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Combining nanomaterials in 3D to build next-generation imaging devices

Man wearing a labcoat.
Oscar Vazquez-Mena. Photos by Erik Jepsen/University Communications

April 12, 2021 -- For years, two-dimensional nanomaterials just one or a few atoms thick have been all the rage in the world of materials science. Take graphene, for example. This one-layer sheet of carbon atoms yields a material that is hundreds of times stronger than steel, highly conductive and super-flexible.

Oscar Vazquez-Mena, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering, is taking these types of materials to the next dimension. His research focuses on integrating different nanoscale materials together in 3D to create an entirely new generation of devices for environmental monitoring, energy harvesting and biomedical applications.

“It opens up so many more possibilities for what we could do with our nanoengineering tools,” said Vazquez-Mena, who recently received a five-year, $500,000 CAREER Award through the National Science Foundation for one such project.

The project involves combining graphene with semiconducting nanoparticles called quantum dots to create devices that can “see” a broad range of different wavelengths of light, such as infrared and ultraviolet, that are invisible to the human eye. These devices, called multi-spectrum photodetectors, could enable cameras to take pictures of infections, poisonous gases and harmful radiation; check for food quality or contamination; and monitor air and water quality. They could also aid vision at night and when it’s foggy.

Closeup of an electronic chip.
Chips integrating graphene and quantum dots.

Vazquez-Mena’s approach would make these devices ultra-thin. “Because we are working with nanomaterials, we can in principle engineer very thin photodetectors on the order of one micrometer, which could easily be integrated into smartphones and other mobile devices for convenient deployment outside of the lab,” he said.

Imaging the brain with ultrasound

In another project, Vazquez-Mena is stacking nanostructures to build 3D arrays that can allow ultrasound to go through the skull and do non-invasive imaging and stimulation of the human brain. Such technology would be useful for treating brain disease and trauma without having to open the skull or insert wires and implants in the brain. It could also allow physicians to rapidly diagnose brain trauma in patients without having to perform costly MRI scans.

Getting ultrasound through the skull and into the brain is no easy task. The human skull is relatively thick and dense, so it either reflects or absorbs ultrasound waves before they can make it to the brain.

To get past this barrier, Vazquez-Mena is engineering a special kind of material—called a metamaterial—composed of nanostructures that can cancel the reflections created by the skull and essentially redirect ultrasound waves to go through it. The metamaterial is made of nanometers-thin membranes of silicon nitride and microscale acoustic cavities. Both components are arranged together in a 3D array that can enable the material to manipulate sound waves in ways that cannot be done with conventional materials.

“This is another example of building 3D constructions based on nanomaterials that achieve new and exciting properties,” Vazquez-Mena said.

This project is funded by a prestigious Director’s Fellowship awarded to Vazquez-Mena by the Defense Advanced Research Projects Agency (DARPA). The multidisciplinary work involves collaboration with UC San Diego mechanical and aerospace engineering professors James Friend and Nicholas Boechler, who are experts in ultrasound acoustics, and with UC San Diego rheumatology professor Monica Guma.

In 2018, Vazquez-Mena received a DARPA Young Faculty award (YFA) to pursue this project. The DARPA YFA recognizes rising stars in junior research positions who are pursuing basic science research and provides $500,000 of funding for a two-year period. As one of the program’s top-performing awardees, Vazquez-Mena was selected for the highly competitive DARPA Director’s Fellowship, which provides up to $500,000 of additional funding and support.

UC San Diego researchers developing COVID-19 vaccine technology -- no refrigeration or second dose needed

Understudied Mutations Have Big Impact on Gene Expression

Variable number tandem repeats modulate genes associated with Alzheimer's disease, obesity, cancer and other conditions

Vineet Bafna, a professor in the UC San Diego Department of Computer Science and Engineering and senior author on the paper

April 9, 2021-- An international team of researchers led by computer scientists at the University of California San Diego have identified 163 variable number tandem repeats (VNTRs) that actively regulate gene expression. In a paper published in Nature Communications this week, the researchers provide new insights into this understudied mechanism, how it may drive disease and other traits and could ultimately impact patient care.

VNTRs are common genomic variations that appear as repeated DNA sequences longer than six base pairs.

“VNTRs have been difficult to identify through sequencing information, particularly short reads,” said Vineet Bafna, a professor in the UC San Diego Department of Computer Science and Engineering and senior author on the paper. “We developed a fast computational method to identify these variations, which gave us a new lens to observe their potential impact on gene expression and disease.”

While VNTRs are one of the most common genetic variations, detecting them has been both challenging and expensive. As a result, genome-wide association studies have mostly ignored VNTRs, excluding a potentially rich repository of disease-causing mutations.

Using the new method they developed, researchers found more than 10,000 VNTRs in a group of 652 people. Of those, 163 changed the way genes were expressed in 46 different tissue types. Nearly half had a particularly strong impact on Alzheimer’s disease, familial cancers, diabetes and other conditions.

“We looked closely at these 163 VNTRs to understand their impact,” said UC San Diego computer science Ph.D. student Mehrdad Bakhtiari. “One was affecting expression levels of a gene called AS3MT, which has been implicated in schizophrenia. The tandem repeat controls gene expression and the expression affects the disease.”

A new neural-network based method

The new computational method,  called adVNTR-NN, rapidly finds VNTRs  in short read genomic sequencing data. Short read technology breaks up DNA samples into relatively small pieces and uses sophisticated algorithms to piece together complete sequences. Popularized by Illumina, short reads are the most common, and least expensive, form of next-generation sequencing.

“Our computational method runs quite fast and it works in the most cost-effective sequencing technologies,” said Bakhtiari, the first author on the paper. “So, it should be easy to scale and easy to use for people outside of research settings, for example, hospitals.”

Next steps

The authors have high confidence in these results, as 91% of the initial findings were validated in two other cohorts. However, there is still more work to do. The researchers want to better quantify the impact VNTRs have on specific genes, as well as determining whether there is indeed a causal link between certain VNTRs and the diseases they have been linked to.

“We’re learning more about the importance of complex and repetitive regions of the genome and the roles they play in human traits,” said Melissa Gymrek, assistant professor in the Computer Science and Engineering department and the School of Medicine and coauthor on the paper. “VNTRs  have been almost impossible to look at in most available sequencing datasets on a large scale.”

The team also wants to study specific conditions, such as autism spectrum disorder, to better understand patients’ VNTR profiles and how those influence their conditions.

“These findings open a whole new window to study the role VNTRs play in gene expression,” said Bafna. “Given that these sequences are physically larger than single nucleotide polymorphisms and are also quite prevalent, these efforts could eventually have a major impact on patient care.”

In addition to Bafna, Bakhtiari, and Gymrek, paper coauthors include Jonghun Park of the Computer Science and Engineering Department, Yuan-Chun Ding and Susan L. Neuhausen of the Beckman Research Institute of City of Hope, Sharona Shleizer-Burko of UC San Diego Department of Medicine, and Bjarni V. Halldórsson and Kári Stefánssonde of CODE Genetics, Reykjavik, Iceland.

 

 

testing

April 9, 2021

Diversifying the ranks of engineering faculty

UC San Diego Jacobs School of Engineering joins program to diversify engineering faculty

The University of California San Diego Jacobs School of Engineering has partnered with University of Michigan to strengthen a program that addresses the lack of diversity in the engineering academia. 

The program, NextProf Pathfinder, is a two-day program developed at Michigan Engineering and aimed at first and second-year PhD students, as well as students in masters programs, in an effort to keep them pursuing careers in academia.

It’s the newest program in a larger effort that began in 2012 as NextProf. To date, more than 144 women and people from underrepresented groups who attended its workshops have achieved tenure-track faculty positions. And UC San Diego Jacobs School of Engineering is the third institution to partner with Michigan Engineering on a NextProf program.

At workshops, participants hear from top faculty and deans from around the U.S. to gain a better understanding of academic life and how to achieve a position in it. They learn best practices in applying and networking for positions, how to set up a lab and what kind of work/life balance they can expect, for example. NextProf Pathfinder, designed for earlier-stage students, teaches participants what types of experiences they should seek out to best position themselves. The NextProf workshops for later-stage students and postdocs focus more on how to leverage those experiences and communicate about them.

The two schools will partner on the NextProf Pathfinder program going forward, with the institutions swapping hosting duties each year. This year, the program will be in Ann Arbor, from October 17-19. The conference will be in San Diego in 2022.

“One of the reasons I’m particularly excited about this partnership is that, given UCSD’s location and the demographics of that region of the country, it will make our workshops more accessible to Latinx graduate students,” said Lola Eniola-Adefoso, a U-M professor of chemical engineering and a University Diversity and Social Transformation Professor. “Latinx faculty members are dramatically underrepresented in academia and this is an important step toward changing that.”

For UC San Diego Jacobs School of Engineering, NextProf Pathfinder represents an important move forward in its broader efforts to create learning and research environments where all engineering and computer science students, staff and faculty thrive.
 

Karen L. Christman, Associate Dean for Faculty, Professor of Bioengineering, UC San Diego Jacobs School of Engineering 

“NextProf Pathfinder is one concrete step in a larger effort to create a broader academic culture where all students—and in particular students who are traditionally underrepresented in engineering—are empowered with the knowledge the networks, the role models and the momentum needed to establish fulfilling and meaningful careers,” said Karen Christman, associate dean for faculty and professor of bioengineering at UC San Diego Jacobs School of Engineering. “Critical to this project is ensuring that students who are traditionally underrepresented in engineering have all that they need to make the jump from graduate student to engineering professor and head of an independent lab. That’s what NextProf Pathfinder is designed to do.”

Engineering is a field which, despite efforts going back decades, remains stubbornly white and male. The number of female faculty members is trending upward in recent years, but only slowly. And the percentage of people from underrepresented groups in faculty positions has been flat for roughly two decades.

Such a monolithic engineering culture has repercussions for society-at-large, as we’ve seen illustrated recently by facial recognition technologies that aren’t accurate for Black faces, for example. Increasing the diversity of academic engineering researchers and educators is seen as an essential step in advancing technologies that don’t exacerbate inequities.

But the current lack of diversity in professor roles can make non-white and non-male candidates feel unwelcome or devalued, Eniola-Adefoso says. Each one that opts for something outside academia, in favor of a career where they feel more at home, can perpetuate the cycle.

NextProf Pathfinder is the newest part of the larger NextProf effort co-founded in 2012 by Alec D. Gallimore, the Robert J. Vlasic Dean of Engineering, the Richard F. and Eleanor A. Towner Professor, an Arthur F. Thurnau Professor, and a professor of aerospace engineering.

NextProf began as a program for third- to fifth-year PhD students and recent doctoral graduates from anywhere in the nation. Since that time it has expanded to three workshops:

  • NextProf Engineering, founded in 2015, is held every spring at U-M and is open to all engineering students and postdocs at U-M.
  • NextProf Pathfinder, founded in 2018, is open to first- and second-year PhD students and master’s students considering a PhD. Before a COVID-19 hiatus in 2020, it had welcomed 73 participants from 32 institutions in its first two years.
  • NextProf Nexus, an expansion of the original NextProf workshop, began in 2018 when the University of California, Berkeley joined as a partner and sponsoring institution. Georgia Tech joined the following year. Now, the three partner universities take turns hosting it.


Katherine Adler is a fifth-year PhD candidate in civil and environmental engineering at Cornell University. She was once a participant in both the NextProf Nexus and Pathfinder programs.

“The Nexus program provided more concrete tools to which I refer as I refine my faculty application materials,” Adler said. “After attending these workshops, I can better visualize my path to becoming a successful research faculty member and better understand the high expectations for faculty candidates.”

Testing

April 3, 2021

Test

UC San Diego Engineering Ranks #9 in U.S. News and World Report Best Engineering Schools Rankings

March 30, 2021 - For the second year in a row, the University of California San Diego Jacobs School of Engineering has ranked #9 in the nation in the influential U.S. News & World Report Rankings of Best Engineering Schools. 

This #9 ranking is up from #11 two years ago, #12 three years ago, #13 four years ago, and #17 five years ago.  

“The Jacobs School of Engineering has earned its ninth place among the nation’s most innovative, distinctive and prestigious engineering schools,” said UC San Diego Chancellor Pradeep K. Khosla. “UC San Diego’s engineers and computer scientists regularly collaborate with students, faculty and staff across our $1.4 billion dollar research enterprise. This unique cooperative, cross-discipline connectivity sparks discoveries and drives innovations that garner national and global recognition."

The Jacobs School of Engineering at UC San Diego leverages engineering and computer science for the public good through education, research and transfer of innovation to society. The #9 ranking brings welcome attention to the Jacobs School's work to create and strengthen interrelated education, research and innovation ecosystems.

“Ranking ninth in the nation is a tribute to the hard work, grit and excellence of our students, staff, faculty, industry partners, collaborators and friends," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. "I look at rankings as recognition rather than definition. It's wonderful to be recognized for some of the ways we are strengthening and growing as a school and as a community."

Research relevance

The UC San Diego Jacobs School of Engineering has launched 14 Agile Research Centers and Institutes since 2014. This effort has driven deeper collaborations within the Jacobs School and across the UC San Diego campus. It has also driven deeper interactions between Jacobs School research teams and collaborators in industry and government labs. The goal is to tackle fundamental, relevant challenges that no individual research lab or company is likely to solve alone. This process of taking on difficult, interdisciplinary challenges involving academia, industry and government provides engaging training and learning environments for Jacobs School of Engineering students. These students go on to graduate as an empowered innovation workforce. 

The most recent institute is a cross-campus collaboration, co-launched with the UC San Diego Division of Physical Sciences, called the UC San Diego Institute for Materials Discovery and Design. Researchers deeply involved in this Institute recently won a prestigious National Science Foundation (NSF) Materials Research Science and Engineering Center (MRSEC)

A few recent research results that have emerged from cross-disciplinary research projects tied to agile research centers and institutes include: a skin patch bringing us closer to wearable, all-in-one health monitor; a robot that doesn't need electronics; and a nano-scale particle for better COVID-19 tests.

San Diego regional innovation ecosystems

The fact that the UC San Diego Jacobs School of Engineering has established itself as a top-nine engineering school adds to San Diego's momentum as a world-class, well-rounded hub for technology and innovation. 

In addition to its #9 ranking, the Jacobs School of Engineering at UC San Diego is the largest engineering school on the U.S. West Coast, according to the latest enrollment data from ASEE. In Fall 2020, the Jacobs School enrolled 9,174 students. The Jacobs School has awarded nearly 15,000 degrees over the last 6 years. 

"The UC San Diego Jacobs School of Engineering is educating the innovation workforce the nation needs," said Pisano. "And more than ever, as a region, we are employing this innovation workforce here in San Diego."

Creating more and better environments for training this innovation workforce is one of the motivations behind Franklin Antonio Hall, which is UC San Diego's new engineering building. It is on schedule to open in Spring 2022.

Students from all across campus will take classes in Franklin Antonio Hall, which will serve as a national model for how to build innovation ecosystems with physical roots and virtual collaboration infrastructure with national and international impact. This is how engineering for the public good will get done in the future.

Bioengineering climbs to #3

In the same US News & World Report Rankings, the Department of Bioengineering at the UC San Diego Jacobs School of Engineering ranked #3 in the nation. This is up from #4 last year in the same ranking. Bioengineering at UC San Diego has ranked among the top four programs in the nation every year for more than a decade.

"The UC San Diego Department of Bioengineering has been inventing and re-inventing the field of bioengineering for more than 50 years, and it continues to take the field in new and exciting directions. I'm thrilled that we have moved up to #3 in the nation," said UC San Diego professor and chair of bioengineering Kun Zhang. "Some of the most influential work that helped launch the field of bioengineering happened here at UC San Diego. Today, our campus remains an incredibly open and vibrant environment. This enables us to recruit some of the most talented young investigators, and continue exploring the next frontiers and embracing non-traditional research directions in the realm of bioengineering."

Bioengineers from UC San Diego recently made headlines around the world for newly published work advancing an effort to develop a gene therapy for chronic pain that could offer a safer, non-addictive alternative to opioids

One of the newest bioengineering faculty at UC San Diego is Lingyan Shi, who is developing new methods and systems for recording what is happening within live cells

Jacobs School rankings

Highly ranked doctoral programs in engineering at the Jacobs School: bioengineering (3); computer engineering (14); electrical engineering (16); aerospace engineering (17); mechanical engineering (17); civil engineering (20).

The full listing of Jacobs School rankings:
2022 US News & World Report Rankings of Best Engineering Schools are here

 

New ways of looking inside living cells

From developing new imaging platforms, to asking new biological questions, and developing new disease diagnostics, UC San Diego bioengineering professor Lingyan Shi is pushing the boundaries of what's possible when we look inside living cells.

UC San Diego bioengineering professor Lingyan Shi

By Becky Ham

March 29, 2021-- Energy from an exquisitely targeted photon can vibrate the chemical bond of molecules like a pluck on a guitar string. Instead of music, these vibrational frequencies allow University of California San Diego bioengineering professor Lingyan Shi to see specific molecules within a living cell.

The cutting-edge imaging technologies used by Shi, who leads the Laboratory of Optical Bioimaging and Spectroscopy at UC San Diego, are a mouthful: stimulated Raman scattering (SRS) microscopy, multiphoton fluorescence microscopy (MPF), and resonance Raman microscopy (RRS). However, they all use light of specific wavelengths to probe chemical vibrational bonds in biological tissues.   

Different molecules such as fats, proteins, and DNA have distinct vibrational modes, and produce a subtle, yet distinct photo-spectral output. This allows researchers to identify these molecules with high chemical and spatial resolution. The powerful techniques don’t disturb living tissues, so they can be used across a variety of applications. For instance, SRS microscopy can generate a digital histological image of a biopsy in mere minutes, without the use of any chemical dyes and minimal sample preparation. Digital histology, which can mimic the staining seen in traditional histology  techniques (see figure 2), may make its way into the operating room as an intraoperative technique that saves time and improves surgical performance. Another application of Raman-based technologies includes the probing of metabolic dynamics and compositions. Various tissues and even diseases like cancer are marked by distinct metabolic changes. Understanding these dynamics will aid in early detection and better understanding of such diseases and nutrition. 

As one of the world’s leading experts in ultrafast optical imaging, the new Assistant Professor of Bioengineering at the UC San Diego Jacobs School of Engineering has no shortage of ideas about the potential of Raman-based technologies. “When we are developing a new technology, a new tool,” she says, “it will definitely inspire us to ask new biological questions.” 

Seeing without Disturbing

One of those questions is: how can we observe very small molecules in the body, without disturbing their natural functions? For her doctoral research, Shi had been tagging very small drug molecules with fluorescent probes to watch how they passed through the blood-brain barrier. But on the molecular scale, “if we consider size of the drug as a ping-pong ball, but the attached fluorescent particle was like another ping-pong ball or even bigger,” she explained. The bulky fluorescent label on the drugs was likely perturbing the drug’s behavior (such as its permeability and diffusion coefficient) in the body.

A 2014 seminar by her postdoctoral mentor Wei Min at Columbia University illustrated how stimulated Raman scattering microscopy could solve this problem. “At the time, I was very biological problem-oriented, and this was just a great tool for my research,” Shi says. “But when I got to know more and more about the technology, I realized that biological questions and imaging technology are mutually inspirational. It’s not unidirectional.”

Today, no single imaging technique reigns supreme in Shi’s lab. She and her students work with a variety of platforms, depending on the biological question at hand. Some techniques are better at seeing deep into living tissue, Shi explains, while others can probe a broader range of chemical bonds. She has also pioneered new ways of using heavy water to tag molecules with an isotope of hydrogen called deuterium (Fig. 3), to follow the metabolic activities under different physiological or pathological conditions. 

As mentioned, a powerful application centers on detecting metabolic changes that occur during tumor formation, when energy-hungry cancer cells metabolize differently than healthy cells. Shi recently led a study that combined several techniques to detect early metabolic changes that distinguish triple-negative breast cancer from less aggressive cancer types.

Triple-negative breast cancer predominantly affects Black and Latina women, and is difficult to detect early in the disease. “But the optical imaging technology we’re developing can tell you a lot about metabolic changes at a very early stage,” says Shi. “Early-stage diagnosis is critical to increase the survival rate among these women and reduce their cost of treatment.

“Homebuilt” Lab

Many of the imaging systems Shi and her students use are not commercially available yet, and they combine instrumentation and probes to fit their needs. “It’s like a homebuilt microscopy platform in my lab,” Shi says.

The researchers are always tinkering with the platforms to improve the image resolution and sensitivity to the optical signal. Shi holds 6 patents as a co-inventor related to optical imaging and is interested in commercializing or licensing some of these technologies.

“The application of these technologies is still in the infant stage,” she explains. “I think we need to do more educational presentations to show what kinds of information we can achieve, and to demonstrate how useful it is.”

Shi is excited to welcome research collaborators at UC San Diego, from biological scientists to genetics experts, and she is eager to mentor passionate students from underrepresented minorities in her lab, at every level from undergraduate to postdoc. 

“We’re very motivated here at UCSD, and the atmosphere is great. I enjoy seeing students become aware of something they didn’t know about before,” she says. “It’s a very happy moment.”

Shi joined the UC San Diego faculty in October 2019, and she says COVID-19 has made setting up a lab more difficult in some ways. At first it was challenging to source supplies, but lately she’s been more worried that the pandemic will keep her from throwing lab dinner parties and birthday celebrations that usually “bring us all together and make it feel like a family.”

“But I try to think positively about it,” Shi says. “This has also given me more time to think about the future research directions we want to explore.”

Research Expo 2021

Robot, heal thyself

Nanoengineers develop self-repairing microbots

March 17, 2021--Living tissue can heal itself from many injuries, but giving similar abilities to artificial systems, such as robots, has been extremely challenging. Now, researchers at the University of California San Diego reporting in Nano Letters have developed small, swimming robots that can magnetically heal themselves on-the-fly after breaking into two or three pieces. The strategy could someday be used to make hardier devices for environmental or industrial clean up, the researchers say. Watch a video of the self-healing swimmers here.

Scientists have developed small robots that can “swim” through fluids and carry out useful functions, such as cleaning up the environment, delivering drugs and performing surgery. Although most experiments have been done in the lab, eventually these tiny machines would be released into harsh environments, where they could become damaged.

Swimming robots are often made of brittle polymers or soft hydrogels, which can easily crack or tear. Senior author and UC San Diego nanoengineering professor Joseph Wang and colleagues wanted to design swimmers that could heal themselves while in motion, without help from humans or other external triggers.

