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Soft skin patch could provide early warning for strokes, heart attacks

Two fingers press down on a soft, electronic patch against the skin.
This soft, stretchy skin patch uses ultrasound to monitor blood flow to organs like the heart and brain. This image was selected as the cover image for the July 2021 issue of Nature Biomedical Engineering.

July 22, 2021 -- Engineers at the University of California San Diego developed a soft and stretchy ultrasound patch that can be worn on the skin to monitor blood flow through major arteries and veins deep inside a person’s body.

Knowing how fast and how much blood flows through a patient’s blood vessels is important because it can help clinicians diagnose various cardiovascular conditions, including blood clots; heart valve problems; poor circulation in the limbs; or blockages in the arteries that could lead to strokes or heart attacks.

The new ultrasound patch developed at UC San Diego can continuously monitor blood flow—as well as blood pressure and heart function—in real time. Wearing such a device could make it easier to identify cardiovascular problems early on.

A team led by Sheng Xu, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering, reported the patch in a paper published July 16 in Nature Biomedical Engineering.

The patch can be worn on the neck or chest. What’s special about the patch is that it can sense and measure cardiovascular signals as deep as 14 centimeters inside the body in a non-invasive manner. And it can do so with high accuracy.

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Ultrasound patch worn on the neck. Images courtesy of Nature Biomedical Engineering

“This type of wearable device can give you a more comprehensive, more accurate picture of what’s going on in deep tissues and critical organs like the heart and the brain, all from the surface of the skin,” said Xu.

“Sensing signals at such depths is extremely challenging for wearable electronics. Yet, this is where the body’s most critical signals and the central organs are buried,” said Chonghe Wang, a former nanoengineering graduate student in Xu’s lab and co-first author of the study. “We engineered a wearable device that can penetrate such deep tissue depths and sense those vital signals far beneath the skin. This technology can provide new insights for the field of healthcare.”

Another innovative feature of the patch is that the ultrasound beam can be tilted at different angles and steered to areas in the body that are not directly underneath the patch.  

This is a first in the field of wearables, explained Xu, because existing wearable sensors typically only monitor areas right below them. “If you want to sense signals at a different position, you have to move the sensor to that location. With this patch, we can probe areas that are wider than the device’s footprint. This can open up a lot of opportunities.”

How it works

The patch is made up of a thin sheet of flexible, stretchable polymer that adheres to the skin. Embedded on the patch is an array of millimeter-sized ultrasound transducers. Each is individually controlled by a computer—this type of array is known as an ultrasound phased array. It is a key part of the technology because it gives the patch the ability to go deeper and wider.

The phased array offers two main modes of operation. In one mode, all the transducers can be synchronized to transmit ultrasound waves together, which produces a high-intensity ultrasound beam that focuses on one spot as deep as 14 centimeters in the body. In the other mode, the transducers can be programmed to transmit out of sync, which produces ultrasound beams that can be steered to different angles.

“With the phased array technology, we can manipulate the ultrasound beam in the way that we want,” said Muyang Lin, a nanoengineering Ph.D. student at UC San Diego who is also a co-first author of the study. “This gives our device multiple capabilities: monitoring central organs as well as blood flow, with high resolution. This would not be possible using just one transducer.”

The phased array consists of a 12 by 12 grid of ultrasound transducers. When electricity flows through the transducers, they vibrate and emit ultrasound waves that travel through the skin and deep into the body. When the ultrasound waves penetrate through a major blood vessel, they encounter movement from red blood cells flowing inside. This movement changes or shifts how the ultrasound waves echo back to the patch—an effect known as Doppler frequency shift. This shift in the reflected signals gets picked up by the patch and is used to create a visual recording of the blood flow. This same mechanism can also be used to create moving images of the heart’s walls. 

A potential game changer in the clinic

For many people, blood flow is not something that is measured during a regular visit to the physician. It is usually assessed after a patient shows some signs of cardiovascular problems, or if a patient is at high risk.

The standard blood flow exam itself can be time consuming and labor intensive. A trained technician presses a handheld ultrasound probe against a patient’s skin and moves it from one area to another until it’s directly above a major blood vessel. This may sound straightforward, but results can vary between tests and technicians.

Since the patch is simple to use, it could solve these problems, said Sai Zhou, a materials science and engineering Ph.D. student at UC San Diego and co-author of the study. “Just stick it on the skin, then read the signals. It’s not operator dependent, and it poses no extra work or burden to the technicians, clinicians or patients,” he said. “In the future, patients could wear something like this to do point of care or continuous at-home monitoring.”

In tests, the patch performed as well as a commercial ultrasound probe used in the clinic. It accurately recorded blood flow in major blood vessels such as the carotid artery, which is an artery in the neck that supplies blood to the brain. Having the ability to monitor changes in this flow could, for example, help identify if a person is at risk for stroke well before the onset of symptoms.

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Ultrasound patch wired to its full experimental setup.

The researchers point out that the patch still has a long way to go before it is ready for the clinic. Currently, it needs to be connected to a power source and benchtop machine in order to work. Xu’s team is working on integrating all the electronics on the patch to make it wireless.

Paper: “Continuous monitoring of deep-tissue haemodynamics with stretchable ultrasonic phased arrays.” Co-authors include Baiyan Qi*, Zhuorui Zhang*, Mitsutoshi Makihata, Boyu Liu, Yi-hsi Huang, Hongjie Hu, Yue Gu, Yimu Chen, Yusheng Lei, Shu Chien and Erik Kistler, UC San Diego; Taeyoon Lee, Yonsei University and Korea Institute of Science and Technology; and Kyung-In Jang, Daegu Gyeonbuk Institute of Science and Technology, Republic of Korea.

*These authors contributed equally

This work was supported by the National Institutes of Health (grant 1R21EB027303-01A1) and the Center for Wearable Sensors at the UC San Diego Jacobs School of Engineering.

UC San Diego among six U.S. institutions in new Wu Tsai Human Performance Alliance

The Joe and Clara Tsai Foundation makes a $220M commitment to create the Wu Tsai Human Performance Alliance, to advance human well-being through the study of peak performance

July 21, 2021--The University of California San Diego is one of six universities invited to participate in the Wu Tsai Human Performance Alliance, which publicly launched on July 21, 2021. 

The Wu Tsai Human Performance Alliance is a scientific collaboration that aims to transform human health on a global scale through the discovery and translation of the biological principles underlying human performance. 

The Alliance was created through a $220M philanthropic investment from the Joe and Clara Tsai Foundation after philanthropists Clara Wu Tsai and Joe Tsai identified an opportunity for broad societal impact by using new insights into the scientific principles underlying athletic performance to improve human fitness and thriving. 

“Scientific funding has traditionally been focused on the study of diseases,” said Clara Wu Tsai, founder of the Wu Tsai Human Performance Alliance. “We are taking the opposite approach and studying the human body at its healthiest and most vital, to enable the thriving of all people – from an Olympic Gold Medal-level athlete to a grandfather lacking the mobility to enjoy a full life.”

The Alliance is a public-private partnership comprised of scientists, clinicians, engineers, coaches, athletes and innovators from UC San Diego; as well as Stanford University; Boston Children’s Hospital, a Harvard Medical School Affiliate; University of Kansas; University of Oregon; and the Salk Institute for Biological Studies. 

