely self-contained for one-time use. Its accuracy is similar to that of PCR tests that are run in high-complexity central labs.

Engelson earned a bachelor’s degree in microbiology and a master’s in bioengineering from UC San Diego. He has led several medical device startups through to acquisition by companies including Medtronic and Stryker, was a partner at medical device incubator The Foundry, and is a venture partner at ShangBay Capital, to name a few career highlights.

He spoke about the process of getting the COVID-19 test kit through FDA emergency use authorization, his time at UC San Diego, and advice for students, in this Q&A.

Q: Lucira had been working on at-home test kits before COVID-19; what was the initial use case for this product?

A: The company was started in 2013, and I joined about two years ago. The original use case was for influenza. Just as central lab testing was extended to point-of-care (POC), Lucira’s technology is now extending POC to anytime/anywhere testing. From a public health standpoint, it is helpful to keep infectious individuals out of circulation. But how is one to know they are infectious if they can’t test themselves at home? With influenza for example, antiviral medications are generally effective only if taken within 48 hours of symptom onset. Many people don’t go to the doctor at all for flu, and when they do, it’s typically three to five days post-symptom onset, and by then it’s too late for an antiviral. As a result, it would be helpful both to individuals as well as the public health to be able to diagnose flu and other infectious diseases at home.

Q: When you and the Lucira team saw the COVID-19 pandemic developing, was there a decision to pivot and rapidly develop a test for this virus instead?

A: There was a pivot. Fortunately, the Lucira test platform is easily adapted to new assays (tests). Within months, our assay team demonstrated that they had developed an effective COVID-19 assay. This was then integrated into our test platform. Meanwhile, the pandemic was continuing, and the decision to prioritize the COVID-19 test was an easy one.

Q: What were some of the main challenges from an engineering and management perspective to getting the COVID-19 at-home test to and through FDA EUA?

A: I give the technical team huge kudos for the work they did in realizing the vision of transforming a central lab molecular diagnostic that runs on large machines, to a tiny, fully disposable handheld device. Significant thoughtfulness by the engineers and biologists who developed this product went into the design. My role was to build an experienced team of other important functions, including commercialization, clinical/regulatory, finance manufacturing/supply chain and quality, around the technical team. I also brought in additional capital. The transition from technology development to a commercial stage company can be challenging, but the risk can be reduced with an experienced team.

Because our test is intended to eventually be a consumer product, it was critical to not only have strong clinical and bench performance, but also to demonstrate that people of all backgrounds could successfully run the Lucira test from its simple, one-page instruction. This is known as usability testing, and significant effort went into creating easy-to-understand instructions along with a simple-to-use test.

Q: Looking back, were there any formative courses, research experiences, or student organizations from your time at UC San Diego that helped prepare you for this experience of rushing a product to FDA EUA in the middle of a pandemic?

A: Originally a New Yorker, my time both at UC San Diego as well as in La Jolla in general in earlier, quieter days was wonderful. UC San Diego was transformative for me in so many ways: socially, academically. I was lucky to find a perfect academic challenge. My biggest takeaways from the UC San Diego experience were a joy of learning and seeing the beginnings of what I was capable of accomplishing. These attributes remain with me today.

I studied microbiology as an undergrad followed by bioengineering in graduate school. The lab research was interesting, but I craved business. It was really the intersection of business and technology that interested me. It’s important to understand that every technical decision within a company also has a business element. How can engineers and scientists make these decisions if they don’t receive accounting and finance at a minimum? I am delighted that the Rady School of Management is there now, and the Institute for the Global Entrepreneur, the Basement, all these new programs to give students exposure to business and entrepreneurship. I would have loved to have taken business classes in my UC San Diego days—how great if current science and engineering students have this opportunity.

Q: Advice for students who want to work in the biotech industry or aspire to a role such as yours?

A: If there’s a chance of doing an internship for the summer in a company, that can be helpful and illuminating. And I would suggest that students take it upon themselves to find companies that could be of interest and just to reach out. Don’t hesitate, just reach out, even to the CEO. He or she will redirect the inquiry most likely.

When I was at UC San Diego, Hybritech was the only startup on the Mesa. I wrote to the CEO and I still have the response letter in which he stated that “we only have five employees right now, so we're not really set up for this”. That’s ok, and I greatly appreciated his reply. Just reach out, take it upon yourself. Exercise your entrepreneurial gene, and don’t expect the system to create opportunities for you. I know the university has programs to try and make connections and that’s great too, but just go for it, be a self-starter and create your own opportunities.

As you construct your resume and cover letters, emphasize not only technical skills but also the critical softer skills such as your experiences collaborating with others, natural leadership and followership skills, independent as well as group problem-solving. Examples always help. Failure is an important teacher, and insights from such experiences can be useful to convey.

Q: Lucira was co-founded by a couple of UC Berkeley engineering alumni. Why did you decide to get involved with Lucira, and what does this say about the UC system?

A: I always pick companies based on the people as well as the market, and the people at Lucira were just stellar. They had toiled for years on the challenging problem of developing the technology. One of the company’s investors recruited me to Lucira. My predecessor had done a really great job of positioning the technology and company.

The UC system rocks. It’s clear that investment in higher education feeds the economy. That’s exactly what we’re witnessing here, and we see it over and over. I am a proponent of higher education and California is lucky to have such an impressive university system.

Engelson is President and CEO of Lucira Health. He is a Trustee Emeritus of the UC San Diego Foundation; Initial Chairman of the Board of Trustees of UC San Diego’s Bioengineering Department; a member of the UC San Diego Division of Biological Sciences Dean’s Leadership Council; and an elected fellow of the American Institute for Medical and Biological Engineering (AIMBE).

This piece originally ran in ThisWeek. 

Making masks smarter and safer against COVID-19

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A new tool for monitoring COVID-19 may one day be right under your nose. Researchers at the University of California San Diego are developing a color-changing test strip that can be stuck on a mask and used to detect SARS-CoV-2 in a person’s breath or saliva.

The project, which received $1.3 million from the National Institutes of Health, is aimed at providing simple, affordable and reliable surveillance for COVID-19 infections that can be done daily and easily implemented in resource-poor settings. It is part of the NIH’s Rapid Acceleration of Diagnostics Radical (RADx-rad) program for COVID-19.

“In many ways, masks are the perfect ‘wearable’ sensor for our current world,” said Jesse Jokerst, professor of nanoengineering at the UC San Diego Jacobs School of Engineering and lead principal investigator of the project. “We’re taking what many people are already wearing and repurposing them so we can quickly and easily identify new infections and protect vulnerable communities.”

The team will create test strips, or stickers, that can be put on any mask (N95, surgical or cloth). They will be designed to detect the presence of protein-cleaving molecules, called proteases, that are produced from infection with the SARS-CoV-2 virus.

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Prototype test strip before use (top) and after use, showing a negative result (bottom).

The idea is that as the user breathes through the mask, particles—including SARS-CoV-2 proteases if the user is infected—will accumulate in the test strip. At the end of the day or during a mask change, the user will conduct the test. The test strip is equipped with a blister pack that the user will squeeze, releasing nanoparticles that change color in the presence of the SARS-CoV-2 proteases. A control line on the test strip will show what a positive result should look like. It would be similar to checking the results of a home pregnancy test.

Jokerst notes that the strips are not meant to replace current COVID-19 testing protocols.

“Think of this as a surveillance approach, similar to having a smoke detector in your house,” he said. “This would just sit in the background every day and if it gets triggered, then you know there’s a problem and that’s when you would look into it with more sophisticated testing,”

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Set of test strips.

The test strips can be easily mass produced via roll-to-roll processing. This would keep costs down to a few cents per strip. “We want this to be affordable enough for daily testing,” Jokerst said. This would allow facilities at high risk such as group homes, prisons, dialysis clinics and homeless shelters to monitor for new infections earlier and more frequently to reduce spread, he said.

Jokerst is teaming up with researchers at UC San Diego School of Medicine to test the strips first on COVID-19-positive saliva samples, then on patients and healthcare workers at Veterans Affairs San Diego Healthcare System.

Co-investigators on the team are William Penny, professor of clinical medicine, and cardiologist at VA San Diego Healthcare System, Louise Laurent, professor of obstetrics, gynecology and reproductive sciences, and Rob Knight, professor of pediatrics, bioengineering and computer science and engineering, and director of the Center for Microbiome Innovation at UC San Diego.

Potential tool against future outbreaks

This technology can translate to future coronavirus outbreaks, Jokerst said. “The proteases we’re detecting here are the same ones present in infections with the original SARS virus from 2003 as well as the MERS virus, so it would not be too far of a stretch to imagine that we could still benefit from this work later on should future pandemics emerge.”

And even with vaccination efforts underway, this surveillance approach could be deployed in parts of the world where vaccines are not yet available or still limited in distribution.

Materials science approach to mask safety

In addition to this work, Jokerst and his team, in collaboration with UC San Diego nanoengineering professor Ying Shirley Meng, have conducted in-depth research on masks to answer a burning question that surfaced early on in the pandemic: Can N95 respirators be safely reused after being disinfected?

The answer, they found, is yes.

Since the start of the COVID-19 pandemic, health care workers have been facing shortages of personal protective equipment. Researchers and medical centers across the U.S. have found ways to decontaminate and reuse N95 respirators to help keep health care workers safe while serving on the front lines. Jokerst, Meng and colleagues wanted to explore exactly how safe and effective the respirators are for reuse.

A paper detailing this work was published in ACS Applied Materials & Interfaces. UC San Diego materials science Ph.D. student Wonjun Yim is the first author on the study.

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SEM images of the filter layer in an N95 respirator before heat treatment (left) and after (right).

The UC San Diego researchers studied the materials science properties of N95 and KN95 respirators before and after decontamination—the process involved heating the respirators in an oven at 70 C (158 F) for 30 minutes at a time, three times total. They used a filtration apparatus to count how many particles in the air are captured by the respirators. They also examined the fibers of the respirators under an electron microscope.

The team discovered that after the heat treatment, the respirators were able to filter out 90 percent of airborne particles—a small drop from their original 95 rating. They also saw no changes in the structure, density or width of the fibers.

“These masks are more reusable than people think. This is good knowledge to have, to know that these still offer significant protection after being heated multiple times,” Jokerst said.

“People right now don’t understand what happens when you breathe on a piece of cloth all day,” he said. “These studies will lay the foundation to get us thinking about how we can use our masks in safer and smarter ways.”

Wearables: Where Are We?

IMDD Seminar: Introduction and Materials for Quantum Communication

Five UC San Diego teams receive $100,000 to support groundbreaking research

Dominique Meyer and Henry Zhang are fusing diverse sensor systems to advance autonomous vehicles.

The Qualcomm Innovation Fellowship (QIF) recognizes creative Ph.D. students, providing them with funding, mentoring and other resources to pursue innovative research. This year, five UC San Diego Jacobs School of Engineering teams were awarded fellowships – four from Computer Science and Engineering and one from Electrical and Computer Engineering.

“This is the most QIF awards UC San Diego has ever received in a single year,” said Sorin Lerner, chair of the computer science department. “We are honored by Qualcomm’s commitment to our students and excited to watch them solve important and impactful research problems.”

Each team will receive $100,000 from Qualcomm to pursue cutting-edge research on autonomous vehicles, natural language processing and other areas.

“It is great to see the UC San Diego engineering graduate students thrive as participants in the Qualcomm Innovation Fellowship program,” said John Smee, Qualcomm’s vice president of Engineering. “Congratulations to all of the student finalists and winners this year.”

Team: Dominique Meyer (Ph.D. 2021) and Henry Zhang (Ph.D. 2024)
Advisors: Professor Henrik Christensen, Director of the Contextual Robotics Institute; Professor Falko Kuester, Structural Engineering; Professor Todd Hylton, Mechanical and Aerospace Engineering and Executive Director of the Contextual Robotics Institute
Project: Spatiotemporal Fusion of Radar, Vision and LIDAR Data for Autonomous Driving

Autonomous vehicles use different sensor types to adapt to road conditions, traffic, weather and other hazards. The value of each sensor type shifts as circumstances change around the vehicles.

Multiple sensing technologies improve performance, but also pull heavily on the vehicle’s minimal processing power.

Building on work conducted at the Autonomous Vehicle Laboratory and DroneLab, Meyer and Zhang are developing a system that adjusts how sensor data is fused based on driving conditions  to create a dynamic sensor fusion algorithm.

“The work on sensor fusion for autonomous driving vehicles the QIF fellows in my group are conducting is a rich data science problem of modeling sensors, fusion of information and generating actionable knowledge to operate in a dynamic and uncertain world,” said Christensen. “Qualcomm’s support for our students is invaluable for their studies, building direct links to real-world problems and helping them establish a broader world view.”

Team: Shuyang Li (Ph.D. 2022) and Bodhisattwa Prasad Majumder (Ph.D. 2022)
Advisor: CSE Associate Professor Julian McAuley
Project: Toward Personalized and Multimodal Conversational Recommender Systems

Working in the Julian McAuley lab, Li and Majumder have been investigating natural language processing to develop a conversational recommender system. The team was one of ten finalists in the Amazon Alexa Prize 2019-2020 for their efforts to build dialog systems that conduct engaging conversations with users.

Li’s research focuses on machine learning for text generation (recipes, news and dialog) and learning from unstructured fact collections. Majumder has designed more personalized and empathetic machine learning systems. He has published on language and dialog generation, common sense reasoning and information extraction.

“We believe this approach can be particularly impactful in a variety of user-facing applications, such as recommendation engines in product marketplaces, ad-targeting systems and customer support,” said McAuley. “For these applications, we must provide explanations that are interpretable by laypeople, and those explanations should be personalized to each individual user. Conversational frameworks increase accessibility, facilitate new forms of interaction and make recommender systems more empathetic.”

Team: Minghua Liu (Ph.D 2024) and Xiaoshuai Zhang (Ph.D. 2024)
Advisor: Computer Science Assistant Professor Hao Su
Project: Learning-Based 3D Mesh Reconstruction

3D reconstruction captures an object’s shape and appearance from sensor data, providing insights that cannot be easily gleaned from 2D observations.

3D data can be presented in several formats, such polygon meshes, which capture geometric shapes more efficiently, making them ideal for autonomous driving. While creating high-quality 3D meshes from point clouds is a prerequisite for many applications, current approaches can be problematic.

To overcome these limitations, the team is developing ways to better handle ambiguous structures, noise and incomplete data to create a system that supports robotics, autonomous driving, augmented reality and other applications.

Team: Sai Bi (Ph.D. 2021) and Zhengquin Li (Ph.D. 2021)
Advisors: Comptuer Science Assistant Professor Manmohan Chandraker and Professor Ravi Ramamoorthi
Project: Physically Motivated Deep Inverse Rendering from Sparse Inputs

Image formation is a complex process, in which lighting, materials and geometry interact to determine final appearance. Inverse rendering reconstructs a scene from a small set of images or sometimes a single image.

Current methods require expensive, carefully calibrated setups, or assume simplified physical models, reducing performance. Even deep learning methods have problems addressing limited data.

“The human eye is sensitive to all these details,” said Chandraker. “That’s why removing these artifacts is so important. For a true augmented reality experience, everything has to be just right.”

Bi and Li are developing inverse rendering networks that require only light-weight setups to handle complex visual effects, such as spatially varying lighting and global illumination. This work could potentially turn mobile phones into powerful augmented reality and 3D modeling devices.

Team: Casey Hardy (Ph.D. 2021) and Abdullah Abdulslam (Ph.D. 2021)
Advisors: Electrical Engineering Assistant Professor Hanh-Phuc Le and Associate Professor Patrick Mercier
Project: Vertical Hybrid Power Delivery for High-Performance Processors and Digital Systems

As data processing requirements increase for mobile devices and autonomous vehicles, the industry needs higher performing processors. However, as performance increases, so do power demands.

Mobile devices must maximize battery life and minimize heat generation, limiting their performance. Autonomous vehicles rely on input/output (I/O) processor pins to handle large amounts of sensor data. However, a large number of pins are needed for power delivery. As a result, power demands can generate data processing bottlenecks. Hardy and Abdulslam are using a novel power converter architecture to operate at optimal efficiency while reducing power losses.

The team’s preliminary analysis shows this architecture can increase power delivery efficiency by up to 12 percent, as well as reducing heat generation and increasing I/O pin availability for laptops, smart phones and autonomous vehicles.

“We really appreciate Qualcomm (QTI) and the QIF program to support us on this project and the opportunity to work closely with QTI engineers to benefit from their immense mass-production experiences for the success of our project,” said Le. “With this support, we are excited to tackle one of the most urgent and challenging problems in modern high-performance computing systems, power delivery and management.”

Computer scientist named inaugural holder of the Halicioglu Endowed Chair in Memory Systems

CSE Professor Steven Swanson is the inaugural holder of the HalicioÄŸlu Endowed Chair in Memory Systems

UC San Diego Computer Science and Engineering (CSE) Professor Steven Swanson is building computer systems that explore how new memory technologies will impact the future of computing.

In recognition of his impressive body of research to create software to support persistent memory, Swanson was recently named the inaugural holder of the HalıcıoÄŸlu Chair in Memory Systems at UC San Diego. The $1 million chair is part of a larger $18.5 million gift made in 2013 to the department by CSE alumnus Taner HalıcıoÄŸlu ’96.

The chair provides a dedicated source of funds, in perpetuity, for the chair holder’s scholarly activities as well as support for graduate students.

“In the face of the COVID-19 pandemic, Professor Swanson’s work is more important than ever before,” said UC San Diego Chancellor Pradeep K. Khosla. “His research, teaching and mentorship not only push the boundaries of human understanding, they inspire our academic community to continue innovating, experimenting and discovering. These efforts are critical to our mission as a public research university.”

The chair is named after HalıcıoÄŸlu, who was Facebook’s first full-time employee when it had only 15 computer servers and 250,000 users. Now he spurs startups in San Diego as an angel investor and is also a lecturer in the computer science department. He’s been recognized as a 2020 Computer Science Distinguished Alumnus, a 2019 Chancellor’s Medalist and a UC San Diego 2019 Outstanding Alumnus.

“Taner’s incredible generosity and support of innovation and the work of Steven Swanson will impact our department, our university and our world for years to come,” said  Sorin Lerner. chair of the Department of Computer Science and Engineering.

“Endowed chairs give faculty members the freedom to pursue revolutionary ideas, inspire the next generation of innovators, and transform our society in fundamental ways,” Swanson said. “I am privileged to be able further this kind of work at UC San Diego and CSE.”

Impacting the Future of Computing

Swanson is the director of the UC San Diego Non-Volatile Systems Laboratory, where his group builds computer systems to explore how new memory technologies will impact the future of computing, with a focus on non-volatile memories that allow programmers to build long-lived data structures that can survive system crashes and power failures.

“This requires the data structures to be extremely robust, but that is hard because systems can fail in so many different ways,” he said.

Their recent research has made it easier for programmers to build these robust data structures. “Rather than relying on the programmer to get it right, we have built a compiler that automatically checks for the properties these data structures need.  This means less testing, fewer bugs and better reliability,” he said. 

Swanson has also been working with colleagues to develop a new course and lab (CSE142 and CSE142L) that teach students how to fully utilize the powerful features that modern processors provide. 

“Based on our experience of what really matters to software developers, we take the students on a ‘grand tour’ of modern CPUs and then have them apply what they’ve learned to optimize machine learning workloads,” he said.

HalıcıoÄŸlu’s gift has also created the HalicioÄŸlu Chair in Computer Architecture at UC San Diego, which is held by Professor Hadi Esmaeilzadehand the Ronald L. Graham Chair of Computer Science held by Professor Ravi Ramamoorthi, both in the computer science deparment. 

New Method Makes Better Predictions of Material Properties Using Low Quality Data

A schematic of the multi-fidelity graph networks approach to more accurately predict material properties.

Advancements in energy technologies, healthcare, semiconductors and food production all have one thing in common: they rely on developing new materials—new combinations of atoms—that have specific properties enabling them to perform a needed function. In the not-too-distant past, the only way to know what properties a material had was by performing experimental measurements or using very expensive computations.

More recently, scientists have been using machine learning algorithms to rapidly predict the properties that certain arrangements of atoms would have. The challenge with this approach is it requires a lot of highly accurate data to train the model, which often does not exist.

By combining large amounts of low-fidelity data with the smaller quantities of high-fidelity data, nanoengineers from the Materials Virtual Lab at UC San Diego have developed a new machine learning method to predict the properties of materials with more accuracy than existing models. Crucially, their approach is also the first to predict the properties of disordered materials—those with atomic sites that can be occupied by more than one element, or can be vacant. They detailed their multi-fidelity graph networks approach on January 14 in Nature Computational Science.

“When you are designing a new material, one of the key things you want to know is if the material is likely to be stable, and what kind of properties it has,” said Shyue Ping Ong, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering and the paper’s corresponding author. “The fundamental problem is that valuable accurate data, such as experimental measurements, is difficult to come by, even though we have large databases of less accurate computed properties. Here, we try to get the best of both worlds – combine the large low-fidelity data and the smaller high-fidelity data to improve the models’ accuracy in high value predictions.”

While other multi-fidelity approaches exist, these methods do not scale well or are limited to only two fidelities of data. They are not as accurate or dynamic as this new multi-fidelity graph network approach, which can work with an unlimited number of data fidelities and can be scaled up very quickly.

In this paper, the nanoengineers looked specifically at materials’ band gaps—a property used to determine electrical conductivity, the color of the material, solar cell efficiency, and more —as a proof-of-concept. Their multi-fidelity graph networks led to a 22–45% decrease in the mean absolute errors of experimental band-gap predictions, compared to a traditional single-fidelity approach. The researchers also showed that their approach can predict high-fidelity molecular energies accurately as well.

“There is no fundamental limitation as to what properties this can be applied to,” said Ong. “The question is which kind of properties we have data on.”

In the near term, Ong’s team plans to use this new method to develop better materials for energy storage, photovoltaic cells and semiconductor devices.

While predicting the properties of ordered materials, the team made another serendipitous discovery—in the graph deep learning model they use, atomic attributes are represented as a learned length-16 embedding vector. By interpolating these learned embedding vectors, the researchers found they were able to also create a predictive model for disordered materials, which have atomic sites that can be occupied by more than one element or can be vacant at times, making them harder to study using traditional methods.

“While the bulk of computational and machine learning works have focused on ordered materials, disordered compounds actually form the majority of known materials,” said Chi Chen, an assistant project scientist in Ong’s lab, and first author of the paper. “Using this approach, multi-fidelity graph network models can reproduce trends in the band gaps in disordered materials to good accuracy.”

This opens the door to much faster and more accurate design of new materials to meet key societal needs.

“What we show in this work is you can actually adapt a machine learning algorithm to predict the properties of disordered materials. In other words, now we are able to do materials discovery and prediction across the entire space of both ordered and disordered materials rather than just ordered materials,” said Ong. “As far as we know, that is a first.”

The work was supported by the Materials Project, an open-science initiative to make the properties of all known materials publicly available to accelerate materials innovation, funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division (DE-AC02-05-CH11231: Materials Project program KC23MP). All data and models from this work have also been made publicly available via the Materials Virtual Lab’s megnet repository on Github

Study Finds Neglected Mutations May Play Important Role in Autism Spectrum Disorder

Melissa Gymrek, a professor at UC San Diego, is the paper's corresponding author. 

Mutations that occur in certain DNA regions, called tandem repeats, may play a significant role in autism spectrum disorders, according to research led by Melissa Gymrek, assistant professor in the UC San Diego Department of Computer Science and Engineering and School of Medicine. The study, which was published in Nature on Jan. 13, was co-authored by UCLA professor of human genetics Kirk Lohmueller and highlights the contributions these understudied mutations can make to disease.

“Few researchers really study these repetitive regions because they’re generally non-coding--they do not make proteins; their function is unclear; and they can be difficult to analyze,” said Gymrek. “However, my lab has found these tandem repeats can influence gene expression, as well as the likelihood of developing certain conditions such as ASD.”   