The researchers made swimmers that were 2 cm long (a little less than an inch) in the shape of a fish that contained a conductive bottom layer; a rigid, hydrophobic middle layer; and an upper strip of aligned, strongly magnetic microparticles. The team added platinum to the tail, which reacted with hydrogen peroxide fuel to form oxygen bubbles that propelled the robot.

When the researchers placed a swimmer in a petri dish filled with a weak hydrogen peroxide solution, it moved around the edge of the dish. Then, they cut the swimmer with a blade, and the tail kept traveling around until it approached the rest of the body, reforming the fish shape through a strong magnetic interaction.

The robots could also heal themselves when cut into three pieces, or when the magnetic strip was placed in different configurations. The versatile, fast and simple self-healing strategy could be an important step toward on-the-fly repair for small-scale swimmers and robots, the researchers say.

Coronavirus circulated undetected months before first COVID-19 cases in Wuhan, China

Study dates emergence as early as October 2019; simulations suggest in zoonotic viruses in most cases die out naturally before causing a pandemic.

The SARS-CoV-2 virus under a microscope. Photo credit: National Institute of Allergy and Infectious Diseases

March 24, 2021--Using molecular dating tools and epidemiological simulations, bioinformaticians and computer scientists at the University of California San Diego, with colleagues at the University of Arizona and Illumina, Inc., estimate that the SARS-CoV-2 virus was likely circulating undetected for at most two months before the first human cases of COVID-19 were described in Wuhan, China, in late-December 2019.

Writing in the March 18, 2021 online issue of Science, they also note that their simulations suggest that the mutating virus dies out naturally more than three-quarters of the time without causing an epidemic.

“Our study was designed to answer the question of how long could SARS-CoV-2 have circulated in China before it was discovered,” said senior author Joel O. Wertheim, associate professor in the Division of Infectious Diseases and Global Public Health at the UC San Diego School of Medicine.

“To answer this question, we combined three important pieces of information: a detailed understanding of how SARS-CoV-2 spread in Wuhan before the lockdown, the genetic diversity of the virus in China, and reports of the earliest cases of COVID-19 in China. By combining these disparate lines of evidence, we were able to put an upper limit of mid-October 2019 for when SARS-CoV-2 started circulating in Hubei province.”

The epidemiological models were designed and run by Ph.D. student Jonathan Pekar, in the UC San Diego bioinformatics program, who is also part of Wertheim’s research group. 

Niema Moshiri, an assistant teaching professor in computer science at the Jacobs School, coded the simulations used in this Science paper. 

Niema Moshiri, an assistant teaching professor in the UC San Diego Department of Computer Science and Engineering, created all the code behind the epidemiological simulations, which can be found here and here on GitHub. The simulations are based on a robust framework for the simultaneous simulation of a transmission network and viral evolution, as well as simulation of sampling imperfections of the transmission network and of the sequencing process. 

Cases of COVID-19 were first reported in late December 2019 in Wuhan, located in the Hubei province of central China. The virus quickly spread beyond Hubei. Chinese authorities cordoned off the region and implemented mitigation measures nationwide. By April 2020, local transmission of the virus was under control but, by then, COVID-19 was pandemic with more than 100 countries reporting cases.

SARS-CoV-2 is a zoonotic coronavirus, believed to have jumped from an unknown animal host to humans. Numerous efforts have been made to identify when the virus first began spreading among humans, based on investigations of early-diagnosed cases of COVID-19. The first cluster of cases — and the earliest sequenced SARS-CoV-2 genomes — were associated with the Huanan Seafood Wholesale Market, but study authors say the market cluster is unlikely to have marked the beginning of the pandemic because the earliest documented COVID-19 cases had no connection to the market.

Regional newspaper reports suggest COVID-19 diagnoses in Hubei date back to at least Nov. 17, 2019, suggesting the virus was already actively circulating when Chinese authorities enacted public health measures.

In the new study, researchers coupled epidemiological simulations with molecular clock evolutionary analyses to try to home in on when the first, or index, case of SARS-CoV-2 occurred. “Molecular clock” is a term for a technique that uses the mutation rate of genes to deduce when two or more life forms diverged — in this case, when the common ancestor of all variants of SARS-CoV-2 existed, estimated in this study to as early as mid-November 2019.

Molecular dating of the most recent common ancestor is often taken to be synonymous with the index case of an emerging disease. However, said co-author Michael Worobey, professor of ecology and evolutionary biology at University of Arizona: “The index case can conceivably predate the common ancestor — the actual first case of this outbreak may have occurred days, weeks or even many months before the estimated common ancestor. Determining the length of that ‘phylogenetic fuse’ was at the heart of our investigation.”

Based on this work, the researchers estimate that the median number of persons infected with SARS-CoV-2 in China was less than one until Nov. 4, 2019. Thirteen days later, it was four individuals, and just nine on December 1, 2019. The first hospitalizations in Wuhan with a condition later identified as COVID-19 occurred in mid December.

Study authors used a variety of analytical tools to model how the SARS-CoV-2 virus may have behaved during the initial outbreak and early days of the pandemic when it was largely an unknown entity and the scope of the public health threat not yet fully realized.

These tools included epidemic simulations based on the virus’s known biology, such as its transmissibility and other factors. In just 29.7 percent of these simulations was the virus able to create self-sustaining epidemics. In the other 70.3 percent, the virus infected relatively few persons before dying out. The average failed epidemic ended just eight days after the index case.

“Typically, scientists use the viral genetic diversity to get the timing of when a virus started to spread,” said Wertheim. “Our study added a crucial layer on top of this approach by modeling how long the virus could have circulated before giving rise to the observed genetic diversity.”

“Our approach yielded some surprising results. We saw that over two-thirds of the epidemics we attempted to simulate went extinct. That means that if we could go back in time and repeat 2019 one hundred times, two out of three times, COVID-19 would have fizzled out on its own without igniting a pandemic. This finding supports the notion that humans are constantly being bombarded with zoonotic pathogens.”

Wertheim noted that even as SARS-CoV-2 was circulating in China in the fall of 2019, the researchers’ model suggests it was doing so at low levels until at least December of that year.

“Given that, it’s hard to reconcile these low levels of virus in China with claims of infections in Europe and the U.S. at the same time,” Wertheim said. “I am quite skeptical of claims of COVID-19 outside China at that time.”

The original strain of SARS-CoV-2 became epidemic, the authors write, because it was widely dispersed, which favors persistence, and because it thrived in urban areas where transmission was easier. In simulated epidemics involving less dense rural communities, epidemics went extinct 94.5 to 99.6 percent of the time.

The virus has since mutated multiple times, with a number of variants becoming more transmissible.

“Pandemic surveillance wasn’t prepared for a virus like SARS-CoV-2,” Wertheim said. “We were looking for the next SARS or MERS, something that killed people at a high rate, but in hindsight, we see how a highly transmissible virus with a modest mortality rate can also lay the world low.”

Konrad Scheffler, Illumina, Inc. was also a co-author.

Funding for this research came, in part, from the National Institutes of Health (grants AI135992, AI136056, T15LM011271), the Google Cloud COVID-19 Research Credits Program, the David and Lucile Packard Foundation, the University of Arizona and the National Science Foundation (grant 2028040).


 

Welcome to the Jacobs School, Class of 2025

Why Commercialization of Carbon Capture and Sequestration has Failed and How it Can Work

Credibility of incentives - a function of policy and politics - is a key, researchers say

Despite extensive support, 80 percent of projects that seek to commercialize carbon capture and sequestration technology have ended in failure. Credit: Coatesy/iStock

March 22, 2021 - There are 12 essential attributes that explain why commercial carbon capture and sequestration projects succeed or fail in the U.S., University of California San Diego researchers say in a recent study published in Environmental Research Letters

The paper was coauthored by Jacobs School alumnus Ryan Hanna, now an assistant research scientist at UC San Diego. 

Carbon capture and sequestration (CCS) has become increasingly important in addressing climate change. The Intergovernmental Panel on Climate Change (IPCC) relies greatly on the technology to reach zero carbon at low cost. Additionallyit is among the few low-carbon technologies in President Joseph R. Biden’s proposed $400 billion clean energy plan that earns bipartisan support. 

In the last two decades, private industry and government have invested tens of billions of dollars to capture CO2 from dozens of industrial and power plant sources. Despite the extensive support, these projects have largely failed. In fact, 80 percent of projects that seek to commercialize carbon capture and sequestration technology have ended in failure. 

“Instead of relying on case studies, we decided that we needed to develop new methods to systematically explain the variation in project outcome of why do so many projects fail,” said  lead author Ahmed Y. Abdulla, research fellow with UC San Diego’s Deep Decarbonization Initiative and assistant professor of mechanical and aerospace engineering at Carleton University. “Knowing which features of CCS projects have been most responsible for past successes and failures allows developers to not only avoid past mistakes, but also identify clusters of existing, near-term CCS projects that are more likely to succeed.”

He added, “By considering the largest sample of U.S. CCS projects ever studied, and with extensive support from people who managed these projects in the past, we essentially created a checklist of attributes that matter and gauged the extent to which each does.”

Credibility of incentives and revenues is key

The researchers found that the credibility of revenues and incentives—functions of policy and politics—are among the most important attributes, along with capital cost and technological readiness, which have been studied extensively in the past.

“Policy design is essential to help commercialize the industry because CCS projects require a huge amount of capital up front,” the authors, comprised of an international team of researchers, note. 

The authors point to existing credible policies that act as incentives, such as the 2018 expansion of the 45Q tax credit. It provides companies with a guaranteed revenue stream if they sequester CO2 in deep geologic repositories.

The only major incentive companies have had thus far to recoup their investments in carbon capture is by selling the CO2 to oil and gas companies, who then inject it into oil fields to enhance the rate of extraction—a process referred to as enhanced oil recovery.

The 45Q tax credit also incentivizes enhanced oil recovery, but at a lower price per CO2 unit, compared to dedicated geologic CO2 storage.   

Beyond selling to oil and gas companies, CO2 is not exactly a valuable commodity, so few viable business cases exist to sustain a CCS industry on the scale that is necessary or envisioned to stabilize the climate.

“If designed explicitly to address credibility, public policy could have a huge impact on the success of projects,” said David Victor, co-lead of the Deep Decarbonization Initiative and professor of industrial innovation at UC San Diego’s School of Global Policy and Strategy.

Results with expert advice from project managers with real-world experience

While technological readiness has been studied extensively and is essential to reducing the cost and risk of CCS, the researchers looked beyond the engineering and engineering economics to determine why CCS continues to be such a risky investment. Over the course of two years, the researchers analyzed publicly available records of 39 U.S. projects and sought expertise from CCS project managers with extensive, real-world experience. 

They identified 12 possible determinants of project outcomes, which are technological readiness, credibility of incentives, financial credibility, cost, regulatory challenges, burden of CO2 removal, industrial stakeholder opposition, public opposition, population proximity, employment impact, plant location, and the host state’s appetite for fossil infrastructure development.

To evaluate the relative influence of the 12 factors in explaining project outcomes, the researchers built two statistical models and complemented their empirical analysis with a model derived through expert assessment.

The experts only underscored the importance of credibility of revenues and incentives; the vast majority of successful projects arranged in advance to sell their captured CO2 for enhanced oil recovery. They secured unconditional incentives upfront, boosting perceptions that they were resting on secure financial footing.

The authors conclude models in the study—especially when augmented with the structured elicitation of expert judgment—can likely improve representations of CCS deployment across energy systems. 

“Assessments like ours empower both developers and policymakers,” the authors write. “With data to identify near-term CCS projects that are more likely to succeed, these projects will become the seeds from which a new CCS industry sprouts.”

Co-authors include Jacobs School alumnus Ryan Hanna, assistant research scientist at UC San Diego; Kristen R Schell, assistant professor at Carleton University; and Oytun Babacan, research fellow at Imperial College London. 

Artificial neuron device could shrink energy use and size of neural network hardware

Goto Flickr
SEM image of the artificial neuron device. Images courtesy of Nature Nanotechnology

March 18, 2021 -- Training neural networks to perform tasks, such as recognizing images or navigating self-driving cars, could one day require less computing power and hardware thanks to a new artificial neuron device developed by researchers at the University of California San Diego. The device can run neural network computations using 100 to 1000 times less energy and area than existing CMOS-based hardware.

Researchers report their work in a paper published Mar. 18 in Nature Nanotechnology.

Neural networks are a series of connected layers of artificial neurons, where the output of one layer provides the input to the next. Generating that input is done by applying a mathematical calculation called a non-linear activation function. This is a critical part of running a neural network. But applying this function requires a lot of computing power and circuitry because it involves transferring data back and forth between two separate units—the memory and an external processor.

Now, UC San Diego researchers have developed a nanometer-sized device that can efficiently carry out the activation function.

“Neural network computations in hardware get increasingly inefficient as the neural network models get larger and more complex,” said corresponding author Duygu Kuzum, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering. “We developed a single nanoscale artificial neuron device that implements these computations in hardware in a very area- and energy-efficient way.”

The new study was performed as a collaboration between UC San Diego researchers from the Department of Electrical and Computer Engineering (led by Kuzum, who is part of the university's Center for Machine-Integrated Computing and Security) and a DOE Energy Frontier Research Center (EFRC led by physics professor Ivan Schuller), which focuses on developing hardware implementations of energy-efficient artificial neural networks.

The device implements one of the most commonly used activation functions in neural network training called a rectified linear unit. What’s particular about this function is that it needs hardware that can undergo a gradual change in resistance in order to work. And that’s exactly what the UC San Diego researchers engineered their device to do—it can gradually switch from an insulating to a conducting state, and it does so with the help of a little bit of heat.

This switch is what’s called a Mott transition. It takes place in a nanometers-thin layer of vanadium dioxide. Above this layer is a nanowire heater made of titanium and gold. When current flows through the nanowire, the vanadium dioxide layer slowly heats up, causing a slow, controlled switch from insulating to conducting.

Chips on a circuit board
Left: Closeups of the synaptic device array (top) and the activation, or neuron, device array (bottom). Right: A custom printed circuit board built with the two arrays.

“This device architecture is very interesting and innovative,” said first author Sangheon Oh, an electrical and computer engineering Ph.D. student in Kuzum's lab. Typically, materials in a Mott transition experience an abrupt switch from insulating to conducting because the current flows directly through the material, he explained. “In this case, we flow current through a nanowire on top of the material to heat it and induce a very gradual resistance change.”

To implement the device, the researchers first fabricated an array of these so-called activation (or neuron) devices, along with a synaptic device array. Then they integrated the two arrays on a custom printed circuit board and connected them together to create a hardware version of a neural network.

The researchers used the network to process an image—in this case, a picture of Geisel Library at UC San Diego. The network performed a type of image processing called edge detection, which identifies the outlines or edges of objects in an image. This experiment demonstrated that the integrated hardware system can perform convolution operations that are essential for many types of deep neural networks.

A building shaped like an upside-down pyramid
Image of Geisel Library used for edge detection (left). Output of the convolution operations for the lateral filter (center) and vertical filter (right).

The researchers say the technology could be further scaled up to do more complex tasks such as facial and object recognition in self-driving cars. With interest and collaboration from industry, this could happen, noted Kuzum.

“Right now, this is a proof of concept,” Kuzum said. “It’s a tiny system in which we only stacked one synapse layer with one activation layer. By stacking more of these together, you could make a more complex system for different applications.”

Paper: “Energy Efficient Mott Activation Neuron for Full Hardware Implementation of Neural Networks.”

This work was supported by the Office of Naval Research, Samsung Electronics, the National Science Foundation, the National Institutes of Health, a Qualcomm Fellowship and the U.S. Department of Energy, Office of Science through an Energy Frontier Research Center.

How to speed up muscle repair

Drawing of muscle fiber
Illustration of skeletal muscle fiber. Credit: Kavitha Mukund

March 17, 2021 -- A study led by researchers at the University of California San Diego Jacobs School of Engineering provides new insights for developing therapies for muscle disease, injury and atrophy. By studying how different pluripotent stem cell lines build muscle, researchers have for the first time discovered how epigenetic mechanisms can be triggered to accelerate muscle cell growth at different stages of stem cell differentiation.

The findings were published Mar. 17 in Science Advances.

“Stem cell-based approaches that have the potential to aid muscle regeneration and growth would improve the quality of life for many people, from children who are born with congenital muscle disease to people who are losing muscle mass and strength due to aging,” said Shankar Subramaniam, distinguished professor of bioengineering, computer science and engineering, and cellular and molecular medicine at UC San Diego and lead corresponding author on the study. “Here, we have discovered that specific factors and mechanisms can be triggered by external means to favor rapid growth.”

The researchers used three different human induced pluripotent stem cell lines and studied how they differentiate into muscle cells. Out of the three, one cell line grew into muscle the fastest. The researchers looked at what factors made this line different from the rest, and then induced these factors in the other lines to see if they could accelerate muscle growth.

They found that triggering several epigenetic mechanisms at different time points sped up muscle growth in the “slower” pluripotent stem cell lines. These include inhibiting a gene called ZIC3 at the outset of differentiation, followed by adding proteins called beta-catenin transcriptional cofactors later on in the growth process.

“A key takeaway here is that all pluripotent stem cells do not have the same capacity to regenerate,” Subramaniam said. “Identifying factors that will prime these cells for specific regeneration will go a long way in regenerative medicine.”

Next, the team will explore therapeutic intervention, such as drugs, that can stimulate and accelerate muscle growth at different stages of differentiation in human induced pluripotent stem cells. They will also see whether implanting specific pluripotent stem cells in dystrophic muscle can stimulate new muscle growth in animals. Ultimately, they would like to see if such a stem cell-based approach could regenerate muscle in aging humans.

Paper: “Temporal mechanisms of myogenic specification in human induced pluripotent stem cells.” Co-authors of the study include Priya Nayak, UC San Diego; Alexandre Colas, Sanford Burnham Prebys Medical Discovery Institute; Mark Mercola, Stanford University; and Shyni Varghese, Duke University.

Defending human-robot teams against adversaries goal of computer science grant

Computer science professor Kamalika Chaudhuri is part of a MURI grant going to multiple institutions. Her work is on Cohesive and Robust Human-Bot Cybersecurity Teams.  

March 16, 2021-- UC San Diego computer science professor Kamalika Chaudhuri is part of a multi-university team that has won a prestigious US Department of Defense Multidisciplinary University Research Initiative (MURI) Award to develop rigorous methods for robust human-machine collaboration against adversaries. 

Chaudhuri will receive $750,000 to fund her research on the project titled Cohesive and Robust Human-Bot Cybersecurity Teams, which aims to develop rigorous parameters for Human-Bot Cybersecurity teams with the goal of developing a cohesive team that is not vulnerable to active human and machine learning (ML) adversaries. 

“We now know how to develop machine learning methods that are robust to adversaries, yet in many applications, humans work in coordination with machine learning software, and adversaries can still disrupt the process,” said Chaudhuri, whose research interests lie in the foundations of trustworthy machine learning. “This project will investigate in detail how that can happen, and how we can design algorithms and tools to be robust to these adversaries."

Cybersecurity is the most challenging task that the Department of Defense (DoD) faces today. A typical human analyst in a cybersecurity task has to deal with a plethora of information, such as intrusion logs, network flows, executables, and provenance information for files. Real cybersecurity scenarios are even more challenging: an active adversarial environment, with large amounts of information and techniques that neither humans nor machines can handle alone. 

In addition to human analysts, machine learning (ML) bots have become part of these cybersecurity teams. ML bots reduce the burden on human analysts by filtering information, thus freeing up cognitive resources for tasks related to the high-level mission.

The team will first focus on ways to build trust within the HBCT by investigating techniques to produce explanations for the human analysts of how the ML bots work. These explanations will be presented in an appropriate vocabulary for the analysts and will be specific to the task of the HBCT, providing valuable insight for the human analysts so they will trust the ML model and reduce manual effort.

The group will also research how analysts integrate information to arrive at decisions, as well as their mental models of how bots operate. This will allow them to take a step towards automating the decision-making process. Moreover, the mental model can help design robust ML models that are more specific to the task of the HBCT.

Adaptability will be key as well. Human-bot team dynamics change as new adversaries with different capabilities arise, and adversaries adapt in response to new team strategies. Adversaries interactive learning must be taken into account to develop methods for the entire team to adaptto adversaries in an interactive manner.

Chaudhuri and her research group will develop methods that can improve generalization capabilities of current machine learning methods to rare inputs, bolster the quality of explanations provided by them and design principled solutions for adversarial robustness. 

“This will build on some of our prior and current work in the area of interactive learning, as well as principled methods for defending against adversaries,” she said. 

Since its inception in 1985, the tri-Service MURI program has convened teams of investigators with the hope that collective insights drawn from research across multiple disciplines could facilitate the advancement of newly emerging technologies and address the Department’s unique problem sets. Complementing the Department’s single-investigator basic research grants, the highly competitive MURI program has made immense contributions to both national defense and society at large. Innovative technological advances from the MURI program help drive and accelerate current and future military capabilities and find multiple applications in the commercial sector.

Seven universities comprise the research team, which is led by Somesh Jha at the University of Wisconsin-Madison: Carnegie Mellon University, University of California San Diego, Pennsylvania State University, University of Melbourne, Macquarie University, and University of Newcastle. Benjamin Rubinstein of the University of Melbourne will lead the Australian team, or AUSMURI, funded by the Australian Government. The team brings together diverse expertise spanning computer security, machine learning, psychology, decision sciences, and human-computer interaction

 


 

Researchers at UC San Diego Unveil New Interactive Web Tool for Visualizing Large-Scale Phylogenetic Trees

March 17, 2021

The proliferation of sequencing technologies and an ever-increasing focus on ‘omic studies over the past several years have spawned massive quantities of data and many tools to process and analyze the results. As these tools have evolved, so has the need for even greater scale and the ability to visualize complex data sets in more efficient ways.

Born of these needs for advancement, a team of researchers with the Center for Microbiome Innovation (CMI) at the University of California San Diego (UC San Diego), led by Kalen Cantrell and Marcus W. Fedarko, unveiled EMPress, a new interactive visualization tool, in an article published in mSystems on March 16, 2021. The paper, entitled “EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets,” showcases the tool’s functionality, versatility, and scalability, and explores some of the potential applications in visualization and data analysis.

"Although there are many excellent existing tools for visualizing trees, we wanted to create a tool that could be used within a web browser and could scale to really large trees," Fedarko remarked when discussing the development process. "Another motivation was that there were many custom features that no existing tool, to our knowledge, supported - for example, the ability to interactively link samples in an ordination with a phylogenetic tree, showing the sequences contained within each sample, or going the opposite way, the samples containing a given sequence."