The big-picture motivation of the Alliance extends to empowering all humans to perform at peak physical, intellectual and emotional capacity. 

"UC San Diego is one of six world-renowned institutions selected to help launch the Wu Tsai Human Performance Alliance," said UC San Diego Chancellor Pradeep K. Khosla. "We are uniquely equipped to help build upon fundamental, applied and clinical expertise to empower all people to perform at peak physical, intellectual and emotional capacity. UC San Diego brings to the Alliance dynamic, multi-scale modelling expertise as well as the capacity to generate bedrock experimental and clinical data that will drive new ‘living models’ of human performance and recovery. We look forward to continuing our tradition of collaborative research with friends and new partners."

 

The UC San Diego arm of the Alliance is led by Andrew McCulloch, a professor in the departments of Bioengineering and Medicine at UC San Diego and director of UC San Diego’s campus-wide Institute of Engineering in Medicine.

UC San Diego activities within the Alliance are organized around two grand challenges: a scientific project, the Multiscale Athlete, led by McCulloch; and an applied project, the Triton Center for Performance and Injury Science, led by Sam Ward, a professor in the departments of Orthopaedic Surgery and Radiology at UC San Diego Health. 

Multiscale Athlete 

For the Multiscale Athlete "moonshot" project, UC San Diego researchers are creating new generations of computational models of the musculoskeletal system. The new models will go well beyond representing a static picture of the muscles, bones, tendons and ligaments in the human body. The goal, instead, is to bring these mathematical models "to life" by incorporating biological processes so that a person’s whole-body athletic model can change and adapt over time to reflect things like injuries or changes in training regimens. 

The researchers are using the term "multiscale" because biological research is performed at multiple "scales." From small to large, these biological scales include the genetic, molecular, cellular, tissue, and organ systems scales. Through the Multiscale Athlete project and the Alliance’s Digital Athlete project at Stanford University, the UC San Diego researchers aim to weave new information and insights from all these different biological scales into whole-body mathematical models of athletic performance.

 

One of the big goals of these living models is to provide useful insights and predictions that are based on what is actually happening, at multiple scales, in a person’s muscles, bones, ligaments and tendons at any given time based on things like a particular exercise regime, a specific diet, an injury, or the details of an individual’s sleep patterns. 

"Our multiscale modeling teams are critical glue that will connect the other research teams across the Alliance. We are a synergistic layer that will make the Alliance much greater than the sum of the individual parts," said McCulloch. "UC San Diego is a recognized world-leader in multiscale modeling of living systems. It’s tremendously exciting to have this opportunity to apply our expertise to the important challenge of understanding the science of human performance and improving human thriving."

Triton Center for Performance and Injury Science

What makes the difference between being a good athlete and a great athlete? Can we predict when a dancer is at risk of injury? What can accelerate an athlete’s recovery? 

These are the kinds of questions that drive the UC San Diego researchers, and the larger efforts of the Alliance more generally. 

"The goal is to understand how the underlying biology behaves in many different human performance contexts," said Ward, who leads the Triton Center for Performance and Injury Science at UC San Diego, which is one of the Innovation Hubs of the Alliance.

"Our concept is to figure out how to fold dynamic models of molecular biology, cell biology and physiology into larger scale models of human movement to aid decision making related to performance, training, and recovery. You can ask questions and do experiments in models that you can’t do in humans. But to make the models useful, you need to get great experimental data and rigorous validation to make sure that the models represent what’s actually happening in the human body during and after training, performance, and recovery."

 

With a new "biobank" of tissue samples, ethically collected from athletes as well as laboratory animals, UC San Diego-led teams will generate new biological measurements that will feed into the engineering models in order to accurately represent what’s happening in the human body during and after exercise training and injury. 

"What sorts of training or rest will be most effective for a baseball pitcher near the end of a long season? How do we precisely pair a therapy to a specific individual with a specific injury? To make these kinds of mappings, you need to understand what’s happening biologically in the underlying tissues," said Ward.

It is the interaction between mechanics and biology that the UC San Diego team believes will create breakthroughs in our understanding of peak athletic performance, and peak human performance, more generally. 

"If you don’t understand what’s going on with the underlying biological ‘state’ of tissues, in the cells themselves, you can’t make a prediction about what is going to cause an injury, improve training, or accelerate healing," said Ward. 

Putting the pieces together

Through the Multiscale Athlete moonshot project and the Performance and Injury Science innovation hub, the UC San Diego teams are pulling in the same direction. 

UC San Diego researchers will use tissue samples from the biobank to run laboratory experiments looking for biological information at multiple scales that offers insights on athletic performance, or injury recovery.  

One of the likely scenarios is the following: first, researchers identify genetic, molecular or cellular information in laboratory experiments on tissue samples that point to new ideas about athletic performance or recovery after exercise or after injury. Laboratory experiments will inform and validate the team’s computer simulations, which will inspire additional experiments. 

The researchers will then be able to apply insights that emerge from this feedback loop between laboratory experiments and computational models to predict what will occur in humans, in terms of anatomy and physiology. Biomarkers in sweat, saliva or blood of human athletes; or information that can be picked up via non-invasive imaging tools, will help the research teams translate their insights to humans.   

To dive deeper into the actual experiences of elite athletes, the UC San Diego researchers are also collaborating with UC San Diego Athletics and other groups in the San Diego community. 

“In athletics, as in life, we know that injuries occur when demand exceeds capacity. The Wu Tsai Human Performance Alliance provides an excellent opportunity to understand better the success factors driving physical readiness associated with optimal performance in sport and life," said Matt Kritz, PhD, Senior Associate Athletic Director for Athletic Performance and Health at UC San Diego.

Scientific advances and successes that emerge from the Alliance will be freely accessible to everyone—to scientists, to athletes and coaches, to clinicians and health care personnel, to technology designers, and to the general public. The aim is to enable people with all kinds of bodies to thrive at every stage of life.

 

UC San Diego projects and collaborators include:

Multiscale Models of Musculoskeletal Tissue States

Andrew McCulloch, UC San Diego Departments of Bioengineering and Medicine

Systems Biology of Musculoskeletal Tissue States

Padmini Rangamani, UC San Diego Department of Mechanical and Aerospace Engineering
Pradipta Ghosh, UC San Diego School of Medicine 

Mechanobiology of Cell and Matrix interactions

Adam Engler, UC San Diego Department of Bioengineering
Stephanie Fraley, UC San Diego Department of Bioengineering 

Biomechanics of Musculoskeletal Tissues

Daniela Valdez-Jasso, UC San Diego Department of Bioengineering
Andrew McCulloch, UC San Diego Department of Bioengineering

Performance Evolution

Kimberly Cooper, UC San Diego Division of Biological Sciences 

Triton Center for Performance and Injury Science

Sam Ward, UC San Diego Health Sciences
Robert Sah, UC San Diego Department of Bioengineering
UC San Diego Athletics
Rady Children’s Hospital  

UC San Diego among six U.S. institutions in new Wu Tsai Human Performance Alliance

The Joe and Clara Tsai Foundation makes a $220M commitment to create the Wu Tsai Human Performance Alliance, to advance human well-being through the study of peak performance

July 21, 2021--The University of California San Diego is one of six universities invited to participate in the Wu Tsai Human Performance Alliance, which publicly launched on July 21, 2021. 