In the paper, the lab studied around 1,600 “quad” families, which include mother, father, a neurotypical child and a child with ASD. Specifically, they were looking for de novo mutations, which appear in the children but not the parents. This analysis, led by UC San Diego graduate student and first author Ileena Mitra, identified an average of 50 de novo mutations at tandem repeats in each child, regardless of whether they were affected by autism. 

On average, there were more mutations in ASD children, and while the increase was statistically significant, it was also relatively modest. However, using a novel algorithmic tool developed by UC San Diego bioengineering undergraduate and second author Bonnie Huang, the researchers showed tandem repeat mutations predicted to be most evolutionarily deleterious were found at higher rates in ASD children.

“In our initial analysis, the ratio between the number of mutations in ASD children and neurotypical children was around 1.03, so barely above one,” said Gymrek. “However, after we applied Bonnie’s tool, we found relative risk increased about two-and-a-half fold. The kids with autism had more severe mutations compared to the controls.”

Finding so many previously undiscovered tandem repeat mutations is significant, as it matches the number of point mutations (single alterations in the A, C, G, T bases that make up DNA) typically found in each child.

The study also produced a wealth of information about the many factors that can influence these de novo mutations. For example, children with older fathers had more tandem repeat mutations, quite possibly because sperm continues to divide – and accumulate mutations – during a man’s lifetime. However, the changes in repeat length coming from mothers were often larger, though the reasons for this are unclear.

“The mutations from dad tended to be plus or minus one copy,” said Gymrek. “However, mutations from mom were usually plus or minus two or more copies, so we’d see more dramatic events when they came from the mother.” 

This approach highlighted a number of genes that had already been linked to ASD, as well as new candidates, which the lab is now exploring.

“We want to learn more about what these novel ASD genes are doing,” said Gymrek. “It’s exciting because repeats have so much more variation compared to point mutations. We can learn quite a bit from a single location on the genome.”

Patterns of de novo tandem repeat mutations and their role in autism

The team includes UC San Diego researchers Ileena Mitra, Bioinformatics and Systems Biology Program; Bonnie Huang, Department of Bioengineering; Nima Mousavi, Department of Electrical and Computer Engineering; Nichole Ma, Department of Medicine; Michael Lamkin, Department of Electrical and Computer Engineering; Richard

Yanicky, Department of Medicine; Sharona Shleizer-Burko, Department of Medicine; and Melissa Gymrek; and Kirk E. Lohmueller from the departments of Ecology and Evolutionary Biology and Human Genetics at UCLA. 

UC San Diego professor Bernhard O. Palsson named Y.C. Fung Endowed Chair in Bioengineering

University of California San Diego professor Bernhard O. Palsson  has been named the Y.C. Fung Endowed Chair in Bioengineering at the Jacobs School of Engineering. Palsson is also a professor of pediatrics, and Director of the Center for Biosustainability.   

University of California San Diego professor Bernhard O. Palsson  has been named the Y.C. Fung Endowed Chair in Bioengineering at the Jacobs School of Engineering. Palsson is also a professor of pediatrics, and Director of the Center for Biosustainability

Palsson’s research focuses on developing experimental and computational models of the red blood cell, E. coli, CHO cells, and several human pathogens to establish their systems biology. His Systems Biology Research Group leverages high-power computing to build interactive databases of biological information and is increasingly focused on Genome Design and Engineering.

"Bernhard Palsson is a true intellectual pioneer and international thought leader who knows how to translate fundamental research into biotechnological impact. The positive outcomes of his research, and the work done by the many people he has educated and mentored, are breathtaking," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. "Bernhard truly exemplifies the can-do, will-do, must-do spirit of Y.C. Fung and the endowed chair professorship created in his honor.” 

"I am honored to be awarded this chair as Y.C. Fung has been one of my role models, was one of the founders of our field, and was such an honorable and dignified individual. I shared many memorable moments with him in my early years at UCSD. I have fond memories of him and admire his legacy," said Palsson. (More about Y.C. Fung: Bioengineering Pioneer Y.C. Bert Fung Turns 100; Obituary for Y.C. Bert Fung

"Following Shu Chien who was the first and only holder of the Y.C. Fung Endowed Chair in Bioengineering adds to the prestige of the history of the chair. I can only hope to be able to continue this history of excellence. These are big shoes to fill," said Palsson. (More about Shu Chien: Pioneering bioengineer Shu Chien retires after 31 years at UC San Diego)

Palsson was named for the 7th year in a row as one of the world’s most influential researchers in their fields, according to a December 2020 research citation report from the Web of Science Group. His most cited paper, entitled, “What is flux balance analysis?” was published in Nature Biotechnology in 2010. He was inducted into the National Academy of Engineering in 2006.

Palson previously held the Pierre Galletti Chair in Bioengineering Innovation in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering where he is a senior faculty member in the Department of Bioengineering, which ranks 4th in the nation for biomedical/bioengineering (US News and World Report Ranking of Best Engineering Schools, published March 2020). Bioengineering has ranked among the top four programs in the nation every year for more than a decade.

"Dr. Palsson is an outstanding world leader in systems biology and genome-scale modeling in bacteria and human cells," said UC San Diego bioengineering professor emeritus Shu Chien. "He is an inspiring educator who has written definitive textbooks on Systems Biology and Tissue Engineering, in the true tradition of Professor Fung. He is an ideal holder of the Y.C. Fung endowed chair."

Remembering UC San Diego engineering professor Siavouche "Sia" Nemat-Nasser

University of California San Diego engineering professor emeritus Siavouche "Sia" Nemat-Nasser passed away on January 4, 2021 due to complications of acute myeloid leukemia (AML). He was 84 years old.  

University of California San Diego engineering professor emeritus Siavouche "Sia" Nemat-Nasser passed away on January 4, 2021 due to complications of acute myeloid leukemia (AML). He was 84 years old. 

Professor Nemat-Nasser was a Distinguished Professor of Mechanics and Materials in the Department of Mechanical and Aerospace Engineering at the UC San Diego Jacobs School of Engineering. He officially retired from UC San Diego in 2019 but remained active as a researcher through his Center of Excellence for Advanced Materials (CEAM). 

He was born in Tehran, Iran, and immigrated to the US in 1958 to complete his undergraduate degree at Sacramento State College (now University). He earned his MS and PhD degrees from UC Berkeley in 1961 and 1964, respectively.

He joined the UC San Diego faculty twice, first from 1966 to 1970. He went on to a brilliant 15-year career at Northwestern University. He then returned to the UC San Diego faculty in 1985 where he served as the Director of CEAM until his retirement.

Upon his return to UC San Diego, he set out to create a materials science program, which included helping to recruit a series of young and talented scholars. He went on to serve as the Founding Director of the Materials Science and Engineering Program, which remains an integrated campus-wide graduate degree program that has achieved global recognition. Nemat-Nasser also initiated a program on the mechanical behavior of materials. Both programs became magnets for researchers globally, and recognition by the community followed, along with support from the National Science Foundation which funded the Institute for Mechanics and Materials at UC San Diego where Nemat-Nasser played an important role. 

In many contexts and with many different material types, he studied how materials fail and why. His work enabled the design of more resistant, useful, and safer materials for a wide range of applications, including building materials for civil infrastructure; materials for space stations that can withstand meteorite impacts; and materials for biotechnology and defense.

Renowned both as a strong theoretician and innovative experimentalist, he studied a broad range of advanced materials including ceramics, ceramic composites, high strength alloys and superalloys, rocks and geomaterials, and advanced metallic and polymeric composites with electromagnetic, self-healing, and self-sensing functionality; ionic polymer-metal composites as soft actuators/sensors, and shape-memory alloys. 

In addition, Nemat-Nasser and his research teams developed or co-developed many of the novel research instruments used in their laboratories.

Over a prolific academic career, he published more than 500 scientific articles which have over 33,000 citations according to Google Scholar. 

Nemat-Nasser served as Founding editor in chief of the journal Mechanics of Materials, a position he held for 37 years until his retirement. He also authored, co-authored or edited over 20 books and proceedings including the book series Mechanics Today and the book series Mechanics of Elastic and Inelastic Solids. Notable scholarly works include his book Micromechanics: Overall Properties of Heterogeneous Materials (with co-author M. Hori), and Plasticity, A Treatise on Finite Deformation of Heterogeneous Inelastic Materials.

In 2001, he was elected a member of the National Academy of Engineering for pioneering micromechanical modeling and novel experimental evaluations of the responses and failure of modes of heterogeneous solids and structures. Among his numerous honors, he received the highest awards in mechanics, the Timoshenko Medal in 2008, and the ASME Gold Medal in 2013 (see video).

Teaching and mentoring were crucial to Nemat-Nasser. He advised more than 70 PhD students and 30 post-doctoral researchers during his career, and throughout, taught undergraduate courses in mechanics and mathematics. In 2015 he was awarded the UC San Diego Academic Senate Distinguished Teaching Award for his teaching of undergraduate students which integrated inventive and alternative teaching methods that were simple yet highly effective. 

In a 2008 UCSD TV video segment, he expressed his passion for teaching and training future generations of researchers. He relished the process of working with graduate students who then would be intellectual partners from whom he could learn. Many of his former students and postdocs have become leaders in the field of mechanics.  

Academic awards that bear Sia Nemat-Nasser's name have been created with both the American Society of Mechanical Engineers (ASME) focused on underrepresented minorities and women in engineering, and the Society for Experimental Mechanics (SEM). 

In 2016, Nemat-Nasser and his wife Éva generously established the Roghieh Chehre-Azad Distinguished Professorship within the UC San Diego Division of Arts and Humanities to foster new projects and future works exploring the music, art, literature and history of Persian culture at UC San Diego.

At the time, Nemat-Nasser noted that the gift served to honor his mother "Chehre-Azad,” a well-known actor in Iran who pursued her passion of acting at great personal risk when women performing on stage in Iran was taboo.

He was fond of the Persian poets Ferdowsi, and Omar Khayyam, who also was a great mathematician and astronomer. Nemat-Nasser himself translated poetry from Farsi to English. He also wrote his own poetry in Farsi, illustrated it, and translated it into English. 

A person of great energy, discipline, and dedication, he swam for one hour every day until 2018. In past years, he was known to enter La Jolla Cove at night and swim alone in the ocean, to the dismay of his wife Éva. 

Nemat-Nasser is survived by his wife Éva, six children: Michaela, Elizabeth, Katherine, David, Syrus, Shiba, and grandchildren: Lilith, DJ, Jack, and Arastoo. 

The family has asked that in lieu of flowers, gifts can be made to the Roghieh Chehre-Azad Distinguished Professorship at UC San Diego (K3993).

$1.2 Million Grant Funds a New Generation of Healthcare Telemanipulation Robots

Researchers at UC San Diego, UCLA, UC Irvine and San Diego State University have been awarded a $1.2 million UC Multicampus Research Programs and Initiatives (MRPI) grant to develop an advanced class of mobile telemanipulation robots. These easy-to-operate, low-cost  robots called UC Iris will be used to grasp objects, open doors and perform other tasks to advance telehealth, allowing healthcare workers to safely conduct remote exams and providing quarantined Californians a safe way to interact outside their homes.

“COVID-19 is exacerbating societal inequities and will continue to affect our existence for years to come,” said project lead Laurel Riek,  a professor in UC San Diego’s Computer Science and Engineering department and director of the university’s Healthcare Robotics Lab. “Two groups are at extremely high risk for infection, adverse physical and mental health outcomes and extended isolation: Frontline healthcare workers and people who cannot leave their homes due to high infection risk. This project will develop new telehealth robotic technologies to support both groups.”

A healthcare worker can remotely operate UC-Iris to safely treat isolated patients (left). People at high risk of infection unable to leave home can use UC-Iris to engage with their communities, such as an art class with friends at a cultural center (left).

Entitled Robot-facilitated Health Equity in Post-Pandemic California and Beyond, the team      will develop state-of-the-art mobile robots with advanced tactile sensing, manipulation, and haptics technologies (which transmit information through touch). This will allow operators to feel truly immersed in a remote location and give them a sense of presence and touch. Veronica Santos, professor of Mechanical and Aerospace Engineering and director of the Biomechatronics Lab at UCLA, and Veronica Ahumada-Newhart, human-robot interaction scientist at UC Irvine and director of the Technology and Social Connectedness Lab are co-principal investigators on the team.      

For healthcare workers, these new  robots will help conduct remote exams. Throughout the COVID-19 pandemic,  clinicians have largely relied on static telehealth technologies, such as Zoom and telemedicine carts, to reduce infection risks. However, they must physically deliver these technologies; train patients to use them; and troubleshoot technical issues – all at the patient’s bedside – mitigating their benefits. In addition, existing technologies lack touch and independent mobility, key features many clinicians need. 

Outside of hospitals, millions are at high risk for infection, including people with cancer, those with suppressed immune systems and older adults. These individuals have been further isolated by the pandemic, putting them at increased risk for depression, suicide, dementia and other conditions. 

To address this, the team will advance inexpensive, user-friendly robotic systems that give quarantined people new opportunities to “leave” home and interact with society.

“We will be designing new haptic interfaces, tactile sensing modalities and shared control methods for telemanipulation,” said Riek. “For healthcare workers, these robots will enable new ways to safely treat patients. For people who are isolated, they will provide new opportunities to engage with their loved ones and their communities.”  

Laurel Riek, the project lead and a professor in UC San Diego’s Computer Science and Engineering department and director of the university’s Healthcare Robotics Lab

The researchers will also study optimal ways to deploy the technology. The team will work closely with healthcare workers across the UC system, including emergency medicine specialists and hospitalists, to integrate UC Iris into critical care settings. They will also explore how these robots can improve quality of life for isolated groups and increase their independence. 

“We are specifically focused on Latino communities, as they are the most tragically affected by COVID-19 in California, representing 71% of fatalities among those 18 to 64,” said Riek. “We will explore ways the robots can help them engage and feel included in their communities without risking in-person gatherings.”

The Team

The multidisciplinary research team includes internationally-recognized experts in robotics, haptics, health informatics and psychology.

  • Dr. Laurel Riek (UC San Diego) will lead the overall project, coordinating research activities across the UC campuses, and leading development of the new mobile telemanipulation robotic system, including creating new shared control methods.
  • Dr. Veronica Santos (UCLA) brings expertise in artificial tactile sensing/perception, grasp and manipulation with human, prosthetic and robotic hands to lead development of new haptics technologies that support teleoperator embodiment.
  • Dr. Veronica Ahumada-Newhart (UCI) is an expert in health informatics and developmental psychology and will lead efforts to develop telerobots that support robot-mediated inclusion.
  • Dr. Tania Morimoto (UC San Diego) contributes expertise in human-in-the-loop interfaces, including low-cost haptics, to accommodate a wide range of age and experience levels. Morimoto will lead efforts to create new haptic display technology.
  • Dr. Jacquelynne Eccles (UCI), one of the leading developmental scientists of her generation, will support virtual inclusion efforts on the project.
  • Dr. Kristen Wells (SDSU), brings extensive expertise in clinical psychology and behavioral science, particularly in health equity and health disparities.

Ocean acidification is transforming California mussel shells

By Mario Aguilera

UC San Diego researchers have found that the shells of California mussels, a critical species found along the Pacific Coast, are weakening as a result of ocean acidification.

The large mollusk known as the California mussel makes its home in the rocky shoreline along the Pacific Coast from Mexico to Alaska. Considered a “foundational” animal, Mytilus californianus provides homes for hundreds of other species and offers a rich food source for species ranging from spiny lobsters to humans.

As the waters off our coasts change due to human influences, scientists at the University of California San Diego are finding that the composition of California mussel shells is weakening as it becomes more tolerant of acidic conditions.

Scientists have known that rising levels of human-produced carbon dioxide that are increasingly absorbed into the world’s oceans will have an impact on sea life. But as ocean waters increasingly acidify, tracking impacts on specific species has been difficult to gauge over time. Most of what we know about species’ responses to acidifying waters comes from short-term experiments that suggest these increases in ocean acidity—causing a lowering of seawater pH and less availability of carbonate ions to make shells—can lead to less fortified shells and more vulnerable animals.

But not every species from these studies responds the same way, with some even appearing to do better under these conditions. This makes long-term studies looking at how increases in temperature and ocean acidification impact species extremely valuable for understanding and ultimately making predictions about future vulnerability of these species.

UC San Diego Biological Sciences graduate students Elizabeth Bullard and Alex Neu traveled the Pacific Coast from La Jolla to Washington state collecting mussels that would form a comparison to mussels collected in the 1950s.

Comparing new data with samples collected in the 1950s, UC San Diego Division of Biological Sciences graduate student Elizabeth Bullard and Professor Kaustuv Roy found that ocean acidification is transforming the composition of California mussel shells from mostly the mineral aragonite to the mineral calcite. The results are published in the Proceedings of the National Academy of Sciences.

Aragonite is much stronger than calcite and makes for a better shell to protect against predators and wave energy, two things that are expected to increase with warming waters. Calcite, on the other hand, is much weaker but does not dissolve as easily as aragonite—making a better shell material if the waters are acidifying. Experts had expected aragonite, the stronger of the two substances, to emerge as the dominant mussel shell mineral due to its preference to form in warmer waters. Instead, the new study has shown that the weaker but more stable calcite mineral is now the dominant shell substance, a response linked to increases in ocean water acidity.

“We found that these mussels are indeed secreting more calcite today than they were 60 years ago,” said Bullard. “Lower pH eats away the shells these animals are able to create, so it’s considered a major problem for marine organisms. There are 303 species that are associated with the California mussel, so if we lose the mussel we lose other species, some of which are really important to things like our fisheries and recreation.”

In the late 1950s, Caltech scientist James Dodd traveled the Pacific Coast from La Jolla to Washington state, collecting mussels along the way. His specimen sampling led to a valuable baseline of information about mussels and their shell composition, including the ratio of aragonite to calcite. One of the results of his work was a stark geographical contrast between cold northern waters, where mussels mostly featured calcitic shells, with the warmer southern waters where aragonite was the dominant shell mineral.

Professor Olivia Graeve with members of her lab

To find out how the shell mineral profile has changed across six decades, Bullard similarly traveled the coastline with her lab mate, graduate student Alex Neu, in 2017 and 2018 to collect new specimens in a survey that geographically replicated Dodd’s sampling. With more than 100 shell samples collected, Bullard then spent days meticulously grinding each shell down to a fine dust to dissect their composition—up to 16 hours of grinding for one shell in some cases.

“If you put too much heat or pressure on aragonite it will convert to calcite,” said Bullard. “Calcite is extremely stable but aragonite isn’t. In order to really make sure the ratio is accurate you have to be super careful and hand grind the specimens down to a super fine powder.”

Finally, project collaborator Professor Olivia Graeve and her materials science group in the UC San Diego Jacobs School of Engineering conducted X-ray diffraction analysis on each sample to determine their mineral profiles.

“By combining our expertise in crystallography of materials with our collaborator’s expertise in ecology, we were able to make a real impact on our understanding of humans’ long-term effects on other species,” said Graeve. “This type of interdisciplinary research is what’s required to continue advancing science and engineering for the benefit of our world.”

The results told a new story. Instead of a geographical boundary between north and south California mussel shells, the new survey revealed that acidic waters are reducing shell aragonite throughout the coast, leading to calcite as the dominant shell mineral.

“James Dodd’s data fit in a world where the balance of temperature and ocean pH was very different from that today,” said Roy, a professor in the Section of Ecology, Behavior and Evolution (EBE). “For me it was surprising how big the effect was in 60 years. That’s not a huge amount of time as these things go, but the effect was striking.”

The researchers were surprised to find that ocean pH and changing amounts of carbonate availability, not temperature, played such a strong role in influencing shell mineralogy. It’s a finding that would not be possible without Dodd’s critical baseline work.

“This study highlights the importance of utilizing long-term data sets and large spatial comparisons to understand and test predictions about species responses to a changing world,” the authors write in the paper.

Bullard and Roy are now probing deeper into shell viability questions. They are conducting lab experiments to test how this change from aragonite to calcite might impact the strength and overall function of the mussel shell.

Co-authors of the paper include: Elizabeth Bullard, Ivan Torres, Tianqi Ren, Olivia Graeve and Kaustuv Roy.

A grant from NASA and the Jeanne Marie Messier Memorial Endowment Fund (EBE) supported this research.

2020 Jacobs School student highlights

Alumna spotlight: Bridget Benson, electrical engineering professor at Cal Poly

Moving forward, looking back

How will the UC San Diego Jacobs School of Engineering emerge on the other side of the COVID-19 pandemic? The ground has shifted in many ways, and it's up to us to respond, evolve and adapt.

As we look back at 2020 and move forward in 2021, there are two high-level moves we are also making. These moves are designed to ensure the Jacobs School emerges more ready than ever to confront the challenges, injustices, and societal and innovation needs laid bare by the pandemic.

First, the Jacobs School has initiated and strengthened a series of culture-building programs. The goal is to ensure that we empower all of our students, faculty and staff to do the creative and innovative technical work they are so capable of (more details below).

Second, we are facilitating critical national and international conversations on research. In particular, how academia, industry and government can partner and collaborate in new ways. The goal is to build on the existing research enterprise in order to increase the pull through of innovation to society. Getting this right will inevitably lead to an ever more diverse and empowered innovation workforce.

"Framed by this work on culture building and more effective research partnerships, I'm pleased and humbled to share some of the momentum we've built this year and over the last handful of years," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. "I offer my deepest gratitude to everyone in our Jacobs School community."

A few of our Jacobs School 2020 wins are captured in this video.



Jacobs School Momentum: looking back and looking forward

World-class faculty
We have hired more than 130 new faculty into the Jacobs School over the last 7 years. More than 36% of these new professors are women and/or from other groups traditionally underrepresented in engineering and computer science.

Growing research enterprise
At $212M, our research expenditures are up 34% over the last 5 years.

Rising reputation
We jumped to #9 in the nation this year, in the closely watched US News and World Report Best Engineering Schools rankings. This is up from #17 just four years ago.

Innovation workforce
We have awarded nearly 15,000 Jacobs School degrees over the last 6 years. More than 9,170 talented students enrolled in Fall 2020.

Research relevance
We have launched 14 new agile research centers and institutes since 2014 to drive deeper and more relevant collaborations that tackle the fundamental challenges no research lab or company can solve alone.

Franklin Antonio Hall
We are on schedule for our Spring 2022 opening of Franklin Antonio Hall. Our new building will serve as a model for how to build innovation ecosystems with physical roots and virtual infrastructure with national and international impact. This is how engineering for the public good will get done in the future.

Culture building
As I mentioned above, we are working hard to build a school culture where every student, staff member and professor is empowered to bring their whole self to the classroom, lab, office, and screen. Just this year, we launched the Student and Faculty Racial Equity Task Force; the Racial Equity Fellows Program; the Jacobs School Research Ethics Initiative; and the Jacobs School Anthropology, Performance, and Technology Program. The Jacobs School is a key part of the new Changemaker Institute at UC San Diego. We are also celebrating 10 years of the IDEA Engineering Student Center; and we are proud to be collaborating with our UC San Diego Office for Equity, Diversity, and Inclusion.

 

 

Jacobs School alumni kickstart Dean's Scholars of Excellence program

December 15, 2020-- Education is the great equalizer.

Jacobs School of Engineering alumni Mary Bui-Pham and Dan Pham have seen this play out in their own lives, having both arrived in the U.S. as Vietnamese immigrants who didn’t speak English or have any money to their names-- Mary with her family at age 13 and Dan in his 20s. Yet they were able to work their way up to leadership roles at top tech firms like Yahoo, HP, and Indeed, all thanks to an education.

“I think of myself coming to the U.S., 13 years old, not knowing any English; my father going from being the administrator of a fairly famous research institute to getting a job as a stock clerk in the hospital because his degrees were not recognized, and my mother having to take a seamstress job in a shirt factory even though she didn’t know how to sew,” said Bui-Pham. “Fast forward to now, and I have a Ph.D., I’m a senior leader for a company that helps millions of people get jobs, and I just gave my school an endowed scholarship. All within my lifetime. And all because I got an education and I worked hard. Why can’t that story be replicated again and again?”

The Bui Pham family in front of Geisel Library at UC San Diego.