Aside from interactively integrating ordinations with trees, EMPress also introduces the ability to animate a tree’s changes over time. While other tools have included a temporal dimension to trees, the ability to animate the tree alongside an ordination is a novel feature that the team believes will enhance the exploratory analysis of ‘omic data sets.

What began as an undergraduate project at UC San Diego’s Early Research Scholars Program has since grown into a collaboration that spans both academia and industry. The team at CMI has worked closely with IBM Research’s Artificial Intelligence for Healthy Living Center throughout the process, as well as researchers at the Simons Foundation, Cornell University, and Justus Liebig University.

Developing a tool that was not only web-based but capable of storing, processing, and visualizing such large phylogenetic trees presented numerous challenges. As the scale of microbiome and other ‘omic studies has continued to grow, so too has the technical complexity required to accommodate and analyze the large, complex data sets those studies produce.

FIG 1 Earth Microbiome Project paired phylogenetic tree (including 756,377 nodes) and unweighted UniFrac ordination (including 26,035 samples). (a) Graphical depiction of EMPress’ unified interface with fragment insertion tree (left) and unweighted UniFrac sample ordination (right). Tips are colored by their phylum-level taxonomic assignment; the barplot layer is a stacked barplot describing the proportions of samples containing each tip summarized by level 1 of the EMP ontology. Inset shows summarized sample information for a selected feature. The ordination highlights the two samples containing the tip selected in the tree enlarged to show their location. (b) Subset of EMP samples with pH information: the inner barplot ring shows the phylum-level taxonomic assignment, and the outer barplot ring represents the mean pH of all the samples where each tip was observed. (c) pH distributions summarized by phylum-level assignment with median pH indicated by dotted lines. Interactive figures can be accessed at https://github.com/knightlab-analyses/empress-analyses.

"We resolved some of these issues by creating our own custom WebGL, shaders which are capable of visualizing millions of points, and implementing high-performance data structures such as the balanced parentheses tree that helped drastically reduce the memory footprint of EMPress," according to Cantrell. As the code has been refined and optimized through several phases of development, it has enabled the analysis of larger and larger data sets, including a tree with over 750,000 nodes. 

While the article in mSystems represents the tool’s formal unveiling, it has already seen use in several studies and applications. Researchers at the CMI utilized EMPress in their recently published analysis of the composition and microbial load of the human oral microbiome. Additionally, epidemiologists with UC San Diego’s Return to Learn program have been using the tool to help manage the university’s response to the COVID-19 pandemic. These applications have provided critical feedback and facilitated improvements to continue streamlining the analyses for which EMPress is designed.

As development continues, there are several planned features, including the ability to explore time-series data, potential anomaly detection, implementing support for annotating various types of data, and further improving performance to allow for larger data sets. The tool’s source code is available on GitHub, and the team is eager to see how their peers expand upon their work.

“Just as EMPress builds on the many existing tree visualization tools in the literature (iTOL, PHYLOViZ, Anvi'o, SigTree, FigTree, ggtree, TopiaryExplorer, MicroReact, Archaeopteryx, etc.), we're sure that other tools will pop up soon enough that build on the concepts used in EMPress -- we look forward to seeing how the landscape of these tools changes in the future,” Fedarko added.

 

FIG 2 EMPress is a versatile exploratory analysis tool adaptable to various ‘omics data types. (a) RoDEO differential abundance of microbial functions from metatranscriptomic sequencing of COVID-19 patients (n = 8) versus community-acquired pneumonia patients (n = 25) and versus healthy control subjects (n = 20). The tree represents the four-level hierarchy of the KEGG enzyme codes. The barplot depicts significantly differentially abundant features (P , 0.05) in COVID-19 patients. Clicking on a tip produces a pop-up insert tabulating the name of the feature, its hierarchical ranks, and any feature annotations. (b) Global FoodOmics Project LC-MS data. Stacked barplots indicate the proportions of samples (n = 70) (stratified by food) containing the tips in an LC-MS Qemistree of food-associated compounds, with tip nodes colored by their chemical superclass. (c) De novo tree constructed from 16S rRNA sequencing data from 32 oral microbiome samples. Samples were taken before (n = 16) and after (n = 16) subjects (n = 10) brushed their teeth; each barplot layer represents a different differential abundance method’s measure of change between before- and after-brushing samples. The innermost layer shows estimated log-fold changes produced by Songbird, the middle layer shows effect sizes produced by ALDEx2, and the outermost layer shows the W-statistic values produced by ANCOM (see Materials and Methods). The tree is colored by tip nodes’ phylum-level taxonomic classifications. Interactive figures can be accessed at https://github.com/knightlab-analyses/empress-analyses.

 

Additional co-authors include Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Mehrbod Estaki, Qiyun Zhu, Erfan Sayyari, George Armstrong, Anupriya Tripathi, Julia M. Gauglitz, Clarisse Marotz, Nathaniel L. Matteson, Cameron Martino, Se Jin Song, Austin D. Swafford, Pieter C. Dorrestein, Kristian G. Andersen, Yoshiki Vázquez-Baeza, and Rob Knight, all at UC San Diego; Stefan Janssen at Justus Liebig University; Niina Haiminen and Laxmi Parida at the IBM Thomas J. Watson Research Center; Kristen L. Beck and Ho-Cheol Kim at the IBM Almaden Research Center; James T. Morton at the Simons Foundation; Jon G. Sanders at Cornell University; and Anna Paola Carrieri at IBM Research Europe.

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

Writing a New Chapter on Innovation

UC San Diego establishes local chapter of National Academy of Inventors

 

March 17, 2021 - The University of California San Diego is the first University of California campus to establish a chapter of the National Academy of Inventors (NAI), a move that will help the campus build and sustain a more robust innovation ecosystem. This designation provides tools and resources to help UC San Diego raise the profile of its inventions and technologies, encourage innovations on campus and educate student entrepreneurs.

“Invention is in our DNA,” said Chancellor Pradeep K. Khosla, an NAI fellow who was recognized for his work in enhancing cybersecurity. “Since 2014, UC San Diego has seen a 153% increase in licensed startups, a 120% increase in industry funding, and a 78% increase in licenses. Just last year, our research program generated more than 500 new invention disclosures, including over 200 new patents. Establishing a local NAI chapter will help further develop our students, create stronger connections to the region’s flourishing community of inventors, and showcase UC San Diego’s growing research prowess.”

An NAI chapter designation gives the UC San Diego community access to networks and tools that can facilitate inventorship and entrepreneurism in students, faculty and staff. Chapter members will be able to participate in annual meetings, network with inventors around the world and meet participants from organizations like the U.S. Patent and Trademark Office. They’ll also be able to submit articles to NAI’s journal Technology and Innovation.

The chapter will have a faculty advisory board to discuss metrics for success and programming opportunities, as well as strategic priorities for the coming year. The inaugural board includes faculty from across campus, including Health Sciences, the Rady School of Management and the Jacobs School of Engineering to ensure representation across UC San Diego’s innovation ecosystem.

Innovation programming helps faculty and students potentially turn research into products, such as this wearable patch that can heat or cool the skin. (cr: David Baillot/UC San Diego Jacobs School of Engineering)

“Students, staff and faculty from all parts of campus will be most welcome in the new chapter," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. "Speaking as an engineer, educator and inventor, I know firsthand that we get the best solutions when we look at challenges from all directions. We need everyone at the innovation and invention table.” 

Pisano was inducted into the National Academy of Inventors in 2019  based on the impact of medical devices that treat arterial diseases, currently being commercialized via a startup company.

While NAI fellows are inducted into the academy through a formal nomination process, chapter members will apply locally through UC San Diego’s Office of Innovation and Commercialization. Students will have the unique opportunity to become honorary members and have access to mentorship and professional development resources.

TODAY’S INNOVATION FOR TOMORROW’S WORLD

Student entrepreneurs are supported by programs like The Basement and will be able to join the NAI chapter as honorary members. (cr: Erik Jepsen/UC San Diego)

The university’s commitment to innovation and entrepreneurship runs deep and goes beyond the campus borders. While programs like Institute for the Global EntrepreneurThe Basement and StartR at the Rady School of Management support students and faculty in their startup endeavors, capital projects like the Design and Innovation Building and Downtown Park & Market “The U” promise to strengthen the connection between the campus and industry partners, government entities and community members.

“UC San Diego prioritizes innovation, technology transfer and entrepreneurship for the sustained economic prosperity of the region,” said Associate Vice Chancellor for Innovation and Commercialization Paul Roben. “Our recent designation as an NAI Chapter will allow us to connect with world-renowned inventors, while nurturing and mentoring innovators, business owners and the workforce of tomorrow.” 

Upcoming events supporting and celebrating campus innovation include the grand opening of the Design and Innovation Building, a Student Inventor and Startup Showcase focused on “Enriching Human Life and Society,” and the NAI Investor Awards.

“Launching an official NAI Chapter is an amazing step at creating a united innovation ecosystem on campus and within your community to celebrate and share the importance of academic innovation and invention,” said NAI Director Jayde Stewart. “The NAI is honored and proud to have you as members and look forward to celebrating the successes of your students and faculty innovators through your local Chapter.”

The National Academy of Inventors was founded in 2010 to recognize and encourage inventors, enhance the visibility of academic technology, and educate and mentor innovation-minded students. NAI boasts over 1,000 fellows and 250 institutions worldwide. In total, the fellows have formed more than 9,000 companies and generated over $190 billion from nearly 11,000 licensed inventions. UC San Diego is home to 13 NAI fellows, including current and emeritus faculty.

Writing a New Chapter on Innovation

UC San Diego establishes local chapter of National Academy of Inventors

March 17, 2021--The University of California San Diego is the first University of California campus to establish a chapter of the National Academy of Inventors (NAI), a move that will help the campus build and sustain a more robust innovation ecosystem. This designation provides tools and resources to help UC San Diego raise the profile of its inventions and technologies, encourage innovations on campus and educate student entrepreneurs.

“Invention is in our DNA,” said Chancellor Pradeep K. Khosla, an NAI fellow who was recognized for his work in enhancing cybersecurity. “Since 2014, UC San Diego has seen a 153% increase in licensed startups, a 120% increase in industry funding, and a 78% increase in licenses. Just last year, our research program generated more than 500 new invention disclosures, including over 200 new patents. Establishing a local NAI chapter will help further develop our students, create stronger connections to the region’s flourishing community of inventors, and showcase UC San Diego’s growing research prowess.”

An NAI chapter designation gives the UC San Diego community access to networks and tools that can facilitate inventorship and entrepreneurism in students, faculty and staff. Chapter members will be able to participate in annual meetings, network with inventors around the world and meet participants from organizations like the U.S. Patent and Trademark Office. They’ll also be able to submit articles to NAI’s journal Technology and Innovation.

The chapter will have a faculty advisory board to discuss metrics for success and programming opportunities, as well as strategic priorities for the coming year. The inaugural board includes faculty from across campus, including Health Sciences, the Rady School of Management and the Jacobs School of Engineering to ensure representation across UC San Diego’s innovation ecosystem.

Innovation programming helps faculty and students potentially turn research into products, such as this wearable patch that can heat or cool the skin. (cr: David Baillot/UC San Diego Jacobs School of Engineering)

“Students, staff and faculty from all parts of campus will be most welcome in the new chapter," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. "Speaking as an engineer, educator and inventor, I know firsthand that we get the best solutions when we look at challenges from all directions. We need everyone at the innovation and invention table.” 

Pisano was inducted into the National Academy of Inventors in 2019  based on the impact of medical devices that treat arterial diseases, currently being commercialized via a startup company.

While NAI fellows are inducted into the academy through a formal nomination process, chapter members will apply locally through UC San Diego’s Office of Innovation and Commercialization. Students will have the unique opportunity to become honorary members and have access to mentorship and professional development resources.

TODAY’S INNOVATION FOR TOMORROW’S WORLD

 

The university’s commitment to innovation and entrepreneurship runs deep and goes beyond the campus borders. While programs like Institute for the Global EntrepreneurThe Basement and StartR at the Rady School of Management support students and faculty in their startup endeavors, capital projects like the Design and Innovation Building and Downtown Park & Market “The U” promise to strengthen the connection between the campus and industry partners, government entities and community members.

“UC San Diego prioritizes innovation, technology transfer and entrepreneurship for the sustained economic prosperity of the region,” said Associate Vice Chancellor for Innovation and Commercialization Paul Roben. “Our recent designation as an NAI Chapter will allow us to connect with world-renowned inventors, while nurturing and mentoring innovators, business owners and the workforce of tomorrow.” 

Upcoming events supporting and celebrating campus innovation include the grand opening of the Design and Innovation Building, and a Student Inventor and Startup Showcase focused on “Enriching Human Life and Society.”

Student entrepreneurs are supported by programs like The Basement and will be able to join the NAI chapter as honorary members. (cr: Erik Jepsen/UC San Diego)

“Launching an official NAI Chapter is an amazing step at creating a united innovation ecosystem on campus and within your community to celebrate and share the importance of academic innovation and invention,” said NAI Director Jayde Stewart. “The NAI is honored and proud to have you as members and look forward to celebrating the successes of your students and faculty innovators through your local Chapter.”

The National Academy of Inventors was founded in 2010 to recognize and encourage inventors, enhance the visibility of academic technology, and educate and mentor innovation-minded students. NAI boasts over 1,000 fellows and 250 institutions worldwide. In total, the fellows have formed more than 9,000 companies and generated over $190 billion from nearly 11,000 licensed inventions. UC San Diego is home to 13 NAI fellows, including current and emeritus faculty.

Swift Sewage-Sifting System Boosts Efforts to Forecast and Mitigate the Spread of COVID-19

March 11, 2021- 

As the COVID-19 pandemic proliferated in early 2020, tracking the spread of a frequently asymptomatic virus presented a novel challenge for public health officials. Diagnostic testing was often unavailable and not fast enough to act as a useful forecasting tool.

While symptoms can take several days to appear, the virus immediately begins replicating in the gastrointestinal tract, and traces of it end up in the infected individuals’ stool. Researchers at the University of California San Diego (UC San Diego) quickly determined that testing sewage for viral markers would allow for earlier detection of infections and potential outbreaks.

The wastewater sampling initiative began as a pilot program on the UC San Diego campus in the summer of 2020 with only six collection sites but quickly grew as they determined that environmental testing was a key to preventing the spread of COVID-19. However, the manual work involved in concentrating samples was a roadblock to scaling the surveillance program beyond the university.

“Viral concentration is typically the biggest bottleneck in wastewater analyses since it's laborious and very time-consuming. Here, we optimized that step via automation with liquid-handling robots,” said Smruthi Karthikeyan, a postdoctoral researcher at UC San Diego School of Medicine. The automated system not only increases the number of samples that can be processed concurrently - 24 in 40 minutes - it also removes the potential for human error and accelerates the timeline from the collection of samples to viral detection, enabling a more rapid response to positive results.

This project marked the first collaboration between the Center for Microbiome Innovation (CMI) and the Center for Machine-Integrated Computing & Security (CMICS), both research centers are part of UC San Diego Jacobs School of Engineering. The system is described in a new paper entitled “High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County”, published March 2, 2021, in mSystems.

As a result of the increased scale at which wastewater samples were tested, the team could track viral detection patterns from a far higher-level perspective than before. “In this paper, we observed strong correlations and forecasting potential between viral content in daily wastewater samples from the Point Loma wastewater treatment plant and positive COVID-19 cases reported for San Diego county when modeled with temporal information,” according to Nancy Ronquillo, a graduate student researcher with the CMICS.

While the system is already enabling health officials to forecast the spread of COVID-19 with greater speed and accuracy, efforts continue to expand what data can be extracted from wastewater. Karthikeyan noted that performing viral genome sequencing of the samples could help track the prevalence of different variants of SARS-CoV-2 and model the impact they’re having on viral spread throughout the community. On a more granular level, the team is studying the dynamics of viral shedding and transmission at UC San Diego, which will ultimately aid the university in safely reopening the campus under the Return to Learn program.

"The Center for Microbiome Innovation and Center for Machine-Integrated Computing & Security collaboration accelerated the trace viral pathogen detection modeling in large-scale wastewater sampling throughout San Diego," remarked Andrew Bartko, executive director of the CMI. "We're grateful to contribute to this interdisciplinary team and generate impactful developments in the fight against COVID-19. We look forward to leveraging our complementary technologies and expertise in the future."

Additional co-authors include Pedro Belda-Ferre, Destiny Alvarado, Tara Javidi, Christopher A. Longhurst, and Rob Knight, all at UC San Diego.


 

Tracking infection dynamics in San Diego County. (A) Map showing the San Diego sewer mains (depicted in purple) that feed into the influent stream at the primary wastewater treatment plant (WWTP) at Point Loma. Overlaid are the cumulative cases recorded from the different zip codes in the county during the course of the study. The caseload was counted by cases per zip code from areas draining into the WWTP. The sizes of the circles are proportional to the diagnostic cases reported from each zone, and the color gradient shows the number of cases per 100,000 residents. (B) Daily new cases reported by the county of San Diego. (C) SARS-CoV-2 viral gene copies detected per liter of raw sewage determined from N1 Cq values corrected for PMMoV (pepper mild mottle virus) concentration. All viral concentration estimates were derived from the processing of two sample replicates and two PCR replicates for each sample (error bars show the standard deviations [SD]).

 

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

 

Structural engineers get hands-on experience with composite materials

Students test the performance of the blades they designed and built using composite materials.

March 11, 2021-- Structural engineering students at the Jacobs School got hands-on experience designing, manufacturing and analyzing structures made from composite materials through the Design of Composite Structures course, held in-person thanks to UC San Diego’s Return to Learn policies.

“This is actually a pretty unique class that I don't think you find in engineering departments across the country in terms of the subject matter, and also that it’s taught at the undergrad level,” said Hyonny Kim, a professor of structural engineering at UC San Diego. “Composite materials are high performance materials used to make aerospace structures and space structures. They’re extremely light, strong, and stiff. The class is about how we design them, manufacture them, and quantitatively analyze them.”

The course, held in the fall quarter, started off in a reduced-capacity setting indoors, with half of the students completing a lab project one week, and the other half the following week. When county COVID-19 requirements shifted to outdoor only-education, Kim and his team of dedicated graduate teaching assistants moved the course outside. 

“I felt and observed that the students really enjoyed this,” said Kim. “I think they got a lot out of it, coming to campus, having some direct interaction with instructors. There was a lot of good learning as well as just the psychological benefits of feeling engaged with school, being able to have some social interaction with their teammates. I think it was all around really good for all the students.”

Kim and the TAs prepared individual lab kits for each student taking the course remotely.

In order to make this lab course work for the 26 students in-person as well as the 17 students taking the course remotely, Kim and the TAs created individual kits for each of the three lab projects, that students picked up or had shipped to them.

For the labs, students first made a flat plate with carbon fiber/epoxy composite to get accustomed to the process of using composite materials. They then made a carbon fiber structural channel beam with a different type of composite that is what’s called pre-impregnated (prepreg), where the epoxy is already combined with the fibers; this prepreg material is what most high-end aerospace structures are made with. For the third lab, students made beams out of fiberglass with a foam core. 

They put this understanding of composites to use for the final project: a competition to see which team could build the most efficient wind turbine blades using a glass fiber/epoxy composite. The student teams had to figure out what angle and configuration to set the blades; build them as light and aerodynamic as possible; and have them generate the most power from a controlled fixed-speed wind source. 

Students working on lab assignments outside.

Each team of five students included two who were completely remote, and were responsible for designing the 3D-printed part that was used to position their team’s blades in the wind turbine. 

“We really tried to give everyone, including the remote students, as close to a hands-on role as possible,” Kim said, noting that after months of quarantining and being isolated from friends, instructors and the campus, students seemed to really appreciate the opportunity to meet safely in person. 

Students made carbon fiber structural channel beams with prepreg material.

“The class seemed to work really well,” said Kim “I really emphasized the right culture to the students: a no blame, no shame culture where if they, lets say, got sick or were exposed or had concerns because of X, Y or Z, they didn’t need to justify telling me they couldn’t or shouldn’t come to class that week. I broadcast that message really clearly, and I thought the students were fantastic. They were excellent and very responsible about that.”

Many of these students are now in the structural engineering capstone design course this quarter, co-taught by Kim, who is also teaching a Repair of Aerospace Structures class that also conducts labs outside. 

Computer science student brings Black beauty products to UC San Diego

Jaida Day, a math-computer science student, started Black Beauty Near You to make beauty products more accessible for UC San Diego students. Photos courtesy of Jaida Day.

March 11, 2021--When Jaida Day arrived at UC San Diego to begin her undergraduate studies, she found a welcoming campus environment, peers and faculty to push her academically, beautiful beaches and opportunities to get involved in student organizations. But she also found there was something missing.

“I grew up in Los Angeles where I could go down the street and find the products I need for my hair and my skin, things of that sort, because there are other people who look like me in that area,” said Day. “But coming to La Jolla, I realized the beauty supply stores, the CVS, even the markets on campus, they don't have what I need for my hair and skin.”

Her options? Drive 30 minutes to the closest beauty supply that carried the items she needed; order her hygiene necessities online and have them shipped; or stock up at home during breaks and bring the products back to campus with her. With no car and only a few trips home each year, she recognized she wasn’t the only student facing this dilemma, and decided to take action.

“I was talking to my mom about it and she said ‘Well, you should come up with something to fix that.’ So that’s pretty much how Black Beauty Near You came about.”

The mathematics-computer science student put her web development skills to use, and launched her Black Beauty Near You business with a goal of making Black hair and skin care products more accessible to UC San Diego students. Through her website, people can order brushes, combs, bobby pins, braid charms, scalp oil, edge control, durags, makeup and other items they need.

For a time, Black Beauty Near You had a physical setup in the Black Resource Center’s The Shop, but with COVID-19 restrictions, sales are now all online. Day delivers the items to students on campus, and frequently changes up her inventory to reflect student requests.

To Day, this is just the first step, a stopgap measure until more permanent solutions are put in place. The UC San Diego Black Student Union—of which Day is co-publicity manager—is working with university administration to try and get more of these products that Black students need in markets on campus.

“My mind goes far. I know this isn't the only school where there's not Black beauty products on campus, and it would be nice if there could be better access to these items at more universities. It doesn’t have to be through Black Beauty Near You, but perhaps in the future I’ll find a way to help universities get these products on their campus, because I think it’s just a disconnect of knowing what is needed.”