The Wu Tsai Human Performance Alliance is a scientific collaboration that aims to transform human health on a global scale through the discovery and translation of the biological principles underlying human performance. 

The Alliance was created through a $220M philanthropic investment from the Joe and Clara Tsai Foundation after philanthropists Clara Wu Tsai and Joe Tsai identified an opportunity for broad societal impact by using new insights into the scientific principles underlying athletic performance to improve human fitness and thriving. 

“Scientific funding has traditionally been focused on the study of diseases,” said Clara Wu Tsai, founder of the Wu Tsai Human Performance Alliance. “We are taking the opposite approach and studying the human body at its healthiest and most vital, to enable the thriving of all people – from an Olympic Gold Medal-level athlete to a grandfather lacking the mobility to enjoy a full life.”

The Alliance is a public-private partnership comprised of scientists, clinicians, engineers, coaches, athletes and innovators from UC San Diego; as well as Stanford University; Boston Children’s Hospital, a Harvard Medical School Affiliate; University of Kansas; University of Oregon; and the Salk Institute for Biological Studies. 

The big-picture motivation of the Alliance extends to empowering all humans to perform at peak physical, intellectual and emotional capacity. 

"UC San Diego is one of six world-renowned institutions selected to help launch the Wu Tsai Human Performance Alliance," said UC San Diego Chancellor Pradeep K. Khosla. "We are uniquely equipped to help build upon fundamental, applied and clinical expertise to empower all people to perform at peak physical, intellectual and emotional capacity. UC San Diego brings to the Alliance dynamic, multi-scale modelling expertise as well as the capacity to generate bedrock experimental and clinical data that will drive new ‘living models’ of human performance and recovery. We look forward to continuing our tradition of collaborative research with friends and new partners."

 

The UC San Diego arm of the Alliance is led by Andrew McCulloch, a professor in the departments of Bioengineering and Medicine at UC San Diego and director of UC San Diego’s campus-wide Institute of Engineering in Medicine.

UC San Diego activities within the Alliance are organized around two grand challenges: a scientific project, the Multiscale Athlete, led by McCulloch; and an applied project, the Triton Center for Performance and Injury Science, led by Sam Ward, a professor in the departments of Orthopaedic Surgery and Radiology at UC San Diego Health. 

Multiscale Athlete 

For the Multiscale Athlete "moonshot" project, UC San Diego researchers are creating new generations of computational models of the musculoskeletal system. The new models will go well beyond representing a static picture of the muscles, bones, tendons and ligaments in the human body. The goal, instead, is to bring these mathematical models "to life" by incorporating biological processes so that a person’s whole-body athletic model can change and adapt over time to reflect things like injuries or changes in training regimens. 

The researchers are using the term "multiscale" because biological research is performed at multiple "scales." From small to large, these biological scales include the genetic, molecular, cellular, tissue, and organ systems scales. Through the Multiscale Athlete project and the Alliance’s Digital Athlete project at Stanford University, the UC San Diego researchers aim to weave new information and insights from all these different biological scales into whole-body mathematical models of athletic performance.

 

One of the big goals of these living models is to provide useful insights and predictions that are based on what is actually happening, at multiple scales, in a person’s muscles, bones, ligaments and tendons at any given time based on things like a particular exercise regime, a specific diet, an injury, or the details of an individual’s sleep patterns. 

"Our multiscale modeling teams are critical glue that will connect the other research teams across the Alliance. We are a synergistic layer that will make the Alliance much greater than the sum of the individual parts," said McCulloch. "UC San Diego is a recognized world-leader in multiscale modeling of living systems. It’s tremendously exciting to have this opportunity to apply our expertise to the important challenge of understanding the science of human performance and improving human thriving."

Triton Center for Performance and Injury Science

What makes the difference between being a good athlete and a great athlete? Can we predict when a dancer is at risk of injury? What can accelerate an athlete’s recovery? 

These are the kinds of questions that drive the UC San Diego researchers, and the larger efforts of the Alliance more generally. 

"The goal is to understand how the underlying biology behaves in many different human performance contexts," said Ward, who leads the Triton Center for Performance and Injury Science at UC San Diego, which is one of the Innovation Hubs of the Alliance.

"Our concept is to figure out how to fold dynamic models of molecular biology, cell biology and physiology into larger scale models of human movement to aid decision making related to performance, training, and recovery. You can ask questions and do experiments in models that you can’t do in humans. But to make the models useful, you need to get great experimental data and rigorous validation to make sure that the models represent what’s actually happening in the human body during and after training, performance, and recovery."

 

With a new "biobank" of tissue samples, ethically collected from athletes as well as laboratory animals, UC San Diego-led teams will generate new biological measurements that will feed into the engineering models in order to accurately represent what’s happening in the human body during and after exercise training and injury. 

"What sorts of training or rest will be most effective for a baseball pitcher near the end of a long season? How do we precisely pair a therapy to a specific individual with a specific injury? To make these kinds of mappings, you need to understand what’s happening biologically in the underlying tissues," said Ward.

It is the interaction between mechanics and biology that the UC San Diego team believes will create breakthroughs in our understanding of peak athletic performance, and peak human performance, more generally. 

"If you don’t understand what’s going on with the underlying biological ‘state’ of tissues, in the cells themselves, you can’t make a prediction about what is going to cause an injury, improve training, or accelerate healing," said Ward. 

Putting the pieces together

Through the Multiscale Athlete moonshot project and the Performance and Injury Science innovation hub, the UC San Diego teams are pulling in the same direction. 

UC San Diego researchers will use tissue samples from the biobank to run laboratory experiments looking for biological information at multiple scales that offers insights on athletic performance, or injury recovery.  

One of the likely scenarios is the following: first, researchers identify genetic, molecular or cellular information in laboratory experiments on tissue samples that point to new ideas about athletic performance or recovery after exercise or after injury. Laboratory experiments will inform and validate the team’s computer simulations, which will inspire additional experiments. 

The researchers will then be able to apply insights that emerge from this feedback loop between laboratory experiments and computational models to predict what will occur in humans, in terms of anatomy and physiology. Biomarkers in sweat, saliva or blood of human athletes; or information that can be picked up via non-invasive imaging tools, will help the research teams translate their insights to humans.   

To dive deeper into the actual experiences of elite athletes, the UC San Diego researchers are also collaborating with UC San Diego Athletics and other groups in the San Diego community. 

“In athletics, as in life, we know that injuries occur when demand exceeds capacity. The Wu Tsai Human Performance Alliance provides an excellent opportunity to understand better the success factors driving physical readiness associated with optimal performance in sport and life," said Matt Kritz, PhD, Senior Associate Athletic Director for Athletic Performance and Health at UC San Diego.

Scientific advances and successes that emerge from the Alliance will be freely accessible to everyone—to scientists, to athletes and coaches, to clinicians and health care personnel, to technology designers, and to the general public. The aim is to enable people with all kinds of bodies to thrive at every stage of life.