It will be replicated more frequently thanks to the Bui-Pham family, who have donated the funds to endow a scholarship supporting students with outstanding academic merit, including students who have made or show potential to contribute to diversity, equity and inclusion; first generation; and low-income engineering students.  Their gift launched the larger Jacobs School of Engineering Dean’s Scholars of Excellence program, a school-wide scholarship program meant to advance equal access to a Jacobs School education.  

Thanks to a $10,000 seed gift from an anonymous Jacobs School faculty emeritus, gifts of any amount can now be directed to the Dean’s Scholars of Excellence program, supporting these student scholarships. 

"We have a responsibility to ensure that a Jacobs School education is accessible to as many students as possible. Diversity is critical to innovation, and moving forward as a nation, we must find more and more effective ways to tap our entire talent pool," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. "Mary and Dan understand on a personal level the effect that education can have on one person, and the transformative impact it can have on a society. I’m grateful and honored to work with them to launch the Dean’s Scholars of Excellence program, providing outstanding students with the financial support to pursue their academic goals.”

Bui-Pham earned her Ph.D. in Chemical Engineering at the UC San Diego Jacobs School of Engineering, where she met Dan, a master’s student also working in Professor Kal Seshadri’s lab one summer. It was fireworks-- or more like an explosion-- from the beginning; a pressure gauge on a gas tank Dan was using for an experiment malfunctioned, causing a minor explosion, but catching Mary’s attention in the process. They’ve been together since. 

After earning her Ph.D., Bui-Pham conducted research as a postdoctoral scholar, doing computational modeling of flames. Her computational background set her up for a job with NetGravity, which eventually merged with Google. She then went to Yahoo, where she was the chief-of-staff for the division of Publisher Products, before moving into her current role as Vice President of Strategy and Operations at Indeed, where she helps shape and implement the employment platform’s long-term roadmap. After earning his master’s degree in mechanical engineering at the Jacobs School, Dan worked at disk drive design and storage firm Quantum Corporation, before working his way up from procurement and software engineer to Program Manager at Hewlett Packard.

“I’ve always been very grateful to UC San Diego,” Bui-Pham said. “I made amazing friends, I met my husband, I had the best time in grad school, and I want to pay it forward.”

The inaugural Bui Pham Family Engineering Endowed Scholarship recipient will be named in Fall 2021. The family hopes that their gift and the larger Dean’s Scholars of Excellence program will help propel students with the drive to succeed on a trajectory similar to the one they’ve lived. 

“I think 10 years from now we’ll have a whole generation of amazingly educated, productive citizens, who would be also thinking about ‘how do I pay it forward,’” Bui-Pham said. “We all need to have that gratitude and understand that you don't get anywhere by yourself. We all stand on others’ shoulders. Sometimes just a tiny boost is all we need.”

The goal of the Dean’s Scholars of Excellence program is to continue advancing equal access and success for the most promising engineering minds from all communities. With the help of visionary supporters, we can shape the next generation of diverse problem-solvers who will rise to the challenge of creating tomorrow’s sustainable technologies. To support students through the Dean’s Scholars of Excellence program, select the Jacobs School Dean's Scholars of Excellence fund here. For more information, contact: David Strachan, Director of Development, (858) 761-1379, dstrachan@eng.ucsd.edu

The Bui Pham’s gift contributes to the Campaign for UC San Diego—a university-wide comprehensive fundraising effort concluding in 2022. Together with philanthropic partners, UC San Diego will continue its nontraditional path toward revolutionary ideas, unexpected answers, lifesaving discoveries and planet-changing impact. To learn more, visit the Campaign for UC San Diego website.

UC San Diego Celebrates 25 Years of Wireless Research Leadership

December 15, 2020-- The University of California San Diego Center for Wireless Communications (CWC) is celebrating 25 years of partnering with industry to push the bounds of wireless technologies while training the wireless workforce of the future. 

At the UC San Diego Center for Wireless Communication's 5G and Beyond Forum in November 2020, researchers from academia, industry and government presented on both 5G innovations and visions for 6G. The symposium also looked back at some of the Center’s impactful research and activities over the last three decades.

Looking forward, UC San Diego is engaging in national and international conversations focused on creating wireless research ecosystems and infrastructure through public-private partnerships that facilitate both innovation and workforce development. The general idea is to create scalable research ecosystems and infrastructure that can be accessed virtually and encourage development of future wireless technologies, use-case exploration for 6G and beyond, and the training of tomorrow's wireless workforce.

"I'm thrilled to be actively engaged with the Center for Wireless Communications, and all of our faculty, industry partners, and the wider wireless research community. We are working together to ensure that we have the wireless research infrastructure necessary to drive innovation and empower future generations of wireless engineers," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering.

Wireless firms are already partnering with researchers at UC San Diego and elsewhere to create research infrastructure such as digital replicas of wireless networks. Building on this kind of shared, virtual research infrastructure will be crucial for collecting the data necessary to bring 6G-enabled technologies to fruition, explained Sujit Dey, who is an electrical and computer engineering professor at UC San Diego and Director of the Center for Wireless Communications.

“The Center for Wireless Communications has invested a lot of time into creating application-specific network testbeds -- we’re doing it for our smart transportation program for connected autonomous vehicles, as well as our connected health program for mixed-reality remote healthcare" said Dey. "We’re lucky to have industry partners that make this realistic, but it’s not possible for everyone to be doing this. I hope industry, academia and government can come together in creating digital replicas, digital twins, to not only have testbeds nationally, but to have these digital twins that replicate real situations and gather tremendous amounts of data we otherwise could not. For example with driving, we cannot drive unsafely. But with a digital twin you could get that data.”

Making transportation smarter

In addition to looking deep into the 6G future and beyond, researchers are also innovating and improving 5G connectivity. At the CWC Forum, UC San Diego engineers shared several research areas they’re focused on, including smart transportation and the hardware required to enable up to a trillion connected devices.

A session on connected and autonomous vehicles featured a number of projects at the UC San Diego Jacobs School of Engineering that are focused on improving how well self-driving cars can “see” and communicate with each other.

One example is a technology developed by the lab of UC San Diego electrical and computer engineering professor Dinesh Bharadia that could enable self-driving cars to navigate safely in bad weather. It consists of multiple radar sensors working together like multiple eyes to create a fuller view of the road, even when it’s not clear outside. The setup can accurately predict the dimensions of a car moving in fog. Bharadia is working with Toyota and Honda for further research and development. He says this new technology could provide a cheap alternative to lidar.

Improving self-driving cars’ vision will also require reconciling images taken by sensors at different viewpoints. A camera from a vehicle and a camera from a lamp post, for example, can both see the same object, but they might not know it is the same because they are viewing it from different angles, said Truong Nguyen, a professor of electrical and computer engineering at UC San Diego. To address this issue, Nguyen and his lab developed algorithms that can find features that are common between these pictures and match them to objects. The algorithms work in both 2D images and 3D point clouds. The researchers are currently optimizing the algorithms for real-time computation.

As more cars and streets become outfitted with cameras and sensors, an emerging opportunity and challenge will be fusing live data from all of these different sources, obtaining intelligent perception of the environment, and sharing the insights with all the vehicles and even other road users like pedestrians and bicyclists.

Sujit Dey, the Center for Wireless Communications director, is working with CWC colleagues and industry partners to develop intelligent roadside units to perform these tasks. The idea is that vehicles—both autonomous and human-driven—would send data from on-board cameras, radar and lidar sensors to the roadside units, which would fuse and process the data, and then provide enhanced perception to vehicles and other road users to improve advanced driver assistance systems, and to autonomous vehicles for more efficient path planning and navigation. Because all of this hefty computer processing will consume a lot of power, Dey and colleagues are building units that are powered by renewable energy so they can reduce their carbon footprint.

Connected vehicle technologies will also require high-throughput data rates. Millimeter wave directional beams can accommodate these increases in data use, but the problem is they are susceptible to blockage from buildings and human bodies. They are also hard to manage when tracking moving objects.

UC San Diego electrical and computer engineering professor Xinyu Zhang is exploring ways to make millimeter wave technology practical for connected vehicle applications. His lab built a testbed at the UC San Diego campus to explore the feasibility and challenges of millimeter wave-connected vehicles. The researchers discovered that millimeter waves can boost link speed by orders of magnitude in best case scenarios, but this requires deploying a significantly large number of base stations on site. The good news, Zhang noted, is that since road segments have simple geometries, base stations can easily “spot-light” on vehicles using their directional beams to maintain connectivity. The researchers are exploring machine learning algorithms that can make the base stations intelligent enough to harness such advantages.

Circuits for a more connected world

The future will experience an explosive growth in the number of connected devices being used worldwide. By 2035, we can expect that number to be a trillion, said UC San Diego electrical and computer engineering professor Patrick Mercier.

But to get to that number, engineers need to figure out how to improve the power management of these devices, he noted. The battery life of a typical IoT device ranges from a few hours to a few days. The largest fraction of that battery power is being spent by the radio subsystems.

By only waking up a wireless device when necessary, the wake-up receiver (chip stack to the left of the penny) can cut down on power use and extend battery life. The system includes a miniaturized antenna (gold-colored plate below the receiver). Photos by David Baillot/UC San Diego Jacobs School of Engineering

Mercier’s lab is working on solving this power problem by building ultra-low power wake-up radios. As their name implies, these radios wake up a device only when it needs to communicate and perform its function. This allows the device to stay dormant the rest of the time and reduce power use. The latest wake-up radio from the Mercier lab boasts a power consumption of 4.4 microwatts and is compatible with both WiFi and Bluetooth. Mercier says the technology could improve the battery life of small IoT devices from months to years.

A number of UC San Diego electrical engineering professors are at the cutting edge of building hardware elements for next generation 5G systems. These include power amplifiers with highly efficient supply modulators (Peter Asbeck and Hanh-Phuc Le); phased arrays that transmit and receive over a wide band (Gabriel Rebeiz); and digital phase-locked loops with state-of-the-art performance (Ian Galton).

Envisioning 6G

While 5G connectivity is still being rolled out and improved for users around the globe, wireless industry and academic leaders are already exploring what the next generation of connectivity—6G—will look like, and starting the research required to enable it.

A panel of experts from Samsung Research, Qualcomm, Nokia, Ericsson and UC San Diego agreed that the specific technical capabilities of 6G are still being hashed out, but some rough estimates do exist.

While 5G connectivity in 2021 is expected to have speeds of 100 gigabits per second and latency of 500 microseconds, 6G connectivity is expected to increase the speed of transmission to 1 terabyte per second, with latency as low as 100 microseconds.

Use cases for these high data rates and low latency include truly immersive extended reality experiences, as well as mobile holograms and "digital twins" which refers to recreating physical entities in a virtual world to study, alter and interact with them.

The panelists also agreed that they expect 6G connectivity should be entering the wireless market within the next 10 years, perhaps as early as 2028. What research is required from academic researchers to enable these speed and latency improvements?

On the semiconductor side, improving radio-frequency integrated circuits (RFICs) to function at terahertz bandwidth will be key. In addition to moving into terahertz bandwidth, research into dynamic spectrum sharing options is needed.

“The wireless industry is incredibly grateful for the existence of the Center for Wireless Communications,” said Martha Dennis, a technologist, venture capitalist and a member of the CWC’s founding executive council at the recent CWC 25th anniversary forum. Over the center’s 25 year lifespan, more than 40 companies have become members.

As wireless technologies are incorporated into more and more industries, services and products, the number and diversity of companies partnering with CWC is sure to rise.   

Bioengineering alumnus named to Forbes 30 Under 30

Major Upgrade Under Way at the World's Largest Outdoor Shake Table

Dec. 14, 2020 -- Earlier this year in San Diego, two giant cranes lifted the 330,000 lb. steel  floor, or platen, off the world’s largest outdoor shake table, revealing a complex network of pipes, wires and catwalks. 

This was the first step in a major $16.3 million upgrade to the seismic simulator funded by the National Science Foundation. Over the next 10 months, the facility will undergo major construction. When completed in October 2021, the shake table will be able to reproduce multi-dimensional earthquake motions with unprecedented accuracy. 

“We take a lot of pride in having such accuracy,”  said Joel Conte, principal investigator of the UC San Diego shake table and a professor in the Department of Structural Engineering. 

“It’s very, very difficult to achieve on such a large shake table.” 

“We will be able to replicate, in full 3D, the combined effect of all the motions of an earthquake applied to a structure, as well as the interaction between soil and building, and soil liquefaction,” he added. 

The principle behind the table is relatively simple: various structures are built on top of the facility’s floor, or platen, which is connected to a series of horizontal and vertical actuators, or pistons that move back and forth, simulating earthquake motions. The movements follow precise earthquake records researchers have gathered from around the world.

Each structure on the table is wired with hundreds of sensors recording how it fared during earthquake simulations--the data acquisition system will be completely overhauled during the upgrade as well. Data analysis from the tests has led to many changes in the nation’s building codes in the shake table’s 15-year history.

Until this year, the facility could only simulate backward and forward ground motions, or what is known as one degree of freedom. Thanks to the NSF funds, it is getting more actuators, and more power, so that it can also simulate up and down, left and right, as well as pitch, roll and yaw motions, which is known as six degrees of freedom (6-DOF).

Reproducing earthquake motions in 6-DOF is key because during a temblor, the ground may move in any direction. For example, during the 1994 Northridge earthquake in the Los Angeles area, bridge columns punched through bridge decks, hinting at a strong vertical ground motion component. Similarly, during the 1971 San Fernando earthquake, the buildings twisted and swayed, hinting that the ground was probably rotating. 

“We will be able to achieve the ultimate level of validation for new retrofit methods, new materials, new components and new construction methods,” Conte said. 

After the upgrade, the facility also will be able to test the tallest and heaviest test specimens in the world, from multi-story buildings, to bridge columns, bridge bents, and wind turbines, with a full range of ground motions that can occur during an earthquake.

Shake table impact

Professor Joel Conte is the principal investigator at UC San Diego's shake table. 

In the 15 years of operations of the shake table, known as the LHPOS,T in its one degree of freedom configuration, a total of 34 major research projects have been tested on the shake table. The research 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, tunnels and retaining walls. It also has helped validate the use of innovative technologies to make buildings more likely to withstand earthquakes.

For example, in San Francisco, approximately 6,000 soft-story wood-frame buildings are being retrofitted to make them safer in strong earthquakes. Full-scale testing of retrofit systems for these “soft-story” wood frame buildings on the UC San Diego shake table, led by Professor John van de Lindt from Colorado State University, was critical to make this possible.

Research by Professor Jose Restrepo at UC San Diego, co-principal investigator for the NSF upgrade grant, and Professor Robert Fleischman at the University of Arizona, led to new design standards for so-called floor diaphragms, which transfer seismic forces from building floors to columns, walls and eventually foundations.

10-story building test

The first structure to undergo tests on the shake table after the upgrade will be a full-scale 10-story building made from cross-laminated timber. The goal of these tests, led by Shiling Pei, a professor at the Colorado School of Mines, will be to gather critical fundamental data to design wood buildings as tall as 20 stories that do not suffer significant damage during large earthquakes. That is, not only can occupants leave the building unharmed, but they can also return and resume living in the building shortly after an earthquake.

The operation and maintenance of the UC San Diego shake table is currently funded through a five-year grant from NSF’s Natural Hazards Engineering Research Infrastructure (NHERI) Program.

 

A smart ring shows it's possible to detect fever before you feel it

Subjects used the Oura ring to track their temperature. 

Dec. 14, 2020 -- Temperature data collected by wearable devices worn on the finger can be reliably used to detect the onset of fevers, a leading symptom of both COVID-19 and the flu, according to a team of researchers from the University of California San Diego, UC San Francisco and MIT Lincoln Lab.

Researchers published their results in a paper titled  “Feasibility of continuous fever monitoring using wearable devices” in the Dec. 14 issue of the journal Scientific Reports. They emphasize that the study is a proof-of-concept effort with data from only 50 participants reporting COVID-19. 

The Scientific Reports paper is the first published result from TemPredict, a study of more than 65,000 people wearing a ring manufactured by Finnish startup Oura, that records temperature, heart rate, respiratory rate and levels of activity. The goal of the study is to develop an algorithm that can predict the onset of symptoms such as fever, cough and fatigue, which are characteristic of COVID-19. Researchers say they hope to reach that goal by the end of the year. They also hope the algorithms will allow public health officials to act faster to contain the virus’ spread.  

“This isn’t just a science problem, it’s a social problem,” said Benjamin Smarr, the paper’s corresponding author and a  professor in the Department of Bioengineering and the Halicioglu Data Sciences Institute at UC San Diego. “With wearable devices that can measure temperature, we can begin to envision a public COVID early alert system.”

But users from diverse backgrounds  would need to feel safe sharing their data for such efforts to really work, Smarr added.  The data is stripped of all personal information, including location, and each subject is known by a random identifying number.

Smarr is TemPredict’s data analytics lead. Ashley Mason, a professor in the Department of Psychiatry and the Osher Center for Integrative Medicine at UC San Francisco, is the principal investigator of the study. 

“If wearables allow us to detect COVID-19 early, people can begin physical isolation practices and obtain testing so as to reduce the spread of the virus,” Mason said. In this way, an ounce of prevention may be worth even more than a pound of cure.” 

Wearables such as the Oura ring can collect temperature data continuously throughout the day and night, allowing researchers to measure people’s true temperature baselines and identify fever peaks more accurately. “Temperature varies not only from person to person but also for the same person at different times of the day,” Smarr said. 

The study, he explains, highlights the importance of collecting data continuously over long periods of time. Incidentally, the lack of continuous data is also why temperature spot checks are not effective for detecting COVID-19. These spot checks are the equivalent of catching a syllable per minute in a conversation, rather than whole sentences, Smarr said. 

Benjamin Smarr, a professor in the Department of Bioengineering and the Halicioglu Data Science Institute, is the paper's corresponding author. 

In the Scientific Reports paper, Smarr and colleagues noticed that fever onset often happened before subjects were reporting symptoms, and even to those who never reported other symptoms. “It supports the hypothesis that some fever-like events may go unreported or unnoticed without being truly asymptomatic,” the researchers write. “Wearables therefore may contribute to identifying rates of asymptomatic [illness] as opposed to unreported illness, [which is] of special importance in the COVID-19 pandemic.”

The 50 subjects in the study all owned Oura rings and had had COVID-19 before joining TemPredict. They provided symptom summaries for their illnesses and gave researchers access to the data their Oura rings had collected during the period when they were sick. The signal for fever onset was not subtle, Smarr said. “The chart tracking people who had a fever looked like it was on fire.” 

The data collected as part of the subsequent TemPredict study included 65,000 subjects, and these data will be stored at the San Diego Supercomputer Center at UC San Diego, where a team led by Ilkay Altintas is building a portal to enable other researchers to access these data for other analyses. 

“The data collected has great potential to be linked with other datasets making individual and societal scale models be combined to further understand the disease,” said Ilkay Altintas, the chief data science officer at the San Diego Supercomputer Center, who is . The easier we can make to share the data and optimize the use of it through digital technologies, the quicker other researchers will make use of it in their studies.”

Researchers also are keeping up efforts to recruit a diverse pool of subjects that reflects the U.S. population. 

“We need to make sure that our algorithms work for everyone,” Smarr said. 

In future, researchers plan to expand their early detection methods to other infectious diseases, such as the flu. 

Smarr has worked as a consultant with Oura within the last 12 month and received compensation, although not during this research project. 

Feasibility of continuous fever monitoring using wearable devices

Benjamin Smarr, UC San Diego Department of Bioengineering and Halicioglu Data Science Institute

Kirstin Aschbacher, UC San Francisco and Oura

Sarah M. Fisher, Anoushka Chowdhary, Kerena Puldon, Adam Rao, Frederick Hecht and Ashley E. Mason UCSF

Stephan Dilchert, City University of New York and preValio LLC, Minneapolis

Passing of Shao-chi Lin, Professor Emeritus of Engineering at UC San Diego

Shao-chi Lin, Professor Emeritus of Engineering at the University of California San Diego, died on October 8, 2020 at the age of 95. He is remembered by former students and colleagues as a talented and caring teacher, mentor and researcher; and an active member of the campus community.

Lin was an internationally renowned engineer who specialized in gas dynamics, which has applications in many areas including the re-entry of spacecraft into earth's atmosphere after space travel.

UC San Diego Professor Emeritus Forman Williams remembers Lin as an experimentalist who had excellent theoretical understanding, which is a powerful combination. Lin's dual strengths in theory and experimentation fed his passion for making real-world impacts through research, teaching, and mentorship.

UC San Diego professor Sol Penner recruited Lin to UC San Diego in 1964, where he joined the newly formed Aerospace and Mechanical Engineering Sciences (AMES) Department as a professor of engineering physics.

A world-class mentor

Lin taught and mentored many UC San Diego students over the years. Two students who earned PhDs under his guidance, and who were driven, like Lin, by a desire to make real-world impacts, are Robert Akins BA ’74, M.S. ’77, Ph.D. ’83, and Richard Sandstrom, BA ’72, M.S. ’76, Ph.D. ’79.

Grounded in expertise on excimer lasers that were part of Lin's research program at UC San Diego, Akins and Sandstrom founded Cymer. This San Diego based company grew to lead the world in the design and manufacture of laser light sources used for making computer chips for computers, phones and many other electronic devices.

"He was a strong intersection of a practical hardware guy and a very good theoretician," said Sandstrom, who explained that Lin instilled the importance of backing up experimental research with a good theoretical foundation. Lin pushed his students to keep asking themselves "What's behind it?"

There are different kinds of personalities you find among professors, explained Akins. "Some are extremely academic, some are outward focused. Dr. Lin was able to blend very strong academics with being very involved in real life," said Akins. "In one of his graduate classes on gas dynamics, the only question on the final was to calculate the peak temperature on the heat shield of a re-entering Apollo space capsule. It was as short as that. You had to come up with a ballpark answer."

Akins fondly recalled Lin's ability to quickly walk through a calculation rationale, making numerous assumptions and calculating units, and then asking students to check his calculations. "You would find he was pretty close, maybe 10% off. He could do that again and again and again."

21st Century China Center

In 2012, Lin and his wife Lily helped to found the 21st Century China Center in the School of Global Policy and Strategy (GPS) at UC San Diego. Lei Guang, director of the Center, described Lin as the “gentlest, kindest, and most sincere person” who only wished for the two countries to get along. "He was proud of the role the Center plays in bridging the understanding between the Chinese and American people."

“Professor Lin was a role model for all of us," says Susan Shirk, research professor and Chair of the 21st Century China Center at UC San Diego. "He achieved great professional success in the United States, and retained a strong love for the Chinese culture and people."

Lin was born in Guangzhou, China on January 5, 1925. He earned his undergraduate degree from National Central University in Chongqing, China in 1946. He went on to earn a Ph.D. in aerospace engineering from Cornell University in 1952, under the guidance of professor Arthur Kantrowitz. Lin worked for a company founded by Kantrowitz called Avco-Everett Research Lab (AERL) in Everett, Massachusetts as a principal research scientist from 1955 to 1964.  

Human connection and inspiration

"Dr. Lin was always very accessible. He was very good to all his students," said Sandstrom, who recalled that Lin and his wife Lily were always looking out for a circle of visiting students and other young people, some family some not.

In 2006, in the context of a planned gift that Shao-chi and Lily communicated to UC San Diego regarding an endowed chair professorship, Lin said, “The best reward has been seeing my students become successful professors, entrepreneurs and leaders.”

Outside the laboratory, Lin and Lily lived an active and full life. Ballroom dancing, downhill skiing, and travel were shared passions. They took annual January ski trips together until Lin turned 90. He also maintained a pilot's license. Shao-Chin and Lily were actively engaged with the Friends of the International Center at UC San Diego for many years.

In a UC San Diego alumni magazine profile, Akins and Sandstrom cite the research laboratory run by Lin, where they collaborated together for years, as particularly impactful to their futures. “Professor Lin had an entrepreneurial spirit and was an incredibly talented physicist and engineer. The way he ran his group had a huge impact on Rick and I. We conduct a lot of our meetings here at Cymer the way he conducted them at UCSD.”