In addition to working towards her math-computer science major—a combination of the mathematical theory and methods used in computer science, along with computer programming, structure, and algorithms—Day is also the web development chair of the Women in Computing undergraduate student organization, and was an intern for the Black Resource Center (BRC). She has a knack for finding ways to use her technical skills to empower her communities.

Day selling her products at the Black Resource Center's The Shop. With COVID-19 restrictions, sales are now all online.

As a BRC intern, Day organized an event called Engineering Orgs Near You, bringing engineering student organizations to the Black Resource Center to recruit new members and share what they do. For her internship final project, she created a website called Magnifying San Diego, where people new to campus can find information on local places to hang out, get their hair or nails done, eat, or find a therapist, with a focus on the Black community.

“Jaida is a brilliant, motivated, and self-less scholar and person. She was an exemplar as an intern at the BRC, but she has also continued to be a dedicated and active member of the Black community at UC San Diego,” said Porsia Curry, director of the Black Resource Center. “Her yearlong project not only blew us away, but continues to be a tremendous resource for Black students. Our center and community are better because of her contributions.”

As WiC’s web development chair, she led the development of the group’s new website, developed entirely from scratch.

“I had never done that before, I had always used templates to develop a website, but never from scratch,” said Day. “So, I was nervous. But WiC is the best community ever; they’re so welcoming, so supportive, so helpful. Myself and some of our other board members got together virtually every week over the summer to work on the website, and we got it done.”

Her advice to students is to branch out and try new things.

“If I had never gone to that first WiC meeting, I would have never had this supportive community in my actual major. Because it’s one thing to hang around with people I identify with as my race, but it’s another to be with people who get the struggle of being a computer science student. So definitely try to find your community or communities on campus. Go to those different org meetings, you never know what you’ll find.”

Always thinking big picture, Day also had advice for increasing underrepresented groups in the computer science field as a whole, and here at UC San Diego.

For starters, more computer science camps and coding programs like Kode with Klossy, where Day got her first introduction to computer science, are needed, particularly in underserved areas.

“The summer after my junior year I did a two-week coding boot camp program through Kode with Klossy, and I thought OK that’s what I want to do; I know I’m good at math and think I like computer science, so why not do both,” said Day. “More of those programs and classes in schools or even like the coding camp I did would be a good start, just so students can have the option to see if they like it. Because if I hadn’t done that coding camp, I would not be a computer science student. I couldn't even tell you what I’d be doing.”

Looking closer to campus, Day said she knows the UC San Diego admissions team is researching ways to reach more diverse groups of students and encourage them to attend UC San Diego, but emphasized the importance of this work.

“I probably only know one Black woman computer science student in each grade level,” she said. “We have to do better at bringing in more Black CS students. It’s isolating in class, and while I’ve gotten over it, it can be really isolating as a first year student when you come in and don’t see anyone that looks like you. We definitely have to do better with that.”

In October 2020, the Jacobs School of Engineering launched a Student and Faculty Racial Equity Task Force to assess and improve its efforts to create equitable learning and working environments, as one piece of UC San Diego’s larger efforts to address this issue. Learn more through the Office of Equity, Diversity and Inclusion. The Department of Computer Science and Engineering and the Division of Physical Sciences (which administers the Math-Computer Science major) are also actively engaged in addressing diversity issues.

With gene therapy, scientists develop opioid-free solution for chronic pain

March 10, 2021 -- A gene therapy for chronic pain could offer a safer, non-addictive alternative to opioids. Researchers at the University of California San Diego developed the new therapy, which works by temporarily repressing a gene involved in sensing pain. It increased pain tolerance in mice, lowered their sensitivity to pain and provided months of pain relief without causing numbness.

The researchers report their findings in a paper published Mar. 10 in Science Translational Medicine.

The gene therapy could be used to treat a broad range of chronic pain conditions, from lower back pain to rare neuropathic pain disorders—conditions for which opioid painkillers are the current standard of care.

woman in business attire
Ana Moreno, UC San Diego bioengineering alumna and CEO and co-founder of Navega Therapeutics

“What we have right now does not work,” said first author Ana Moreno, a bioengineering alumna from the UC San Diego Jacobs School of Engineering. Opioids can make people more sensitive to pain over time, leading them to rely on increasingly higher doses. “There’s a desperate need for a treatment that’s effective, long-lasting and non-addictive.”

The idea for such a treatment emerged when Moreno was a Ph.D. student in UC San Diego bioengineering professor Prashant Mali’s lab. Mali had been investigating the possibility of applying CRISPR-based gene therapy approaches to rare as well as common human diseases. Moreno’s project focused on exploring potential therapeutic avenues. One day, she came across a paper about a genetic mutation that causes humans to feel no pain. This mutation inactivates a protein in pain-transmitting neurons in the spinal cord, called NaV1.7. In individuals lacking functional NaV1.7, sensations like touching something hot or sharp do not register as pain. On the other hand, a gene mutation that leads to overexpression of NaV1.7 causes individuals to feel more pain.

When Moreno read this, it clicked. “By targeting this gene, we could alter the pain phenotype,” she said. “What’s also cool is that this gene is only involved in pain. There aren’t any severe side effects observed with this mutation.”

Non-permanent gene therapy

Moreno had been working on gene repression using the CRISPR gene editing tool as part of her dissertation. Specifically, she was working with a version of CRISPR that uses what’s called “dead” Cas9, which lacks the ability to cut DNA. Instead, it sticks to a gene target and blocks its expression.

Moreno saw an opportunity to use this approach to repress the gene that codes for NaV1.7. She points out an appeal of this approach: “It’s not cutting out any genes, so there are no permanent changes to the genome. You wouldn’t want to permanently lose the ability to feel pain,” she said. “One of the biggest concerns with CRISPR gene editing is off-target effects. Once you cut DNA, that’s it. You can’t go back. With dead Cas9, we’re not doing something irreversible.”

Mali, who is a co-senior author of the study, says that this use of dead Cas9 opens the door to using gene therapy to target common diseases and chronic ailments.

“In some common diseases, the issue is that a gene is being misexpressed. You don’t want to completely shut it down,” he said. “But if you could turn down the dose of that gene, you could bring it to a level where it is not pathogenic. That is what we are doing here. We don’t completely take away the pain phenotype, we dampen it.”

Moreno and Mali co-founded the spinoff company Navega Therapeutics to work on translating this gene therapy approach, which they developed at UC San Diego, into the clinic. They teamed up with Tony Yaksh, an expert in pain systems and a professor of anesthesiology and pharmacology at UC San Diego School of Medicine. Yaksh is a scientific advisor to Navega and co-senior author of the study.

Early lab studies

The researchers engineered a CRISPR/dead Cas9 system to target and repress the gene that codes for NaV1.7. They administered spinal injections of their system to mice with inflammatory and chemotherapy-induced pain. These mice displayed higher pain thresholds than mice that did not receive the gene therapy; they were slower to withdraw a paw from painful stimuli (heat, cold or pressure) and spent less time licking or shaking it after being hurt.

The treatment was tested at various timepoints. It was still effective after 44 weeks in the mice with inflammatory pain and 15 weeks in those with chemotherapy-induced pain. The length of duration is still being tested, researchers said, and is expected to be long-lasting. Moreover, the treated mice did not lose sensitivity or display any changes in normal motor function.

To validate their results, the researchers performed the same tests using another gene editing tool called zinc finger proteins. It’s an older technique than CRISPR, but it does the same job. Here, the researchers designed zinc fingers that similarly bind to the gene target and block expression of NaV1.7. Spinal injections of the zinc fingers in mice produced the same results as the CRISPR-dead Cas9 system.

“We were excited that both approaches worked,” Mali said. “The beauty about zinc finger proteins is that they are built on the scaffold of a human protein. The CRISPR system is a foreign protein that comes from bacteria, so it could cause an immune response. That’s why we explored zinc fingers as well, so we have an option that might be more translatable to the clinic.”

The researchers say this solution could work for a large number of chronic pain conditions arising from increased expression of NaV1.7, including diabetic polyneuropathy, erythromelalgia, sciatica and osteoarthritis. It could also provide relief for patients undergoing chemotherapy.

And due to its non-permanent effects, this therapeutic platform could address a poorly met need for a large population of patients with long-lasting (weeks to months) but reversible pain conditions, Yaksh said.

“Think of the young athlete or wounded war fighter in which the pain may resolve with wound healing,” he said. “We would not want to permanently remove the ability to sense pain in these people, especially if they have a long life expectancy. This CRISPR/dead Cas9 approach offers this population an alternative therapeutic intervention—that’s a major step in the field of pain management.”  

Researchers at UC San Diego and Navega will next work on optimizing both approaches (CRISPR and zinc fingers) for targeting the human gene that codes for NaV1.7. Trials in non-human primates to test for efficacy and toxicity will follow. Researchers expect to file for an IND and to commence human clinical trials in a couple years.

Paper title: “Long-lasting Analgesia via Targeted in situ Repression of NaV1.7.” Co-authors include Fernando Alemán, Glaucilene F. Catroli, Matthew Hunt, Michael Hu, Amir Dailamy, Andrew Pla, Sarah A. Woller, Nathan Palmer, Udit Parekh, Daniella McDonald, Amanda J. Robers, Vanessa Goodwill, Ian Dryden, Robert F. Hevner, Lauriane Delay and Gilson Gonçalves dos Santos.

This work was supported by UC San Diego Institutional Funds and the National Institutes of Health (grants R01HG009285, RO1CA222826, RO1GM123313, R43CA239940, R43NS112088, R01NS102432, R01NS099338).

Disclosure: Ana Moreno, Fernando Alemán, Prashant Mali and Tony Yaksh have a financial interest in Navega Therapeutics. The terms of these arrangements have been reviewed and approved by the University of California San Diego in accordance with its conflict of interest policies.

'Wearable microgrid' uses the human body to sustainably power small gadgets

March 9, 2021 -- Nanoengineers at the University of California San Diego have developed a “wearable microgrid” that harvests and stores energy from the human body to power small electronics. It consists of three main parts: sweat-powered biofuel cells, motion-powered devices called triboelectric generators, and energy-storing supercapacitors. All parts are flexible, washable and can be screen printed onto clothing.

The technology, reported in a paper published Mar. 9 in Nature Communications, draws inspiration from community microgrids.

“We’re applying the concept of the microgrid to create wearable systems that are powered sustainably, reliably and independently,” said co-first author Lu Yin, a nanoengineering Ph.D. student at the UC San Diego Jacobs School of Engineering. “Just like a city microgrid integrates a variety of local, renewable power sources like wind and solar, a wearable microgrid integrates devices that locally harvest energy from different parts of the body, like sweat and movement, while containing energy storage.” 

Stretchable electronics on a white long sleeved shirt
The wearable microgrid uses energy from human sweat and movement to power an LCD wristwatch and electrochromic device. Photos by Lu Yin

The wearable microgrid is built from a combination of flexible electronic parts that were developed by the Nanobioelectronics team of UC San Diego nanoengineering professor Joseph Wang, who is the director of the Center for Wearable Sensors at UC San Diego and corresponding author on the current study. Each part is screen printed onto a shirt and placed in a way that optimizes the amount of energy collected.

Biofuel cells that harvest energy from sweat are located inside the shirt at the chest. Devices that convert energy from movement into electricity, called triboelectric generators, are positioned outside the shirt on the forearms and sides of the torso near the waist. They harvest energy from the swinging movement of the arms against the torso while walking or running. Supercapacitors outside the shirt on the chest temporarily store energy from both devices and then discharge it to power small electronics.

Harvesting energy from both movement and sweat enables the wearable microgrid to power devices quickly and continuously. The triboelectric generators provide power right away as soon as the user starts moving, before breaking a sweat. Once the user starts sweating, the biofuel cells start providing power and continue to do so after the user stops moving.

“When you add these two together, they make up for each other’s shortcomings,” Yin said. “They are complementary and synergistic to enable fast startup and continuous power.” The entire system boots two times faster than having just the biofuel cells alone, and lasts three times longer than the triboelectric generators alone.

The wearable microgrid was tested on a subject during 30-minute sessions that consisted of 10 minutes of either exercising on a cycling machine or running, followed by 20 minutes of resting. The system was able to power either an LCD wristwatch or a small electrochromic display—a device that changes color in response to an applied voltage—throughout each 30-minute session.

Greater than the sum of its parts

Stretchable electronics on a white shirt
Biofuel cells harvest energy from sweat.

The biofuel cells are equipped with enzymes that trigger a swapping of electrons between lactate and oxygen molecules in human sweat to generate electricity. Wang’s team first reported these sweat-harvesting wearables in a paper published in 2013. Working with colleagues at the UC San Diego Center for Wearable Sensors, they later updated the technology to be stretchable and powerful enough to run small electronics.

The triboelectric generators are made of a negatively charged material, placed on the forearms, and a positively charged material, placed on the sides of the torso. As the arms swing against the torso while walking or running, the oppositely charged materials rub against each and generate electricity.

Stretchable electronics on a white shirt
Triboelectric generator harvests energy from movement.

Each wearable provides a different type of power. The biofuel cells provide continuous low voltage, while the triboelectric generators provide pulses of high voltage. In order for the system to power devices, these different voltages need to be combined and regulated into one stable voltage. That’s where the supercapacitors come in; they act as a reservoir that temporarily stores the energy from both power sources and can discharge it as needed.

Yin compared the setup to a water supply system.

“Imagine the biofuel cells are like a slow flowing faucet and the triboelectric generators are like a hose that shoots out jets of water,” he said. “The supercapacitors are the tank that they both feed into, and you can draw from that tank however you need to.”

Stretchable electronics on a white shirt
Supercapacitors store energy and discharge it to other electronic devices that the user is wearing.

All of the parts are connected with flexible silver interconnections that are also printed on the shirt and insulated by waterproof coating. The performance of each part is not affected by  repeated bending, folding and crumpling, or washing in water—as long as no detergent is used.

The main innovation of this work is not the wearable devices themselves, Yin said, but the systematic and efficient integration of all the devices.

“We’re not just adding A and B together and calling it a system. We chose parts that all have compatible form factors (everything here is printable, flexible and stretchable); matching performance; and complementary functionality, meaning they are all useful for the same scenario (in this case, rigorous movement),” he said.

Other applications

This particular system is useful for athletics and other cases where the user is exercising. But this is just one example of how the wearable microgrid can be used. “We are not limiting ourselves to this design. We can adapt the system by selecting different types of energy harvesters for different scenarios,” Yin said.

The researchers are working on other designs that can harvest energy while the user is sitting inside an office, for example, or moving slowly outside.

Paper: “A Self-Sustainable Wearable Multi-Modular E-Textile Bioenergy Microgrid System.” Co-authors include Kyeong Nam Kim*, Jian Lv*, Farshad Tehrani, Muyang Lin, Zuzeng Lin, Jong-Min Moon, Jessica Ma, Jialu Yu and Sheng Xu.

*These authors contributed equally to this work.

This work was supported by the UC San Diego Center for Wearable Sensors and the National Research Foundation of Korea.

Adhesion, contractility enable metastatic cells to go against the grain

Schematic of cells migrating over a step gradient. For durotactic cells, higher tractions and longer bond lifetimes on the stiff side drive adhesion maturation and net migration toward the stiffer substrate. For adurotactic cells, tractions balance across the boundary due to longer bond lifetimes on the soft side of the step gradient.

March 9, 2021--Bioengineers at the University of California San Diego and San Diego State University have discovered a key feature that allows cancer cells to break from typical cell behavior and migrate away from the stiffer tissue in a tumor, shedding light on the process of metastasis and offering possible new targets for cancer therapies. 

It has been well documented that cells typically migrate away from softer tissue to stiffer regions within the extracellular matrix—a process called durotaxis. Metastatic cancer cells are the rare exception to this rule, moving away from the stiffer tumor tissue to softer tissue, and spreading the cancer as they migrate. What enables these cells to display this atypical behavior, called adurotaxis, and migrate away from the stiffer tumor hasn’t been well understood.

Building off previous research led by bioengineers in UC San Diego Professor Adam Engler’s lab, which found that weakly adherent, or less sticky, cells migrated and invaded other tissues more than strongly adherent cells, the team has now shown that the contractility of these weakly adherent cells is what enables them to move to less stiff tissue. By chemically reducing the contractility of weakly adherent cells, they become durotactic, migrating toward stiffer tissue; increasing the contractility of strongly adherent cells makes them migrate down the stiffness gradient. The researchers reported their findings on March 9 in Cell Reports. 

“The main takeaway here is that the less adherent, more contractile cells are the ones that don’t exhibit typical durotactic behavior,” said Benjamin Yeoman, a bioengineering PhD student in the joint program at UC San Diego and SDSU, and first author of the study. “But beyond that, we see this in several different types of cancer, which opens up the possibility that maybe there’s this commonality between different types of carcinomas that could potentially be a target for a more universal treatment.”

To find out what enables this atypical behavior, Yeoman first used computational models developed in bioengineer Parag Katira’s lab in the SDSU Department of Mechanical Engineering, to try and pinpoint what was different about the cells that were able to move against the stiffness gradient. The models showed that changing a cell’s contractile force could modulate the cell’s adhesion strength in an environment of a certain stiffness, which would change their ability to be durotactic. To confirm the computational results, Yeoman used a microfluidic flow chamber device designed for previous research on cell adherence in Engler’s lab, to experiment with the contractility of real cancer cells from breast cancer, prostate cancer and lung cancer cell lines. 

“It worked perfectly,” said Katira, co-corresponding author of the paper. “It was really an ideal collaboration, where you have experimental results that show something is different; then you have a computational model that predicts it and explains why something is happening; and then you go back and do experiments to actually test if that’s going on. All of these blocks fell into place to bring this interesting result.”

The microfluidic cell-sorting device developed in Engler’s lab allowed the researchers to isolate cells based on adhesion strength. Credit: Benjamin Yeoman

The parallel plate flow chamber device used to test the computational theory was designed by engineers in Engler’s lab studying the effect of adherence on cell metastasis and cancer recurrence, and first described in Cancer Research in February 2020. Using this patent pending device, the researchers now isolated cells based on adhesion strength, and seeded them onto photopatterned hydrogels with alternating soft and stiff profiles. The researchers used time-lapse video microscopy to watch how the cells moved, and found that strongly adherent cells would durotax, moving to stiffer sections, while weakly adherent cells would migrate to softer tissue. 

After investigating several potential mechanisms within the cell enabling this behavior, the team focused on contractility as a key marker of its ability to adurotax. By modulating the number of active myosin motors within the cell— a marker of contractile ability—they were able to get previously durotactic cells to migrate away from stiffer tissue, and previously adurotactic, weakly adherent cells to migrate up the stiffness gradient.

The researchers hope that this work, and the further development of the microfluidic cell sorting device, will enable better assessments of disease prognosis in the future. Their ultimate aim is to be able to use the parallel plate flow chamber as a way to measure the metastatic potential of a patient’s cells, and use that as a predictor for cancer recurrence to drive more effective treatments and outcomes. 

“Understanding the mechanisms that govern invasion of many different tumor types enables us to better use this device to sort and count cells with weak adhesion and their percentage in a tumor, which may correlate with poor patient outcomes,” said Adam Engler, professor of bioengineering at UC San Diego and co-corresponding author of the paper. 

The researchers cautioned that this discovery doesn’t preclude other mechanisms from playing a role in the metastasis of cells. It does, however, highlight the important role that adherence and contractility do play, which needs to be studied further.

“The point is not to say that nothing else can drive cells away from a tumor,” said Katira. “There could be other drivers for metastasis, but this is clearly an important mechanism, and the fact that cells can do this across lung, breast and pancreatic cancer cells tells us this is generalizable.”

Going forward, the engineers plan to study other parameters that may contribute to adurotaxis; investigate the effect of different types of tumor environments on a cell’s ability to adurotax; and move from the individual cell scale to the population scale, to see how adhesion and contractility function and can be modulated when there is a mixed population of cells with unique mechanical properties.

This project was funded by grants from the National Science Foundation, National Institutes of Health and the Army Research Office. 

Three-layered masks most effective against large respiratory droplets

The droplet impacting on the mask surface is recorded at 20,000 frames per second. These time sequence images of droplet impingement on a single-, double-, and triple-layer masks show the total number count of atomized droplets is significantly higher for the single-layer mask in comparison with the double-layer mask, while only a single droplet penetrates through the triple-layer mask. Credit: Basu et al, Science Advances, March 5 2021

March 5, 2021-- If you are going to buy a face mask to protect yourself and others from COVID-19, make sure it’s a three-layered mask. You might have already heard this recommendation, but researchers have now found an additional reason why three-layered masks are safer than single or double-layered alternatives. 

While this advice was originally based on studies that showed three layers prevented small particles from passing through the mask pores, researchers have now shown that three-layered surgical masks are also most effective at stopping large droplets from a cough or sneeze from getting atomized into smaller droplets. These large cough droplets can penetrate through the single- and double-layer masks and atomize to much smaller droplets, which is particularly crucial since these smaller droplets (often called aerosols) are able to linger in the air for longer periods of time. Researchers studied surgical masks with one, two and three layers to demonstrate this behavior. 

The researchers reported their results in Science Advances on March 5

The team notes that single and double-layer masks do provide protection in blocking some of the liquid volume of the original droplet and are significantly better than wearing no mask at all. They hope their findings on ideal mask pore size, material thickness, and layering could be used by manufacturers to produce the most effective masks designs.

Using a droplet generator and a high-speed time-lapse camera, the team of engineers from the University of California San Diego, Indian Institute of Science and University of Toronto found that, counterintuitively, large respiratory droplets containing virus emulating particles (VEPs) actually get atomized when they hit a single-layer mask, and many of these VEPs pass through that layer. Think of it like a water droplet breaking into smaller droplets as it’s being squeezed through a sieve. For a 620 micron droplet—the size of a large droplet from a cough or sneeze—a single-layer surgical mask only restricts about 30 percent of the droplet volume; a double-layer mask performs better, restricting about 91 percent of the droplet volume; while a three layer mask has negligible, nearly zero droplet ejection. This video illustrates the research as well.

“While it is expected that large solid particles in the 500–600-micron range should be stopped by a single-layer mask with average pore size of 30 micron, we are showing that this is not the case for liquid droplets,” said Abhishek Saha, professor of mechanical and aerospace engineering at UC San Diego and a co-author of the paper. “If these larger respiratory droplets have enough velocity, which happens for coughs or sneezes, when they land on a single-layer of this material it gets dispersed and squeezed through the smaller pores in the mask.” 

Schematic diagram of viral load getting trapped inside the mask layer. Droplets and virus are not drawn to scale. Basu et al, Science Advances, March 5 2021

This is a problem. Droplet physics models have shown that while these large droplets are expected to fall to the ground very quickly due to gravity, these now smaller, 50-80 micron-sized droplets coming through the first and second layer of a mask will linger in the air, where they can spread to people at larger distances. 