 

UC San Diego projects and collaborators include:

Multiscale Models of Musculoskeletal Tissue States

Andrew McCulloch, UC San Diego Departments of Bioengineering and Medicine

Systems Biology of Musculoskeletal Tissue States

Padmini Rangamani, UC San Diego Department of Mechanical and Aerospace Engineering
Pradipta Ghosh, UC San Diego School of Medicine 

Mechanobiology of Cell and Matrix interactions

Adam Engler, UC San Diego Department of Bioengineering
Stephanie Fraley, UC San Diego Department of Bioengineering 

Biomechanics of Musculoskeletal Tissues

Daniela Valdez-Jasso, UC San Diego Department of Bioengineering
Andrew McCulloch, UC San Diego Department of Bioengineering

Performance Evolution

Kimberly Cooper, UC San Diego Division of Biological Sciences 

Triton Center for Performance and Injury Science

Sam Ward, UC San Diego Health Sciences
Robert Sah, UC San Diego Department of Bioengineering
UC San Diego Athletics
Rady Children’s Hospital  

Calling all couch potatoes: this finger wrap can let you power electronics while you sleep

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This thin, flexible strip can be worn on a fingertip and generate small amounts of electricity when a person’s finger sweats or presses on it.

July 13, 2021 -- A new wearable device turns the touch of a finger into a source of power for small electronics and sensors. Engineers at the University of California San Diego developed a thin, flexible strip that can be worn on a fingertip and generate small amounts of electricity when a person’s finger sweats or presses on it.

What’s special about this sweat-fueled device is that it generates power even while the wearer is asleep or sitting still. This is potentially a big deal for the field of wearables because researchers have now figured out how to harness the energy that can be extracted from human sweat even when a person is not moving.

This type of device is the first of its kind, said co-first author Lu Yin, a nanoengineering Ph.D. student at the UC San Diego Jacobs School of Engineering. “Unlike other sweat-powered wearables, this one requires no exercise, no physical input from the wearer in order to be useful. This work is a step forward to making wearables more practical, convenient and accessible for the everyday person.”

The new wearable energy harvester is described in a paper published July 13 in Joule.

The device also generates extra power from light finger presses—so activities such as typing, texting, playing the piano or tapping in Morse code can also become sources of energy.

“We envision that this can be used in any daily activity involving touch, things that a person would normally do anyway while at work, at home, while watching TV or eating,” said Joseph Wang, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering and the study’s senior author. “The goal is that this wearable will naturally work for you and you don’t even have to think about it.”

The device derives most of its power from sweat produced by the fingertips, which are 24-hour factories of perspiration. It’s a little-known fact that the fingertips are one of the sweatiest spots on the body; each one is packed with over a thousand sweat glands and can produce between 100 to 1000 times more sweat than most other areas on the body.

“The reason we feel sweatier on other parts of the body is because those spots are not well ventilated,” said Yin. “By contrast, the fingertips are always exposed to air, so the sweat evaporates as it comes out. So rather than letting it evaporate, we use our device to collect this sweat, and it can generate a significant amount of energy.”

But not just any sweat-fueled device can work on the fingertip. Collecting sweat from such a small area and making it useful required some innovative materials engineering, explained Yin. The researchers had to build different parts of the device to be super absorbent and efficient at converting the chemicals in human sweat into electrical energy.

Yin worked on this project with UC San Diego nanoengineering Ph.D. students Jong-Min Moon and Juliane Sempionatto, who are the study’s other co-first authors, as part of a team led by Wang, who is also the director of the Center for Wearable Sensors at UC San Diego. Wang and his team pioneered sweat-fueled wearables 8 years ago. Since then, they have been building on the technology to create new and better ways to power wearables using sustainable sources, such as the wearers themselves and their surroundings.

This latest energy harvesting technology is especially unique in that it could serve as a power source anytime, anywhere. It does not have the same limitations as, say, solar cells, which only work under sunlight, or thermoelectric generators, which only work when there’s a large temperature difference between the device and the surroundings.

How it works

The device is a thin, flexible strip that can be wrapped around the fingertip like a Band-Aid. A padding of carbon foam electrodes absorbs sweat and converts it into electrical energy. The electrodes are equipped with enzymes that trigger chemical reactions between lactate and oxygen molecules in sweat to generate electricity. Underneath the electrodes is a chip made of what’s called a piezoelectric material, which generates additional electrical energy when pressed.

As the wearer sweats or presses on the strip, the electrical energy gets stored in a small capacitor and is discharged to other devices when needed.

The researchers had a subject wear the device on one fingertip while doing sedentary activities. From 10 hours of sleep, the device collected almost 400 millijoules of energy—this is enough to power an electronic wristwatch for 24 hours. From one hour of casual typing and clicking on a mouse, the device collected almost 30 millijoules.

And this is just from one fingertip. Strapping devices on the rest of the fingertips would generate 10 times more energy, the researchers said.

“By using the sweat on the fingertip—which flows out naturally regardless of where you are or what you’re doing—this technology provides a net gain in energy with no effort from the user. This is what we call a maximum energy return on investment,” said Wang.

“Compare this to a device that harvests energy as you exercise,” explained Yin. “When you are running, you are investing hundreds of joules of energy only for the device to generate millijoules of energy. In that case, your energy return on investment is very low. But with this device, your return is very high. When you are sleeping, you are putting in no work. Even with a single finger press, you are only investing about half a millijoule.”

In other experiments, the researchers connected their energy harvester to an electronic system consisting of a chemical sensor connected to a small low-power display, which shows a numerical reading of the sensor’s data. Either pressing the energy harvester 10 times every 10 seconds or simply wearing it on the fingertip for two minutes was enough to power both the sensor and the display. In one experiment, the researchers hooked up their device to a vitamin C sensor that they developed in the lab. They had a subject take a vitamin C pill and then use the finger-powered system to read their vitamin C level. In another experiment, the researchers showed that their system could also be used with a lab-built sodium sensor to read the sodium ion level of a saltwater solution.

“Our goal is to make this a practical device,” said Yin. “We want to show that this is not just another cool thing that can generate a small amount of energy and then that’s it—we can actually use the energy to power useful electronics such as sensors and displays.”

To that end, the team is making further improvements to the device so that it is more efficient and durable. Future studies will include combining it with other types of energy harvesters to create a new generation of self-powered wearable systems.

Paper: “A Passive Perspiration Biofuel Cell: High Energy Return on Investment.” Co-authors include Muyang Lin, Mengzhu Cao, Alexander Trifonov, Fangyu Zhang, Zhiyuan Lou, Jae-Min Jeong, Sang-Jin Lee and Sheng Xu, UC San Diego.

This work was supported by the Center for Wearable Sensors at the UC San Diego Jacobs School of Engineering. 

Artificial Intelligence Could Be New Blueprint for Precision Drug Discovery

Mathematical approach could transform drug development by searching for disease targets, then predicting if a drug will be successful

July 12, 2021--Writing in the July 12, 2021 online issue of Nature Communications, researchers at University of California San Diego describe a new approach that uses machine learning to hunt for disease targets and then predicts whether a drug is likely to receive FDA approval. 