Akins recently elaborated a bit more on this point.

"We ran our weekly review meetings exactly how he ran his meetings. We fell back on the virtues of integrity, passion to succeed, and innovation. Looking back, I see the influence Dr. Lin had on the way we ran the company," said Akins.

Sandstrom's advice for graduate students rings out like another lesson learned from Lin: "Keep in touch with your advisor after you are out of graduate school. They are a great resource for you when you are out in your career."

Honoring Professor Lin

Gifts to honor Shao-chi Lin can be made to the Mechanical and Aerospace Engineering Excellence and Innovation Fund (E3889) at the UC San Diego Jacobs School of Engineering.
 

This flexible and rechargeable battery is 10 times more powerful than state of the art

Dec. 11, 2020 -- A team of researchers has developed a flexible, rechargeable silver oxide-zinc battery with a five to 10 times greater areal energy density than state of the art. The battery also is easier to manufacture; while most flexible batteries need to be manufactured in sterile conditions, under vacuum, this one can be screen printed in normal lab conditions. The device can be used in flexible, stretchable electronics for wearables as well as soft robotics.  

The team, made up of researchers at the University of California San Diego and California-based company ZPower, details their findings in the Dec. 7 issue of the journal Joule. 

“Our batteries can be designed around electronics, instead of electronics needed to be designed around batteries,”  said Lu Yin, one of the paper’s co-first authors and a Ph.D. student in the research group of UC San Diego’s nanoengineering Professor Joseph Wang.

The areal capacity for this innovative battery is 50 milliamps per square centimeter at room temperature--this is 10-20 times greater than the areal capacity of a typical Lithium ion battery. So for the same surface area, the battery described in Joule can provide 5 to 10 times more power.  

“This kind of areal capacity has never been obtained before,” Yinvsaid.  “And our manufacturing method is affordable and scalable.”

The new battery has higher capacity than any of the flexible batteries currently available on the market. That’s because the battery has a much lower impedance--the resistance of an electric circuit or device to alternative current. The lower the impedance, the better the battery performance against high current discharge.

“As the 5G and Internet of Things (IoT) market grows rapidly, this battery that outperforms commercial products in high current wireless devices will likely be a main contender as the next-generation power source for consumer electronics“ said Jonathan Scharf the paper’s co-first author and a Ph.D. candidate in the research group of UC San Diego’s nanoengineering Professor Ying Shirley Meng.

The batteries successfully powered a flexible display system equipped with a microcontroller and Bluetooth modules. Here too the battery performed better than commercially available Li coin cells. 

The printed battery cells were recharged for more than 80 cycles, without showing any major signs of capacity loss. The cells also remained functional in spite of repeated bending and twisting. 

“Our core focus was to improve both battery performance and the manufacturing process,” said Ying Shirley Meng, director of the UC San Diego Institute for Materials Discovery and Design and one of the paper’s corresponding authors. 

To create the battery, the researchers used a proprietary cathode design and chemistry from ZPower.  Wang and his team contributed their expertise in printable, stretchable sensors and stretchable batteries. Meng and her colleagues provided their expertise in advanced characterization for electrochemical energy storage systems and characterized each iteration of the battery prototype until it reached peak performance. 

The recipe to better performance

The battery’s exceptional energy density is due to its silver oxide-zinc, (AgO-Zn)chemistry. Most commercial flexible batteries use a Ag2O-Zn chemistry. As a result, they usually have limited cycle life and have low capacity. This limits their use to low-power, disposable electronics. 

AgO is traditionally considered unstable. But ZPower’s AgO cathode material relies on a proprietary lead oxide coating to improve AgO’s electrochemical stability and conductivity. 

As an added benefit, the AgO-Zn chemistry is responsible for the battery’s low impedance. The battery’s printed current collectors also have excellent conductivity, which also helps achieve lower impedance. 

Improved manufacturing

But AgO had never been used in a screen-printed battery before, because it is highly oxidative and chemically degrades quickly. By testing various solvents and binders, researchers in Wang’s lab at UC San Diego were able to find an ink formulation that makes AgO viable for printing . As a result, the battery can be printed in only a few seconds once the inks are prepared. It is dry and ready to use in just minutes. The battery could also be printed in a roll-to-roll process, which would increase the speed and make manufacturing scalable. 

The batteries are printed onto a polymer film that is chemically stable, elastic and has a high melting point (about 200 degrees C or 400 degrees Fahrenheit) that can be heat sealed. Current collectors, the zinc anode, the AgO cathode and their corresponding separators each constitute a stacked screen-printed layer.

The team is already at work on the next generation of the battery, aiming for cheaper, faster charging devices with even lower impedance that would be used in 5G devices andsoft robotics that require high power and customizable and flexible form factors.  .


 

 











 

Finding Worth in Waste: How Wastewater Monitoring Helps Reduce the Spread of SARS-CoV-2 at UC San Diego

Wastewater testing

Center for Microbiome Innovation director Rob Knight (above) and his research team regularly visit all sites to collect and test samples. Photo Credit – UC San Diego, Erik Jepsen

Early detection is one of the keys to reducing the spread of SARS-CoV-2 - the virus that causes COVID-19 - and a wastewater monitoring system developed by the UC San Diego Center for Microbiome Innovation (CMI) is proving to be an invaluable tool.

While symptoms of COVID-19 generally take four or five days to appear, traces of the virus can be detected much earlier. Once a person has been exposed to SARS-CoV-2, the virus replicates in the gastrointestinal tract and travels into stool, eventually reaching sewage systems from toilets and showers. By monitoring wastewater outflow, viral activity can be discovered near the onset of an infection, including presymptomatic and asymptomatic cases.

The Environmental Testing/Wastewater Work Group is led by Rob Knight, professor and director of the Center for Microbiome Innovation at UC San Diego; Smruthi Karthikeyan, postdoctoral researcher in the Department of Pediatrics; and Bob Neuhard, executive director of the Operational Strategic Initiatives, and serves as an integral component of UC San Diego's Return to Learn Program. Using real-time quantitative polymerase chain reaction (RT-qPCR) analysis, wastewater samples are tested for genetic material unique to the coronavirus. The CMI integrates researchers and technologies to rapidly perform these tests on a large scale, enabling more efficient surveillance capacity for the university.

"Building capabilities to solve applied problems is where the Center for Microbiome Innovation excels," according to Andrew Bartko, executive director of the CMI. "We strive to integrate the world-class expertise, technologies, and resources we have available into collaborative teams that yield impactful results." Both the wastewater testing initiative and the Return to Learn program have garnered national acclaim, including recent coverage in the New York Times and Los Angeles Times.

The program began with six sample collection points during the summer and expanded to 52 sites in late November, with plans to reach 200 sites in the coming months. As the number of collection sites grow, the system will cover the entire campus and provide more granular data on where viral shedding is occurring. The increase in collection capacity has already paid dividends, as traces of the coronavirus were detected throughout late November and early December. When a positive sample is detected in wastewater, the university sends out an alert that encourages anyone who was in buildings where the virus was detected to get tested immediately. Infected students are then moved to isolated housing, preventing wider outbreaks and significantly reducing public spread of the virus.

This early detection has been vital to UC San Diego’s low infection rate, which has consistently been nearly an order of magnitude below San Diego County’s numbers. Even as the virus has surged throughout the county, UC San Diego has maintained a positivity rate of less than 1% among its student body.

With a continued focus on early detection and mitigation by studying the virus’s interaction with the microbiome, the CMI is committed to helping the university protect its community of students, faculty, and staff as they return to campus.

 

 This piece was written by CMI’s contributing editor Cassidy Symons

Windmill kit provides introduction to structures and design

December 10, 2020-- This fall, students in the Introduction to Structures and Design course at the Jacobs School of Engineering were able to get hands-on experience designing aerodynamic, efficient and earthquake-safe structures even during a quarter of hybrid in-person and remote learning. This was made possible by a take-home windmill kit designed by a local startup company CORI. The curriculum using these building kits was developed by UC San Diego structural engineering teaching professor Lelli Van Den Einde as a design-build competition to meet the learning objectives of the course.


While 120 of the 140 students in the introductory structural engineering course opted to take it in-person, the traditional team project builds of years past weren’t realistic due to campus social distance policies. To make it possible for students—remote and in person-- to still get a hands-on design and build experience during the lab class, students each received their own CORI windmill kit containing cardboard, dowels, string and 3D connectors. 


The goal? To design a windmill capable of raising a water bottle off the ground, and a supporting tower to resist wind and seismic loads as efficiently as possible.


“My class is about introducing students to fundamental structural engineering concepts that they will learn more deeply during their education at UC San Diego, as well as introducing the possible tracts they can take in structural engineering,” said Van Den Einde. “We want them to be exposed to the four different focus sequences they could choose. We have civil structures which are bridges and buildings; aerospace structures which include airplanes; geostructures which are foundations and retaining walls; and structural health monitoring which assesses the integrity of all structures in real time.” 


Van Den Einde initially contemplated developing a term project and sending each student a different project kit for each of the four structural engineering tracts, but the costs for that quickly added up. Instead, she teamed up with CORI to design the windmill project, which focuses on the Civil and Aerospace tracts.
“Students have to use aerodynamic principles to design the blades for the windmill—they design the shape of the blades, number of blades, and angle of inclination to get the most efficiency out of their windmill.


Additionally, the windmill sits on top of a tower, and we want them to design the tower in a way that can resist what we call lateral loads like earthquakes or wind loads. So it’s a cool project because it uses simple cardboard material, but students can apply the principles they’re learning in class about loads, material properties, structural analysis, and aerodynamics, getting that basic intro to engineering intuition.”


The course had been meeting in the EnVision Arts and Engineering Maker Space, but went remote during week 9 and was moved to an outdoor classroom during the last week of the course, so that the structures could be physically tested. The students had have a competition to see whose design is the most efficient based on a predefined performance index that includes the amount of materials used as a proxy for cost, the efficiency of lifting the water bottle, and the maximum strength that the windmill tower can resist under lateral loads.

“We appreciate the opportunity to work with Professor Van Den Einde and the UC San Diego Jacob School of Engineering on this lab experience, and how the flexibility of Cori allowed us to develop the ideal kit for their needs and budget,” said Howard Chan of CORI. 

When Strains of E.coli Play Rock-Paper-Scissors, It's Not the Strongest That Survives

Bacteria is all around us—not just in bathrooms or kitchen counters, but also inside our bodies, including in tumors, where microbiota often flourish. These “small ecologies” can hold the key to cancer drug therapies and learning more about them can help development new life-saving treatments.

What happens when different strains of bacteria are present in the same system? Do they co-exist? Do the strongest survive? In a microbial game of rock-paper-scissors, researchers at the University of California San Diego’s BioCircuits Institute uncovered a surprising answer. Their findings, titled “Survival of the weakest in non-transitive asymmetric interactions among strains of E. coli,” appeared in a recent edition of Nature Communications.

The research team consisted of Professor of Bioengineering and Molecular Biology Jeff Hasty; Michael Liao and Arianna Miano, both bioengineering graduate students; and Chloe Nguyen, a bioengineering undergraduate. They engineered three strains of E. coli (Escherichia coli) so that each strain produced a toxin that could kill one other strain, just like a game of rock-paper-scissors.

When asked how the experiment came about, Hasty commented, “In synthetic biology, complex gene circuits are typically characterized in bacteria that are growing in well-mixed liquid cultures. However, many applications involve cells that are restricted to grow on a surface. We wanted to understand the behavior of small engineered ecologies when the interacting species are growing in an environment that is closer to how bacteria are likely to colonize the human body.”

diagram of e.coli strains

Diagram of engineered strains including one toxin and two immunity genes. Each toxin targets a different essential biological component of E.coli cells. Cr: BioCircuits Institute/UC San Diego

The researchers mixed the three populations together and let them grow on a dish for several weeks. When they checked back they noticed that, across multiple experiments, the same population would take over the entire surface—and it wasn’t the strongest (the strain with the most potent toxin). Curious about the possible reasons for this outcome, they devised an experiment to unveil the hidden dynamics at play.

There were two hypotheses: either the medium population (called “the enemy of the strongest” as the strain that the strongest would attack) would win or the weakest population would win. Their experiment showed that, surprisingly, the second hypothesis was true: the weakest population consistently took over the plate.

Going back to the rock-paper-scissor analogy, if we assume the “rock” strain of E.coli has the strongest toxin, it will quickly kill the “scissor” strain. Since the scissor strain was the only one able to kill the “paper” strain, the paper strain now has no enemies. It’s free to eat away at the rock strain slowly over a period of time, while the rock strain is unable to defend itself.

To make sense of the mechanism behind this phenomenon, the researchers also developed a mathematical model that could simulate fights between the three populations by starting from a wide variety of patterns and densities. The model was able to show how the bacteria behaved in multiple scenarios with common spatial patterns such as stripes, isolated clusters and concentric circles. Only when the strains were initially distributed in the pattern of concentric rings with the strongest in the middle, was it possible for the strongest strain to take over the plate.

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It is estimated microbes outnumber human cells 10 to 1 in the human body and several diseases have been attributed to imbalances within various microbiomes. Imbalances within the gut microbiome have been linked to several metabolic and inflammatory disorders, cancer and even depression. The ability to engineer balanced ecosystems that can coexist for long periods of time may enable exciting new possibilities for synthetic biologists and new healthcare treatments. The research that Hasty’s group is conducting may help lay the foundation to one day engineer healthy synthetic microbiomes that can be used to deliver active compounds to treat various metabolic disorders or diseases and tumors.

Vice Chancellor for Research Sandra Brown said, “Bringing together molecular biology and bionengineering has allowed discovery with the potential to improve the health of people around the world.  This is a discovery that may never have occurred if they weren’t working collaboratively. This is another testament to the power of UC San Diego’s multidisciplinary research.”

The BioCircuits Institute (BCI) is a multidisciplinary research unit that focuses on understanding the dynamic properties of biological regulatory circuits that span the scales of biology, from intracellular regulatory modules to population dynamics and organ function. BCI seeks to develop and validate theoretical and computational models to understand, predict and control complex biological functions. The institute is comprised of over 50 faculty from UC San Diego and other local institutions, including Scripps Research, the Salk Institute and the Sanford-Burnham Medical Research Institute.

This work was supported by the National Institute of General Medical Sciences of the National Institutes of Health (grant R01-GM069811). Michael Liao is supported by the National Science Foundation Graduate Research Fellowship (grant DGE-1650112).

Researchers discover a new superhighway system in the Solar System

Dec. 9, 2020--Researchers have discovered a new superhighway network to travel through the Solar System much faster than was previously possible. Such routes can drive comets and asteroids near Jupiter to Neptune’s distance  in under a decade and to 100 astronomical units in less than a century. They could be used to send spacecraft to the far reaches of our planetary system relatively fast, and to monitor and understand near-Earth objects that might collide with our planet.

In their paper, published in the Nov. 25 issue of Science Advances, the researchers observed the dynamical structure of these routes, forming a connected series of arches inside what’s known as space manifolds that extend from the asteroid belt to Uranus and beyond. This newly discovered “celestial autobahn” or “celestial highway” acts over several decades, as opposed to the hundreds of thousands or millions of years that usually characterize Solar System dynamics.

"Simply put, these highways are entirely produced by the planets," said Aaron Rosengren, a professor in the Department of Mechanical and Aerospace Engineering at UC San Diego, and one of the paper's authors. "Asteroids, comets, etc., are candidates to travel along them, but do not produce their own 'fast routes'. Jupiter, being the most massive body in our planetary system, is responsible for most of the structures we've discovered, but each planet generates similar 'arches' and all of these structures can interact to produce quite complicated routes for transport."

The most conspicuous arch structures are linked to Jupiter and the strong gravitational forces it exerts. The population of Jupiter-family comets (comets having orbital periods of 20 years) as well as small-size solar system bodies known as Centaurs, are controlled by such manifolds on unprecedented time scales. Some of these bodies will end up colliding with Jupiter or being ejected from the Solar System. 

The planets 'carry' their highways with them during their orbital motion about the Sun, and each planet has its own 'network of celestial autobahns'. Routes originating from the different planets can cross mutually, which was previously known. Such complexities are almost impossible to describe mathematically, but the great power and scope of modern computers and numerical methods do allow researchers to at least visualize them in two- and three-dimensions. 

The structures were resolved by gathering numerical data about millions of orbits in our Solar System and computing how these orbits fit within already-known space manifolds. The results need to be studied further, both to determine how they could be used by spacecraft, or how such manifolds behave in the vicinity of the Earth, controlling the asteroid and meteorite encounters, as well as the growing population of artificial man-made objects in the Earth-Moon system. 

When Strains of E.coli Play Rock-Paper-Scissors, It's Not the Strongest That Survives

10 Jacobs School Faculty Named in 2020 List of Highly Cited Researchers

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December 08, 2020 -- Ten professors at the University of California San Diego Jacobs School of Engineering are among the world’s most influential researchers in their fields, according to a new research citation report from the Web of Science Group.

The Jacobs School of Engineering faculty members are among 52 professors and researchers at UC San Diego named in the prestigious list of Highly Cited Researchers in 2020. Researchers earned this distinction by producing multiple publications that rank in the top 1% by citations in their field over the past 11 years.

“Our faculty and researchers continue to influence their fields with top-quality, innovative work,” said UC San Diego Chancellor Pradeep K. Khosla. “Their inclusion on this list of highly cited researchers is one measure of their impact in groundbreaking research taking place across the globe. UC San Diego shines because of our unique, multi-discipline research climate, where collaborators work together to advance the frontiers of knowledge.”

UC San Diego was ranked 8th globally for institutions with the most highly cited researchers. More than 6,000 researchers from around the world made the list in 2020.

"Here at the Jacobs School, we are working hard to develop and strengthen research ecosystems that allow our faculty, students and industry partners to ask and answer some of the most difficult questions that no single researcher, lab or company can address alone," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. "I'd like to congratulate our highly cited researchers for their research accomplishments and for their larger contributions to the growing momentum of our research and education enterprise here at the Jacobs School."

The ten Highly Cited Jacobs School researchers are listed below.

Ludmil Alexandrov, professor of bioengineering. Alexandrov maps the mutational processes in cancer and devises better strategies for preventing it.

Most cited paper: “Signatures of mutational processes in human cancer,” published in Nature, 2013.

Trey Ideker, professor of genetics and bioengineering. Ideker seeks to comprehensively map connections between the many genes and proteins in a cell and how these connections trigger or prevent disease. His current work focuses on DNA mutations that cause cancer.

Recent paper: “Using deep learning to model the hierarchical structure and function of a cell,” published in Nature Methods, 2018.

Rob Knight, professor of pediatrics, bioengineering, computer science and engineering, and director of the Center for Microbiome Innovation. Knight studies microbiomes in a range of settings, including but not limited to the human body, and how they can be manipulated to benefit health and the environment. Recently, Knight has been involved in campus programs performing COVID-19 clinical testing and wastewater detection of SARS-CoV-2.

Most cited paper: “QIIME allows analysis of high-throughput community sequencing data,” published in Nature Methods, 2010.

Nathan E. Lewis, professor of pediatrics and bioengineering and co-director of the CHO Systems Biology Center. Lewis’s research focuses on building computational models to guide engineering of mammalian cells for drug and vaccine manufacturing. He also uses systems biology approaches to study complex genetic, metabolic and molecular pathways underlying childhood disorders, such as autism.

Most cited paper: “Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0,” published in Nature Protocols, 2011.

Prashant Mali, professor of bioengineering. Mali’s expertise is in the fields of genome engineering and regenerative medicine. He has helped pioneer the development of CRISPR/Cas9, a powerful genome editing tool with wide applications in both basic biology and human therapeutics.

Recent paper: “Defining the Teratoma as a Model for Multi-lineage Human Development,” published in Cell, 2020.

Ying Shirley Meng, Zable Endowed Chair in Energy Technologies, professor of nanoengineering and director of the Institute for Materials Discovery and Design. Meng’s research focuses on functional nano- and micro-scale materials for energy storage and conversion—especially for batteries of all shapes and sizes.

A highly cited paper: “Identifying surface structural changes in layered Li-excess nickel manganese oxides in high voltage lithium ion batteries: A joint experimental and theoretical study,” published in Energy & Environmental Science, 2011.

Bernhard O. Palsson, Galletti Professor of Bioengineering, professor of pediatrics and Director of the Center for Biosustainability. Palsson’s research focuses on developing experimental and computational models of the red blood cell, E. coli, CHO cells, and several human pathogens to establish their systems biology. His Systems Biology Research Group leverages high-power computing to build interactive databases of biological information and is increasingly focused on Genome Design and Engineering.

Most cited paper: “What is flux balance analysis?” published in Nature Biotechnology, 2010.

Joseph Wang, SAIC Endowed Chair, distinguished professor of nanoengineering, director of the Center for Wearable Sensors and co-director of the Institute of Engineering in Medicine Center for Mobile-Health Systems and Applications. Wang’s research focuses on developing micro- and nanomotors and wearable sensors for medical, military, security and environmental applications.

A highly cited paper: “Electrochemical glucose biosensors,” published in Chemical Reviews, 2008.

Kun Zhang, Leo and Trude Szilard Chancellor’s Endowed Chair, professor and chair of bioengineering. Zhang develops technologies for single-cell sequencing of the genome, transcriptome and epigenome, as well as imaging of human tissues. These technologies enable Zhang and colleagues to build 3D, digital single-cell maps of the human brain and organs in the respiratory and urinary systems. His work aims to provide a deeper understanding of the functions and malfunctions of organs in the human body at the level of individual cells.

A highly cited paper: ”Somatic coding mutations in human induced pluripotent stem cells,” published in Nature, 2011.

Liangfang Zhang, professor of nanoengineering, co-director of the Center for Nano-Immuno Engineering and faculty member of the Institute of Engineering in Medicine. Zhang’s revolutionary work in the field of nanomedicine focuses on developing nanoparticles that perform therapeutic tasks in the body without being rejected by the immune system. He invented a technology to disguise synthetic nanoparticles in the skins of natural cells (i.e. red blood cells, white blood cells, cancer cells and others). These cell-coated nanoparticles have shown promise in fighting drug-resistant bacterial infections; training the immune system to fight cancer; and treating rheumatoid arthritis and other diseases.

A highly cited paper: “Erythrocyte membrane-camouflaged polymeric nanoparticles as a biomimetic delivery platform,” published in Proceedings of the National Academy of Sciences, 2011.

UC San Diego nanoengineer Liangfang Zhang inducted into National Academy of Inventors

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Liangfang Zhang

December 08, 2020 -- Liangfang Zhang, professor of nanoengineering and director of the chemical engineering program at the UC San Diego Jacobs School of Engineering, has been named a 2020 fellow of the National Academy of Inventors (NAI). Each NAI fellow has demonstrated a prolific spirit of innovation in creating or facilitating outstanding inventions that have made a tangible impact on the quality of life, economic development and the welfare of society. Election to NAI fellow status is the highest professional distinction accorded solely to academic inventors.

Zhang is recognized for his revolutionary work in the field of nanomedicine, which focuses on nanomaterials for medical applications. He invented a way to make nanoparticles perform therapeutic tasks in the body without being rejected by the immune system. His method is to disguise synthetic nanoparticles as the body’s own cells—red blood cells, white blood cells, platelets, beta cells, cancer cells and others—by coating them with natural cell membranes from human cells.

Zhang’s cell membrane coating technology made its debut in a 2011 study, which showed that polymeric nanoparticles disguised as red blood cells can evade clearance by the immune system. Zhang and his team later showed that these cell-mimicking nanoparticles can be used to treat MRSA (methicillin-resistant Staphylococcus aureus) infections in mice. These so-called red blood cell “nanosponges” work by absorbing toxins produced by MRSA and safely removing them from the bloodstream. Red blood cells are one of the primary targets of MRSA toxins, so the nanosponges serve as decoys by luring these toxins away and trapping them so they can no longer go on and destroy actual red blood cells.

“I like to test new ideas and invent new technologies. More importantly, I also like to facilitate the translation of these inventions, aiming to benefit the public in large, especially the patient populations,” Zhang said.