The team of engineers— which also includes Professors Swetaprovo Chaudhuri from University of Toronto, and Saptarshi Basu of the Indian Institute of Science— were well-versed in this type of experiment and analysis, though they were used to studying the aerodynamics and physics of droplets for applications including propulsion systems, combustion, or thermal sprays. They turned their attention to respiratory droplet physics last year when the COVID-19 pandemic broke out, and since then, have been studying the transport of these respiratory droplets and their roles in transmission of Covid-19 type diseases

“We do droplet impact experiments a lot in our labs,” said Saha. “For this study, a special generator was used to produce a relatively fast-moving droplet. The droplet was then allowed to land on a piece of mask material—that could be a single layer, double, or triple layer, depending on which we’re testing. Simultaneously, we use a high-speed camera to see what happens to the droplet.”

Using the droplet generator, they’re able to alter the size and speed of the droplet to see how that affects the flow of the particle. 

Going forward, the team plans to investigate the role of different mask materials, as well as the effect of damp or wet masks, on particle attrition. 

Coronavirus-like particles could ensure reliability of simpler, faster COVID-19 tests

Series of test tubes containing yellow and pink liquid
RT-LAMP test samples showing positive (yellow) and negative (pink) results. Image credit: Soo Khim Chan

March 2, 2021 -- Rapid COVID-19 tests are on the rise to deliver results faster to more people, and scientists need an easy, foolproof way to know that these tests work correctly and the results can be trusted. Nanoparticles that pass detection as the novel coronavirus could be just the ticket.

Such coronavirus-like nanoparticles, developed by nanoengineers at the University of California San Diego, would serve as something called a positive control for COVID-19 tests. Positive controls are samples that always test positive. They are run and analyzed right alongside patient samples to verify that COVID-19 tests are working consistently and as intended.

The positive controls developed at UC San Diego offer several advantages over the ones currently used in COVID-19 testing: they do not need to be kept cold; they are easy to manufacture; they can be included in the entire testing process from start to finish, just like a patient sample; and because they are not actual virus samples from COVID-19 patients, they do not pose a risk of infection to the people running the tests.

Researchers led by Nicole Steinmetz, a professor of nanoengineering at UC San Diego, published their work in the journal Biomacromolecules.

This work builds on an earlier version of the positive controls that Steinmetz’s lab developed for the RT-PCR test, which is the gold standard for COVID-19 testing. The positive controls in the new study can be used not only for the RT-PCR test, but also for a cheaper, simpler and faster test called the RT-LAMP test, which can be done on the spot and provide results in about an hour.

Having a hardy tool to ensure these tests are running accurately—especially for low-tech diagnostic assays like the RT-LAMP—is critical, Steinmetz said. It could help enable rapid, mass testing of COVID-19 in low-resource, underserved areas and other places that do not have access to sophisticated testing equipment, specialized reagents and trained professionals.

Upgraded positive controls

Goto Flickr
Coronavirus-like nanoparticles, made from plant viruses and bacteriophage, could serve as positive controls for the RT-LAMP test. Image credit: Soo Khim Chan

The new positive controls are essentially tiny virus shells—made of either plant virus or bacteriophage—that house segments of coronavirus RNA inside. The RNA segments include binding sites for both of the primers used in the PCR and LAMP tests.

“This design creates an all-in-one control that can be used for either one of these assays, making it very versatile,” said first author Soo Khim Chan, who is a postdoctoral researcher in Steinmetz’s lab.

The team developed two types of positive controls. One was made from plant virus nanoparticles. To make them, the researchers infected cowpea plants in the lab with cowpea chlorotic mottle virus and then extracted the viruses from the plants. Afterwards, the researchers removed the virus’ RNA and replaced it with a custom-made RNA template containing specific yet non-infectious sequences from the SARS-CoV-2 virus. The resulting nanoparticles consist of coronavirus RNA sequences packaged inside plant virus shells.

The other positive control was made from bacteriophage nanoparticles. It involved a similar recipe. The researchers infected E. coli bacteria with custom-made plasmids—rings of DNA—that contain specific fragments of sequences (which are also non-infectious) from the SARS-CoV-2 virus, as well as genes coding for surface proteins of a bacteriophage called Qbeta. This process caused the bacteria to produce nanoparticles that consist of coronavirus RNA sequences packaged inside bacteriophage shells.

The plant virus and bacteriophage shells are key to making these positive controls so sturdy. They protect the coronavirus RNA segments from breaking down at warmer temperatures—tests showed that they can be stored for a week at temperatures up to 40 C (104 F). The shells also protect the RNA during the first step of the PCR and LAMP tests, which involves breaking down cells in the sample—via enzymes or heat—to release their genetic material for testing.

These protections are not present in the positive controls currently used in COVID-19 testing (naked synthetic RNAs, plasmids or RNA samples from infected patients). That’s why existing controls either require refrigeration (which makes them inconvenient to handle, costly to ship and store) or have to be added at a later stage of the test (which means that means scientists will not know if something went wrong in the first steps).

As a next step, the researchers are looking to partner up with industry to implement this technology. The positive controls can be adapted to any established RT-PCR or RT-LAMP assay, and using them would help negate false readouts, Steinmetz’s team said.  Plus, these positive controls can be easily produced in large quantities by molecular farming in plants or microbial culture fermentation, which is good news for translating them to large-scale manufacturing.

“With mutants and variants emerging, continued testing will be imperative to keep the population safe,” Steinmetz said. “The new technology could find utility in particular for at-home tests, which may have a higher rate of false readouts due to the less controlled experimental conditions.”

Paper title: “Virus-Like Particles as Positive Controls for COVID-19 RT-LAMP Diagnostic Assays.”

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

KRISTEN VACCARO AND THE SCIENCE OF SOCIAL MEDIA

 

February 11, 2021 -- New assistant professor Kristen Vaccaro came to UC San Diego’s Computer Science and Engineering Department from the University of Illinois Urbana-Champaign, where she recently earned her Ph.D. After spending several years in chilly Illinois, she’s pleased to be wintering in San Diego.

“It was very cold,” said Vaccaro, “and very  flat. It’s been a pleasure to go hiking again.”

Weather notwithstanding, Vaccaro chose CSE because she was impressed by the faculty and students here.

“It was a virtual visit, which was weird,” she said. “I hadn't been to San Diego before, so I was really coming in blind, but I had so much fun on the visit, talking with everyone. That was 90% of my decision.”

Understanding Social Media

Vaccaro earned her B.A. in physics at Reed College, worked as a software engineer at the MITRE Corporation for several years and circled back to grad school at the University of Illinois. Her research focuses on giving users more say in how social media works.

“My work looks at how we can design machine learning systems to improve user agency and control,” said Vaccaro. “There are increasingly large numbers of decisions that get made about people through automated decision-making systems. How can we take a more human-centered approach when building these systems? How do we give people a sense of agency?”

These can be tricky questions. Sometimes people get too many choices and are simply overwhelmed. Facebook already has more than 100 control settings, but most people don’t know how to effectively use them. In fact, Vaccaro’s research has identified a kind of control setting placebo effect, which she likens to the Close Door button on an elevator. Nobody has any idea what it does – if anything.

“We did one study where we gave people control setting access for their newsfeeds,” she said. “Sometimes the control settings worked properly, but in some cases we also coded them to      malfunction. People were just as satisfied with the malfunctioning settings as the functioning ones.”

Vaccaro and others have also identified a variety of social media folk theories – which can lead to odd tricks people adopt to customize their feeds. Some people like a post and subsequently hide it. They want to show their friend some love; however, they don’t want the algorithm to show them similar posts.

Does liking and hiding work? Nobody really knows. Outside of Facebook, there’s no way to run a controlled experiment where people can change their news feed on one screen and leave the other alone. However, understanding these folk theories can offer new design insights.

“The control settings are there,” said Vaccaro. “People care about them, but they don't know where they are, and they can't tell whether they're working. Maybe we can take the more natural ways people have of thinking about a platform and leverage those to curate control settings, be their virtual valet.”

Vaccaro also wonders if current design is too seamless, hiding what’s really going on under the hood. She thinks a more “seamful” approach, in which people can see problems in real time and react appropriately, might be more helpful. She compares it to hearing an unnerving rattle in your car.

In addition, Vaccaro wants to help people understand their privacy choices and improve their experience when they disagree with a platform. “How can you design content moderation systems so that people have a say in how their community is governed?” she asks.

Teaching and Learning

Vaccaro likes to incorporate student-driven elements into her courses. It engages her classes and sometimes offers unique topics. During one fall quarter class, she let students to pick 10% of the topics.

“Some of the student choices were things I would've picked already, like AR/VR,” she said. “Others were things I absolutely would not have chosen myself. The students wanted to talk about depression and stress and how that connects to  social media. I would never, in a million years, have picked that topic. But the students were interested, and it led to a great discussion.”

Outside the classroom, she has been exploring San Diego, particularly the excellent hiking. “I go out weekdays, early in the morning, so there’s less traffic – Torrey Pines, Peñasquitos, Cowles Mountain. I have two books on San Diego area hikes, and I hope to do them all.”

Meet computer scientist Kristen Vaccaro and the science of social media

CSE Assistant Professor Kristen Vaccaro is one of four new faculty members to join the distinguisehd community of CSE faculty over the next two academic years. 

March 2, 2021 -- New assistant professor Kristen Vaccaro came to UC San Diego’s Department of Computer Science and Engineering from the University of Illinois Urbana-Champaign, where she recently earned her Ph.D. After spending several years in chilly Illinois, she’s pleased to be wintering in San Diego.

“It was very cold,” said Vaccaro, “and very flat. It’s been a pleasure to go hiking again.”

Weather notwithstanding, Vaccaro chose UC San Diego because she was impressed by the faculty and students here.

“It was a virtual visit, which was weird,” she said. “I hadn't been to San Diego before, so I was really coming in blind, but I had so much fun on the visit, talking with everyone. That was 90% of my decision.”

Understanding Social Media

Vaccaro earned her bachelor's in physics at Reed College, worked as a software engineer at the MITRE Corporation for several years and circled back to grad school at the University of Illinois. Her research focuses on giving users more say in how social media works.

“My work looks at how we can design machine learning systems to improve user agency and control,” said Vaccaro. “There are increasingly large numbers of decisions that get made about people through automated decision-making systems. How can we take a more human-centered approach when building these systems? How do we give people a sense of agency?”

These can be tricky questions. Sometimes people get too many choices and are simply overwhelmed. Facebook already has more than 100 control settings, but most people don’t know how to effectively use them. In fact, Vaccaro’s research has identified a kind of control setting placebo effect, which she likens to the Close Door button on an elevator. Nobody has any idea what it does – if anything.

“We did one study where we gave people control setting access for their newsfeeds,” she said. “Sometimes the control settings worked properly, but in some cases we also coded them to malfunction. People were just as satisfied with the malfunctioning settings as the functioning ones.”

Vaccaro and others have also identified a variety of social media folk theories – which can lead to odd tricks people adopt to customize their feeds. Some people like a post and subsequently hide it. They want to show their friend some love; however, they don’t want the algorithm to show them similar posts.

Does liking and hiding work? Nobody really knows. Outside of Facebook, there’s no way to run a controlled experiment where people can change their news feed on one screen and leave the other alone. However, understanding these folk theories can offer new design insights.

“The control settings are there,” said Vaccaro. “People care about them, but they don't know where they are, and they can't tell whether they're working. Maybe we can take the more natural ways people have of thinking about a platform and leverage those to curate control settings, be their virtual valet.”

Vaccaro also wonders if current design is too seamless, hiding what’s really going on under the hood. She thinks a more “seamful” approach, in which people can see problems in real time and react appropriately, might be more helpful. She compares it to hearing an unnerving rattle in your car.

In addition, Vaccaro wants to help people understand their privacy choices and improve their experience when they disagree with a platform. “How can you design content moderation systems so that people have a say in how their community is governed?” she asks.

Teaching and Learning

Vaccaro likes to incorporate student-driven elements into her courses. It engages her classes and sometimes offers unique topics. During one fall quarter class, she let students pick 10% of the topics.

“Some of the student choices were things I would've picked already, like AR/VR,” she said. “Others were things I absolutely would not have chosen myself. The students wanted to talk about depression and stress and how that connects to  social media. I would never, in a million years, have picked that topic. But the students were interested, and it led to a great discussion.”

Outside the classroom, she has been exploring San Diego, particularly the excellent hiking. “I go out weekdays, early in the morning, so there’s less traffic – Torrey Pines, Peñasquitos, Cowles Mountain. I have two books on San Diego area hikes, and I hope to do them all.”

Weakness is strength for this low-temperature battery

Goto Flickr
Simulated structures of the binding between a lithium ion and electrolyte molecules. Image courtesy of John Holoubek/Nature Energy

February 25, 2021 -- Nanoengineers at the University of California San Diego have discovered new fundamental insights for developing lithium metal batteries that perform well at ultra-low temperatures; mainly, that the weaker the electrolyte holds on to lithium ions, the better. By using such a weakly binding electrolyte, the researchers developed a lithium metal battery that can be repeatedly recharged at temperatures as low as -60 degrees Celsius—a first in the field.

Researchers report their work in a paper published Feb. 25 in Nature Energy.

In tests, the proof-of-concept battery retained 84% and 76% of its capacity over 50 cycles at -40 and -60 degrees Celsius, respectively. Such performance is unprecedented, researchers said.

Other lithium batteries that have been developed for use in sub-freezing temperatures are capable of discharging in the cold but need warmth when charging. That means an extra heater must be brought on board to use these batteries in applications such as outer space and deep-sea exploration. The new battery, on the other hand, can be both charged and discharged at ultra-low temperature.

This work—a collaboration between the labs of UC San Diego nanoengineering professors Ping Liu, Zheng Chen and Tod Pascal—presents a new approach to improving the performance of lithium metal batteries at ultra-low temperature. Many efforts so far have focused on choosing electrolytes that don’t freeze up so easily and can keep lithium ions moving quickly between the electrodes. In this study, UC San Diego researchers discovered that it’s not necessarily how fast the electrolyte can move the ions, but how easily it lets go of them and deposits them on the anode.

“We found that the binding between the lithium ions and the electrolyte, and the structures that the ions take in the electrolyte, mean either life or death for these batteries at low temperature,” said first author John Holoubek, a nanoengineering Ph.D. student at the UC San Diego Jacobs School of Engineering.

The researchers made these discoveries by comparing battery performance with two types of electrolytes: one that binds weakly to lithium ions, and one that binds strongly. Lithium metal battery cells with the weakly binding electrolyte performed better overall at -60 degrees Celsius; it was still running strong after 50 cycles. In contrast, cells with the strongly binding electrolyte stopped working after just two cycles.

After cycling the cells, the researchers took them apart to compare the lithium metal deposits on the anodes. The differences were also stark. Deposits were smooth and uniform in the cells with the weakly binding electrolyte, but chunky and needle-like in the cells with the strongly binding electrolyte. 

Details matter

The differences in battery performance all come down to nanoscale interactions, the researchers said. “How lithium ions interact with the electrolyte at the atomic level not only enables sustainable cycling at very, very low temperature, but also prevents dendrite formation,” Chen said.

To understand why, the team took a detailed look at these interactions using computational simulations and spectroscopic analysis. In one of the electrolytes, called diethyl ether (or DEE), the researchers observed molecular structures consisting of lithium ions weakly bound to the surrounding electrolyte molecules. In the other electrolyte, called DOL/DME, the researchers observed structures that feature strong binding between the ions and electrolyte molecules.

These structures and binding strengths are important, the researchers said, because they ultimately dictate how lithium deposits on the anode surface at low temperature. In weakly bound structures like those observed in the DEE electrolyte, Holoubek explained, lithium ions can easily leave the electrolyte’s hold, so it doesn’t take much energy to get them to deposit anywhere on the anode surface. This is why deposits are smooth and uniform in DEE. But in strongly bound structures, like those in DOL/DME, more energy is needed to pull lithium ions away from the electrolyte. As a result, lithium will prefer to deposit where the anode surface has an extremely strong electric field—anywhere there’s a sharp tip. And lithium will continue to pile up on that tip until the cell short circuits. This is why deposits are chunky and dendritic in DOL/DME.

“Figuring out the different types of molecular and atomic structures that lithium forms, how lithium coordinates with certain atoms—these details matter,” said Pascal, who directed the computational studies. “By understanding fundamentally how these systems come together, we can come up with all kinds of new design principles for the next generation of energy storage systems. This work demonstrates the power of nanoengineering, where figuring out what happens at the small scale enables the design of devices at the large scale.”

Compatible cathode

These fundamental insights enabled the team to design a cathode that’s compatible with the electrolytes and anode for low-temperature performance. It is a sulfur-based cathode made with materials that are low-cost, abundant and environmentally benign—no expensive transition metals are used.

“The significance of this work is really two-fold,” said Liu, whose lab designed the cathode and has been optimizing the cycling performance of such a cathode in DEE for normal conditions. “Scientifically, it presents insights that are contrary to conventional wisdom. Technologically, it is the first rechargeable lithium metal battery that can deliver meaningful energy density while being fully operated at -60 C. Both aspects present a complete solution for ultra-low temperature batteries.”

Paper title: “Tailoring Electrolyte Solvation for Li Metal Batteries Cycled at Ultra-Low Temperature.”

This work was supported by a NASA Space Technology Graduate Research Opportunity, and in part by a NASA early career faculty award and by the U.S. Department of Energy.

Protecting our oceans with AI Technology: Q&A with Saakib Akbany of Remora

Human-centered mobility and transportation options for disadvantaged communities is the goal of new partnership

UC San Diego researchers are working hand in hand with community organizations and the San Diego Association of Governments

Feb. 24, 2021--The University of California San Diego is teaming up with several community-based organizations and the San Diego Association of Governments to improve access to transportation for the county’s low-income and underserved neighborhoods. The team is adopting a human-centered design approach to their work to try and repair the harm done by car-oriented transportation policies of the past. 

The project was selected this month to be part of the inaugural Civic Innovation Challenge, a partnership of the National Science Foundation, the Department of Energy and the Department of Homeland Security. The competition’s goal is to empower communities to tackle issues such as transit, housing affordability and operating safe schools during the COVID-19 pandemic. 

The UC San Diego team is one of 52 groups across 30 states to receive a $50,000 award during the first stage of the competition. The teams have four months to refine their projects, after which NSF will select a smaller number of groups to receive awards of up to $1 million for ready-to-implement pilot projects with the potential to produce scalable, sustainable and transferable solutions to address community-identified challenges. 

The UC San Diego team is headed by Todd Hylton and Colleen Emmenegger of the  Contextual Robotics Institute and the Design Lab. Contextual Robotics Institute Director Henrik Christensen is also a co-principal investigator on the grant.  Thanks to the $50,000 NSF award, researchers will assess the challenges and feasibility of an integrated mobility service with representative communities. With the help of partner community organizations, they will conduct day-in-a-life interviews and real-world observations. They will also deploy questionnaires and wearable sensors in several disadvantaged communities.

Working with SANDAG, the team will employ data-driven methodologies including the analysis demographic data, transportation services data, survey data and transportation modeling in these same communities.

The project’s primary research objective is to assess the integration of these techniques and their utility in understanding the needs of disadvantaged communities and in formulating solutions that are both responsive and feasible. 

In the project’s second stage, the team will implement an integrated mobility pilot in one of these communities that is responsive to the real needs of the community; addresses the long-term strategic plan for transportation and sustainability in the region; and can be expanded to other communities in the region. 

“We anticipate that the pilot will demonstrate improved access to employment, recreation, shopping, education and public transit via the integration of mobility services including, for example, pooled ride-hailing, neighborhood electric vehicles, microtransit, e-scooters, e-bikes, and carshare,” Hylton said. 

The project intends not only to address needs in particular San Diego communities, but also to inform SANDAG’s planners about the types of services, incentives, and operating models that are needed to ensure alignment with a community’s needs as they implement a bold vision of the 2021 Regional Plan known as the “5 Big Moves.”


 

Computer scientist studies the importance of extra-chromosomal DNA

With ground-breaking approaches and a new company, Vineet Bafna and colleagues are taking a different path to control cancer

CSE Professor Vineet Bafna is working to determine how ecDNA drives cancer, which could eventually lead to new anti-cancer therapies. 

Feb. 23, 2021--Cancer is a genetic disease that can lay waste to DNA. In many cases, error correction mechanisms mutate, removing the quality control circuits that maintain genes, setting the stage for more mutations.

But sometimes the changes are even more profound. Chunks of DNA are duplicated and break away from their home chromosomes, forming small, circular islands of extrachromosomal DNA (ecDNA). Under a microscope, chromosomes look like they’ve been hit by a sledgehammer.

UC San Diego Computer Science and Engineering (CSE) Professor Vineet Bafna is fascinated by ecDNA and is working with biologists to measure its impact. These structural changes, and the associated gene duplications, can amplify genes that drive rampant cell division, as well as genes that make tumors treatment resistant, giving them an outsized impact on cells.

“There’s been a lot of research that suggests high copies of oncogenes – genes that are proliferative in nature – lead to poor outcomes,” says Bafna. “But what is not clear is how these copy number variations arise. How is it a gene can make 20, 50, 100 copies?”

Bafna and colleagues are working to answer these questions and help determine how ecDNA drives cancer. They hope these insights will eventually lead to new anti-cancer therapies.

Taking an Algorithmic Approach

Since the human genome was sequenced, many researchers have focused almost exclusively on single letter changes in oncogenes and how these affect cellular function. While this has been a fruitful path, structural changes to chromosomes have been somewhat neglected. Working closely with UC San Diego pathology professor Paul Mischel and others, Bafna has been developing computational approaches to identify ecDNA and other chromosomal changes.

“The question I’m interested in is: How can we determine what is causing a complex structural rearrangement based on a genomic signature?” said Bafna.

The Bafna lab developed machine learning techniques to detect ecDNA in cellular images. These techniques can spot ecDNA when cultured cancer cells enter metaphase, the second stage of cell division, when chromosomes become quite compact.

From there, it’s just a matter of counting. Conducted jointly with the Mischel lab, these studies have analyzed thousands of images and found ecDNA in virtually every cancer subtype – hiding in plain sight.

Unfortunately, these imaging techniques are difficult to deploy with patient tumors, from which only DNA, isolated from chromosomes, can be extracted. To get around this, Bafna and colleagues examine short (150 to 300 base pair) ecDNA fragments in tumor samples and compare them to reference genomes. If the two ends of these ecDNA fragments match a reference chromosome, this strongly indicates the region detached from that chromosome.