The study findings could measurably change how researchers sift through big data to find meaningful information with significant benefit to patients, the pharmaceutical industry and the nation’s health care systems. 

Pradipta Ghosh, MD, is senior author of the study and professor in the departments of Medicine and Cellular and Molecular Medicine at UC San Diego School of Medicine.

“Academic labs and pharmaceutical and biotech companies have access to unlimited amounts of ‘big data’ and better tools than ever to analyze such data. However, despite these incredible advances in technology, the success rates in drug discovery are lower today than in the 1970s,” said Dr. Pradipta Ghosh, senior author of the study and professor in the departments of Medicine and Cellular and Molecular Medicine at UC San Diego School of Medicine. 

“This is mostly because drugs that work perfectly in preclinical inbred models, such as laboratory mice, that are genetically or otherwise identical to each other, don’t translate to patients in the clinic, where each individual and their disease is unique. It is this variability in the clinic that is believed to be the Achilles heel for any drug discovery program.” 

In the new study, Ghosh and colleagues replaced the first and last steps in preclinical drug discovery with two novel approaches developed within the UC San Diego Institute for Network Medicine (iNetMed), which unites several research disciplines to develop new solutions to advance life sciences and technology and enhance human health. 

The researchers used the disease model for inflammatory bowel disease (IBD), which is a complex, multifaceted, relapsing autoimmune disorder characterized by inflammation of the gut lining. Because it impacts all ages and reduces the quality of life in patients, IBD is a priority disease area for drug discovery and is a challenging condition to treat because no two patients behave similarly.

“Our study shows how the likelihood of success in phase III clinical trials, for any target, can be determined with mathematical precision,” said Debashis Sahoo, PhD, co-senior author of the study who leads PreCSN and is associate professor in the departments of Pediatrics and Computer Science at UC San Diego School of Medicine and UC San Diego. 

 “Our approach could provide the predictive horsepower that will help us understand how diseases progress, assess a drug’s potential benefits and strategize how to use a combination of therapies when current treatment is failing,” Sahoo said.

The first step, called target identification, used an artificial intelligence (AI) methodology developed by The Center for Precision Computational System Network (PreCSN), the computational arm of iNetMed. The AI approach helps model a disease using a map of successive changes in gene expression at the onset and during the progression of the disease. What sets this mapping apart from other existing models is the use of mathematical precision to recognize and extract all possible fundamental rules of gene expression patterns, many of which are overlooked by current methodologies. 

Soumita Das, PhD, is co-senior author of the study, director of the HUMANOID center and an associate professor in the Department of Pathology at UC San Diego School of Medicine.

The underlying algorithms ensure that the identified gene expression patterns are ‘invariant’ regardless of different disease cohorts. In other words, PreCSN builds a map that extracts information that applies to all IBD patients. 

“In head-to-head comparisons, we demonstrated the superiority of this approach over existing methodologies to accurately predict ‘winners’ and ‘losers’ in clinical trials,” said Ghosh. 

The last step, called target validation in preclinical models, was conducted in a first-of-its-kind Phase ‘0’ clinical trial using a living biobank of organoids created from IBD patients at The HUMANOID Center of Research Excellence (CoRE), the translational arm of iNetMed. 

The Phase ‘0’ approach involves testing the efficacy of the drugs identified using the AI model on human disease organoid models—cultured human cells in a 3D environment that mimic diseases outside of the body. In this case, an IBD-afflicted gut-in-a-dish. 

“The ‘phase 0’ trial concept was developed because most drugs fail somewhere between phases I and III. Before proceeding to patients in the clinic, ‘phase 0’ tests efficacy in the human disease models, where ineffective compounds can be rejected early in the process, saving millions of dollars,” said Soumita Das, PhD, co-senior author of the study, director of the HUMANOID center and an associate professor in the Department of Pathology at UC San Diego School of Medicine.

Biopsy tissues for the study were taken during colonoscopy procedures involving IBD patients. Those biopsies were used as the source of stem cells to grow organoids. 

“There were two major surprises. First, we saw that despite being away from the immune cells in the gut wall and the trillions of microbes that are in the gut lining, these organoids from IBD patients showed the tell-tale features of a leaky gut with broken cell borders,” said Das.

“Second, the drug identified by the AI model not only repaired the broken barriers, but also protected them against the onslaught of pathogenic bacteria that we added to the gut model. These findings imply that the drug could work in both acute flares as well as for maintenance therapy for preventing such flares.”

The researchers found the computational approach had a surprisingly high level of accuracy across diverse cohorts of IBD patients, and together with the Phase ‘0’ approach, they developed a first-in-class therapy to restore and protect the leaky gut barrier in IBD. 

Debashis Sahoo, PhD, is co-senior author of the study who leads PreCSN and is associate professor in the departments of Pediatrics and Computer Science at UC San Diego School of Medicine and UC San Diego

The authors said next steps include testing if the drug that passed the human phase ‘0’ trial in a dish can pass phase III trials in clinic; and whether the same methodologies can be used with other diseases, ranging from diverse types of cancers and Alzheimer’s disease to non-alcoholic fatty liver disease. 

“Our blueprint has the potential to shatter status quo and deliver better drugs for chronic diseases that have yet to have good therapeutic solutions,” said Ghosh.

Co-authors include: Lee Swanson, Ibrahim Sayed, Gajanan Katkar, Stella-Rita Ibeawuchi, Yash Mittal, Rama Pranadinata, Courtney Tindle, Mackenzie Fuller, Dominik Stec and John Chang, all with UC San Diego. 

This study was supported in part, the National Institutes of Health (grants AI141630, DK107585, R56 AG069689, UG3TR003355, UG3TR002968, R01-AI55696, T32 DK 007202, 1TL1TR001443, 3R01DK107585-02S1), the DiaComp Pilot and Feasibility Award (R00-CA151673, R01-GM138385), Padres Pedal the Cause/C3 Collaborative Translational Cancer Research Award (#PTC2017), the Leona M. and Harry B. Helmsley Charitable Trust and The American Association of Immunologists Intersect Fellowship Program for Computational Scientists and Immunologists. 

Disclosure: Soumita Das, Debashis Sahoo and Pradipta Ghosh have a patent on the methodology.

Ishwar K. Puri named USC vice president for research

Women in Engineering --Anna Pridmore, P.E., Ph.D.

Machine learning enhances non-verbal communication in online classrooms

If concertmaster (top left) looks at her camera, it will appear to the musicians that she is looking at all of them. But gaze tracking system shows she is looking at Walter (second row center), and labels the concertmaster’s video feed with the cue “Walter” so the entire class knows intended gaze recipient. The cue updates continuously when she looks at another musician – establishing non-verbal communication with the ensemble.

June 21, 2021--Researchers in the Center for Research on Entertainment and Learning (CREL) at the University of California San Diego have developed a system to analyze and track eye movements to enhance teaching in tomorrow’s virtual classrooms – and perhaps future virtual concert halls.

UC San Diego music and computer science professor Shlomo Dubnov, an expert in computer music who directs the Qualcomm Institute-based CREL, began developing the new tool to deal with a downside of teaching music over Zoom during the COVID-19 pandemic.