Zhang currently has 108 issued and pending patents worldwide, of which more than 90 have been licensed to several biotechnology and pharmaceutical companies for clinical translation.

In 2014, Zhang co-founded the startup company Cellics Therapeutics to further develop and commercialize the red blood cell nanosponges. The company is currently on schedule to advance them to human clinical trials.

Cellics recently received an award of up to $15 M from Boston-based accelerator CARB-X to further development of another nanosponge platform: macrophage nanosponges—nanoparticles cloaked in the cell membranes of macrophages—designed to treat sepsis. The company is building on work from a 2017 study, in which Zhang and colleagues report that treatment with macrophage nanosponges protected mice from lethal sepsis caused by E. coli bacteria. In a similar vein to their red blood cell counterparts, the macrophage nanosponges work by luring and trapping bacterial molecules called endotoxins that play a key role in sepsis, as well as pro-inflammatory cytokines produced by the immune system.

In a recent study from the Zhang laboratory, researchers report that macrophage nanosponges could also serve as part of a potential treatment for COVID-19. The work, which is in the early stages, shows that both macrophage nanosponges and lung epithelial cell nanosponges greatly reduce the ability of SARS-CoV-2 to infect host cells and replicate. The lung epithelial cell nanosponges act as lung cell decoys to bait and trap SARS-CoV-2, while the macrophage nanosponges neutralize SARS-CoV-2 and the cytokine storm that the virus can cause.

“I like to think of the fundamental cause of a problem or challenge, which allows me to think of a solution from outside the box,” Zhang said. “Take the cellular nanosponge technology as an example—I did not focus on how to target and kill the pathogens. Instead, I looked at how to protect the host cells that the pathogens attack. The idea is that no matter how different pathogens are and how often they mutate, these pathogens share some similarity in terms of their mechanism of action. They attack certain host cells and destroy them.”

“I got the inspiration to develop cellular nanodecoys by using the target host cell membranes to attract and neutralize the pathogens or their virulence factors,” Zhang added. “This treatment strategy can be broad; so broad that it can be used to treat all pathogens and their mutations as long as they attack the host cells. This initial idea of cellular nanosponges came to me almost 10 years ago and we have now proved its broad applicability in various disease models.”

Zhang’s cell membrane coating technology has produced a suite of other therapeutic nanoparticles, such as ones that can be used to treat rheumatoid arthritis; train the immune system to fight cancer; and deliver drugs to specific sites in the body.

Electrical engineer selected to lead Intel AI project

Farinaz Koushanfar, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering, has been selected by Intel to lead one of nine inaugural research projects for the Private AI Collaborative Research Institute. The Institute, a collaboration between Intel, Avast and Borsetta, aims to advance and develop technologies in privacy and trust for decentralized artificial intelligence (AI). The companies issued a call for research proposals earlier this year and selected the first nine research projects to be supported by the institute at eight universities worldwide.

At UC San Diego, Koushanfar, who is co-director of the Center for Machine Integrated Computing and Security, will lead a project on Private Decentralized Analytics on the Edge (PriDEdge). Her team will focus on easing the computational burden of training and data management in federated machine learning (FL) by evaluating the cryptographic primitives and devising new hardware-based primitives that complement existing resources on Intel processors. The new primitives include accelerators for homomorphic encryption, Yao's garbled circuit, and Shamir's secret sharing. Placing several cryptographic primitives on the same chip will ensure optimal usage by enabling resource sharing among these primitives. The UC San Diego team also plans to design efficient systems through the co-optimization of the FL algorithms, defense mechanisms, cryptographic primitives, and the hardware primitives.

The Private AI Collaborative Research Institute will focus its efforts on overcoming five main obstacles of the current centralized approach:

·  Training data is decentralized in isolated silos and often inaccessible. Most data stored at the edge is privacy-sensitive and cannot be moved to the cloud.

·  Today’s solutions are insecure and require a single trusted data center. Centralized training can be easily attacked by modifying data anywhere between collection and cloud. There is no framework for decentralized secure training among potentially untrusting participants.

·  Centralized models become obsolete quickly. Infrequent batch cycles of collection, training, and deployment lead to outdated models, making continuous and differential retraining not possible.

·  Centralized compute resources are costly and throttled by communication and latency. It requires vast data storage and compute as well as dedicated accelerators to make training viable.

·  Federated machine learning (FL) is limited. While FL can access data at the edge, it cannot reliably guarantee privacy and security.

Learn more about the Private AI Collaborative Research Institute and the inaugural university awardees.

The UC San Diego Center for Microbiome Celebrates 14 Researchers on Highly Cited Researchers 2020 List

The UC San Diego Center for Microbiome (CMI) is proud to announce that 14 of our academics have been named on the annual Highly Cited Researchers™ 2020 list from making up 27% of the 52 names listed from UC San Diego.

Pieter Dorrestein - cross-field
Jack Gilbert - microbiology
Christopher Glass - molecular biology and genetics
Trey Ideker - cross-field
Michael Karin - (listed in 2 fields) immunology molecular biology and genetics
Rob Knight - (listed in 4 fields) biology & biochemistry, environment & ecology, microbiology, molecular biology & genetics
Rohit Loomba - clinical medicine
Prashant Mali - biology and biochemistry
Daniel McDonald - microbiology
Bernhard Palsson - biology and biochemistry
Ming Tsuang - psychiatry/psychology
Yoshiki Vazquez-Baeza - cross-field
Joseph Wang - chemistry
Kun Zhang -  cross-field

We are incredibly proud that this year our faculty director and founder of the CMI, Rob Knight, was included in four separate areas of study (biology & biochemistry, environment & ecology, microbiology, and molecular biology & genetics). Out of the 6,389 highly cited researchers, Knight is the only researcher listed in four areas of study.

The Center for Microbiome Innovation exists to inspire, nurture, and sustain vibrant collaborations between UC San Diego Microbiome experts and industry. The Center encompasses a large range of expertise in microbiome sampling, a broad range of technologies (metagenomics, metabolomics, metatranscriptomics), and data analysis using high-performance algorithms, machine learning, and modeling. The ultimate goal is to increase knowledge of the microbiome’s impact on human health and the environment with an eye to providing innovative solutions and treatment to major diseases as well as prolonging wellness.

The highly anticipated annual list identifies researchers who demonstrated significant influence in their chosen field or fields through the publication of multiple highly cited papers during the last decade. Their names are drawn from the publications that rank in the top 1% by citations for field and publication year in the Web of Science™ citation index.

Read about UC San Diego’s ranking 8th globally for most highly cited researches here
You can read about Web of Science’s methodology on their website
The full 2020 Highly Cited Researchers list and executive summary can be found online here

#HighlyCited2020

UC San Diego and LINK-J Seminar Series

Quantum sensing in stone

Joint webinar with Kyushu University

Virus-like probes could help make rapid COVID-19 testing more accurate, reliable

November 30, 2020 -- Nanoengineers at the University of California San Diego have developed new and improved probes, known as positive controls, that could make it easier to validate rapid, point-of-care diagnostic tests for COVID-19 across the globe.

The positive controls, made from virus-like particles, are stable and easy to manufacture. Researchers say the controls have the potential to improve the accuracy of new COVID-19 tests that are simpler, faster and cheaper, making it possible to expand testing outside the lab.

“Our goal is to make an impact not necessarily in the hospital, where you have state-of-the-art facilities, but in low-resource, underserved areas that may not have the sophisticated infrastructure or trained personnel,” said Nicole Steinmetz, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering.

Positive controls are a staple in the lab—they are used to verify that a test or experiment indeed works. The positive controls that are primarily used to validate today’s COVID-19 tests are naked synthetic RNAs, plasmids or RNA samples from infected patients. But the issue is RNA and plasmids are not stable like viral particles. They can degrade easily and require refrigeration, making them inconvenient and costly to ship around the world or store for long periods of time.

In a paper published Nov. 25 in ACS Nano, UC San Diego researchers led by Steinmetz report that by packaging segments of RNA from the SARS-CoV-2 virus into virus-like particles, they can create positive controls for COVID-19 tests that are stable—they can be stored for a week at temperatures up to 40 C (104 F), and retain 70% of their activity even after one month of storage—and can pass detection as the novel coronavirus without being infectious.

Illustration of nanoparticles
Illustration and TEM image of SARS-CoV-2 positive control made from plant virus-based nanoparticles (left) and bacteriophage nanoparticles (right). Image courtesy of Soo Khim Chan/ACS Nano

The team developed two different controls: one made from plant virus nanoparticles, the other from bacteriophage nanoparticles. Using them is simple. The controls are run and analyzed right alongside a patient sample, providing a reliable benchmark for what a positive test result should look like.

To make the plant virus-based controls, the researchers use the cowpea chlorotic mottle virus, which infects black-eyed pea plants. They essentially open the virus, remove its RNA contents, replace them with a synthesized RNA template containing specific sequences from the SARS-CoV-2 virus, then close everything back up.

The process to make the bacteriophage-based controls starts with plasmids, which are rings of DNA. Inserted into these plasmids are the gene sequences of interest from the SARS-CoV-2 virus, as well as genes coding for surface proteins of the bacteriophage Qbeta. These plasmids are then taken up by bacteria. This process reprograms the bacteria to produce virus-like particles with SARS-CoV-2 RNA sequences on the inside and Qbeta bacteriophage proteins on the outside.

Both controls were validated with clinical samples. A big advantage, the researchers point out, is that unlike the positive controls used today, these can be used in all steps of a COVID-19 test.

“We can use these as full process controls—we can run the analysis in parallel with the patient sample starting all the way from RNA extraction,” said first author Soo Khim Chan, a postdoctoral researcher in Steinmetz’s lab. “Other controls are usually added at a later step. So if something went wrong in the first steps, you won’t be able to know.”

So far, the researchers have adapted their controls for use in the CDC-authorized RT-PCR test. While this is currently the gold standard for COVID-19 testing, it is expensive, complex, and can take days to return results due to the logistics of sending samples off to a lab with PCR capability.

Steinmetz, Chan and colleagues are now working on adapting the controls for use in less complex diagnostic tests like the RT-LAMP test that can be done on the spot, out of the lab and provide results right away.

“It’s a relatively simple nanotechnology approach to make low-tech assays more accurate,” Steinmetz said. “This could help break down some of the barriers to mass testing of underserved populations in the U.S. and across the world.”

Paper title: “Biomimetic Virus-like Particles as Severe Acute Respiratory Syndrome Coronavirus 2 Diagnostic Tools.”

This work was funded in part by grants from the National Science Foundation: RAPID CBET-2032196 and RAPID CMMI-2027668, as well as the University of California: UCOP-R00RG2471 and a Galvanizing Engineering in Medicine (GEM) Award.

CleaNN: unsupervised, embedded defense against neural Trojan attacks

ExampleTrojans: (a)BadNets with a stickynote and TrojanNN with (b)square and (c)watermark triggers

San Diego, Calif., Nov. 25, 2020-- Engineers at UC San Diego have developed a new defense against neural network Trojan attacks on autonomous devices such as cars, drones, or security cameras. Their algorithm and hardware co-designed solution is the first end-to-end framework that enables the online real time mitigation of these Trojan attacks for embedded deep neural network algorithms.

The CleaNN defense is completely unsupervised, meaning it doesn’t require access to Trojan samples or any labeled data sets. It is the first defense to recover the ground-truth labels of Trojan data without performing any model training or fine-tuning.

Researchers also developed a customized hardware stack that is specifically designed to optimize the performance of their defense algorithm so that it can work in real time settings. They trained CleaNN on image analysis tasks, but they believe it would work on other types of data as well. 

Currently, most methods to detect if a machine learning model has been compromised by a Trojan attack are implemented before the model is used on any device, and require large data sets or lots of computational power. Researchers in the Center for Machine-Integrated Computing and Security at UC San Diego took a different approach, aiming to create a defense that would identify and inoculate against Trojans in real time while the device is functioning.

Their CleaNN algorithm continually runs in the background, embedded in the autonomous device while it goes about its set task. The algorithm is constantly checking the state of the neural network model and its inputs, and if it detects a Trojan trying to make the model mispredict, it removes the malicious effect the Trojan was trying to achieve and reverts back to the original task or ground truth.

In tests using state-of-the-art Trojan attacks, CleaNN brought down the attack success rate to 0% for a variety of physical and complex digital Trojans, with a minimal drop in the accuracy of the underlying Deep Neural Network. The team presented CleaNN on Nov. 2 at the International Conference on Computer-Aided Design.  

(a)Example Trojan data with watermark and square triggers, (b) reconstruction error heatmap, and (c) output mask from the outlier detection module.

 The researchers developed CleaNN by using a legacy signal processing algorithm, a field which had taken a back seat for about a decade in favor of neural networks and deep learning architectures. The engineers went back to a statistical analysis and sparse recovery approach, which not only worked, but also requires less computational power, making it possible to run the algorithm directly on the embedded computing device such as a drone or an autonomous car.

“What we have right now is an algorithm that is not based on deep learning or modifying the model in anyway,” said Mojan Javaheripi, an electrical engineering PhD student and co-first author of the paper. “This is something that is just based on sparse recovery of the signals. Because what we observed was when you add a Trojan pattern in the data, there are some nuances in the behavior of the signals all throughout the network, both in the input space and also as you’re propagating the input throughout the network, you can see there is suspicious behavior rising.”

CleaNN consists of two core modules: a Discrete Cosine Transform (DCT) that transforms the input image to the frequency domain, and then performs sparse recovery on the extracted frequency components and reconstructs the original signal using sparse approximation.

The second module, a feature analyzer, investigates patterns in the latent features extracted by the victim neural network to find abnormal structures. A sparse recovery module within this feature analyzer denoises input features for use in the remaining layers of the neural network, allowing CleaNN to recover the ground-truth labels for Trojan samples by removing the Trojan triggers entering the network.

"The significance of the work is in achieving a real time detection for the first time, while maintaining a very good accuracy,” said Farinaz Koushanfar, professor of electrical and computer engineering at UC San Diego and co-director of the Center for Machine-Integrated Computing and Security. “The AI models form the core computing engines in modern time sensitive applications such as autonomous driving, financial applications, and disaster response. Introduction of CleaNN just-in-time defense provides a paradigm shift in robustness of AI-based solutions against the nefarious backdoor attacks.”

While attacks and defenses in machine learning have become a cat and mouse game, the researchers cite CleaNN’s unsupervised defense establishment and its success in detecting state-of-the-art Trojan attacks BadNet and TrojanNN as reason to be optimistic that the embedded algorithm will be successful against future iterations of Trojan attacks.

“Our algorithm doesn’t make any assumptions about the type of Trojan, its size, pattern or anything,” said Javaheripi. “Our defense is constructed without any knowledge of what the attack might look like. It worked well on existing attacks out there, so I’m hopeful it would work against new, future attacks as well.”

Eustaquio Aguilar Ruiz Named Alan Turing Memorial Scholarship Recipient

Eustaquio Aguilar Ruiz has received the Alan Turing Memorial Scholarship, which recognizes a student majoring in programs touching on networked systems who is active in supporting the LGBT+ community.

Eustaquio Aguilar Ruiz, a senior majoring in physics with a specialization in computational physics, has received the 2020-2021 Alan Turing Memorial Scholarship from UC San Diego’s Center for Networked Systems (CNS). This is the fifth year that CNS has recognized a student majoring in programs touching on networked systems who is active in supporting the LGBT+ community.

CNS established the Alan Turing Memorial Scholarship in 2015 to pay homage to the cofounder of computer science, Alan Turing, the famed cryptanalyst, and mathematician. His work accelerated the Allied victory in World War II by more than a year. After the war, Turing was persecuted for his orientation as a gay man. He died by suicide in 1954.

“The Turing Scholarship at UC San Diego is a unique way that we, as a community, show how much we value diversity, particularly diversity aimed at the LGBT+ community. Diversity is essential to strengthening our center and is in line with our university’s mission,” said CNS Co-director and Computer Science and Engineering Associate Professor George Porter.

Ruiz arrived in the United States from Mexico when he was two years old. Through financial hardship, Ruiz and his mother and stepfather have persevered. Ruiz has been able to charter his academic path with his ultimate goal in mind– to obtain a higher education degree, which had been unimaginable for his ancestors. “Joining college made me feel liberated, but I also felt, more than ever, the personal responsibility of continuing to assist those in my community,” said Ruiz.

The adversity Ruiz faces as a gay Latino first-generation college student has fueled him to actively serve the communities with which he identifies. During his college career, he has been involved with the UC San Diego LGBT Resource Center, the Queers and Allies of Eleanor Roosevelt College, and he is in his third year of serving as a peer mentor for the First-Generation Student Success Coaching Program. With the skills he has learned, he has fostered an inclusive and empowering environment for more than 50 first-generation college students from UC San Diego. Ruiz is currently involved with the UC San Diego oSTEM organization, but he said when he first attempted to join more STEM-related organizations, “I felt so misplaced.”

“I feel that many who are LGBT+, along with other marginalized identities, struggle with finding a welcoming place. The Alan Turing Memorial Scholarships represent hope and opportunity for students with complex and diverse identities in the LGBT+ communities,” he said.

The scholarship is open to undergraduates who are active supporters of the LGBT+ community and majoring in computer science, computer engineering, public policy, communications, and other programs touching on networked systems. It is awarded to students based on academic merit, with a preference for those with demonstrated financial need.

CNS reached its endowment goal of $250,000 in February 2020. Many individual donors and corporate donors made this possible, including a generous donation from the Amateur Radio Digital Communications (ARDC) in memory of Brian Kantor, WB6YT, a UC San Diego alumnus who worked at UC San Diego for 47 years and founded the ARDC.

ECE department launches virtual alumni mentorship program

November 19, 2020-- In an effort to keep students and alumni engaged and connected to campus resources during months of remote school and work, the Jacobs School’s Electrical and Computer Engineering (ECE) Department’s Alumni Advisory Board launched an ECE Alumni Mentorship Program (AMP) in October.

The six month program pairs a current ECE student with an alumnus who shares similar interests, not just in terms of academics and research, but broader hobbies or personal interests as well. In addition to two recommended mentor-mentee meetings a month, the whole group of participants meets for one or two additional group activities each month, including social events and discussion or guest speaker sessions.

Participation has been sky-high.

“We’ve had an overwhelming response,” said Stefanie Battaglia, the program director. “We went into this thinking if we could get 50 students and 50 mentors that would be great. And out of the gates we’ve doubled that.”

117 students and 98 alumni are participating in this inaugural session of the program.

Hamna Khan, an electrical engineering alumna who now works for Northrop Grumman developing solar array hardware for space vehicles, is president of the ECE Alumni Advisory Board. She said the idea for this mentorship program started last spring, when students, faculty, staff and alumni suddenly found themselves dealing with remote learning and work requirements.

“We knew the pandemic wasn’t going to end right away,” said Khan. “We had a feeling we had to figure out what it is we can do while we’re at home. We started talking to students, we talked to faculty, and we came up with this idea of why don’t we try this mentorship program? We’re helping students who feel even more lost and confused, and connecting with alumni who are eager to help.”

Khan spent days reading through every single participant’s answers to a long list of questions designed to ensure the mentors and mentees have enough interests in common to have meaningful conversations—from technical interests to hobbies, larger topics they care about such as climate change, social justice, intellectual property, or space for example, to areas where the students felt they needed help and areas the alumni felt they could offer advice.

The theme for fall quarter’s meetings is preparing for job interviews—how to polish LinkedIn profiles, resumes, conducting mock interviews and helping students develop the confidence to apply for roles they’re interested in.

Themes for winter and spring quarter will depend on feedback from alumni and students, but will include advice on being successful in the classroom, joining student organizations and getting involved in research opportunities on campus.

Given the levels of participation for this first cohort of AMP, Khan said she anticipates this will be an ongoing annual program, starting each fall and running through spring quarter. Return mentors and mentees are welcome to reapply each year, and will be matched with a new partner. And new participants are always welcome.

“It’s been great to see how many alumni are participating in this that have never gotten involved before—so many new faces,” said Khan. “A couple were also interested in the Alumni Advisory Board and I love that we’re getting more people to understand that we’re here to help everyone and build a stronger ECE community.”

Learn more about ECE AMP and get involved: https://sites.google.com/view/ece-amp

Alumni-led Lucira Health earns 1st FDA authorization for at-home COVID test

San Diego, Calif., Nov. 18, 2020 --On Tuesday, the Food and Drug Administration gave emergency use authorization to the first rapid at-home COVID-19 test, developed by Lucira Health. Erik Engelson, a UC San Diego bioengineering and microbiology alumnus, is president and CEO of Lucira Health.

Erik Engelson, president and CEO of Lucira Health, and UC San Diego bioengineering alumnus.

The Lucira COVID-19 All-In-One Test Kit is a molecular (real-time loop mediated amplification reaction) test that uses a simple nasal swab to return results in 30 minutes, at home. Lucira says the test will cost less than $50, and requires a prescription from a health care provider.

The test works by swirling the self-collected sample swab in a vial that is then placed in the test unit. In 30 minutes or less, the results can be read directly from the test unit’s light-up display.

Read more about the test in the New York Times.

Engelson earned his bachelor’s degree in microbiology from UC San Diego, and then a master’s in bioengineering from the Jacobs School of Engineering at UC San Diego. Engelson is a Trustee Emeritus of the UC San Diego Foundation; Initial Chairman of the Board of Trustees of UC San Diego’s Bioengineering Department; a member of the UC San Diego Division of Biological Sciences Dean’s Leadership Council; and an elected fellow of the American Institute for Medical and Biological Engineering (AIMBE).

 

UC San Diego Engineers Send Soil Into Outer Space To Tackle Mudslides On Earth

Upgraded radar can enable self-driving cars to see clearly no matter the weather

San Diego, Calif., Nov. 17, 2020 -- A new kind of radar could make it possible for self-driving cars to navigate safely in bad weather. Electrical engineers at the University of California San Diego developed a clever way to improve the imaging capability of existing radar sensors so that they accurately predict the shape and size of objects in the scene. The system worked well when tested at night and in foggy conditions.

The team will present their work at the Sensys conference Nov. 16 to 19.

Inclement weather conditions pose a challenge for self-driving cars. These vehicles rely on technology like LiDAR and radar to “see” and navigate, but each has its shortcomings. LiDAR, which works by bouncing laser beams off surrounding objects, can paint a high-resolution 3D picture on a clear day, but it cannot see in fog, dust, rain or snow. On the other hand, radar, which transmits radio waves, can see in all weather, but it only captures a partial picture of the road scene.

Enter a new UC San Diego technology that improves how radar sees.

“It’s a LiDAR-like radar,” said Dinesh Bharadia, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering. It’s an inexpensive approach to achieving bad weather perception in self-driving cars, he noted. “Fusing LiDAR and radar can also be done with our techniques, but radars are cheap. This way, we don’t need to use expensive LiDARs.”

The system consists of two radar sensors placed on the hood and spaced an average car’s width apart (1.5 meters). Having two radar sensors arranged this way is key—they enable the system to see more space and detail than a single radar sensor.  

Goto Flickr
Multi-radar system predicting the dimensions of cars in live traffic. Red boxes are the predictions, blue boxes are the ground truth measurements. Image credit: Kshitiz Bansal

During test drives on clear days and nights, the system performed as well as a LiDAR sensor at determining the dimensions of cars moving in traffic. Its performance did not change in tests simulating foggy weather. The team “hid” another vehicle using a fog machine and their system accurately predicted its 3D geometry. The LiDAR sensor essentially failed the test.

Two eyes are better than one

The reason radar traditionally suffers from poor imaging quality is because when radio waves are transmitted and bounced off objects, only a small fraction of signals ever gets reflected back to the sensor. As a result, vehicles, pedestrians and other objects appear as a sparse set of points.

“This is the problem with using a single radar for imaging. It receives just a few points to represent the scene, so the perception is poor. There can be other cars in the environment that you don’t see,” said Kshitiz Bansal, a computer science and engineering Ph.D. student at UC San Diego. “So if a single radar is causing this blindness, a multi-radar setup will improve perception by increasing the number of points that are reflected back.”