Working with Mischel and Professor Roel Verhaak at the Jackson Laboratory in Maine, Bafna applied these genomic methods to more than 3,000 tumor samples and found ecDNA in over 20% of the tumors, with higher frequencies in glioblastomas, lung and kidney cancers.

Grand Challenges    

These structural defects have become increasingly important for the scientific community. Interrogating ecDNA is one in a series of Cancer Grand Challenges, which offer $25 million awards to researchers who can answer important questions about cancer pathology.

“What are the biological mechanisms involved in ecDNA generation?” asked Bafna. “What's the role of ecDNA in the evolution of cancer? Can we model and predict ecDNA evolution? Can we target any vulnerabilities therapeutically? These are questions we’ve been trying to answer anyway, so this is a big deal for us.”

The researchers also believe it’s time to translate their discovery research into treatments. Two years ago, Bafna and Mischel co-founded Boundless Bio, a San Diego life sciences company working to find ecDNA-focused therapeutics.

“We are taking what we’ve learned about ecDNA vulnerabilities and identifying molecules that could potentially target those vulnerabilities,” says Bafna. “We believe this will give us another tool to fight cancer.”

New material is next step toward stable high-voltage long-life solid-state sodium-ion batteries

The Zr-Cl unit and the orange/brown "cloud" that surrounds the green Zr shows rotation.

Feb. 23, 2021-- A team of researchers designed and manufactured a new sodium-ion conductor for solid-state sodium-ion batteries that is stable when incorporated into higher-voltage oxide cathodes. This new solid electrolyte could dramatically improve the efficiency and lifespan of this class of batteries. A proof of concept battery built with the new material lasted over 1000 cycles while retaining 89.3% of its capacity--a performance unmatched by other solid-state sodium batteries to date. 

Researchers detail their findings in the Feb. 23, 2021 issue of Nature Communications. 

Solid state batteries hold the promise of safer, cheaper, and longer lasting batteries. Sodium-ion chemistries are particularly promising because sodium is low-cost and abundant, as opposed to the lithium required for lithium-ion batteries, which is mined at a high environmental cost. The goal is to build batteries that can be used in large-scale grid energy storage applications, especially to store power generated by renewable energy sources to mitigate peak demand. 

“Industry wants batteries at cell-level to cost $30 to $50 per kWh,” about one-third to one-fifth of what it costs today, said Shirley Meng, a professor of nanoengineering at the University of California San Diego, and one of the paper’s corresponding authors. “We will not stop until we get there.”

The work is a collaboration between researchers at UC San Diego and UC Santa Barbara, Stony Brook University, the TCG Center for Research and Education in Science and Technology in Kolkata, India, and Shell International Exploration, Inc.

For the battery described in the Nature Communications study, researchers led by UC San Diego nanoengineering professor Shyue Ping Ong ran a series of computational simulations powered by a machine learning model to screen which chemistry would have the right combination of properties for a solid state battery with an oxide cathode. Once a material was selected as a good candidate, Meng’s research group experimentally fabricated, tested, and characterized it to determine its electrochemical properties. 

By rapidly iterating between computations and experiments, the UC SanDiego team settled on a class of halide sodium conductors made up of sodium, yttrium, zirconium and chloride. The material, which they named NYZC, was both electrochemically stable and chemically compatible with the oxide cathodes used in higher voltage sodium-ion batteries. The team then reached out to researchers at UC Santa Barbara to study and understand the structural properties and behavior of this new material.

NYZC is based on Na3YCl6, a well-known material that is unfortunately a very poor sodium conductor. Ong suggested substituting zirconium for yttrium because it would create vacancies and increase the volume of the cell battery unit, two approaches that increase the conduction of sodium ions. Researchers also noted that, in conjunction with the increased volume, a combination of zirconium and chloride ions in this new material undergoes a rotating motion, resulting in more conduction pathways for the sodium ions. In addition to the increase in conductivity, the halide material is much more stable than materials currently used in solid-state sodium batteries. 

“These findings highlight the immense potential of halide ion conductors for solid-state sodium-ion battery applications,” said Ong. “Further, it also highlights the transformative impact that large-scale materials data computations coupled with machine learning can have on the materials discovery process.”

Next steps include exploring other substitutions for these halide materials and increasing the battery’s overall power density, along with working to scale up the manufacturing process. 

The technology has been licensed by UNIGRID, a startup co-founded by UC San Diego NanoEngineering professor Zheng Chen; Erik Wu, a Ph.D. alumnus from Meng’s research group; and Darren H. S. Tan, one of Meng’s Ph.D. students. Meng is the company’s technical advisor.

Funding to support this work was provided by the Energy & Biosciences Institute through the EBI-Shell program and NSF.

The video below shows a simulation of the ZrCl6 unit rotating.

Tracking melting points above 4000 degrees Celsius

With a new grant, a UC San Diego engineer is developing a better platform to study new materials that melt above 4000 degrees Celsius

February 23, 2021: A materials engineer at the University of California San Diego is leading the development of a new research platform for studying high-performance materials, in particular new materials that melt above 4000 degrees Celsius (C). UC San Diego nanoengineering professor Kenneth Vecchio is leading the project, which is funded by a new $800,000 grant from the US Office of Naval Research (ONR), through the Defense University Research Instrumentation Program (DURIP).

The research platform will be built to specifically address the challenges of studying new materials that melt at temperatures higher than 4000C, which is approximately 80 percent of the temperature of the surface of the sun.

This platform will become a national resource for engineers and other researchers who are pushing the limits of materials science. There are many industrial, energy, space and defense applications that would benefit from new solid materials that perform reliably at record-breaking, ultra-high temperatures. Applications include the containment walls for fusion reactors, leading edges of air vehicles that travel five or more times the speed of sound, and new industrial material machining methods. (The tips of cutting tools, for example, can experience temperatures above 3000C at high machining speeds. New cutting tool materials with much higher melting temperatures would enable faster manufacturing.)

Creating and then characterizing materials that don't melt until exposed to ultra-high temperatures presents multiple challenges. In addition to creating candidate materials, researchers need to be able to characterize these materials to demonstrate performance. One of the key metrics is the temperature at which materials melt.

When working at temperatures around 4000C, nothing is simple. For example, how do you test the melting point of new materials that melt at temperatures higher than any containers you might try to hold them in? How do you heat a sample to temperatures in the 4000C range while precisely controlling the temperature? Or how do you determine exactly when a sample at such extreme conditions actually melts?

These are some of the issues that Vecchio and his team plan to solve via an experimental platform he designed and will build thanks to $800K in new funding from the ONR DURIP grant.

New Materials that melt at temperatures higher than 4000C

How do you increase the melting point of materials that already melt at ultra-high temperatures? For the past five years, Vecchio has led a UC San Diego project funded by the ONR Multidisciplinary University Research Initiatives (MURI) Program to focus on this.

The team is taking a new approach to this difficult task. To make sense of their strategy, you first need to know that there are two physical phenomena that largely determine the temperature at which a solid material melts into a liquid.

The first phenomenon is enthalpy. Enthalpy describes the energy associated with keeping a material in its solid form. The higher the enthalpy, the stronger the bond between the two atoms will be, and the higher you have to heat the material to melt it by breaking those bonds.

The second phenomenon is entropy. Entropy is associated with disorder and describes the energy driving the atoms to separate.  

"Melting in a solid occurs when the entropy becomes high enough to exceed the enthalpy," said Vecchio.

Ultra-high-temperature materials development is usually focused on enthalpy. But researchers seem to have reached the limits of the enthalpy approach, at least for materials that do not react with oxygen. The roadblock is due to the fact that the enthalpy of bonding between atoms is largely fixed. That means that once you find materials with the highest enthalpy of bonding, there is little room for increasing the melting temperature of that material via enthalpy.  

In their quest for materials that melt at ever higher temperatures, Vecchio and his team at the UC San Diego Jacobs School of Engineering have turned to the other phenomenon controlling melting temperature: entropy.

Most people have a vague sense that entropy has something to do with chaos or disorder. That notion will come in handy for understanding this new approach to developing materials with record-breaking melting temperatures.
 

Kenneth Vecchio UC San Diego
UC San Diego nanoengineering professor Kenneth Vecchio

"A liquid has a very high level of entropy. Atoms are moving all around in a liquid, that's entropy. If we can make a solid look like a liquid, in terms of its free energy, then there will be less driving force to change from the solid to the liquid state," said Vecchio.

Making a solid "look" like a liquid means increasing the inherent entropy of the material when it's a solid. That's what Vecchio has set out to do. Their strategy is to increase the disorder in new high-temperature solid materials by mixing large numbers of different atoms together.

"We create disorder through atomic mixing," said Vecchio.  

By taking this approach, the researchers are making their solid materials structurally appear more similar to the atomic state of that material's liquid form. This reduces the driving force for the solid to "want" to melt, which can lead to an increase in the temperature at which it melts.

For example, silicon carbide (SiC) is a well-known material with an ultra-high melting point of 2730C. But it would be useful to have related materials that melt at even high temperatures.

Following the entropy-focused approach in previous research, Vecchio and his collaborators replaced the Si atoms with equal amounts of five different metals, which led to new materials with even higher melting temperatures. These new materials, called, high-entropy carbides, or more broadly high-entropy ceramics, are discussed in a research article published in the journal Acta Materialia in 2019.

Vecchio and his team are pursuing another use of entropy as well. More entropy can be added to a solid-material system by adding other molecular and atomic-bonding variations that alone would not increase the melting temperature. But when you add enough of them into the system, the diversity of molecular elements and bonding scenarios further increases entropy, which can increase the temperature at which the solid melts into a liquid.

Researchers must be able to experimentally validate melting temperature and other properties for these kinds of approaches to materials development to lead to new useful materials. That's where the new platform comes in.

High Temperature-X-ray Diffraction platform

The new High Temperature-X-ray Diffraction platform being funded by the ONR DURIP grant to UC San Diego is designed to enable the heating of a sample region to 4500C, while measuring its temperature very accurately, and detecting the onset of melting.
 

Concept for integration of laser heating and high temperature pyrometry into an x-ray diffraction platform to achieve measurement of melting above 4000C.

The system components include: a platform that enables high-speed measurements called a high brightness X-ray diffraction platform; a high power laser to locally heat a small region of a material sample; and a high-tech thermometer (a pyrometer) that records temperatures up to 4500C by measuring the wavelength of light emitted from the heat source.

"The integration of these three tools is a fascinating engineering challenge," said Vecchio.

In order to overcome the 'container problem' in which a container melts before the experimental sample it is supposed to be holding, Vecchio plans to use sample materials as their own containers.

"We will only heat a small circular region in the middle of the sample using the laser," he said.

The remaining perimeter of the sample that is not exposed to the laser will serve as the container that holds the sample as it melts from solid to liquid.

"I look forward to being able to share this unique platform with researchers across the country," said Vecchio. "People have been trying to devise systems to measure melting temperatures of these types of materials, but their biggest scientific problem is they have no method to verify what structure the sample has at the perceived onset of melting. My design will solve this problem," explained Vecchio. "By building our melting system inside an x-ray diffraction platform, we will be able to exactly know the structure and type of material present right at the point of melting, and we will be able to completely verify melting as it has a completely different X-ray diffraction result compared to a solid sample."

He estimates that the facility will be up and running by the end of 2022.

The funded ONR DURIP proposal is entitled “Thermodynamic Measurements of Entropy-Stabilized Ultra-high Temperature Materials.” University of California San Diego NanoEngineering Professor Kenneth Vecchio is the Principal Investigator (PI) on the grant. (ONR award number: N00014-20-1-2872).

Engineer inducted into prestigious biomedical institution

Padmini Rangamani, a professor in the Department of Mechanical and Aerospace Engineering at UC San Diego, is part of the 2021 class of AIMBE Fellows. 

Feb. 22, 2021--Padmini Rangamani, a professor at the Jacobs School of Engineering, has been inducted into the College of Fellows of the American Institute for Medical and Biological Engineering (AIMBE). She was recognized for outstanding contributions to multiscale computational modeling of cellular mechanobiology including spatial signal transduction and membrane trafficking processes.

The College of Fellows comprises the top 2 percent of medical and biological engineers in the country, including the most accomplished and distinguished engineering and medical school chairs, research directors, professors, innovators and successful entrepreneurs. AIMBE Fellows are recognized for their contributions in teaching, research and innovation.

A formal induction ceremony will be held during AIMBE’s 2021 Annual Event on March 26. Rangamani will be inducted along with 174 colleagues who make up the AIMBE Fellow Class of 2021, including two other UC San Diego researchers, Samuel Ward and Jiang Du from the UC San Diego School of Medicine. They join a total of 37 UC San Diego AIMBE Fellows. 

Rangamani's research is focused on understanding the design principles of biological systems. Her long-term research goal is  to understand the  control of  cell shape  by  analyzing biological membranes and their interaction with proteins and the cytoskeleton using principles from transport phenomena. This is a unifying framework that brings together mechanics of the membrane, membrane-bound proteins, and their coupled interactions. 

Her work uses a combination of novel mechanical theories and computational  approaches to simulate  many aspects of cellular membranes, in collaboration with experimentalists. Her areas of focus include transport phenomena in biological membranes, influence of cell shape on biochemical activation of signaling networks and morphological and topological changes to lipid membranes mediated by proteins and cytoskeletal forces.

In addition to her research, Rangamani has been active in advocating for women in science and under-represented groups in science. She recently was part of a group of women deans, chairs and distinguished faculty that authored a call to action to fund Black scientists, published in the journal Cell. Karen Christman, a Jacobs School’s associate dean and a bioengineering professor, was also part of the group. 

Rangamani also was a coauthor of a paper in PLOS Computational Biology titled “Ten simple rules for women principal investigators during a pandemic.” 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. 

AIMBE’s mission is to recognize excellence in, and advocate for, the fields of medical and biological engineering in order to advance society. Since 1991, AIMBE‘s College of Fellows has led the way for technological growth and advancement in the fields of medical and biological engineering. Fellows have helped revolutionize medicine and related fields in order to enhance and extend the lives of people all over the world. They have also successfully advocated public policies that have enabled researchers and business-makers to further the interests of engineers, teachers, scientists, clinical practitioners, and ultimately, patients.

For more information about the AIMBE Annual Event, visit www.aimbe.org


 

This robot doesn't need any electronics

Walking quadruped is controlled and powered by pressurized air

Photos: http://bit.ly/airwalkerpictures

Feb. 17, 2021--Engineers at the University of California San Diego have created a four-legged soft robot that doesn’t need any electronics to work. The robot only needs a constant source of pressurized air for all its functions, including its controls and locomotion systems. 

The team, led by Michael T. Tolley, a professor of mechanical engineering at the Jacobs School of Engineering at UC San Diego, details its findings in the Feb. 17, 2021 issue of the journal Science Robotics.

“This work represents a fundamental yet significant step towards fully-autonomous, electronics-free walking robots,” said Dylan Drotman, a Ph.D. student in Tolley’s research group and the paper’s first author. 

Applications include low-cost robotics for entertainment, such as toys, and robots that can operate in environments where electronics cannot function, such as MRI machines or mine shafts. Soft robots are of particular interest because they easily adapt to their environment and operate safely near humans. 

Most soft robots are powered by pressurized air and are controlled by electronic circuits. But this approach requires complex components like circuit boards, valves and pumps--often outside the robot’s body. These components, which constitute the robot’s brains and nervous system, are typically bulky and expensive. By contrast, the UC San Diego robot is controlled by a light-weight, low-cost system of pneumatic circuits, made up of tubes and soft valves, onboard the robot itself. The robot can walk on command or in response to signals it senses from the environment. 

“With our approach, you could make a very complex robotic brain,” said Tolley, the study’s senior author. “Our focus here was to make the simplest air-powered nervous system needed to control walking.” 

The robot is controlled by complex pneumatic circuits made up tubes and soft valves and powered by pressurized air. 
More pictures: http://bit.ly/airwalkerpictures

The robot’s computational power roughly mimics mammalian reflexes that are driven by a neural response from the spine rather than the brain. The team was inspired by neural circuits found in animals, called central pattern generators, made of very simple elements that can generate rhythmic patterns to control motions like walking and running.

To mimic the generator’s functions, engineers built a system of valves that act as oscillators, controlling the order in which pressurized air enters air-powered muscles in the robot’s four limbs. Researchers built an innovative component that coordinates the robot’s gait by delaying the injection of air into the robot’s legs. The robot’s gait was inspired by sideneck turtles. 

The robot is also equipped with simple mechanical sensors--little soft bubbles filled with fluid placed at the end of booms protruding from the robot’s body. When the bubbles are depressed, the fluid flips a valve in the robot that causes it to reverse direction. 

The Science Robotics paper builds on  previous work by other research groups that developed oscillators and sensors based on pneumatic valves, and adds the components necessary to achieve high-level functions like walking. 

How it works

The robot is equipped with three valves acting as inverters that cause a high pressure state to spread around the air-powered circuit, with a delay at each inverter.

Each of the robot’s four legs has three degrees of freedom powered by three muscles. The legs are angled downward at 45 degrees and composed of three parallel, connected pneumatic cylindrical chambers with bellows. When a chamber is pressurized, the limb bends in the opposite direction. As a result, the three chambers of each limb provide multi-axis bending required for walking. Researchers paired chambers from each leg diagonally across from one another, simplifying the control problem. 

A soft valve switches the direction of rotation of the limbs between counterclockwise and clockwise. That valve acts as what’s known as a latching double pole, double throw switch--a switch with two inputs and four outputs, so each input has two corresponding outputs it’s connected to. That mechanism is a little like taking two nerves and swapping their connections in the brain. 

Next steps

In the future, researchers want to improve the robot’s gait so it can walk on natural terrains and uneven surfaces. This would allow the robot to navigate over a variety of obstacles. This would require a more sophisticated network of sensors and as a result a more complex pneumatic system. 

The team will also look at how the technology could be used to create robots, which are in part controlled by pneumatic circuits for some functions, such as walking, while traditional electronic circuits handle higher functions. 

This work is supported by the Office of Naval Research, grant numbers N00014-17-1-2062 and N00014-18-1-2277.

Electronics-free pneumatic circuits for controlling soft legged robots

Dylan Drotman, Saurabh Jadhav, David Sharp, Christian Chan and Michael T. Tolley, Department of Mechanical and Aerospace Engineering and Contextual Robotics Institute, UC San Diego


 

Delving into Drool's Droves of Data: Quantifying the Microbial Load in Human Saliva

As anyone who has woken up to a blast of morning breath can attest, the human mouth plays host to a vibrant and diverse blend of microbes. Along with its obvious olfactory output, the oral microbiome impacts the digestive tract, immune system, and nearly every other facet of human health.

The mix of bacteria and fungi that comprise the oral microbiome has been studied extensively, yet the actual quantity has been largely untested. How many microbes are at work in the mouth throughout the day? And what are the potential health ramifications of both understanding and managing the microbial load?

Researchers from the Center for Microbiome Innovation at UC San Diego, led by Clarisse Marotz and corresponding author Karsten Zengler, designed a study to measure not just the composition of the oral microbiome, but the microbial load as well, and how it’s affected by daily activities such as eating and brushing one’s teeth. The results, entitled “Quantifying live microbial load in human saliva samples over time reveals stable composition and dynamic load,” were published in mSystems on February 16, 2021.

"While the proportion of bacteria can be the same, the overall numbers can vary from a few to trillions, showcasing the extreme dynamics of our microbial ecosystems,” according to Marotz. “We wanted to quantify how much microbial load can fluctuate in a healthy, host-associated microbiome over time."

The study was performed by collecting salivary samples from participants at specific intervals throughout the day and cross-referenced against perturbations such as meals and dental hygiene. The samples were measured for flow rate, tested for both microbial load and composition, and treated with propidium monoazide, which enabled tests to assess the mix and mass of active microbes.

By removing relic DNA from dead or inactive cells, the study provided a much clearer picture of how the quantity of living microbes ebbs and flows. “These results highlight the importance of removing dead cell signal in microbiome experiments, especially in longitudinal studies where variations over time can be masked by DNA from dead microbes of previous timepoints,” Marotz remarked when discussing the impact of the findings.

Daily dynamics of the human saliva microbiome. The percentage of live microbial cells collected in unstimulated saliva (for 5 minutes) normalized to the first timepoint; samples were collected throughout the course of a day starting from right after waking to before going to bed.

Based on these results, the team is embarking on further studies to determine how these methods can be adapted to other sample sites and microbiomes within the human body. If current testing methods based on the relative abundance of dead bacteria can be refined to focus on live microbes, researchers hope that this will allow for a deeper understanding of how variations in microbial activity are indicators of both health conditions and the progression of diseases.

Additional co-authors include Perris Navarro, Joanna Coker, Pedro Belda-Ferre, and Rob Knight, all at UC San Diego, as well as James T. Morton at the Simons Foundation.

 

 

 

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

New skin patch brings us closer to wearable, all-in-one health monitor

February 15, 2021 -- Engineers at the University of California San Diego have developed a soft, stretchy skin patch that can be worn on the neck to continuously track blood pressure and heart rate while measuring the wearer’s levels of glucose as well as lactate, alcohol or caffeine. It is the first wearable device that monitors cardiovascular signals and multiple biochemical levels in the human body at the same time.

“This type of wearable would be very helpful for people with underlying medical conditions to monitor their own health on a regular basis,” said Lu Yin, a nanoengineering Ph.D. student at UC San Diego and co-first author of the study published Feb. 15 in Nature Biomedical Engineering. “It would also serve as a great tool for remote patient monitoring, especially during the COVID-19 pandemic when people are minimizing in-person visits to the clinic.”

Such a device could benefit individuals managing high blood pressure and diabetes—individuals who are also at high risk of becoming seriously ill with COVID-19. It could also be used to detect the onset of sepsis, which is characterized by a sudden drop in blood pressure accompanied by a rapid rise in lactate level.

Wearable patch on a person's arm
This soft, stretchy patch can monitor the wearer’s blood pressure and biochemical levels at the same time.

One soft skin patch that can do it all would also offer a convenient alternative for patients in intensive care units, including infants in the NICU, who need continuous monitoring of blood pressure and other vital signs. These procedures currently involve inserting catheters deep inside patients’ arteries and tethering patients to multiple hospital monitors.

“The novelty here is that we take completely different sensors and merge them together on a single small platform as small as a stamp,” said Joseph Wang, a professor of nanoengineering at UC San Diego and co-corresponding author of the study. “We can collect so much information with this one wearable and do so in a non-invasive way, without causing discomfort or interruptions to daily activity.”