“In a music classroom, non-verbal communication such as facial affect and body gestures is critical to keep students on task, coordinate musical flow and communicate improvisational ideas,” said Dubnov. “Unfortunately, this non-verbal aspect of teaching and learning is dramatically hampered in the virtual classroom where you don’t inhabit the same physical space.”

To overcome the problem, Dubnov and Ph.D. student Ross Greer recently published a conference paper on a system that uses eye tracking and machine learning to allow an educator to make ‘eye contact’ with individual students or performers in disparate locations – and lets each student know when he or she is the focus of the teacher’s attention.

The researchers built a prototype system and undertook a pilot study in a virtual music class at UC San Diego via Zoom.

“Our system uses a camera to capture the presenter’s eye movements to track where they are looking on screen,” explained Greer, an electrical and computer engineering Ph.D. student in UC San Diego’s Jacobs School of Engineering. “We divided the screen into 91 squares, and after determing the location of the teacher’s face and eyes, we came up with a ‘gaze-estimation’ algorithmm that provides the best estimate of which box – and therefore which student – the teacher is looking at.”

As the system recognizes a change in where the teacher is looking, the algorithm determines the identity of the student and tags his or her name on screen so everyone knows whom the presenter is focusing on.

In the pilot study, Dubnov and Greer found the system to be highly accurate in estimating the presenter’s gaze – managing to get within three-quarters of an inch (2cm) of the correct point on a 27.5 x 13 inches (70x39cm) screen. “In principle,” Greer told New Scientist magazine, “the system should work well on small screens, given enough quality data.”

One downside, according to Dubnov: the further the presenter is from the camera, the eyes become smaller and harder to track, resulting in less accurate gaze estimation. Yet with better training data, higher-quality camera resolution, and further advances in tracking facial and body gestures, he thinks the system could even allow the conductor to wield a baton remotely and conduct a distributed symphony orchestra -- even if every musician is located somewhere else.

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Ross Greer and Shlomo Dubnov, Eye-Tracking Software Could Make Video Calls Fee More LifelikeProceedings of CSME (2021), ISBN: 978-989-758-502-9  DOI: 10.5220/0010539806980708

Bio-inspired hydrogel protects the heart from post-op adhesions

Researchers developed a device to spray the hydrogel during surgeries. Download high resolution version of this image on Flickr.  Image credit:  UC San Diego Jacobs School of Engineering / David Baillot

June 18, 2021-- A hydrogel that forms a barrier to keep heart tissue from adhering to surrounding tissue after surgery was developed and successfully tested in rodents by a team of University of California San Diego researchers. The team of engineers, scientists and physicians also conducted a pilot study on porcine hearts, with promising results.

They describe their work in the June 18, 2021 issue of Nature Communications.

In rats, the hydrogel prevented the formation of adhesions altogether. In a small pilot study, porcine hearts treated with the hydrogel experienced less severe adhesions that were easier to remove. In addition, the hydrogel did not appear to cause chronic inflammation. 

Adhesions--organ tissue sticking to surrounding tissue--are a relatively common problem when surgeons need to operate again at the same site, which happens in 20 percent of cases every year in cardiac surgery. Re-operations are particularly common when the patients are children suffering from cardiac malformations--as the child’s heart grows, additional interventions are needed. 

Adhesions form within the first 30 days post-op and can complicate operations and increase the risk of mortality during interventions. In some cases, they can also interfere with proper heart function or completely prevent a repeat surgery. One of the paper’s senior authors, UC San Diego bioengineering professor Karen Christman, experienced this when one of her uncles couldn’t have  a heart valve repaired because of severe adhesions. 

“Our work is an engineering solution driven by a medical problem,” said Christman, who co-founded a company, Karios Technologies, to bring the hydrogel into the clinic. “And now it’s poised to significantly improve cardiac surgery, both for adults and children.”

The work brought together not only bioengineers and physicians, but also chemists and materials scientists.  

In academic medical centers such as UC San Diego, most surgeons conduct repeat operations and encounter adhesions fairly regularly. In this study, in rats, 70 percent of animals in the control group developed severe adhesions. 

Currently there are no FDA approved products marketed for preventing adhesions after heart surgery.  “This product will have a significant impact on the lives of many patients who potentially require repeat operations, either on the heart or anywhere else in the body,” said Dr. Michael M. Madani, chair of the Division of Cardiovascular and Thoracic Surgery at UC San Diego Health and one of the paper’s co-authors.

How it’s made

By contrast, the hydrogel developed by bioengineers in Christman’s lab is designed specifically to meet both the patients’ and surgeons’ needs. It’s sprayable, so easy to apply. Once sprayed onto tissue, it binds to the heart muscle and turns into a soft, elastic coating that creates a protective barrier, while still allowing for movement. The gel can be easily removed from tissue and dissolves after more than four to six weeks. 

The biggest challenge was making sure that the hydrogel attaches strongly  enough to the heart but doesn’t swell, as swelling can put dangerous pressure on the heart. Christman and team used what’s known as crosslinking chemistry, which consists of linking two molecules together with a covalent bond, to accomplish this. Masaki Fujita, the paper’s first author and a visiting scientist in the Department of Bioengineering at UC San Diego, had the idea of using a compound known as catechol, similar to what mussels use to adhere to rocks, to ensure the hydrogel stayed in place on the heart. 

Catechol contains an amino acid, L-dopa, that is a muscle binding protein. In this case, it was added to the gel base, a water soluble polymer, known as PEG. The result is a hydrogel that sticks onto the organ it is applied to, but then creates a protective barrier that lasts at least up to four weeks before dissolving. By that point, adhesions are less likely to form. To the researchers’ knowledge, it’s the first time this type of formulation has been used for preventing adhesions after surgery.

Spraying device

Left: a rodent heart treated with the hydrogel post-op shows little to no adhesions two weeks post-op. Right: a heart from the control rodent group shows severe adhesions.

Researchers also designed a device to safely and accurately spray the hydrogel inside the area where open heart surgery is being performed. The device houses the hydrogel’s two main components in two different chambers. Each component is made of PEG with different reactive groups that crosslink together to form the hydrogel. One of the solutions also includes the catechol-modified PEG to ensure it stays on the heart. The two mix as they exit the device, forming a gel. The process is akin to using two cans of spray paint, for example blue and yellow, to create a third color, green. 

Next steps and bigger picture

The next step is to do a large-scale trial in pigs to refine dosage and examine how the hydrogel binds to sutures and drains. The ultimate goal is to conduct a human pediatric study in 18 months to two years and bring the product to the FDA for approval in five years.

Karios Technologies is licensing the technology from UC San Diego.  “We want feedback from surgeons,” Gregory, CEO of Karios Technologies said. “We designed this material specifically for use on the heart and ease of use by the surgeon.”

The technology could easily translate to other organs also requiring multiple operations and susceptible to adhesions, researchers said. 

The work was funded by the National Heart, Lung and Blood Institute through the UC Center for Accelerated Innovation, and the National Center for Advancing Translational Sciences through the UC San Diego Center for Clinical and Translational Research Institute. 