The team found that spacing two radar sensors 1.5 meters apart on the hood of the car was the optimal arrangement. “By having two radars at different vantage points with an overlapping field of view, we create a region of high-resolution, with a high probability of detecting the objects that are present,” Bansal said.

A tale of two radars

The system overcomes another problem with radar: noise. It is common to see random points, which do not belong to any objects, appear in radar images. The sensor can also pick up what are called echo signals, which are reflections of radio waves that are not directly from the objects that are being detected.  

More radars mean more noise, Bharadia noted. So the team developed new algorithms that can fuse the information from two different radar sensors together and produce a new image free of noise.

Another innovation of this work is that the team constructed the first dataset combining data from two radars.

“There are currently no publicly available datasets with this kind of data, from multiple radars with an overlapping field of view,” Bharadia said. “We collected our own data and built our own dataset for training our algorithms and for testing.”

The dataset consists of 54,000 radar frames of driving scenes during the day and night in live traffic, and in simulated fog conditions. Future work will include collecting more data in the rain. To do this, the team will first need to build better protective covers for their hardware.

The team is now working with Toyota to fuse the new radar technology with cameras. The researchers say this could potentially replace LiDAR. “Radar alone cannot tell us the color, make or model of a car. These features are also important for improving perception in self-driving cars,” Bharadia said.

Alumni bring advanced 3D printing to space

UC San Diego alumna and NASA astronaut Kate Rubins in front of the Turbine Ceramic Manufacturing Module on the ISS. Three fellow Triton alumni were on the team that developed the device.

San Diego, Calif., Nov. 16, 2020-- UC San Diego alumni have a long history with space—as astronauts, engineers designing rockets and spacecraft, and medical researchers working to better understand human health on Earth by comparing it with the microgravity environment in space.

This was evident this fall, when UC San Diego alumna and NASA astronaut Kate Rubins (’99 biological sciences) installed a Turbine Ceramic Manufacturing Module made by Made In Space, on the International Space Station. Three fellow Triton alumni were part of the Made in Space team that designed, built, and tested the ceramic 3D printing device.

Mechanical and aerospace engineering alumni Matt Napoli (also a member of the MAE Industry Advisory Board), Eugenio Guidi and Noah Paul-Gin now work for Made in Space, and developed the ceramic turbine manufacturing device that will allow astronauts on the ISS to 3D print detailed parts requiring high accuracy in space.

While students at the Jacobs School, Napoli was active in the American Institute of Aeronautics and Astronautics, and Paul-Gin was involved with Global TIES as well as the Innovative Design and Engineering Application Club. Guidi was on the track team for a year, and has fond memories of the junkyard derby, and heading to the desert to launch supersonic rockets for his aerospace engineering senior project.

Read more about this new addition to the ISS in TechCrunch.

Experimenting in space to help prevent mudslides here on Earth

San Diego, Calif., Jan. 12, 2004 -- What can the International Space Station teach us about mudslides here on Earth?

Here is the connection: UC San Diego engineers are trying to better understand the role gravity plays in mudslides. That is why in 18 months, they will launch an experiment to the ISS via SpaceX and NASA to study mudslides in microgravity.

Back here on Earth, structural engineer Ingrid Tomac and her team at the Jacobs School of Engineering at UC San Diego will conduct under Earth’s gravity the same experiments that are happening in space in microgravity. 

“Gravity plays a big role in mudslides, but we do not understand it,” said Tomac, who is a professor in UC San Diego’s Department of Structural Engineering. “The idea is to test in space in microgravity so we can get a baseline.”

Tomac’s ultimate goal is to develop technologies to prevent mudslides. This is particularly important in places where wildfires burn away vegetation and roots, producing wax that coats soil to become water repellent.  When the rainy season comes, water is unable to penetrate the soil. On steep slopes, rain splashes and blankets steep hills and detaches soil particles, which trap air bubbles. Dangerous mudslides follow.

“What happens in mudslides is a three-phase mixture of air, sand and water,” Tomac said. “We want to better understand how these three elements interact, both under gravity and in microgravity.”

The UC San Diego team is partnering with Kentucky-based firm Space Tango. The company is getting $250,000 from NASA to turn the experiments here on earth into something that can be launched up to the ISS. It’s all part of the CubeLabs project, a partnership between NASA and Space Tango to bring to the ISS compact experiments that can either run automatically or be remote-controlled. 
In gravity, solids sink and bubbles rise. Tomac hopes that the experiments on the ISS will allow her to learn how water repellent particles and bubbles aggregate in water in microgravity. The proposed experiments will improve prevention methods and our understanding of mudslides. 

Mudslide-proof glue

In addition to this work with the ISS, Tomac and her team have discovered that spraying Xanthan gum, a common food additive used as a thickener or stabilizer, on eroded slopes creates a protective layer. Xanthan acts like glue that keeps particles of sand on the surface of the slope. As a result, the soil particles remain in place, and clean rainwater just flows downhill. This is a much more manageable scenario than a mudslide.

Xanthan gum is essentially made of sugar and completely biodegradable. It is also inert and will not pollute water tables. After a year or two, it is eventually absorbed in the soil and doesn’t interfere with vegetation growth, all of which will make the soil more stable.

“Spraying this on eroded sites would be a good temporary measure to protect the slopes,” Tomac said. “It wouldn’t have an impact on plants, as opposed to some of the chemicals currently used.”

Tomac’s team is also studying individual drops of water to see how they behave differently     when they fall on regular and hydrophobic soil. They’re also working toward a solution to allow sand to absorb water in deeper layers, preventing mudslides.

“We are looking at the smallest scale to better understand the mechanisms that lead to mudflows,” Tomac said.  

The work is funded by a $400,000 grant from the National Science Foundation, $78,000 from the UC Institute of Transportation Studies and part of Tomac’s $50,000 Hellman Fellowship. 

 

 


 

Meet The Deep Minds of UC San Diego's CSE

CSE's DeepMind Fellows and ML graduate students: (l to r) Ulyana Tkachenko, Anshuman Dewangan and Garrett Wolfe

UC San Diego’s Computer Science and Engineering Department (CSE) is proud to announce the inaugural class of DeepMind Fellows. These fellowships were made possible by a recent generous gift from DeepMind, a London-based leader in artificial intelligence (AI) research and how it’s applied in the real world. UC San Diego is currently one of just three universities in the United States, and one of five in North America, selected to participate in this program.

The fellowships are designed to support machine learning (ML) graduate students. Students from cultural, racial, linguistic, geographic and socioeconomic backgrounds and genders who are underrepresented in ML graduate education are encouraged to apply. DeepMind Fellows receive two-year fellowships that cover tuition along with a stipend, a travel grant and access to a DeepMind mentor. DeepMind also made a one-time gift to CSE’s Diversity, Equity and Inclusion initiative.

“The recipients of the DeepMind Fellowship all had stellar academic performance, a deep interest in ML as a discipline, and had made significant prior contributions to diversity,” said Leo Porter, director of MS programs for the Computer Science and Engineering Department. “This generous fellowship will enable these students to focus on studying the field of ML. We look forward to seeing what these DeepMind Fellows will accomplish in the future."

Meet CSE’s DeepMind Fellows (all CSE master’s students studying ML):

 

Anshuman Dewangan

BS, Business Administration; BA, Statistics; BA, Economics

UC Berkeley

Imagine a future in which you can wear a headset that senses when you're feeling down from patterns in your brain waves and suggests an activity (deep breathing, jogging, calling a friend) to improve your mood based on data that the activity has proven to help you (and others like you) in the past. The DeepMind Fellowship allows me to put my passion for AI and mental health technology into action and begin making this dream a reality.

My mission is to leverage neural and digital data to promote personalized behavior change interventions for better mental and social wellness at scale. Access to mentorship from DeepMind's global and interdisciplinary AI experts will help me navigate through academia and industry to become a thought leader in the space.”

 

Ulyana Tkachenko

BS, Computer Science

UC Riverside

“I look forward to utilizing DeepMind’s mentorships program and professional learning opportunities to create a network of peers who are similarly interested in developing AI for social good.

I recognize many real-world issues where AI applications could identify ways to improve the sociological and ecological state of our world. A key focus of DeepMind is conducting research in areas such as medical health and carbon footprint reduction that provide tangible, positive impact to society. In my undergraduate research, I had firsthand experience utilizing data to better represent and ultimately help alleviate homelessness within Riverside County. As my future career goal, I plan to work on similar projects which directly benefit underprivileged spaces that are often overlooked by mainstream tech.”

 

Garrett Wolfe

BS, Computer Science

UC Irvine

“I hope to use this opportunity provided to me by this fellowship to expand my knowledge of the theory behind AI and the technical skills needed to apply it. I also hope to collaborate with my mentor to gain insight into the more pragmatic and real-world issues that can arise as well as the ethical concerns that it may bring.

My goal is to someday build an equitable education platform with artificially intelligent tutors that can adapt to the specific needs of individual students from all backgrounds. It’s an ambitious and far-off goal, but those are exactly the kind of goals that DeepMind strives to meet. Through this fellowship, with the lessons I learn and the friendships I make, I think it is attainable.”

Read more about DeepMind’s scholarship program and the company’s impact on the future of AI and ML in this blog post.

For more information about the fellowship program or questions, please visit cse.ucsd.edu/graduate/deepmind-fellowships 

Neurons stripped of their identity are hallmark of Alzheimer's disease, study finds

Cartoon of neurons in a human brain
Neurons in patients with familial Alzheimer’s disease revert to an undifferentiated state, leading to loss of neuronal and synaptic function. Image credit: Victoria Caldwell and Andrew Caldwell

San Diego, Calif., Nov. 13, 2020 -- Researchers at the University of California San Diego have identified new mechanisms in neurons that cause Alzheimer’s disease. In particular, they discovered that changes in the structure of chromatin, the tightly coiled form of DNA, trigger neurons to lose their specialized function and revert to an earlier cell state. This results in the loss of synaptic connections, an effect associated with memory loss and dementia.

The findings are published Nov. 13 in Science Advances.

The study was founded on the question: how do neurons in patients with Alzheimer’s disease differ from neurons in healthy individuals?

“It’s a fundamental question that would provide the framework and foundation for understanding Alzheimer’s disease at the cellular level, and thus pave the path for novel therapeutic approaches,” said Shankar Subramaniam, professor of bioengineering at the UC San Diego Jacobs School of Engineering.

Subramaniam worked with an interdisciplinary team of engineers and neuroscientists at UC San Diego to answer this question. They started by taking human induced pluripotent stem cells derived from patients with familial Alzheimer’s disease, which is a hereditary form of Alzheimer’s, and transformed them into neurons. They used next generation sequencing techniques to look at what genes are being expressed in these neurons and how gene expression is regulated, and then compared how they differ in neurons of healthy individuals.

They discovered that neurons derived from the patients de-differentiate to a precursor state.

“In other words, they cease to be neurons,” Subramaniam said. “This is the key defect observed across a diversity of patients with distinct mutations. The consequences to the brain are dramatic, with loss of synaptic connections leading to cognitive decline.”

The researchers observed other defects: neuronal genes are suppressed, so these cells no longer have any instructions telling them that they are neurons; they are in a precursor-like state, which means they can trigger cell growth and division—this is unusual because adult brains do not produce new neurons; and they have inflammation, which signals damage or stress.

The same defects were also observed in post-mortem human brain samples from patients with Alzheimer’s disease. “This was validating for our findings because we weren’t just seeing these mechanisms in the stem cells, but in actual brain samples as well,” Subramaniam said.

The researchers traced all of these mechanisms back to changes in the structure of chromatin. Parts of this structure consist of open regions, where genes are expressed or regulated, and other parts consist of closed regions, where gene expression is repressed. In the diseased neurons, some regions that used to be open are now closed, and vice versa. As a consequence, the neurons are not behaving as they should be, Subramaniam explained.

The team is now working on developing drugs to inhibit these mechanisms.

Environmentally friendly method could lower costs to recycle lithium-ion batteries

San Diego, Calif., Nov. 12, 2020 -- A new process for restoring spent cathodes to mint condition could make it more economical to recycle lithium-ion batteries. The process, developed by nanoengineers at the University of California San Diego, is more environmentally friendly than today’s methods; it uses greener ingredients, consumes 80 to 90% less energy, and emits about 75% less greenhouse gases.

Researchers detail their work in a paper published Nov 12 in Joule.

Microscopic images of cathode materials
SEM image of lithium iron phosphate (LFP) cathode before regeneration (left) and after (right). Image courtesy of Panpan Xu/Joule

The process works particularly well on cathodes made from lithium iron phosphate, or LFP. Batteries made with LFP cathodes are less costly than other lithium-ion batteries because they don’t use expensive metals like cobalt or nickel. LFP batteries also have longer lifetimes and are safer. They are widely used in power tools, electric buses and energy grids. They are also the battery of choice for Tesla’s Model 3.

“Given these advantages, LFP batteries will have a competitive edge over other lithium-ion batteries in the market,” said Zheng Chen, a professor of nanoengineering at UC San Diego.

The problem? “It’s not cost-effective to recycle them,” Chen said. “It’s the same dilemma with plastics—the materials are cheap, but the methods to recover them are not.”

The new recycling process that Chen and his team developed could lower these costs. It does the job at low temperatures (60 to 80 C) and ambient pressure, making it less power hungry than other methods. Also, the chemicals it uses—lithium salt, nitrogen, water and citric acid—are inexpensive and benign.

“The whole regeneration process works at very safe conditions, so we don’t need any special safety precautions or special equipment. That’s why we can make this so low cost for recycling batteries,” said first author Panpan Xu, a postdoctoral researcher in Chen’s lab.

The researchers first cycled commercial LFP cells until they had lost half their energy storage capacity. They took the cells apart, collected the cathode powders, and soaked them in a solution containing lithium salt and citric acid. Then they washed the solution with water, dried the powders and heated them.

The researchers made new cathodes from the powders and tested them in both coin cells and pouch cells. Their electrochemical performance, chemical makeup and structure were all fully restored to their original states.

As the battery cycles, the cathode undergoes two main structural changes that are responsible for its decline in performance. The first is the loss of lithium ions, which creates empty sites called vacancies in the cathode structure. The other occurs when iron and lithium ions switch spots in the crystal structure. When this happens, they cannot easily switch back, so lithium ions become trapped and can no longer cycle through the battery.

The process restores the cathode’s structure by replenishing lithium ions and making it easy for iron and lithium ions to switch back to their original spots. The latter is accomplished using citric acid, which acts as a reducing agent—a substance that donates an electron to another substance. Citric acid transfers electrons to the iron ions, making them less positively charged. This minimizes the electronic repulsion forces that prevent the iron ions from moving back into their original spots in the crystal structure, and also releases the lithium ions back into circulation.

While the overall energy costs of this recycling process are lower, researchers say further studies are needed on the logistics of collecting, transporting and handling large quantities of batteries.

“Figuring out how to optimize these logistics is the next challenge,” Chen said. “And that will bring this recycling process closer to industry adoption.”

Veterans Day 2020 at the UC San Diego Jacobs School of Engineering

San Diego, Calif., Oct. 11, 2020 -- In recognition of Veterans Day, the University of California San Diego Jacobs School of Engineering is sharing the stories of two student veterans (electrical engineer Jack Bae and aerospace engineer Jeffrey Sei), while building for the future. 

"I want the Jacobs School to be the engineering school of choice for veterans and other military-connected students," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. 

There are more than 430 military connected students at UC San Diego, a third of whom study engineering and computer science at the Jacobs School. 

"I am proud of our network of industry partners, the various student organizations providing mentorship programs with alumni, and the people who are stepping up to increase our ability to support veterans and other military-connected students through scholarships and other initiatives," said Pisano. "We are building a Veterans Thought Leaders group here at the Jacobs School to work with me on the academic, personal, and professional development and support of military connected engineering students." 

"My father was a decorated tin-can sailor from the Korean War,” said Pisano. “I know full well the effort and sacrifices people in the military make, therefore is my very great honor to take a moment to say 'thank you' to those men and women who make sacrifices every day to protect and serve this great country.”

 

Jack Bae

Jack Bae had just two quarters left before he earned his undergraduate electrical engineering degree at UC San Diego. That's when the financial pressure hit a boiling point. 

“I had some financial issues and I thought I couldn’t keep going. I already had a student loan so it was stressful, plus I had part time jobs; I was miserable,” Bae said. 

Jack Bae

He decided to put his engineering degree on pause and join the Army for five years, with the intention of using the GI Bill after his service to help pay the tuition for his remaining quarters. That was just over five years ago, and he's now back at UC San Diego in the final quarter of his bachelor’s degree in electrical engineering. When he returned, Bae received support from the Philip and Elizabeth Hiestand Scholarship Endowment for Transfer Engineering Students. 

He was also accepted into the electrical and computer engineering BS/MS program, meaning he’ll spend one more year at the Jacobs School and earn his master’s degree in electrical engineering.

“After I came back I realized I feel really different at school because now I’m not worried about financial issues and I can just focus on school. That feels very satisfying. Even doing homework I was so happy when I came back! I was awaiting that moment for five years,” Bae said.

Bae wanted to serve as an electrical technician in the Army, but that billet wasn’t available when he enlisted, so he opted to work as a mechanic. This often involved working on the transmission and engine of large trucks or tanks. 

His first duty station took him to Korea with an air defense artillery unit. 

“One time the radar was down, and some civilian guys came to fix it so I talked to them a lot and realized they were actually electrical engineers,” Bae said. “I was surprised because when I left school I was focused on the electronic circuits depth, so I had never thought about an electrical engineer working in this kind of defense field. That’s the reason why when I applied for the BS/MS program I applied for the signal and image processing track, because I wanted to learn more about that area.”

Bae is continuing to discover just how broad the field of electrical engineering can be, as a paid systems engineering intern at local medical device company Instrumentation Laboratory. He’s helping them build a device that measures blood clotting levels, to help doctors and nurses know how much of a blood clotting drug to administer to patients.

“I never thought as an electrical engineer I’d be working at a medical device company, but I like the company and the people.”

Jeffrey Sei

Jeffrey Sei

For Jeffrey Sei, a Marine veteran and aerospace engineering student, the decision to serve in the military was about getting more life experience under his belt before choosing whether or what to study. 

“I was actually supposed to go to school in LA straight out of high school, but honestly I had no clue what I wanted to do and I was like ‘I’m just going to do this electrical engineering major just because my uncle did,’ but I had no motivation for it,” Sei said. 

“I wasn’t really stable in life at the time. I didn’t have a stable place, didn’t really have any income. And I wanted that family bonding experience which I always heard a lot about especially in the Marines.”

After four years of active duty and three years as a reservist serving as an aviation ordinance technician—maintaining the weapons systems on the F18 aircraft, including bomb racks and missile launchers—Sei discovered he was more interested in aerospace engineering than electrical, and was particularly intrigued by space.

“I always wanted to help us explore space further, achieve greater goals in space. I think that’s the main reason I decided to go back to school for aerospace engineering because I found something I actually liked to do, unlike when I first was applying for school I just picked electrical engineering because that’s all I knew.”

Sei received the Gregory A. Chauncey and Naomi C. Broering Endowed Engineering Scholarship Fund for Combat Veterans. He is expecting to graduate from UC San Diego with his aerospace engineering degree in the summer of 2021, after which he’s eyeing a position on NASA’s Artemis program. 

“That’s one of the things I’m really excited about,” he said. “When I hear about it I can’t believe we’re doing this. It excites me that we’re trying to go back to the moon and build a base.”

Supporting student veterans

Sei during a layover in Maine on the way to Bahrain. 

Bae and Sei are two of more than 430 military connected students at UC San Diego, a third of whom study engineering. They both received scholarships which helped to cover general living expenses that the GI Bill doesn’t cover. 

“The scholarship helped me out with more general things, I know I have this much extra to use on food or stuff I need to live off," said Sei. "I’m thinking of getting a printer because one of my classes the teacher wants hand written or printed notes, so I’m going to have to print a million notes for midterms, and the scholarship money will help me get a nice printer. I didn’t grow up in a wealthy environment, so every little bit helps.”

One area on campus that has spearheaded efforts to support these students is the Student Veterans Resource Center (SVRC), which focuses on providing services and programs in collaboration with campus partners to support military connected students to achieve personally, academically, and professionally. 

“We are grateful to our campus community for their continuous support of our student veterans,” said Maruth Figueroa, Assistant Vice Chancellor of Student Retention and Success. “It is through these partnerships which honor the strengths and tremendous life experiences of our student veterans that we demonstrate a truly student-centered approach to education.”

In addition to the life experiences, the goal-oriented training, leadership and ethics that help people stand out in the military are also directly relevant to engineering, noted Pisano.

"I want to make sure the Jacobs School does everything it can to attract, retain and make our veterans, and all our military-connected students successful," said Pisano. "To do that, we'll be looking for support and collaboration from our constituents."

"My experience in the Army was really good, serving the country and meeting people I would have never met," said Bae. "It was a great experience."

“I feel like it definitely helped mature me as a person,” Sei said. “Not only with the leadership, but also back then I was extremely shy, and it helped me break out of that shell.”

Alumni battery startup raises $1.25M

Rajan Kumar and Carlos Munoz

San Diego, CA, Oct. 17, 2020--Ateios, a startup founded by Jacobs School of Engineering alumni Rajan Kumar and Carlos Munoz, raised $1.25 million in seed funding.  Ateios has developed a flexible, paper-thin, customizable battery, and is reshaping battery manufacturing with their technique for thin-film batteries. The company spun out from Kumar and Munoz' research into stretchable batteries here at the Jacobs School of Engineering, and was part of the Institute for the Global Entrepreneur. Read the full release here.

IROS 2020: Autonomous mail delivery, robots practicing bartending, and more

San Diego, Calif., Nov. 8, 2020 -- From autonomous vehicles to robots practicing bartending and insect-like robots, engineers at the University of California San Diego are showcasing a broad range of pacers at IROS 2020, which is being held virtually from Oct. 25 to Nov. 25. 

The Contextual Robotics Institute at UC San Diego is a full stack research enterprise, from autonomy, to robots in medicine, to human robot interaction, said institute director Henrik Christensen, who is also a professor in the UC SanDiego Department of Computer Science. 

“The conference is a unique opportunity for the Contextual Robotics Institute to showcase our diverse research portfolio and to engage with the broader audience to demonstrate how robots are changing the world from manufacturing to e-commerce to helping in everyday life,” Christensen said. “IROS is also for the first time putting a significant emphasis on diversity equity and inclusion, which is a great new direction.”

For the first time, the conference is available for free after registration. This year’s theme is Consumer Robotics and Our Future. 

Laurel Riek, a professor in the UC San Diego Department of Computer Science and Engineering, is giving an invited talk at the RoPat20 workshop. She is speaking on “Expressive Patient Simulators for Clinical Education.” 

Nicholas Gravish, a professor in the Department of Mechanical and Aerospace Engineering at UC San Diego, is one of the organizers of a workshop on robotics-inspired biology. In addition, Michael Yip, a professor in the Department of Electrical and Computer Engineering, and one of his PhD students, Florian Richter, are co-organizers of a workshop on cognitive robotics surgery. 