The new patch is a product of two pioneering efforts in the UC San Diego Center for Wearable Sensors, for which Wang serves as director. Wang’s lab has been developing wearables capable of monitoring multiple signals simultaneously—chemical, physical and electrophysiological—in the body. And in the lab of UC San Diego nanoengineering professor Sheng Xu, researchers have been developing soft, stretchy electronic skin patches that can monitor blood pressure deep inside the body. By joining forces, the researchers created the first flexible, stretchable wearable device that combines chemical sensing (glucose, lactate, alcohol and caffeine) with blood pressure monitoring.

“Each sensor provides a separate picture of a physical or chemical change. Integrating them all in one wearable patch allows us to stitch those different pictures together to get a more comprehensive overview of what’s going on in our bodies,” said Xu, who is also a co-corresponding author of the study.

Patch of all trades

The patch is a thin sheet of stretchy polymers that can conform to the skin. It is equipped with a blood pressure sensor and two chemical sensors—one that measures levels of lactate (a biomarker of physical exertion), caffeine and alcohol in sweat, and another that measures glucose levels in interstitial fluid.

The patch is capable of measuring three parameters at once, one from each sensor: blood pressure, glucose, and either lactate, alcohol or caffeine. “Theoretically, we can detect all of them at the same time, but that would require a different sensor design,” said Yin, who is also a Ph.D. student in Wang’s lab.

The blood pressure sensor sits near the center of the patch. It consists of a set of small ultrasound transducers that are welded to the patch by a conductive ink. A voltage applied to the transducers causes them to send ultrasound waves into the body. When the ultrasound waves bounce off an artery, the sensor detects the echoes and translates the signals into a blood pressure reading.

The chemical sensors are two electrodes that are screen printed on the patch from conductive ink. The electrode that senses lactate, caffeine and alcohol is printed on the right side of the patch; it works by releasing a drug called pilocarpine into the skin to induce sweat and detecting the chemical substances in the sweat. The other electrode, which senses glucose, is printed on the left side; it works by passing a mild electrical current through the skin to release interstitial fluid and measuring the glucose in that fluid.

The researchers were interested in measuring these particular biomarkers because they impact blood pressure. “We chose parameters that would give us a more accurate, more reliable blood pressure measurement,” said co-first author Juliane Sempionatto, a nanoengineering Ph.D. student in Wang’s lab.

“Let’s say you are monitoring your blood pressure, and you see spikes during the day and think that something is wrong. But a biomarker reading could tell you if those spikes were due to an intake of alcohol or caffeine. This combination of sensors can give you that type of information,” she said.

Wearable patch on a person's neck
Wearing the patch on the neck provides optimal readout.

In tests, subjects wore the patch on the neck while performing various combinations of the following tasks: exercising on a stationary bicycle; eating a high-sugar meal; drinking an alcoholic beverage; and drinking a caffeinated beverage. Measurements from the patch closely matched those collected by commercial monitoring devices such as a blood pressure cuff, blood lactate meter, glucometer and breathalyzer. Measurements of the wearers’ caffeine levels were verified with measurements of sweat samples in the lab spiked with caffeine.

Engineering challenges

One of the biggest challenges in making the patch was eliminating interference between the sensors’ signals. To do this, the researchers had to figure out the optimal spacing between the blood pressure sensor and the chemical sensors. They found that one centimeter of spacing did the trick while keeping the device as small as possible.

The researchers also had to figure out how to physically shield the chemical sensors from the blood pressure sensor. The latter normally comes equipped with a liquid ultrasound gel in order to produce clear readings. But the chemical sensors are also equipped with their own hydrogels, and the problem is that if any liquid gel from the blood pressure sensor flows out and makes contact with the other gels, it will cause interference between the sensors. So instead, the researchers used a solid ultrasound gel, which they found works as well as the liquid version but without the leakage.

“Finding the right materials, optimizing the overall layout, integrating the different electronics together in a seamless fashion—these challenges took a lot of time to overcome,” said co-first author Muyang Lin, a nanoengineering Ph.D. student in Xu’s lab. “We are fortunate to have this great collaboration between our lab and Professor Wang’s lab. It has been so fun working together with them on this project.”

Next steps

Wearable patch with cables attached at the bottom
The current prototype of the patch needs to be connected with cables to a benchtop machine and power source.

The team is already at work on a new version of the patch, one with even more sensors. “There are opportunities to monitor other biomarkers associated with various diseases. We are looking to add more clinical value to this device,” Sempionatto said.

Ongoing work also includes shrinking the electronics for the blood pressure sensor. Right now, the sensor needs to be connected to a power source and a benchtop machine to display its readings. The ultimate goal is to put these all on the patch and make everything wireless.

“We want to make a complete system that is fully wearable,” Lin said.

Paper: “An epidermal patch for the simultaneous monitoring of haemodynamic and metabolic biomarkers.”

This research was supported by the UC San Diego Center of Wearable Sensors and the National Institutes of Health (grant no. 1R21EB027303-01A1). 

Engineers earn NASA grant to enable flying taxis

An artist’s conception of an urban air mobility environment. Credit: NASA / Lillian Gipson

February 12, 2021-- Imagine fleets of small aircraft able to vertically take off and land from helipads in urban areas, transporting people to and from work; or shuttles with preset routes flying people to the airport or other major hubs.

This futuristic system of flying taxis and shuttles is one step closer to reality thanks to a team of engineers led by the University of California San Diego. They received a $5.8 million University Leadership Initiative grant from NASA to create computational design tools that will help US companies develop more efficient air taxi designs, faster.

“This project is part of a growing field called urban air mobility, an exciting vision enabling point-to-point, on-demand air travel within densely populated areas,” said John Hwang, professor of mechanical and aerospace engineering at the Jacobs School of Engineering at UC San Diego and principal investigator for the project. “We will combine multidisciplinary computational models of urban air mobility vehicles and advanced design optimization algorithms to develop methods and tools for rapidly designing safe, quiet, and affordable vehicle concepts.”

This three-year project will result in a set of open-source simulation and optimization tools that companies can use to design the optimal electric vertical take off and landing (eVTOL) aircraft for their needs. Given several input parameters such as number of passengers, desired cruise speed, and range requirement, these tools will allow engineers to determine the optimal number and shape of rotors, wing shape, structural design, propulsion system sizing, and other design aspects that yield the most cost-efficient vehicle while ensuring it is safe and operates quietly. In addition, the researchers will use these tools to perform vehicle configuration trade studies on safety, noise, and cost, to help companies make their design decisions.

“Given a computational model, state-of-the-art design optimization algorithms can efficiently search for the optimal values of up to tens of thousands of design parameters that minimize or maximize some specified objective, such as vehicle operating cost," said Hwang. "We will develop models for all aspects of the aircraft – such as aerodynamics, structures, acoustics, battery, and motor performance – and leverage these optimization algorithms to navigate the most complex and unintuitive aspects of the eVTOL aircraft design problem.”

Early roll out of this new class of vehicles is expected within five years, with a market study commissioned by NASA estimating these services will be profitable by the 2030s. In fact, United Airlines and startup Archer Aviation just inked a deal to purchase 200 of these eVTOL aircraft, expected to debut in 2024.

Ultimately, this new kind of transportation – a hybrid between a helicopter, airplane and drone – is intended to save time, while limiting travel-related carbon emissions in urban areas by operating purely on electricity.

“The goal of urban air mobility is to ease traffic congestion and reduce travel times. For example, a 90-minute ground commute to a downtown workplace could be reduced to a 15-minute air taxi flight,” said Hwang.

University Leadership Initiative

The team, led by Hwang, is one of five academic groups that received the University Leadership Initiative (ULI) award from NASA. ULI was created to initiate a new type of interaction between NASA’s Aeronautics Research Mission Directorate and US universities, with academic researchers taking the lead on their own research projects that further NASA’s mission.

In addition to Hwang, the team includes UC San Diego engineers David Kamensky, Alicia Kim, and Shirley Meng. The team also includes Seongkyu Lee from UC Davis; Chris Mi from San Diego State University; Andrew Ning from Brigham Young University; Jeffrey Chambers and Adam Grasch from Aurora Flight Sciences; and Tyler Winter of M4 Engineering. In all, the researchers bring expertise in computational modeling and optimization, topology optimization, batteries, acoustics, electric motors, aerodynamics, composite materials, and concept design.

Key aspects of the ULI include a focus on transitioning the research results to industry or government partners to bring them to market; providing research opportunities for students; and promoting greater diversity in the aeronautics field through increased participation of underrepresented groups in engineering.

This project will have an industry advisory board consisting of both established aircraft companies and eVTOL startups. The team will also institute an aeronautics internship program for students, to enhance and coordinate recruiting and mentoring of undergraduate student researchers across all four universities involved. The internship will be run in partnership with the Academic Enrichment Program at UC San Diego, which has experience managing internship programs for first-generation, low-income and underrepresented students in engineering.

In Memoriam: Juan C. Lasheras, Distinguished Mechanical and Aerospace Engineering Professor

February 9, 2021: Juan C. Lasheras, University of California San Diego distinguished professor of Mechanical and Aerospace Engineering and Bioengineering, passed away on February 1, 2021 after a brief battle with cancer. He was 69 years old.  
 

Juan Lasheras
Juan C. Lasheras

Lasheras was a brilliant scholar, a visionary leader, a supportive mentor, a dedicated educator and a larger-than-life presence in the Department of Mechanical and Aerospace Engineering (MAE) and in the Jacobs School of Engineering. More than that, he was a beloved friend and dear colleague.  

Lasheras was instrumental in founding the Aerospace Engineering program at UC San Diego and in forming the Department of Mechanical and Aerospace Engineering (MAE). In 1999, when the Department of Applied Mechanics and Engineering Sciences (AMES) split into the Department of Mechanical and Aerospace Engineering (MAE) and the Department of Structural Engineering, Juan served as the first Chairman of the new MAE department.  

He was also the founding director of the Center for Medical Devices at UC San Diego, and served as the Interim Dean of Engineering in 2012. Since 2007, he held the Stanford S. and Beverly P. Penner Endowed Chair in Engineering or Applied Sciences.  

Beyond UC San Diego, Lasheras received multiple distinctions and awards. He was a member of the National Academy of Engineering, the National Academy of Inventors, and the Spanish Royal Academy of Engineering. He held honorary doctoral degrees from the Universidad Politécnica de Madrid and from Universidad Carlos III.  

Lasheras was born in Valencia, Spain and spent most of his formative years near Murcia where his father, a mathematician by training, was stationed as a Colonel at the Air Force Academy. At age 18, Lasheras began his studies at the Universidad Politécnica de Madrid in Aeronautical Engineering. However, his academic plans were disrupted at the end of his first year by his father's passing. To provide for his family, he moved back to Murcia and, in the following years, worked as a teacher and director of a preparatory school for air force cadet candidates. During that period, Juan was unable to attend college lectures in Madrid, located 300 miles away, and prepared for course exams using class notes shared by his classmates. Despite these challenges, Juan managed to graduate at the top of his class.  

Upon graduation in 1977, Lasheras secured a Guggenheim fellowship to continue his studies at Princeton University, under the guidance of Professor Irv Glassman, a renowned combustion scientist. It was at Princeton that Lasheras began to develop his skills as a creative experimentalist. He designed a combustion facility from scratch that, for the first time, allowed investigation of the mechanisms for explosive (disruptive) burning of multicomponent and emulsified fuel droplets. His pioneering work caught the attention of the research department at the Shell corporation, which hired him as a Research Scientist in 1981 to direct the combustion group at the Royal Dutch Shell Laboratory in Amsterdam.  

In 1983, Lasheras returned to the US as an Assistant Professor in the Department of Mechanical Engineering at the University of Southern California. In the following years, Lasheras used his experimental skills to investigate a number of fluid dynamics problems related to aerospace propulsion applications. For example, his experiments helped clarify the structure and stability of turbulent mixing layers and jets, as well as the regimes of liquid atomization relevant to the design of rocket engines. It was during his time in Los Angeles that Lasheras met Alexis, whom he married in 1985.  

Already a renowned experimentalist, Lasheras joined UC San Diego as Professor in the AMES Department in 1991. While he maintained an active research program addressing flow problems for engineering applications, he also developed an interest in biomedical applications following the deaths of two of his sisters at an early age. With initial guidance from Professor Shu Chien, Distinguished Professor of Bioengineering and Medicine at UC San Diego, Lasheras was able to build a brilliant career working at the interfaces between mechanics, biology, and medicine in a short time.  

Lasheras' work has led to significant advances in biomechanics. He addressed a wide variety of problems and applications at the macroscopic level, including endovascular techniques to induce and control mild hypothermia, unsteady blood flows and the risk of rupture of aortic and intracranial arterial aneurysms. More recently, his work encompassed cerebrospinal flow in the central nervous system and its role in intrathecal drug delivery procedures. His contributions are equally important at the cellular level, including development of a novel, three-dimensional cell-traction-force microscopy method and clarification of some of the biochemical pathways for the generation of the traction forces exerted by cells during migration. Although his work was driven by a fundamental interest in the underlying physical mechanisms, he always remained a true engineer with an interest in the ultimate applications. He held nearly fifty patents, including one for an endovascular blood-cooling catheter that served as a heat exchanger, the first device approved by the FDA to rapidly cool the body temperature after cardiac arrest to protect the brain from the resulting damage.                                                

The research style of Lasheras combined an outstanding ability to identify relevant problems in need of further understanding and quantification along with a profound knowledge of the key physical and biological elements involved. Mastering the central physical phenomena and describing them in a clear and concise manner, he was able to design insightful experiments that revealed the underlying phenomena with minimum associated complexity. Although an experimentalist by training, he was interested in complex problems that require an interdisciplinary approach. His success was a result of his remarkable ability to form and motivate research teams that included individuals from different disciplines who were able to contribute a wide range of research tools. Juan's exceptional interpersonal and communication skills were key in enabling and promoting the collaborative work of people with completely different backgrounds, successfully facilitating the harmonious interaction of biologists and medical doctors with electrical, mechanical, and aerospace engineers.  

Lasheras was also an exceptional communicator. He was known for his ability to explain very complex ideas in simple terms. In any given laboratory meeting he could explain the different roles of viscous and pressure forces in blood flow to a doctor, and then turn around and explain the physiology of a red cell to an engineer. These communication skills made him an extremely effective and well-liked teacher. Students gave him the highest recommendations, and he was awarded the Teacher of the Year Award by the MAE department on multiple occasions and by the Engineering Division’s Tau Beta Pi Engineering Honor Society. He was always sought by campus colleagues to serve on Academic Senate faculty committees.  

Lasheras was extremely generous with his time. He somehow seemed to have endless hours available for either serious discussion or friendly conversation, and he handled both with ease. He never turned down a request when his help or advice was needed. For many years, he served as Chairman of the Board of Advisors at Universidad Carlos III in Spain, where he helped organize their Bioengineering program, along with his friend Shu Chien. It has become the leading program in the country.

Lasheras was also very active in service to the scientific community, notably as an Associate Editor of the Journal of Fluid Mechanics and as a participant in activities of the American Physical Society (APS) and the National Institutes of Health (NIH). Besides spending time as Secretary/Treasurer of the Division of Fluid Mechanics of APS and later as Chair of that division, Lasheras was a member of the APS Executive Council. He chaired the Organizing Committee for two annual meetings, having previously received the F. Frenkiel Award for Fluid Dynamics from APS and having been elected an APS Fellow. He was also strongly involved in NIH studies and served as a Permanent Member of the Study Section on Modeling and Analysis of Biological Systems for seven years. Lasheras contributed deep consideration and time to these activities, always trying to make sure that what was done would be best for the scientific community.  

Beyond all of his professional accomplishments and accolades, Lasheras was a caring and generous person. He had a profound impact on many students, staff, and faculty at UC San Diego. This legacy is evident in countless anecdotes they shared including certain impactful career advice, his role in bringing them to UC San Diego, and the help that he graciously offered to them or to their relatives regarding personal challenges.  

Outside of work, he was an excellent golfer and a skilled chef. In his cooking, he applied the same creativity he used in the laboratory, always ready to try new recipes. He and Alexis loved to entertain friends, students, and colleagues and hosted many memorable gatherings in their La Jolla home.  

Lasheras leaves an extraordinary academic legacy, not only in his scientific contributions but also in the innumerable graduate and undergraduate students, postdocs and colleagues that have benefitted from his teaching and mentorship.  

He is survived by Alexis, his wife of over 35 years, his siblings, Maruja, Arsenio, and Teresa, and his nephews and nieces, Javier, Carmen, Jose Maria, Arsenio, Luz, Jaime, and Robbie.

Elizabeth H. Simmons
Executive Vice Chancellor

Albert P. Pisano
Dean, Jacobs School of Engineering

George Tynan
Professor and Chair, Department of Mechanical and Aerospace Engineering

Deepfake detectors can be defeated, computer scientists show for the first time

February 8, 2021-- Systems designed to detect deepfakes --videos that manipulate real-life footage via artificial intelligence--can be deceived, computer scientists showed for the first time at the WACV 2021 conference which took place online Jan. 5 to 9, 2021.

Researchers showed detectors can be defeated by inserting inputs called adversarial examples into every video frame. The adversarial examples are slightly manipulated inputs which cause artificial intelligence systems such as machine learning models to make a mistake. In addition, the team showed that the attack still works after videos are compressed.

“Our work shows that attacks on deepfake detectors could be a real-world threat,” said Shehzeen Hussain, a UC San Diego computer engineering Ph.D. student and first co-author on the WACV paper. “More alarmingly, we demonstrate that it’s possible to craft robust adversarial deepfakes in even when an adversary may not be aware of the inner workings of the machine learning model used by the detector.”

In deepfakes, a subject’s face is modified in order to create convincingly realistic footage of events that never actually happened. As a result, typical deepfake detectors focus on the face in videos: first tracking it and then passing on the cropped face data to a neural network that determines whether it is real or fake. For example, eye blinking is not reproduced well in deepfakes, so detectors focus on eye movements as one way to make that determination. State-of-the-art Deepfake detectors rely on machine learning models for identifying fake videos.

The extensive spread of fake videos through social media platforms has raised significant concerns worldwide, particularly hampering the credibility of digital media, the researchers point out. “If the attackers have some knowledge of the detection system, they can design inputs to target the blind spots of the detector and bypass it,” said Paarth Neekhara, the paper’s other first coauthor and a UC San Diego computer science student.

Researchers created an adversarial example for every face in a video frame. But while standard operations such as compressing and resizing video usually remove adversarial examples from an image, these examples are built to withstand these processes. The attack algorithm does this by estimating over a set of input transformations how the model ranks images as real or fake. From there, it uses this estimation to transform images in such a way that the adversarial image remains effective even after compression and decompression.

The modified version of the face is then inserted in all the video frames. The process is then repeated for all frames in the video to create a deepfake video. The attack can also be applied on detectors that operate on entire video frames as opposed to just face crops.

The team declined to release their code so it wouldn’t be used by hostile parties.

High success rate

Researchers tested their attacks in two scenarios: one where the attackers have complete access to the detector model, including the face extraction pipeline and the architecture and parameters of the classification model; and one where attackers can only query the machine learning model to figure out the probabilities of a frame being classified as real or fake. In the first scenario, the attack's success rate is above 99 percent for uncompressed videos. For compressed videos, it was 84.96 percent. In the second scenario, the success rate was 86.43 percent for uncompressed and 78.33 percent for compressed videos. This is the first work which demonstrates successful attacks on state-of-the-art Deepfake detectors.

“To use these deepfake detectors in practice, we argue that it is essential to evaluate them against an adaptive adversary who is aware of these defenses and is intentionally trying to foil these defenses,” the researchers write. “We show that the current state of the art methods for deepfake detection can be easily bypassed if the adversary has complete or even partial knowledge of the detector.”

To improve detectors, researchers recommend an approach similar to what is known as adversarial training: during training, an adaptive adversary continues to generate new deepfakes that can bypass the current state of the art detector; and the detector continues improving in order to detect the new deepfakes.

Adversarial Deepfakes: Evaluating Vulnerability of Deepfake Detectors to Adversarial Examples

*Shehzeen Hussain, Malhar Jere, Farinaz Koushanfar, Department of Electrical and Computer Engineering, UC San Diego

Paarth Neekhara,  Julian McAuley, Department of Computer Science and Engineering, UC San Diego


 

Music and computer science professor studies the sounds of COVID

Researchers analyze coughs, vocal utterances to detect COVID-19 infection

UC San Diego music and computer science professor Shlomo Dubnov

February 5, 2021-- Millions of people already use Fitbit and other devices to monitor and track a variety of personal health metrics. Now, a researcher at the University of California San Diego has published data indicating that analyzing voice signals can detect COVID-19 infection when compared with sample audio clips from healthy speakers.

In a research paper on “Robust Detection of COVID-19 in Cough Sounds,” published in the February 2021 issue of Springer Nature’s SN Computer Science journal, UC San Diego music and computer science professor Shlomo Dubnov and colleagues spell out initial results of their work analyzing samples of coughs and utterances from patients diagnosed with the SARS-Cov2 virus against a control group of healthy subjects.

“This work displays high potential for evaluating and automatically detecting COVID-19 from web-based audio samples of an individual’s coughs and vocalizations,” said Dubnov, who co-authored the paper with Lebanese American University professor Pauline Mouawad and recent Jacobs School of Engineering alumnus Tammuz Dubnov. “We showed the robustness of our method in detecting COVID-19 in cough sounds with an overall mean accuracy of 97 percent.” With samples of the sustained vowel sound ’ah’, the accuracy was 99 percent.

“Now we’re kind of hopeful that some of this will be useful for actual applications,” add the paper’s senior author.

The project originated in a master’s thesis by Dubnov’s son Tammuz, who completed his M.S. degree in engineering sciences in UC San Diego’s Mechanical and Aerospace Engineering department in 2020. His topic: “Signal Analysis and Classification of Audio Samples from Individuals Diagnosed with COVID-19”.  Tammuz completed his degree while running a startup, Zuzor, which he founded in 2015.

“My thesis was using artificial intelligence and audio, then COVID happened,” recalls the UC San Diego alumnus. “So that was kind of the genesis of it. I was already doing a lot of work in deep learning, and I was already doing a lot of machine learning before that.  So I wondered: how we could we use this maybe to diagnose something?”