Christman co-founded and holds equity interest in Karios Technologies, a startup that aims to commercialize the hydrogel technology. Dr. Madani is a consultant for the company. Christman, Fujita and Madani are inventors on patents and patent applications related to the work. 

 

Imperfections in jewels used as sensors for new quantum materials

'It Feels Like I'm Talking into a Void': How Do We Improve the Virtual Classroom?

 

A pseudonymous snapshot of a discussion-based lecture at UC San Diego. Most students are not sharing videos and all are muted except the one person who is speaking.

June 17, 2021--The COVID pandemic precipitated a major shift to virtual learning—an unplanned test of whether these technologies can scale effectively. But did they?

Researchers in the UC San Diego Department of Computer Science and Engineering wanted to look beyond the anecdotal evidence to better understand where remote education fell short and how we might improve it. In a study presented at the Association for Computing Machinery’s Conference on Human Factors in Computing Systems (CHI), the team examined faculty and student attitudes towards virtual classrooms and proposed several technological refinements that could improve their experience, such as flexible distribution of student video feeds and enhanced chat functions.

“We wanted to understand instructor and student perspectives and see how we can marry them,” said Nadir Weibel, a computer science associate professor and senior author on the paper. “How can we improve students’ experience and give better tools to instructors?”

The project was initiated and led by computer science Ph.D. student and first author Matin Yarmand. With coauthors Scott Klemmer, a professor of cognitive science and computer science, and Carnegie Mellon University Ph.D. student Jaemarie Solyst, the team interviewed seven UC San Diego faculty members to better understand their experience. Their primary fault with online learning is that many students never turn their cameras on.

“When I’m presenting the lecture content, it feels like I’m talking into a void,” said one professor. “How do I tell whether students are engaged?” asked another. “You have no sense if people are getting it or not getting it.”

The researchers then distributed student surveys. The 102 responses they showed—not surprisingly—that students resist turning on their cameras and often remain muted. Some don’t want their peers to see them; others are eating or performing unrelated tasks; some are unaware video feedback helps instructors; and a hardcore few see no need to turn their cameras on at all.

While students feel awkward asking questions on video, they overwhelmingly like chat functions, which make them more likely to participate. “I’m more comfortable asking questions in chat, since I feel less like I’m interrupting the lecture,” said one respondent. The survey also showed chat rooms drive more community among students. As a result, the authors propose that text communication could promote student engagement and community, even in in-person classrooms.

Students also have trouble connecting with instructors. Online classes lack opportunities for short conversations and questions that can happen during “hallway time” before and after live lectures.

Gathering together, virtually

The Gather lounge contains the instructor’s office in the middle and many other spaces for student collaboration. The red ellipses indicate small group interactions that are taking place before the lecture starts.

In response to these concerns, the researchers have suggested potential solutions. Technology that reads social cues, such as facial expressions or head nods, could provide invaluable feedback for instructors. Video feeds could also be refined to make instructors the center of attention, as they are in real-life classrooms, rather than one of many co-equal video boxes.

Increased chat use could improve both online and in-person classes, as some students have always been reluctant to call attention to themselves.

Weibel and colleagues have also been exploring how virtual reality environments could improve online learning. Using a tool called Gather, they have been testing an instructor lounge, in which students and faculty could meet before or even during class.

“The way Gather works is you move your avatar around in the space, and if it gets close enough to somebody, you can have a one-to-one conversation with just that person,” said Weibel. “Nobody else is part of it. People can just come and talk to me directly or chat with their friends and peers.”

The team is also working on a natural language processing bot that could make the experience more interactive. For example, if two people are struggling on the same assignment, it could connect them to improve collaboration or point to additional resources on Canvas.

The authors believe online classes, such as MOOCs, which were popular before COVID, will continue into the future. Weibel hopes this research and other efforts will refine the technology and improve the online learning experience.

“Some classes will be back in person,” he said. “Some will be only online and some will be hybrid, but I think online learning is probably here to stay.”

AI predicts how patients with viral infections, including COVID-19, will fare

This image shows specialized lung cells (resembling a beaded necklace) that may mount a cytokine storm in response to some viral infections.

June 17, 2021--Debashis Sahoo, a professor in the UC San Diego Department of Computer Science and Engineering and of pediatrics at UC San Diego School of Medicine, along with other researchers at the School of Medicine have used an artificial intelligence algorithm to sift through terabytes of gene expression data — which genes are “on” or “off” during infection — to look for shared patterns in patients with past pandemic viral infections, including SARS, MERS and swine flu.

Two telltale signatures emerged from the study, published June 11, 2021 in eBiomedicine. One, a set of 166 genes, reveals how the human immune system responds to viral infections. A second set of 20 signature genes predicts the severity of a patient’s disease. For example, the need to hospitalize or use a mechanical ventilator. The algorithm’s utility was validated using lung tissues collected at autopsies from deceased patients with COVID-19 and animal models of the infection.

Sahoo co-led the study with Dr. Pradipta Ghosh, professor of cellular and molecular medicine at UC San Diego School of Medicine and Moores Cancer Center, and Soumita Das, associate professor of pathology at UC San Diego School of Medicine.

“These viral pandemic-associated signatures tell us how a person’s immune system responds to a viral infection and how severe it might get, and that gives us a map for this and future pandemics,” said Ghosh.

During a viral infection, the immune system releases small proteins called cytokines into the blood. These proteins guide immune cells to the site of infection to help get rid of the infection. Sometimes, though, the body releases too many cytokines, creating a runaway immune system that attacks its own healthy tissue. This mishap, known as a cytokine storm, is believed to be one of the reasons some virally infected patients, including some with the common flu, succumb to the infection while others do not.

But the nature, extent and source of fatal cytokine storms, who is at greatest risk and how it might best be treated have long been unclear.

“When the COVID-19 pandemic began, I wanted to use my computer science background to find something that all viral pandemics have in common — some universal truth we could use as a guide as we try to make sense of a novel virus,” Sahoo said. “This coronavirus may be new to us, but there are only so many ways our bodies can respond to an infection.”

The data used to test and train the algorithm came from publicly available sources of patient gene expression data — all the RNA transcribed from patients’ genes and detected in tissue or blood samples. Each time a new set of data from patients with COVID-19 became available, the team tested it in their model. They saw the same signature gene expression patterns every time.

From a simple blood draw, gene expression patterns associated with pandemic viral infections could provide clinicians with a map to help define patients’ immune responses, measure disease severity, predict outcomes and test therapies.

“In other words, this was what we call a prospective study, in which participants were enrolled into the study as they developed the disease and we used the gene signatures we found to navigate the uncharted territory of a completely new disease,” Sahoo said.

By examining the source and function of those genes in the first signature gene set, the study also revealed the source of cytokine storms: the cells lining lung airways and white blood cells known as macrophages and T cells. In addition, the results illuminated the consequences of the storm: damage to those same lung airway cells and natural killer cells, a specialized immune cell that kills virus-infected cells.

“We could see and show the world that the alveolar cells in our lungs that are normally designed to allow gas exchange and oxygenation of our blood, are one of the major sources of the cytokine storm, and hence, serve as the eye of the cytokine storm,” Das said. “Next, our HUMANOID Center team is modeling human lungs in the context of COVID-19 infection in order to examine both acute and post-COVID-19 effects.”