Here is a listing of the papers that UC San Diego faculty are contributing to the conference this year: 

Autonomous Vehicle Benchmarking using Unbiased Metrics
David Paz, Po-jung Lai, Nathan Chan, Yuqing Jiang and Henrik I. Christensen

With the recent development of autonomous vehi- cle technology, there have been active efforts on the deployment of this technology at different scales that include urban and highway driving. While many of the prototypes showcased have been shown to operate under specific cases, little effort has been made to better understand their shortcomings and generalizability to new areas. Distance, uptime and number of manual disengagements performed during autonomous driving provide a high-level idea on the performance of an autonomous system but without proper data normalization, testing location information, and the number of vehicles involved in testing, the disengagement reports alone do not fully encompass system performance and robustness. Thus, in this study a complete set of metrics are applied for benchmarking autonomous vehicle systems in a variety of scenarios that can be extended for comparison with human drivers and other autonomous vehicle systems. These metrics have been used to benchmark UC San Diego’s autonomous vehicle platforms during early deployments for micro-transit and autonomous mail delivery applications.

https://arxiv.org/pdf/2006.02518.pdf 

Probabilistic Semantic Mapping for Urban Autonomous Driving Applications
David Paz, Hengyuan Zhang, Qinru Li, Hao Xiang and Henrik I. Christensen

Recent advancements in statistical learning and computational abilities have enabled autonomous vehicle tech- nology to develop at a much faster rate. While many of the architectures previously introduced are capable of op- erating under highly dynamic environments, many of these are constrained to smaller-scale deployments, require constant maintenance due to the associated scalability cost with high- definition (HD) maps, and involve tedious manual labeling. As an attempt to tackle this problem, we propose to fuse image and pre-built point cloud map information to perform automatic and accurate labeling of static landmarks such as roads, sidewalks, crosswalks, and lanes. The method performs semantic segmentation on 2D images, associates the semantic labels with point cloud maps to accurately localize them in the world, and leverages the confusion matrix formulation to construct a probabilistic semantic map in bird’s eye view from semantic point clouds. Experiments from data collected in an urban environment show that this model is able to predict most road features and can be extended for automatically incorporating road features into HD maps with potential future work directions.

https://arxiv.org/pdf/2006.04894.pdf

Neural Manipulation Planning on Constraint Manifolds
Ahmed H. Qureshi, Jiangeng Dong, Austin Choe, and Michael Yip

The presence of task constraints imposes a significant challenge to motion planning. Despite all recent advancements, existing algorithms are still computationally expensive for most planning problems. In this paper, we present Constrained Motion Planning Networks (CoMPNet), the first neural planner for multimodal kinematic constraints. Our approach comprises the following components: i) constraint and environment perception encoders; ii) neural robot configuration generator that outputs configurations on/near the constraint manifold(s), and iii) a bidirectional planning algorithm that takes the generated configurations to create a feasible robot motion trajectory. We show that CoMPNet solves practical motion planning tasks involving both unconstrained and constrained problems. Furthermore, it generalizes to new unseen locations of the objects, i.e., not seen during training, in the given environments with high success rates. When compared to the state-of-the-art constrained motion planning algorithms, CoMPNet outperforms by order of magnitude improvement in computational speed with a significantly lower variance.

https://sites.google.com/view/constrainedmpnet/home

 

Dynamically Constrained Motion Planning Networks for Non-Holonomic Robots
Jacob J. Johnson, Linjun Li, Fei Liu, Ahmed H. Qureshi and Michael C. Yip

Reliable real-time planning for robots is essential in today's rapidly expanding automated ecosystem. In such environments, traditional methods that plan by relaxing constraints become unreliable or slow-down for kinematically constrained robots. This paper describes the algorithm Dynamic Motion Planning Networks (Dynamic MPNet), an extension to Motion Planning Networks, for non-holonomic robots that address the challenge of real-time motion planning using a neural planning approach. We propose modifications to the training and planning networks that make it possible for real-time planning while improving the data efficiency of training and trained models' generalizability. We evaluate our model in simulation for planning tasks for a non-holonomic robot. We also demonstrate experimental results for an indoor navigation task using a Dubins car.
https://arxiv.org/abs/2008.05112

Soft Microrobotic Transmissions Enable Rapid Ground-Based Locomotion
Wei Zhou and Nick Gravish 

In this paper we present the design, fabrication, testing, and control of a 0.4 g milliscale robot employing a soft polymer flexure transmission for rapid ground movement. The robot was constructed through a combination of two methods: smart-composite-manufacturing (SCM) process to fabricate the actuators and robot chassis, and silicone elastomer molding and casting to fabricate a soft flexure transmission. We actuate the flexure transmission using two customized piezoelectric (PZT) actuators that attach to the transmission inputs. Through high- frequency oscillations the actuators are capable of exciting vibrational resonance modes of the transmission which result in motion amplification on the transmission output. Directional spines on the transmission output generate traction force with the ground and drive the robot forward. By varying the excitation frequency of the soft transmission we can control running speed, and when the transmission is oscillated at its resonance frequency we achieve high speeds with a peak speed of 439 mm/s (22 body lengths/s). By exciting traveling waves through the soft transmission, we were able to control the steer- ing direction. Overall this paper demonstrates the feasibility of exciting resonance behavior in millimeter scale soft robotic structures to achieve high-speed controllable locomotion.

http://gravishlab.ucsd.edu/PDF/Zhou_IROS_2020.pdf​

Knuckles that buckle: compliant underactuated limbs with joint hysteresis enable minimalist terrestrial robots
Mingsong Jiang, Rongzichen Song and Nick Gravish

Underactuated designs of robot limbs can enable these systems to passively adapt their joint configuration in response to external forces. Passive adaptation and reconfiguration can be extremely beneficial in situations where manipulation or locomotion with complex substrates is required. A common design for underactuated systems often involves a single tendon that actuates multiple rotational joints, each with a torsional elastic spring resisting bending. However, a challenge of using those joints for legged locomotion is that limbs typically need to follow a cyclical trajectory so that feet can alternately be engaged in stance and swing phases. Such trajectories present challenges for linearly elastic underactuated limbs. In this paper, we present a new method of underactuated limb design which incorporates hysteretic joints that change their torque response during loading and unloading. A double-jointed underactuated limb with both linear and hysteretic joints can thus be tuned to create a variety of looped trajectories. We fabricate these joints inside a flexible legged robot using a modified laminate based 3D printing method, and the result shows that with passive compliance and a mechanically determined joint sequence, a 2-legged minimalist robot can successfully walk through a confined channel over uneven substrates.

http://gravishlab.ucsd.edu/PDF/Jason_Robosoft_2020.pdf​

OrcVIO: Object residual constrained Visual-Inertial Odometry
Mo Shan, Qiaojun Feng, Nikolay Atanasov

Introducing object-level semantic information into simultaneous localization and mapping (SLAM) system is critical. It not only improves the performance but also enables tasks specified in terms of meaningful objects. This work presents OrcVIO, for visual-inertial odometry tightly coupled with tracking and optimization over structured object models. OrcVIO differentiates through semantic feature and bounding-box reprojection errors to perform batch optimization over the pose and shape of objects. The estimated object states aid in real-time incremental optimization over the IMU-camera states. The ability of OrcVIO for accurate trajectory estimation and large-scale object-level mapping is evaluated using real data.

https://natanaso.github.io/ref/Shan_OrcVIO_IROS20.pdf

Dense Incremental Metric-Semantic Mapping via Sparse Gaussian Process Regression
Ehsan Zobeidi, Alec Koppel and Nikolay Atanasov

We develop an online probabilistic metric- semantic mapping approach for autonomous robots relying on streaming RGB-D observations. We cast this problem as a Bayesian inference task, requiring encoding both the geo- metric surfaces and semantic labels (e.g., chair, table, wall) of the unknown environment. We propose an online Gaussian Process (GP) training and inference approach, which avoids the complexity of GP classification by regressing a truncated signed distance function representation of the regions occupied by different semantic classes. Online regression is enabled through sparse GP approximation, compressing the training data to a finite set of inducing points, and through spatial domain partitioning into an Octree data structure with overlapping leaves. Our experiments demonstrate the effectiveness of this technique for large-scale probabilistic metric-semantic mapping of 3D environments. A distinguishing feature of our approach is that the generated maps contain full continuous distributional information about the geometric surfaces and semantic labels, making them appropriate for uncertainty-aware planning.

https://natanaso.github.io/ref/Zobeidi_GPMapping_IROS20.pdf

Fully Convolutional Geometric Features for Category-level Object Alignment
Qiaojun Feng and Nikolay Atanasov
This paper focuses on pose registration of different object instances from the same category. This is required in online object mapping because object instances detected at test time usually differ from the training instances. Our approach transforms instances of the same category to a normalized canonical coordinate frame and uses metric learning to train fully convolutional geometric features. The resulting model is able to generate pairs of matching points between the instances, allowing category-level registration. Evaluation on both synthetic and real-world data shows that our method provides robust features, leading to accurate alignment of instances with different shapes.

https://natanaso.github.io/ref/Feng_CategoryAlignment_IROS20.pdf

Deep Keypoint-Based Camera Pose Estimation with Geometric Constraints
You-Yi Jau, Rui Zhu, Hao Su and Manmohan Chandraker

Estimating relative camera poses from consecutive frames is a fundamental problem in visual odometry (VO) and simultaneous localization and mapping (SLAM), where classic methods consisting of hand-crafted features and sampling-based outlier rejection have been a dominant choice for over a decade. Although multiple works propose to replace these modules with learning-based counterparts, most have not yet been as accurate, robust and generalizable as conventional methods. In this paper, we design an end-to-end trainable framework consisting of learnable modules for detection, feature extraction, matching and outlier rejection, while directly optimizing for the geometric pose objective. We show both quantitatively and qualitatively that pose estimation performance may be achieved on par with the classic pipeline. Moreover, we are able to show by end-to-end training, the key components of the pipeline could be significantly improved, which leads to better generalizability to unseen datasets compared to existing learning-based methods.

https://arxiv.org/abs/2007.15122

 

Eyes on Wildfire

First responder observing real-time ALERTWildfire camera network feeds in UC San Diego’s VRroom, a room-scale visual analytics environment for collaborative big-data analytics.

By Caitlin Scully

San Diego, Calif., Nov. 5, 2020-- As California reacts to a record-breaking 2020 fire season, a backcountry observation network has reached a milestone of installing more than 610 cameras across the state. The cameras are part of the ALERTWildfire camera network, built by UC San Diego’s Scripps Institution of Oceanography, the University of Nevada, Reno and the University of Oregon. The network has become a vital firefighting tool helping first responders confirm and monitor wildfires from ignition through containment.

The ALERTWildfire cameras play a critical role for California as the state grapples with ever-intensifying fire seasons. In 2020, the Operations Southern California Center (OSCC)—the cooperative organization that includes agencies such as the U.S. Forest Service, Department of the Interior and CAL FIRE—predicts temperatures across California to be higher than normal with lower than normal rainfall through December, creating conditions ideal for wildfires.

A new ALERTWildfire camera is installed in October 2020 on the hills above Santa Monica, Calif. by Scripps Institution of Oceanography at UC San Diego personnel Ernest Aaron, Colby Nicholson and Bryan Hoban.

The high-definition ALERTWildfire cameras are able to pan, tilt, zoom and perform 360-degree sweeps approximately every two minutes with 12 high-definition frames per sweep. The cameras also provide 24-hour monitoring with near-infrared night vision capabilities. Each camera can view as far as 60 miles on a clear day and 120 miles on a clear night. Fire agencies and utilities can access actionable real-time data to confirm 911 calls, triangulate on the location of fires at their earliest stages and make critical decisions during and after wildfires.

“The cameras have been a game changer for us in San Diego,” said CAL FIRE San Diego County Unit Chief Tony Mecham. “The cameras have given us real-time situational awareness and have allowed us to make informed decisions much quicker than we used to. It used to take 20 to 30 minutes for our fire ground commanders to get to fires and make decisions, and now with the cameras we are reacting within seconds of the first report. That extra time is significant when it comes to moving resources or needing to start evacuations. It’s making a difference. I can’t even put into words how important those first few minutes are.”

The ALERTWildfire Camera Network got its start as ALERTTahoe, a pilot project in the Lake Tahoe region launched by the Nevada Seismological Laboratory at the University of Nevada, Reno. Built on the backbone of the networking technology used in earthquake detection systems, the ALERTTahoe network expanded rapidly. When UC San Diego and the University of Oregon became partners, the network became ALERTWildfire.

The efficacy of the network to confirm and monitor wildfires was readily apparent and interagency investment created a surge in camera numbers as they quickly became an essential tool. In California, the ALERTWildfire network expansion began in 2017 with 16 cameras in San Diego County funded through San Diego Gas & Electric. From there, additional investment and support to expand the network has come from organizations including Pacific Gas & Electric, Southern California Edison, and most recently CAL FIRE, which contributed $5 million for the installation and network support of 100 additional cameras throughout the state of California that were installed this spring, summer and fall in anticipation of a potentially dangerous 2020 fire season.

“The ALERTWildfire camera network provides actionable real-time data that allows first responders to marshal resources to fight fires in the incipient phase,” said Scripps Oceanography geoscientist Neal Driscoll, director of the ALERTWildfire program at UC San Diego. “These cameras save critical time by allowing rapid confirmation of 911 calls and accurate location of new fires using the ALERTWildfire web-based interface, time that would otherwise be spent sending engines to mountaintops or launching aircraft to confirm fire ignition and location.”

In the last four months, the number of ALERTWildfire cameras has nearly doubled, with growth primarily in California. The team has been on track, and installed the 610th camera in California in mid-October 2020. Currently the ALERTWildfire network also has 41 cameras in Nevada, nine in Oregon, six in Idaho, and one in Washington state.

The to-the-minute information provided by ALERTWildfire allows for enhanced situational awareness that helps first responders adapt quickly to scale fire resources up or down and monitor fire activity. The ALERTWildfire team is working rapidly, with interagency support and funding, to deploy as many cameras as possible as conditions become more conducive to fires.

“In Kern County, ALERTWildfire has provided us the early confirmation necessary to increase the number of firefighters and resources deployed to fires located in communities vulnerable to high-risk wildfires,” says Kern County Battalion Chief Zach Wells, “We get to the fires much earlier than we did last year based on the increased situational awareness the cameras provide. We also share the publicly available camera feeds with firefighters responding to the scene to help them better observe and orient themselves to assist with route selection and evolving conditions.”

A fully-interactive, real-time quilt of ALERTWildfire camera views in UC San Diego’s VRoom.

ALERTWildfire is more than cameras on mountaintops. Behind the scenes, its cyber-infrastructure is created and managed by UN Reno and UC San Diego’s Jacobs School of Engineering. They provide ALERTWildfire with networking, an interactive user interface, “Big Data” management, storage and backups as well as next-generation data processing and wildfire visualization. As the camera network grows, so does the amount of raw data recorded and processed. One year of current camera data usage exceeds one million gigabytes. That amount of data is expected to double annually as the ALERTWildfire Camera Network continues to expand.

“This project brings together a highly interdisciplinary team of faculty, students, and staff at UC San Diego,” said Falko Kuester, ALERTWildfire team member and professor at the Jacobs School of Engineering at UC San Diego. “The team includes members with expertise in earth systems science, computer science and engineering, electrical and computer engineering, mechanical and aerospace engineering, structural engineering, mathematics and physics.”

Currently, ALERTWildfire Camera Network growth comes with greater urgency, as wildfires continue to increase in frequency and intensity. Hotter daytime and warmer nighttime temperatures throughout the year, periodic drought, episodic dry wind events including Santa Anas and Diablos, and stressed and degraded native habitats are some of the many climate change impacts that directly contribute to California’s increased fire risk.

California’s Fourth Climate Change Assessment, released in 2018 and edited by Scripps Oceanography research meteorologist Dan Cayan, found that by the year 2100, if greenhouse gas emissions continue to rise, using traditional fire abatement practices, the average area burned by wildfires would increase 77 percent and the frequency of extreme wildfires burning more than 25,000 acres would increase by nearly 50 percent.

California’s recent catastrophic fires showcase the importance of having a robust camera network. The CZU Lightning Complex Fires outside of Santa Cruz caused devastating losses for the community, and cameras. While the cameras are designed to be resilient, five ALERTWildfire cameras also were burned and rendered inoperable, including the Bonny Doon ALERTWildlfire camera in Santa Cruz County. Three of those cameras have since been replaced, and once all areas are safe to access, the remaining damaged cameras will also be brought back online.

ALERTWildfire cameras can be viewed by the public at any time at alertwildfire.org. The website shows cameras by geographical region, and once a camera is selected, users can create time lapses or explore other cameras in the area.

Each ALERTWildfire partner plays an essential role in broadening the network reach and every new camera is a tool to save lives, property, infrastructure and habitat.

'Monster tumors' could offer new glimpse at human development

Histology image in pink of a teratoma
Histology image of a teratoma.

San Diego, Calif., Nov. 4, 2020 -- Finding just the right model to study human development—from the early embryonic stage onward—has been a challenge for scientists over the last decade. Now, bioengineers at the University of California San Diego have homed in on an unusual candidate: teratomas.

Teratomas—which mean “monstrous tumors” in Greek—are tumors made up of different tissues such as bone, brain, hair and muscle. They form when a mass of stem cells differentiates uncontrollably, forming all types of tissues found in the body. Teratomas are generally considered an undesired byproduct of stem cell research, but UC San Diego researchers found an opportunity to study them as models for human development.

Researchers report their work in a paper published Nov. 4 in Cell.

“We’ve been fascinated with the teratoma for quite a while,” said Prashant Mali, a professor of bioengineering at the UC San Diego Jacobs School of Engineering. “Not only is the teratoma an intriguing tumor to look at in terms of the diversity of cell types, but it also has regions of organized tissue-like structures. This prompted us to explore its utility in both cell science and cell engineering contexts.”

“There’s no other model like it. In just one tumor, you can study all of these different lineages, all of these different organs, at the same time,” said Daniella McDonald, an M.D/Ph.D. candidate in Mali’s lab and co-first author of the study. “Plus, it’s a vascularized model, it has a three-dimensional structure and it’s human-specific tissue, making it the ideal model for recreating the context in which human development happens.”

The team used teratomas grown from human stem cells injected under the skin of immunodeficient mice. They analyzed the teratomas with a technique called single-cell RNA sequencing, which profiles the gene expression of individual teratoma cells. The researchers were able to map 20 cell types, or “human lineages” (brain, gut, muscle, skin, etc.) that were consistently present in all the teratomas they analyzed.

The researchers then used the gene editing technology CRISPR-Cas9 to screen and knock out 24 genes known to regulate development. They found multiple genes that play roles in the development of multiple lineages.

“What’s remarkable about this study is that we could use the teratoma to discover things in a much faster way. We can study all of these genes on all of these human lineages in a single experiment,” said co-first author Yan Wu, who worked on this project as a Ph.D. student in the labs of Mali and UC San Diego bioengineering professor Kun Zhang. “With other models, like organoids, that separately model one lineage at a time, we would have had to run many different experiments to come up with the same results as we did here.”

“Teratomas are a very unique type of human tissue. When examined through the lens of single-cell sequencing, we can see that they contain most major representative cell types in the human body. With that understanding, we suddenly have an extremely powerful platform to understand, manipulate and engineer human cells and tissues in a far more sophisticated way than what was previously possible,” Zhang said.

The researchers also showed that they can “molecularly sculpt” the teratoma to be enriched in one lineage—in this case, neural tissue. They accomplished this feat using a microRNA gene circuit, which acts like a molecular chisel by carving away unwanted tissues—these are selectively killed off using a suicide gene—and leaving behind the lineage of interest. The researchers say this has applications in tissue engineering.

“We envision that this study will set a new foundation in the field. Hopefully, other scientists will be using the teratoma as a model for future discoveries in human development,” McDonald said.

Infection by Confection: COVID-19 and the Risk of Trick-or-Treating

Researchers say viral transmission risk is low, even when candies are handled by infected persons, but handwashing and disinfecting collected sweets reduces risk even further

San Diego, Calif., Oct. 30, 2020 -- Like a specter, the question looms: How risky is trick-or-treating with SARS-Cov-2, the virus that causes COVID-19, in the air — and possibly on the candy? 

In a study published October 30, 2020 in the journal mSystems, researchers at University of California San Diego and San Diego State University analyzed the viral load on Halloween candy handled by patients with COVID-19. 

SARS-CoV-2 is primarily transmitted by respiratory droplets and aerosols. The risk of infection by touching fomites — objects or surfaces upon which viral particles have landed and persist —is relatively low, according to multiple studies, even when fomites are known to have been exposed to the novel coronavirus. Nonetheless, the risk is not zero.

“The main takeaway is that although the risk of transmission of SARS-CoV-2 by surfaces, including candy wrappers, is low, it can be reduced even further by washing your hands with soap before handling the candy and washing the candy with household dishwashing detergent afterwards,” said co-senior author Rob Knight, professor of computer science and pediatrics and director of the Center for Microbiome Innovation at UC San Diego. “The main risk is interacting with people without masks, so if you are sharing candy, be safe by putting it in dish where you can wave from six feet away.” Knight led the study with Forest Rohwer, viral ecologist at San Diego State University, and Dr. Louise Laurent, professor at UC San Diego School of Medicine.

For their study, the researchers enrolled 10 recently diagnosed COVID-19 patients who were asymptomatic or mildly symptomatic and asked them to handle Halloween candy under three different conditions: 1) normally with unwashed hands; 2) while deliberately coughing with extensive handling; and 3) normal handling after handwashing.

The candy was then divided into two treatments — no post-handling washing (untreated) and washed with household dishwashing detergent — followed by analyses using real-time reverse transcription polymerase chain reaction, the same technology used to diagnose COVID-19 infections in people, and a second analytical platform that can conduct tests on larger samples more quickly and cheaply. Both produced similar findings.  

On candies not washed post-handling, researchers detected SARS-CoV-2 on 60 percent of the samples that had been deliberately coughed on and on 60 percent of the samples handled normally with unwashed hands. However, the virus was detected in only 10 percent of the candies handled after handwashing. 

Not surprisingly, the dishwashing detergent was effective for reducing the viral RNA on candies, with reducing the viral load by 62.1 percent. 

They had also planned to test bleach, “but importantly, we noted that bleach sometimes leaked through some of the candy wrappers, making it unsafe for this type of cleaning use,” Rohwer said.

The study authors underscored that the likely risk of SARS-CoV-2 transmission from candy is low, even if handled by someone with a COVID-19 infection, but it can be reduced to near-zero if the candy is handled only by people who have first washed their hands and if it is washed with household dishwashing detergent for approximately a minute after collection.

Additional co-authors include: Rodolfo A. Salido, Sydney C. Morgan, Celestien G. Magallenes, Clarisse Marotz, Peter DeHoff, Pedro Belda-Ferre, Stefan Aigner, Deborah M. Kado, Gene W. Yeo, Jack A. Gilbert, all at UC San Diego; and Maria I. Rojas of San Diego State University.

Full study: https://msystems.asm.org/content/5/6/e01074-20 

 

 

Energizing Plastics Renewability, Recycling Efforts

San Diego, Calif., Oct. 30, 2020 -- The U.S. Department of Energy (DOE) has announced more than $27 million in funding for 12 projects that will support the development of advanced renewable plastics and new recyclable-by-design plastics. Two of the dozen projects—collectively funded for more than $4 million—belong to UC San Diego researchers: Professor of Chemistry and Biochemistry, and Director of the Center for Renewable Materials, Michael Burkart and Professor of Nanoengineering Jon Pokorski, both part of the university’s Institute for Materials Discovery and Design.

Jon Pokorski
Jon Pokorski, professor of nanoengineering at the UC San Diego Jacobs School of Engineering

Part of DOE’s Plastics Innovation Challenge, these projects will help improve existing recycling processes that break plastics into chemical building blocks, which can in turn be used to make new products. For example, Burkart, Skip Pomeroy (chemistry and biochemistry) and Stephen Mayfield (biology) have developed algae-based polyurethane foams used in commercial products like surfboards and flip-flops that are partially biodegradable. The new $2 million from the DOE toward their project will further their goal of achieving full renewability.

“While we had achieved 50 percent renewability in our polyurethanes, our goals have been to achieve 100 percent renewability and also increase content that comes from algae,” said Burkart. “At the same time, we want to ensure full biodegradability. This proposal will achieve all of these goals by integrating the achievements we have made in chemistry and biology into commercially relevant materials.”

Mayfield explained that the team’s previous research used enzymes from organisms degrading the foams and showed that they could be used to depolymerize the polyurethane products. “We then showed that we could isolate the depolymerized products and use those to synthesize new polyurethane monomers, completing a ‘bioloop,’ or full recyclability,” he said, adding the funding will help them get closer to that goal.

Burkart, principal investigator on the project, Pomeroy and Mayfield will be working with Ryan Simkovsky (UC San Diego) and Alissa Kendall (UC Davis), who will do life-cycle analysis. Their cost-share partners on the project are BASF, Algenesis and REEF. 