After completing his thesis, Tammuz wanted to continue the research and approached his father at UC San Diego, who was also focused on machine learning and audio – but for different applications. “I've been working on voice or musical instrument sounds, but also on singing and spoken voice,” said Dubnov, a longtime participant in the Qualcomm Institute at UC San Diego. “We're talking pretty much about sound texture, of the little details of sound, the repetition of small sound elements. We had these techniques as part of our research toolkit, so it was sort of a leap of faith to see if we could actually discriminate between COVID and non COVID.”

The machine-learning models developed for the study were “trained” on data (self-submitted audio samples) collected by the Corona Voice Detect project, a partnership between Carnegie Mellon University and the Israel-based company Voca.ai. The recordings contained audio of each individual coughing three times and then uttering the sustained vowel “ah”.

The researchers applied a combined method from nonlinear dynamics to detect COVID-19 in vocal signals – offering a reliability that could also allow detection at an earlier stage. “The robust results of our model have the potential to substantially aid in the early detection of the disease on the onset of seemingly harmless coughs,” said professor Dubnov.

The researchers insist that their model is not intended for independently diagnosing COVID-19. “I wouldn't rely on an AI to diagnose or not diagnose,” insisted Tammuz. “We're hoping more to position it like an early warning system for doctors.”

Shlomo Dubnov agrees. “It would hopefully help physicians decide whether standard tests may be necessary for a diagnosis,” he said. “It also offers a non-invasive way to do surveillance testing at the population level, including analyzing vocal sounds from microphone arrays in public spaces.”

Example of graphical sound 'fingerprints' indicating a COVID-19-related dry cough.

“COVID is a terrible respiratory disease that we're all facing now, but I'm optimistic that the vaccine will work and COVID will hopefully be a thing of the past,” said Tammuz. “But as part of this project, I ended up talking to a lot of doctors and maybe the bright side of all this is that this technology can be used for other diseases.”

Indeed, there are audio signatures associated with a broad array of medical conditions, ranging from asthma and chronic obstructive pulmonary disease to bronchitis, tuberculosis and congestive heart failure. “We have a whole list of diseases that it could be beneficial for,” he explained. “So that's kind of the commercial opportunity here.”

Professor Dubnov is now teaming with his son’s software company Zuzor on a joint proposal for a Small Business Innovation Research (SBIR) seed grant from the National Science Foundation. Their goal: to aggregate much larger datasets related to different diseases – data they will need in order to train models to do much deeper feature extraction that, for instance, would allow them to differentiate cough sounds across many different diseases.

Said Zuzor’s Tammuz Dubnov: “There are diseases that have a huge impact on many, many lives, so if we can help even a little bit with that, that could have really big implications.”

Lightening the data center energy load

UC San Diego engineers earn ARPA grant to enable efficiency through photonics

A proof-of-concept setup for an optically switched network. Photo by David Baillot

February 3, 2021-- Electrical engineers and computer scientists at UC San Diego are on the front lines of global efforts to reduce the energy used by data centers. The potential impact is great: the US government estimates that data centers currently consume more than 2.5% of U.S. electricity. This figure is projected to double in about eight years due to the expected growth in data traffic. 

The UC San Diego Jacobs School of Engineering team has been awarded a total of $7.5 million from the US Advanced Research Projects Agency-Energy (ARPA-E) and the California Energy Commission to advance nation-wide efforts to double data center energy efficiency in the next decade through deployment of new photonic— light based—network topologies. 

In particular, the UC San Diego team is focused on developing solutions to enable the thousands of computer servers within a data center to communicate with each other over advanced light and laser-based networks that replace existing electrical switches with optical switches developed within the ARPA-E program. 

“The photonic devices we’re developing aren’t actually used within the servers per se: instead, the devices connect the servers within the datacenter network using a more efficient optical  network,” said George Papen, a professor of electrical and computer engineering at UC San Diego and co-principal investigator on the project. 

“By removing bottlenecks in the network, the computer servers, which account for the majority of power in the data center, operate more efficiently. Our project, supported by ARPA-E, aims to double the server power efficiency by transforming the network into a high-speed interconnect free of these bottlenecks,” said George Porter, a professor of computer science at UC San Diego and co-principal investigator.

What’s an optical switch?

So how do these data center networks pass bits of information and computation commands around today? They use a technology called electrical packet switching, in which a message is broken down into smaller groups, or packets of data. These packets of data are converted to electrical signals and sent through a cable to a network switch, where they’re routed to the desired location and pieced back together into the original message. Network switches are physical, electrical devices with ports for wired connections, that direct the flow of data from many machines.

Unlike electronic switches, optical switches aren’t bound by the limitations of electronics to transmit data. Instead, optical switches make direct “light path” connections from input ports to output ports. Since no conversion between optical and electrical data is required at every switch, optical switches don’t have the latency or electronic logjam issues that existing network switches have, and require less power to route data. 

Using an optical network instead of an electrical network can produce a more efficient network with a larger data rate to each server. This can increase the energy efficiency of the servers, which consume most of the energy in a data center. One goal of the project is to demonstrate that the cost of such an optical network can drop below the cost of adding the additional semiconductor chips required to get the same data rate on existing electrical networks. 

“It would be lower cost in part because you’re using less energy, but also in part because if you wanted to build a very high speed network using existing commercial technology, the cost of adding additional chips to build bigger switches increases dramatically,” said Porter. “It’s not a linear relationship of double-the-speed for double-the-money; you can think of it almost like double the speed for quadruple the cost. On the other hand, optics, at these very high speeds, follows a more linear cost relationship.”

Developing a proof-of-concept

In phase one of the Lightwave Energy Efficient Datacenters (LEED)  project in the  ARPA-E Enlitened program, which ran from 2017-2019, Papen, Porter and UC San Diego colleagues Joe Ford, a professor in the Department of Electrical and Computer Engineering, and Alex Snoeren, a professor in the Department of Computer Science and Engineering, developed the photonic technology and network architecture required to enable this scale of optical switching. The collaboration between electrical engineers—who designed a new type of optical switch—and computer scientists—who developed the protocol to allow it to work at a data center scale—was key. 

Their success hinged on a new type of optical switch conceptualized by UC San Diego alumnus Max Mellette, co-founder and CEO of spinout company inFocus Networks. Instead of the full crossbar architecture that was previously used, which allows any node in the data center to talk to any other node, his idea was to create a switch that had more limited connectivity, thereby enabling faster speeds.

The key insight was to develop a network protocol that would enable this faster but less-connected architecture to communicate in a way that would still deliver the performance required. By working closely with computer scientists led by Porter and Snoeren, the team made it happen. 

By the end of Phase 1, this new optical switch was functional, able to run applications and receive data in a testbed setting. Now in Phase 2, the team is working with collaborators at Sandia National Laboratories on scaling up the architecture to function with larger amounts of data and more nodes. The goal for Phase 2 is a realistic testbed demonstration that an optical network architecture provides significant value to end-users. 

A storied history of photonics

There was a good reason this UC San Diego team was selected for the Enlitened program: it was here that, more than a decade ago, then-postdoc Porter was part of a research team also including Papen, that assembled and demonstrated the first data center testbed using an optically switched network. The paper describing this work has been cited more than 1,000 times.

Since then, Porter, Papen, Ford, Snoeren and colleagues in both the electrical engineering and computer science departments and the Center for Networked Systems have worked closely to further develop and refine the technology, and work towards making it a commercially viable reality. 

“We were the first to show we could build testbeds with optically switched networks for data centers,” Porter said. “Papen and I have been meeting multiple times a week for 10 years, supervising students together, and working on this optical data center concept for a decade; it’s a real example of what can happen when computer scientists and electrical engineers work closely together.” 

While their optical data center is still in the proof-of-concept phase, researchers agree there will come a time when the cost of adding more and more semiconductor chips to drive faster speeds simply won’t be cost competitive, putting aside the energy concerns. At that point, optical systems will become much more appealing. It’s hard to know when exactly that will be, but researchers predict it could be as soon as five years from now, and likely within 10. 

“Nonetheless, there's so much work to do to be able to validate that indeed if we can’t continually scale chips, what applications should we first apply optical switching? That will take a significant effort to sort  out,” Papen said. The researchers are working with national labs and private companies to test optical switches on various live applications to help answer this question.

Difficult, future-looking work such as this optical data center project is a perfect example of the role academic research institutions play in the innovation ecosystem.

“This is a really hard problem to solve, and hard problems take a long time,” Papen said. “Being able to devote the time to this, and collaborate with faculty and students from across the entire engineering school, is what makes this type of transformative development possible.”

Islands without structure inside metal alloys could lead to tougher materials for transportation, energy and defense

January 29, 2021: An international team of researchers produced islands of amorphous, non-crystalline material inside a class of new metal alloys known as high-entropy alloys. 

This discovery opens the door to applications in everything from landing gears, to pipelines, to automobiles. The new materials could make these lighter, safer, and more energy efficient.  

The team, which includes researchers from the University of California San Diego and Berkeley, as well as Carnegie Mellon University and University of Oxford, details their findings in the Jan. 29 issue of Science Advances. 

“These present a bright potential for increased strength and toughness since metallic glasses (amorphous metals) have a strength that is vastly superior to that of crystalline metals and alloys,” said Marc Meyers, a professor in the Department of Mechanical and Aerospace Engineering at UC San Diego, and the paper’ s corresponding author. 

Using transmission electron microscopy, which can identify the arrangement of atoms, the researchers concluded that this amorphization is triggered by extreme deformation at high velocities. It is a new deformation mechanism that can increase the strength and toughness of these high entropy alloys even further.

Proposed hierarchical deformation mechanism paradigm for the equi- atomic CrCoNi-based HEAs subjected to increasing degrees of deformation.

The research is based on seminal work by Brian Cantor at the University of Oxford, and Jien-Wei Yeh at National Tsing Hua University in Taiwan. In 2004, both researchers led teams that reported the discovery of high-entropy alloys. This triggered a global search for new materials in the same class, driven by numerous potential applications in the transportation, energy, and defense industries.

 “Significant new developments and discoveries in metal alloys are quite rare,” Meyers said. 

Amorphization in extreme deformation of the CrMnFeCoNi high-entropy alloy

Shiteng Zhao and Robert O. Ritchie, University of California Berkeley; Zezhou Li, Wen Yang and Marc A. Meyers, University of California San Diego; Chaoyi Zhu, Carnegie Mellon University; Zhouran Zhang, David E. J. Armstrong and Patrick S. Grant, University of Oxford.  


 

Women in STEM: Picture a Scientist

Bioengineering Diversity Council's Town Hall addresses issues of gender parity

January 29, 2021: Women from all different stages of their scientific careers, from undergraduate students through the UC San Diego Vice Chancellor for Research, met virtually to share their experiences as women in STEM for the UC San Diego Bioengineering Diversity Council’s Winter Quarter Town Hall. Stephanie Fraley, professor of bioengineering and chair of the Bioengineering Diversity Council, mediated a discussion among six panelists addressing topics from the film “Picture a Scientist,” including gendered harassment and discrimination. 

In addition to Fraley, the panelists included Sandra Brown, UC San Diego Vice Chancellor for Research; Dr. Sangeeta Bhatia, professor of engineering at MIT and director of the Marble Center for Cancer Nanomedicine at MIT; Daniela Valdez-Jasso, a professor of bioengineering at UC San Diego; Maya Rowell, a bioengineering PhD student and a Jacobs School Racial Equity Fellow; and Rafaela Simoes-Torigoe, a bioengineering undergraduate student. 

During the discussion, the panelists shared their experiences navigating the “minority time tax,” developing a work-life balance, setting boundaries for the diversity-promoting efforts they’re asked to participate in, and addressing the outright bullying and stereotyping they’ve witnessed. The group also shared some actionable steps to create a truly inclusive research community. 

Read a thorough recap of the discussion here. 

The UC San Diego Bioengineering Diversity Council promotes the interests and advancement of women and minorities in the bioengineering department at the Jacobs School of Engineering. 

A call to end funding discrimination against Black scientists in the United States

Network of female biomedical engineering researchers issues call to action in Cell

Karen Christman, one of the paper's co-authors, is an associate dean at the Jacobs School and a professor in the UC San Diego Department of Bioengineering.

January 26, 2021: Representatives from a network of women deans, chairs and distinguished faculty in biomedical engineering are calling upon the National Institutes of Health and other funding agencies to address disparities in allocating support to Black researchers.  The group made the call to action in the Jan. 26, 2021 issue of the journal Cell

Two engineering faculty at the University of California San Diego are coauthors: Karen Christman, associate dean at the Jacobs School of Engineering and bioengineering professor, and Padmini Rangamani, professor of mechanical and aerospace engineering. 

In examining the racial inequities and injustices that prevent Black faculty from equitably contributing to science and achieving their full potential, insufficient federal funding for research by Black scientists rose to the top as a key issue. 

According to studies of the allocation of National Institutes of Health research funding,  Black applicant award rates for research funding has stood at about 55 percent of that of white principal investigators of similar academic achievement.  Despite internal reviews of the reasons behind this disparity, and promises to do better, the funding gap continues. 

Efforts have been made to improve the pipeline to encourage Black students to prepare for and enter careers as researchers and college and university faculty. But once on the job, lack of research funding can derail these careers.  Many universities look to faculty members’ ability to support their research as part of their decisions on tenure and promotions. As a result, NIH funding disparity can end the careers of Black scientists.  In addition, without adequate research funding, these scientists can become discouraged and leave their professions.  

 

This means that fewer Black scientists remain to serve as role models and mentors for the next generation.  It also means that many important research questions vital to society are not being asked, because the perspectives, creativity, and knowledge of a diverse population of scientists are not being tapped. The public also does not see the faces or hear the voices of Black scientific experts speaking on vital issues.  

The authors of the paper make several recommendations on how research funding disparities can be eliminated.  Among the steps funding agencies might take are:

Explicitly state that racism persists in the U.S. research enterprise and that it must be expelled

Develop federal funding institute policies to immediately achieve racial funding equity

Incorporate diversity into research proposal scoring criteria; prioritize research teams that exemplify diversity; and diversify proposal review panels

Train funding agency leadership and staff as well as grant reviewers and recipients, to recognize and stop racism

“Scientific colleagues, let us each use our voices and actions to now overcome our profession’s racism and serve as antiracist agents of change,” the researchers wrote in Cell. 

They recommended ways  individual scientists and universities, colleges and institutes can move forward.  These recommendations include recognizing how they might be unintentionally contributing to systemic racism in their academic roles.  Academia, they write, must also move forward from statements of solidarity to transformative organizational changes.

In closing, the authors also look to the private sector, such as philanthropists and industrial leaders whose companies depend on scientific innovation, and to foundations and professional societies, to help offset racial disparities in research funding. The biotech company Genentech is held up as an example of leadership in reducing racial disparities in science, with its creation of a research funding awards program for Black scientists. 

Together, private and public sectors can enhance the creativity and innovation of their science and bring forward the greater good of society by funding innovative ideas and robust talents of Black scientists.

The corresponding authors on the paper, “Fund Black Scientists,” are senior author Omolola Eniola-Adefeso, the University Diversity and Social Transformation Professor of Chemical Engineering at the University of Michigan, and lead author Kelly R. Stevens, Assistant Professor of Bioengineering and Laboratory Medicine and Pathology at the University of Washington School of Medicine and UW College of Engineering.  Stevens also is an investigator at the UW Medicine Institute for Stem Cell and Regenerative Medicine. 

Other engineering faculty researchers co-authoring the paper are: Kristyn S. Masters University of Wisconsin-Madison; Princess Imoukhuede and Lori A. Setton, Washington University St. Louis; Karmella A. Haynes, Emory University; Elizabeth Cosgriff-Hernandes and Shelly Sakiyama-Elbert, University of Texas at Austin; Muyinatu A. Lediju Bell, Johns Hopkins University; Padmini Rangamani and Karen Christman, University of California San Diego; Stacey Finley, University of Southern California;  Rebecca Willits and Abigail N. Koppes, Northeastern University; Naomi Chesler, University of California-Irvine; Josephine Allen, University of Florida, Gainesville; Joyce N. Wong, Boston University; Hana El-Samad and Tejal Desai, University of California San Francisco also contributed to the Cell paper. 

 

 


 

The Spectacular Synthesis of Spider Silk

How bioengineering could bring greater sustainability to the apparel industry

Triton 5: Ji-San Lee '11

Sourcing Viral Surveillance Supplies at the Pharmacy: Understanding Consumer-Grade Materials' Viability as SARS-CoV-2 Testing Media

As the COVID-19 pandemic grew and quickly took hold of the world, one of the biggest challenges in the response efforts was determining the most effective approach to monitoring the virus’s spread. That task has become all the more critical as regional and national governments have been tasked with balancing the protection of public health against the reality that society is ill-equipped to handle a prolonged shutdown.

Even as rapid research led to more efficient testing methods, early efforts to detect SARS-CoV-2 - the virus that causes COVID-19 - were hampered by a lack of available materials approved by public health agencies such as the CDC and WHO. Questions quickly arose as to whether more widely available sampling supplies were viable alternatives.

To address these questions, a team of researchers at the Center for Microbiome Innovation at UC San Diego set out to determine whether consumer-grade materials were a safe replacement, as well as testing whether alternative storage solutions were viable options for preserving and transporting samples. Their findings, titled “Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment,” were published in Microbiome Journal on January 22, 2021.

"One of the main problems at the beginning of the pandemic in the US was supply chain shortages. Since medical- and research-grade swabs are used for sample collection during testing, we wanted to determine if consumer-grade swabs were a possible option for COVID-19 screening and testing," according to Jeremiah J Minich of the Scripps Institute of Oceanography at UC San Diego, one of the paper's lead authors.

The study approached this problem by performing a series of viral detection experiments using five different consumer-grade swabs composed of varying materials, as well as one CDC-approved swab as a control. All of the swabs were then placed in 95% ethanol and evaluated in terms of RNase activity.

Prior to this study, it was generally believed that consumer-grade swabs would contain too many contaminants to serve as sampling materials effectively. "However, our work showed that, at least in the case of SARS-CoV-2 detection, wooden-shafted and cotton-tipped swabs are suitable, provided the material is extracted from the swab head itself rather than relying on the material to be present in the surrounding fluid which is typically assessed for viral presence" noted corresponding author Austin D. Swafford, Director of Research-Innovations at the Center for Microbiome Innovation.

These findings are a boon to government and health agencies in their work to safely reopen educational and economic sectors of society. The ability to monitor the built environment for the virus using readily available materials allows for orders of magnitude more testing than previously thought.

"As we continue our efforts to monitor the environment for SARS-CoV-2 in public settings such as our hospitals, campus, and K-12 schools, we seek to provide a path to scalable, affordable monitoring. Consumer-grade surface swabs will enable a wider range of applications where the deployment of clinical-grade materials is not economically feasible," said co-author Rob Knight, professor and director of the Center for Microbiome Innovation at UC San Diego. Those efforts are expected to pay dividends quickly via UC San Diego’s Safer at School Early Alert (SASEA) program. SASEA will soon be utilizing inexpensive and readily available surface detection methods - informed largely by this study’s results - to help provide a safe path for San Diego-area students to return to their classrooms.

Comparison of CDC-approved SYN swabs, consumer-grade CGp, and bulk TMI swab congruence compared to clinical-grade hospital tests using synthetic-tipped plastic-shafted NP swabs for twenty participants in the clinical setting. a SARS-CoV-2-positive patients (n = 16) sampled with three swab types across three environments: nares, floor, and bedrail. “+” samples (dark grey = SYN, red = CGp, blue = TMI) refer to samples which tested positive for SARS-CoV-2 out of the total samples tested for that particular swab type (light-grey bar). Percentage of positive tests per swab type are below the x axis for each environmental sample. b SARS-CoV-2-negative patients (n = 4) with three swab types across three environments: nares, floor, and bedrail.

While the paper’s findings have wide-ranging implications, the benefits of deploying consumer-grade supplies to detect the virus are particularly significant in developing nations, where supply chain shortages presented even greater logistical challenges. Dr. Miguel Angel Garcia Bereguiain, of Universidad de Las Americas in Quito, Ecuador, noted the implications for his nation’s response to the pandemic. "Ecuador has experienced supply shortages at different levels of SARS-CoV-2 diagnosis, from swabs to PCR kits. During the swab shortage, public health authorities could have asked local producers to provide cotton swabs to avoid diagnosis disruption," he commented. "With this new information available, hopefully in the coming future, this problem will be avoided."

Following this research, there are further ongoing studies centered upon expanding and refining the ability to detect SARS-CoV-2 in the built environment as a means of reducing the pandemic’s spread, as well as better informing the response to future viral threats. “Hopefully, the lessons we've learned here can help set the stage for a more rapid, affordable, and widespread, perhaps citizen-scientist accessible, response to monitoring and combating current and future outbreaks,” Swafford added when discussing the study’s conclusions.

Additional co-authors include Farhana Ali, Clarisse Marotz, Pedro Belda-Ferre, Leslie Chiang, Justin P. Shaffer, Carolina S. Carpenter, Daniel McDonald, Jack Gilbert, Sarah M. Allard, Eric E Allen, and Daniel A. Sweeney, all at UC San Diego.

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

IMDD Seminar: The Innovation Ecosystem at UC San Diego

Campus Resources to Help you Translate your Research into Products and Services

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. 

File photo from 2014

January 21, 2021: 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.

January 21, 2021: 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

Goto Flickr

January 21, 2021: 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. (Read an updated FAQ with project leader and UC San Diego nanoengineering professor Jesse Jokerst on the Jacobs School blog.)

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?

The latest from Jacobs School of Engineering professors and alumni pioneering the industry.

IMDD Seminar: Introduction and Materials for Quantum Communication

Dr. Bhagawan Sahu on January 28

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. Photo taken prior to COVID-19 pandemic.

January 19, 2021: 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

Multi-fidelity approach also enables property prediction for disordered materials

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

UC San Diego and UCLA researchers find tandem repeats, which are also associated with Huntington’s disease, may contribute to ASD

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

January 13, 2021: 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.   

January 13, 2021: 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 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.  

January 13, 2021: 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

UC MRPI award will develop advanced telehealth robots to protect healthcare workers and help isolated people connect with their communities.

January 12, 2021: 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

New analyses reveal how over 60 years a critical marine species has responded to ocean acidification

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

The Jacobs School of Engineering is preparing to emerge from the pandemic stronger and more relevant than ever

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

Advance could pave the way for early warning system on COVID-19 and flu using wearables

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

The device is screen-printed, making it cheaper and easier to manufacture

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

New research from UC San Diego reveals hidden dynamics of bacteria colonies

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

Goto Flickr

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

Gift from worldwide leader in AI research will give a boost to machine learning graduate students and diversity efforts at 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

Goto Flickr

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 gif