According to Pomeroy, the environmentally unfriendly practice of producing nearly indestructible plastic commercial products began about 60 years ago and, if not addressed, will result in 12 billion metric tons of plastic in landfills or the natural environment by 2050.

“When you look around, plastics are ubiquitous. They’re not just part of the things we use every day, but they’re also now part of our oceans, our beaches, our forests—they are taking a major toll on our environment,” Pokorski said. “The problem is compounded by the fact that these plastics just stick around for way too long before they even begin to break down.”

Adam Feist
Adam Feist, research scientist in the UC San Diego Department of Bioengineering

Pokorski, along with UC San Diego bioengineer Adam Feist, is leading a project to develop a different kind of biodegradable plastic—one filled with bacterial spores that will aid in breaking down the material at the end of its life-cycle. Funding from the $2 million DOE award will enable the team to explore and optimize bacterial strains for biodegrading thermoplastic polyurethanes and their byproducts, and then incorporate these strains into different polymer formulations to see which will work best. Collaborators Jason Locklin (University of Georgia, New Materials Institute) and a team at BASF led by Arif Rahman will work on determining biodegradation protocols and scaling up the processes, respectively.

“We’re making bacteria part of the plastic to jump start its degradation,” Feist said. “Ultimately, these plastics will have the performance and properties we want, for the duration we need them for, and then degrade as soon as possible after that.”

The BOTTLE: Bio-Optimized Technologies to Keep Thermoplastics out of Landfills and the Environment funding opportunity is jointly funded by the Office of Energy Efficiency and Renewable Energy’s (EERE) Bioenergy Technologies Office and Advanced Manufacturing Office. The projects are part of DOE’s Plastics Innovation Challenge, which draws on the research capabilities of DOE National Laboratories, universities, and industry to accelerate innovations in energy-efficient plastics recycling technologies.

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.

San Diego, Calif., Nov. 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.

“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

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.

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.”

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. 

The model

The model 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. 
 

$39 Million to better integrate renewables into power grid

San Diego, Calif., Oct. 29. 2020 -- The National Science Foundation has awarded $39 million to a team of engineers and computer scientists at the University of California San Diego to build a first-of-its-kind testbed to better understand how to integrate distributed energy sources such as solar panels, wind turbines, smart buildings and electric vehicle batteries into the power grid. The goal is to make the testbed available to outside research teams and industry by 2025. 

The major driver for the project is the need to decarbonize the electrical grid, protect it from cybersecurity attacks and make it more resilient. To provide 50 percent—or more—of power from clean energy sources, power grids will have to be able to leverage distributed energy sources, and reliably manage dynamic changes, while minimizing impact on customer quality of service.

“We will be replicating the entire California power grid on one campus,”  said Jan Kleissl, a professor in the Department of Mechanical and Aerospace Engineering at UC San Diego and the project’s principal investigator.

Jan Kleissl is the principal investigator on the grant and director of DERConnect. He is a professor in the Department of Mechanical and Aerospace Engineering.

The creation of the testbed, DERConnect, addresses an outstanding national need for large-scale testing capabilities across universities, national labs, industry, utility companies, and Independent System Operators to validate future technologies for autonomous energy grids in real-word scenarios.  In fact, a major, current obstacle to the adoption of such technologies in the operations of real energy systems is the development of realistic test cases on a realistic scale.

Most utilities struggle with the fact that renewable and distributed energy sources are not as stable as traditional sources, such as natural-gas power plants. Solar panel output depends on the weather, for example, as do wind turbines. At the other end of the grid, electric vehicles need charging for only a certain amount of time every day, and when not in use could be used as temporary batteries to store energy from renewables.

As a result, while the number and diversity of distributed energy resources on the power grid is rapidly expanding, the adoption of these resources for power-grid balancing is hindered by concerns about safety, reliability and cost.

 “This created the classic ‘chicken-and-egg’ situation, where the economics and impact of distributed energy resources cannot be demonstrated, because there are too few of them  due to limited buy-in from Independent System Operators, and other practical concerns,” Kleissl said. 

Offering utilities, researchers, industry,  and other entities a testbed with real-world communications challenges is essential to solve these problems and develop new distributed control theories, algorithms, and applications. The envisioned testbed is built upon a number of technical innovations at UC San Diego that create a microgrid encompassing distributed energy resources, including energy storage, electrical vehicles and independent electrical and thermal systems in buildings. This distributed system is monitored and controlled by computing and networking systems that make it accessible to local and remote researchers as a programmable platform.

“The ultimate goal of any grid is reliability, and it is a top concern at UC San Diego, as we must  constantly power medical centers and major research facilities,” said Gary Matthews, vice chancellor resource management and planning for UC San Diego. “The ability to interact with buildings and change their energy profile intelligently both enhances grid stability and saves a tremendous amount of energy. We support this living laboratory at the highest level, as this grant allows us to put infrastructure in place for future research, collaborating with leading scientists on real world solutions.”

DERConnect will include more than 2500 distributed energy resources, or DERs, on the campus’ microgrid, with its fuel cell and solar panels, a dozen classroom and office buildings, as well as 300 charging stations for electric vehicles. It will also entail the construction of a new energy storage testing facility on the East Campus. 

An upgrade to the microgrid will give researchers real time control over heating, ventilation and air conditioning systems, lighting, solar panels, battery storage and EVs. The testbed’s control center will be housed in Robinson Hall on the UC San Diego campus, which will be turned into a full controllable building that can be disconnected from the campus’ grid at any time.  

The bulk of the construction will take place this coming academic year. Researchers hope to be able to begin testing their equipment in 2022. 

DERConnect will be the first integrated platform in the United States that matches the needed experimental evaluation and validation for the implementation of DER technologies, protocols, and standards. A wide range of smart grid implementation use cases and testing procedures will be established to provide controlled laboratory evaluations of DER control algorithms, emerging technologies, and protocols in areas such as distributed and renewable energy integration, energy storage systems, advanced distribution management, advanced metering infrastructure, and cybersecurity. DERConnect will be able to explore which architectures and corresponding resource aggregation approaches allow consumers and grid operators to adapt their operations to achieve significant improvements in system-wide operational cost and renewables integration.

Sonia Martinez, a professor in the Department of Mechanical and Aerospace Engineering at UC San Diego, is the project's deputy director. 

UC San Diego is building on experience from NODES, a three-year, $2.88 million grant from ARPA-E, led by Professor Sonia Martinez in the Department of Mechanical and Aerospace Engineering, who is also the CO-PI on DERConnect. NODES’ aim was to develop transformational grid management and control technologies to facilitate the integration of renewables and DERs, increase operational efficiency, and reduce carbon footprint. NODES involved the same research team and constitutes the intellectual backbone of DERConnect in the development and preliminary testing of algorithms for decentralized control of DERs.  The testing carried out at the UC San Diego microgrid was among the most successful ones due to the number of devices, their diversity, and the alignment with real-world operating conditions. Building on this experience, DERConnect strives to be a plug-and-play experience for users with a much larger number of devices, minimal overhead for users in terms of platform readiness, and failsafe system that allows experiments at any time of the day.

Experiments and algorithms

DERConnect will provide advanced controls, sensors, and data analytics to optimize building energy use, while maintaining and even improving comfort for occupants. For example, the Computer Science and Engineering building is instrumented with over 4,500 sensing and control points. Every control unit can be controlled, from the position of air dampers to the speed of supply air fans to a room. DERConnect will upgrade 12 additional buildings with advanced control infrastructure that enables researchers to access operating conditions and set various operating parameters in real-time through novel programming methods and tools. This capability is particularly important as indoor operating conditions in buildings with central air handling become an important focus for researchers and building operators to reduce the spread of infectious diseases. 

Researchers plan to conduct experiments to optimize learning conditions for students by changing airflow, temperature, humidity and lighting conditions in classrooms. Similarly, researchers could make changes in the energy prices at EV charging stations and see how this impacts customer willingness to delay charging to benefit the power grid. 

Outreach efforts and education 

Solar trees on the top floor of the Gilman Parking structure at UC San Diego.

The testbed will also become a training ground for students in the new Systems Engineering program at the UC San Diego Jacobs School of Engineering as well as data-driven research and capstone projects tied toThe Halıcıoğlu Data Science Institute at UC San Diego.

Outreach efforts for elementary through high schools will take the form of a Research Experience for Teachers program, targeting 10 teachers coming from schools with a high number of students under-represented in engineering. Classes will also be able to tour the testbed and related lesson plans will be provided to their teachers.

The team will also work with Santa Fe Community College in New Mexico to develop a course focused on local data and technologies to inform planning, operations and maintenance, and the decarbonization of microgrids. 

In addition, the team will offer microgrid workshops for Native American tribes. The workshops will offer training sessions on key aspects of the infrastructure design and construction, on-site tours of the facility construction area, and tours of local microgrid facilities. Workshop participants will include tribe members involved in planning and construction of microgrids, as well as students training in various aspects of microgrid and DER planning and installation.

Professional seminars and workshops will raise awareness of DERConnect for senior researchers and engineers at Sempra Energy, San Diego Gas & Electric, Southern California Edison, and other utilities and energy companies, with the goal of both promoting the testbed to enlarge the user base as well as to train them in novel concepts for renewable energy integration.

The team

In addition to Kleissl, who will serve as director of DERConnect, the research team includes co-PIs professors Sonia Martinez, serving as deputy director, Jorge Cortes and Raymond de Callafon, in the Department of Mechanical and Aerospace Engineering; and Professor Rajesh Gupta, director of The Halicioglu Data Science Institute at UC San Diego. Additional senior personnel include Professors David Victor and Josh Graff Zivin from the School of Global Policy and Strategy; Ping Liu, a nanoengineering professor and director of the UC San Diego Sustainable Power and Energy Center; Mike Ferry and Antonio Tong from the Center for Energy Research; Ilkay Altintas and Amarnath Gupta from the San Diego Supercomputing Center; and UC San Diego Energy Manager John Dilliott, in Facilities Management and Planning. Researchers developed a detailed cybersecurity plan together with UC San Diego Chief Information Security Officer Michael Corn. Sharon Franks and Wendy Groves in the Office of Research Affairs Research Proposal Development Service provided strategic advice throughout the proposal development and review process. Industry partners include Johnson Controls and Sunspec SunSpec Alliance.


 

Designing batteries for easier recycling could avert a looming e-waste crisis

This article originally appeared in The Conversation. Written by Zheng Chen, UC San Diego professor of nanoengineering, and Darren H. S. Tan, PhD candidate in chemical engineering. 

 

San Diego, Calif., Oct. 22, 2020 -- As concern mounts over the impacts of climate change, many experts are calling for greater use of electricity as a substitute for fossil fuels. Powered by advancements in battery technology, the number of plug-in hybrid and electric vehicles on U.S. roads is increasing. And utilities are generating a growing share of their power from renewable fuels, supported by large-scale battery storage systems.

These trends, coupled with a growing volume of battery-powered phones, watches, laptops, wearable devices and other consumer technologies, leave us wondering: What will happen to all these batteries once they wear out?

Despite overwhelming enthusiasm for cheaper, more powerful and energy-dense batteries, manufacturers have paid comparatively little attention to making these essential devices more sustainable. In the U.S. only about 5% of lithium-ion batteries – the technology of choice for electric vehicles and many high-tech products – are actually recycled. As sales of electric vehicles and tech gadgets continue to grow, it is unclear who should handle hazardous battery waste or how to do it.

As engineers who work on designing advanced materials, including batteries, we believe it is important to think about these issues now. Creating pathways for battery manufacturers to build sustainable production-to-recycling manufacturing processes that meet both consumer and environmental standards can reduce the likelihood of a battery waste crisis in the coming decade.

Hazardous contents

Batteries pose more complex recycling and disposal challenges than metals, plastics and paper products because they contain many chemical components that are both toxic and difficult to separate.

Some types of widely used batteries – notably, lead-acid batteries in gasoline-powered cars – have relatively simple chemistries and designs that make them straightforward to recycle. The common nonrechargeable alkaline or water-based batteries that power devices like flashlights and smoke alarms can be disposed directly in landfills.

However, today’s lithium-ion batteries are highly sophisticated and not designed for recyclability. They contain hazardous chemicals, such as toxic lithium salts and transition metals, that can damage the environment and leach into water sources. Used lithium batteries also contain embedded electrochemical energy – a small amount of charge left over after they can no longer power devices – which can cause fires or explosions, or harm people that handle them.

Moreover, manufacturers have little economic incentive to modify existing protocols to incorporate recycling-friendly designs. Today it costs more to recycle a lithium-ion battery than the recoverable materials inside it are worth.

As a result, responsibility for handling battery waste frequently falls to third-party recyclers – companies that make money from collecting and processing recyclables. Often it is cheaper for them to store batteries than to treat and recycle them.

Recycling technologies that can break down batteries, such as pyrometallurgy, or burning, and hydrometallurgy, or acid leaching, are becoming more efficient and economical. But the lack of proper battery recycling infrastructure creates roadblocks along the entire supply chain.

For example, transporting used batteries over long distances to recycling centers would typically be done by truck. Lithium batteries must be packaged and shipped according to the U.S. Department of Transportation’s Class 9 hazardous material regulations. Using a model developed by Argonne National Laboratory, we estimate that this requirement increases transport costs to more than 50 times that of regular cargo.

A proposed procedure for recycling solid-state battery packs directly and harvesting their materials for reuse. Tan et al.

Safer and simpler

While it will be challenging to bake recyclability into the existing manufacturing of conventional lithium-ion batteries, it is vital to develop sustainable practices for solid-state batteries, which are a next-generation technology expected to enter the market within this decade.

A solid-state battery replaces the flammable organic liquid electrolyte in lithium-ion batteries with a nonflammable inorganic solid electrolyte. This allows the battery to operate over a much wider temperature range and dramatically reduces the risk of fires or explosions. Our team of nanoengineers is working to incorporate ease of recyclability into next-generation solid-state battery development before these batteries enter the market.

Conceptually, recycling-friendly batteries must be safe to handle and transport, simple to dismantle, cost-effective to manufacture and minimally harmful to the environment. After analyzing the options, we’ve chosen a combination of specific chemistries in next-generation all-solid-state batteries that meets these requirements.

Our design strategy reduces the number of steps required to dismantle the battery, and avoids using combustion or harmful chemicals such as acids or toxic organic solvents. Instead, it employs only safe, low-cost materials such as alcohol and water-based recycling techniques. This approach is scalable and environmentally friendly. It dramatically simplifies conventional battery recycling processes and makes it safe to disassemble and handle the materials.

Compared to recycling lithium-ion batteries, recycling solid-state batteries is intrinsically safer since they’re made entirely of nonflammable components. Moreover, in our proposed design the entire battery can be recycled directly without separating it into individual components. This feature dramatically reduces the complexity and cost of recycling them.

Our design is a proof-of-concept technology developed at the laboratory scale. It is ultimately up to private companies and public institutions, such as national laboratories or state-run waste facilities, to apply these recycling principles on an industrial scale.

Rules for battery recycling

Developing an easy-to-recycle battery is just one step. Many challenges associated with battery recycling stem from the complex logistics of handling them. Creating facilities, regulations and practices for collecting batteries is just as important as developing better recycling technologies. China, South Korea and the European Union are already developing battery recycling systems and mandates.

One useful step would be for governments to require that batteries carry universal tags, similar to the internationally recognized standard labels used for plastics and metals recycling. These could help to educate consumers and waste collectors about how to handle different types of used batteries.

Markings could take the form of an electronic tag printed on battery labels with embedded information, such as chemistry type, age and manufacturer. Making this data readily available would facilitate automated sorting of large volumes of batteries at waste facilities.

It is also vital to improve international enforcement of recycling policies. Most battery waste is not generated where the batteries were originally produced, which makes it hard to hold manufacturers responsible for handling it.

Such an undertaking would require manufacturers and regulatory agencies to work together on newer recycling-friendly designs and better collection infrastructure. By confronting these challenges now, we believe it is possible to avoid or reduce the harmful effects of battery waste in the future.

Portable and Noncontact Imaging System for Characterizing Composite Delamination

Professors Ken Loh and Hyonny Kim

San Diego, Calif., Oct. 22, 2020 -- Carbon fiber-reinforced polymer (CFRP) composites are widely used in various Naval aircraft structures, as well as in many civilian aerospace, automotive, and industrial structural components. However, composites can sustain complex damage modes, where even low-velocity impact can result in subsurface delamination. The aim of this research is to target the time-consuming elements of current Navy ultrasonic inspection methods and to demonstrate improved damage characterization in reduced time, while also lessening the burden on technicians to prepare, inspect, and report component damage. For this project funded by the Office of Naval Research, and in collaboration with NAVAIR ISSC North Island, the goal is to develop a noncontact, portable, nondestructive inspection system for imaging and characterizing delamination in CFRP composites. A prototype planar electrical capacitance tomography electrode array and imaging algorithm were developed. The system was used to image damaged CFRP specimens, which were subjected to hammer impact tests to induce subsurface delamination. The volumetric permittivity image, as obtained by the noncontact imaging system, revealed significant dielectric property changes near the point of impact. The results were compared with a corresponding ultrasonic C-scan image of the same specimen and confirmed the presence of subsurface damage at the center. Overall, the technology is expected to directly visualize the physical properties of the panel, as well as damage features embedded in the part.

Start-up receives up to $15 M to develop nanoparticle therapy for sepsis licensed from UC San Diego

San Diego, Calif., Oct. 21, 2020 -- San Diego-based Cellics Therapeutics, which was co-founded by UC San Diego nanoengineering Professor Liangfang Zhang, has received an award of up to $15 M from Boston-based accelerator CARB-X to develop a macrophage cellular nanosponge—nanoparticles cloaked in the cell membranes of macrophages—designed to treat sepsis.

CARB-X, which stands for Combating Antibiotic-Resistant Bacteria Biopharmaceutical Accelerator, is a global non-profit partnership dedicated to supporting early development of antibacterial R&D to address the rising threat of drug-resistant bacteria. 

In a paper published in Proceedings of the National Academy of Sciences in 2017, Zhang collaborated with the laboratory of Professor Victor Nizet at UC San Diego School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences to show that macrophage nanosponges can safely neutralize bacterial molecules that play a key role in sepsis, called endotoxins, as well as pro-inflammatory cytokines produced by the immune system. In this work, treatment with macrophage nanosponges protected mice from lethal sepsis caused by E. coli bacteria. The CARB-X award further validates the potential of macrophage cellular nanosponges to neutralize diverse inflammatory factors that play key biological roles in sepsis and other human diseases. As demonstrated in another recent study from the Zhang laboratory, this work could likewise position macrophage cellular nanosponges as a treatment for COVID-19 given its ability to neutralize SARS-CoV-2 and cytokine storm that the virus can cause.

The CARB-X funds will go to Cellics and the Nizet Laboratory to develop an appropriate animal model for bacterial sepsis to carefully assess the therapeutic potential of the nanosponges. Researchers will also identify the appropriate cell line to be used for manufacturing the nanosponges. The ultimate goal is to advance Cellics’ manufacturing capabilities and scale up production of the nanosponges. Cellics is currently on schedule to advance its lead product candidate, a red blood cell nanosponge for the treatment of MRSA pneumonia, to human clinical trials.

“Cellics is dedicated to the development of biomimetic nanomedicines to treat life threatening diseases. Our macrophage nanosponge technology leverages the natural receptors on human macrophage membranes to neutralize bacterial pore-forming toxins, endotoxins, and inflammatory cytokines that underlie sepsis,” said Dr. Steve Chen, president and chief medical officer, Cellics Therapeutics, Inc.

“Sepsis is a leading cause of death around the world that is made worse by the lack of effective preventatives and treatments for drug-resistant bacterial infections. Effective treatments are urgently needed,” said Erin Duffy, CARB-X R&D Chief. “CARB-X funds and supports early development of innovative antibiotics and other treatments that target the most dangerous drug-resistant bacteria. Cellics’ nanosponge product, if successful, could potentially transform the treatment of sepsis and save lives.”

Sepsis

Sepsis occurs when the body launches an uncontrolled immune response to an infection, triggering widespread inflammation that can lead to organ failure, septic shock and even death. The U.S. Centers for Disease Control and Prevention estimate that more than 1.5 million Americans get sepsis and about 250,000 die from this condition each year. A 2020 study in the leading medical journal The Lancet estimated that sepsis-related deaths represent 19.7% of all global deaths, exceeding cancer as a cause of human mortality.

Sepsis is usually treated with antibiotics. But while antibiotics can potentially eliminate sepsis-causing bacteria, they can’t keep inflammation in check.

Inflammation is triggered when macrophages recognize that the toxic endotoxins secreted by sepsis-causing bacteria are dangerous. In response, macrophages release proteins called pro-inflammatory cytokines, which in turn activate additional macrophages and other immune cells to produce more cytokines, setting off a dangerous domino effect of inflammation throughout the body.

Most recently, cytokine storm has emerged as a major issue in COVID-19, leading to organ injury and failure, and ultimately, if left unchecked, to death.

There is no currently approved treatment for sepsis. “To effectively manage sepsis, you need to manage this cytokine storm,” said Zhang.

Nanosponges stop the cascade that leads to sepsis by trapping endotoxins and pro-inflammatory cytokines onto their macrophage cell membranes, thus neutralizing them. The injected nanosponges vastly outnumber the organism’s own macrophages, ensuring that sepsis and a cytokine storm can be avoided. Also, since the nanosponges are covered in actual macrophage cell membranes, they can pass as the body’s own immune cells and circulate within the bloodstream without being evicted.

The nanosponge platform

Sepsis-fighting nanosponges are one example of the cell membrane cloaking technology pioneered by Zhang’s lab. His group develops new nanomedicine therapies by disguising nanoparticles as the body’s own cells. Previous examples include red blood cell nanosponges to combat and prevent MRSA infections;  nanoparticles cloaked in platelet cell membranes to repair wounded blood vessels; and cancer cell membrane cloaked nanoparticles to elicit multi-antigenic antitumor immunity for cancer immunotherapy.

In 2014, Zhang cofounded Cellics to further develop and commercialize this nanosponge technology. The company’s proprietary platform technology strips cell membranes of their intracellular contents and creates cellular nanosponges from these membranes to be leveraged as a therapeutic product. These nanosponges are designed to counteract diverse disease pathologies by acting as biomimetic decoys to sequester and neutralize biological molecules that would otherwise attack host cells.

Product development at Cellics currently emphasizes using nanosponges made of human red blood cell membranes and white blood cell membranes for the treatment of bacterial infections and inflammatory diseases. A similar working principle can be applied with membranes of other cell types, making cellular nanosponges suitable for large and diverse disease areas, including MRSA and COVID-19.

The mission of Cellics is to employ innovative biomimetic nanomedicines to address serious diseases with a high unmet medical need. The company’s initial primary focus at this time is on autoimmune and inflammatory diseases and difficult-to-treat infectious diseases. Cellics also aims to develop best-in-class vaccines for various diseases. The company is currently on schedule to advance its lead product candidate CTI-005 to human clinical trials for the treatment of MRSA pneumonia.

2021 Talanta Medal awarded to Professor Joseph Wang

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.

 

https://immunology.sciencemag.org/content/5/51/eaaz1974.abstract

 

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.

Affiliations:
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

 BIOENGINEERING

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

 

COMPUTER SCIENCE AND ENGINEERING

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

 

ELECTRICAL AND COMPUTER ENGINEERING

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

 

MECHANICAL AND AEROSPACE ENGINEERING

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

 

NANOENGINEERING

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

 

STRUCTURAL ENGINEERING

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

Tests

New anode material could lead to safer fast-charging batteries

Goto Flickr
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
ebateman@eng.ucsd.edu
858.336.1251

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

https://doi.org/10.1038/s41586-020-2609-x

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. 

Funding

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

https://doi.org/10.1038/s41467-020-17316-z

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.  

MesoMaterials

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
ebateman@eng.ucsd.edu

 

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.

Authors

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

Contributors

Qiangzhe Zhang, Jiarong Zhou and Anna N. Honko contributed equally to the work

Funding

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: 

http://friend.ucsd.edu/madsplit/

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

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
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
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

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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.  

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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