The researchers think the information might also help guide treatment approaches for patients experiencing a cytokine storm by providing cellular targets and benchmarks to measure improvement.

To test their theory, the team pre-treated rodents with either a precursor version of Molnupiravir, a drug currently being tested in clinical trials for the treatment of COVID-19 patients, or SARS-CoV-2-neutralizing antibodies. After exposure to SARS-CoV-2, the lung cells of control-treated rodents showed the pandemic-associated 166- and 20-gene expression signatures. The treated rodents did not, suggesting that the treatments were effective in blunting cytokine storm.

“It is not a matter of if, but when the next pandemic will emerge,” said Ghosh, who is also director of the Institute for Network Medicine and executive director of the HUMANOID Center of Research Excellence at UC San Diego School of Medicine. “We are building tools that are relevant not just for today’s pandemic, but for the next one around the corner.”

Co-authors of the study include: Gajanan D. Katkar, Soni Khandelwal, Mahdi Behroozikhah, Amanraj Claire, Vanessa Castillo, Courtney Tindle, MacKenzie Fuller, Sahar Taheri, Stephen A. Rawlings, Victor Pretorius, David M. Smith, Jason Duran, UC San Diego; Thomas F. Rogers, Scripps Research and UC San Diego; Nathan Beutler, Dennis R. Burton, Scripps Research; Sydney I. Ramirez, La Jolla Institute for Immunology; Laura E. Crotty Alexander, VA San Diego Healthcare System and UC San Diego; Shane Crotty, Jennifer M. Dan, La Jolla Institute for Immunology and UC San Diego.

Funding for this research came, in part, from the National Institutes for Health (grants R00-CA151673, R01-GM138385, R01-AI141630, CA100768, CA160911, R01DK107585, R01-AI155696, R00RG2628, R00RG2642 and U19-AI142742), UC San Diego Sanford Stem Cell Clinical Center, La Jolla Institute for Immunology Institutional Funds, and VA San Diego Healthcare System.

Researchers translate a bird's brain activity into song

Study demonstrates the possibilities of a future speech prosthesis for humans

ALT TEXT
Zebra finch. Photo by iStock_thawats

June 16, 2021 -- It is possible to re-create a bird’s song by reading only its brain activity, shows a first proof-of-concept study from the University of California San Diego. The researchers were able to reproduce the songbird’s complex vocalizations down to the pitch, volume and timbre of the original.

Published June 16 in Current Biology, the study lays the foundation for building vocal prostheses for individuals who have lost the ability to speak.

“The current state of the art in communication prosthetics is implantable devices that allow you to generate textual output, writing up to 20 words per minute,” said senior author Timothy Gentner, a professor of psychology and neurobiology at UC San Diego. “Now imagine a vocal prosthesis that enables you to communicate naturally with speech, saying out loud what you’re thinking nearly as you’re thinking it. That is our ultimate goal, and it is the next frontier in functional recovery.”

The approach that Gentner and colleagues are using involves songbirds such as the zebra finch. The connection to vocal prostheses for humans might not be obvious, but in fact, a songbird’s vocalizations are similar to human speech in various ways. They are complex, and they are learned behaviors.

“In many people’s minds, going from a songbird model to a system that will eventually go into humans is a pretty big evolutionary jump,” said Vikash Gilja, a professor of electrical and computer engineering at UC San Diego who is a co-author on the study. “But it’s a model that gives us a complex behavior that we don’t have access to in typical primate models that are commonly used for neural prosthesis research.”

The research is a cross-collaborative effort between engineers and neuroscientists at UC San Diego, with the Gilja and Gentner labs working together to develop neural recording technologies and neural decoding strategies that leverage both teams’ expertise in neurobiological and behavioral experiments.

The team implanted silicon electrodes in male adult zebra finches and monitored the birds’ neural activity while they sang. Specifically, they recorded the electrical activity of multiple populations of neurons in the sensorimotor part of the brain that ultimately controls the muscles responsible for singing.

The researchers fed the neural recordings into machine learning algorithms. The idea was that these algorithms would be able to make computer-generated copies of actual zebra finch songs just based on the birds’ neural activity. But translating patterns of neural activity into patterns of sounds is no easy task.

“There are just too many neural patterns and too many sound patterns to ever find a single solution for how to directly map one signal onto the other,” said Gentner.

To accomplish this feat, the team used simple representations of the birds’ vocalization patterns. These are essentially mathematical equations modeling the physical changes—that is, changes in pressure and tension—that happen in the finches’ vocal organ, called a syrinx, when they sing. The researchers then trained their algorithms to map neural activity directly to these representations.


Bird song sample: number of a bird in the study, followed by its own natural recorded song and then the reproduced, biomechanical version of the same song.

This approach, the researchers said, is more efficient than having to map neural activity to the actual songs themselves.

“If you need to model every little nuance, every little detail of the underlying sound, then the mapping problem becomes a lot more challenging,” said Gilja. “By having this simple representation of the songbirds’ complex vocal behavior, our system can learn mappings that are more robust and more generalizable to a wider range of conditions and behaviors.”

The team’s next step is to demonstrate that their system can reconstruct birdsong from neural activity in real time.

Part of the challenge is that songbirds’ vocal production, like humans’, involves not just output of the sound but a constant monitoring of the environment and constant monitoring of the feedback. If you put headphones on humans, for example, and delay when they hear their own voice, disrupting just the temporal feedback, they’ll start to stutter. Birds do the same thing. They’re listening to their own song.  They make adjustments based on what they just heard themselves singing and what they hope to sing next, Gentner explained. A successful vocal prosthesis will ultimately need to work on a timescale that is similarly fast and also intricate enough to accommodate the entire feedback loop, including making adjustments for errors.

“With our collaboration,” said Gentner, “we are leveraging 40 years of research in birds to build a speech prosthesis for humans—a device that would not simply convert a person’s brain signals into a rudimentary set of whole words but give them the ability to make any sound, and so any word, they can imagine, freeing them to communicate whatever they wish.”

Paper: “Neurally driven synthesis of learned, complex vocalizations.” Co-authors include Ezequiel M. Arneodo, Shukai Chen and Daril E. Brown, all at UC San Diego.

This work was supported by the National Institutes of Health (grant R01DC018446), the Kavli Institute for the Brain and Mind (IRG no. 2016-004), the Office of Naval Research (MURI N00014-13-1-0205) and a Pew Latin American Fellowship in the Biomedical Sciences.

Declaration of interests: Vikash Gilja is a compensated consultant of Paradromics, Inc., a brain-computer interface company.

Genetically engineered nanoparticle delivers dexamethasone directly to inflamed lungs

June 16, 2021--Nanoengineers at the University of California San Diego have developed immune cell-mimicking nanoparticles that target inflammation in the lungs and deliver drugs directly where they’re needed. As a proof of concept, the researchers filled the nanoparticles with the drug dexamethasone and administered them to mice with inflamed lung tissue. Inflammation was completely treated in mice given the nanoparticles, at a drug concentration where standard delivery methods did not have any efficacy. 

The researchers reported their findings in Science Advances on June 16.

Schematic of a genetically engineered cell membrane-coated nanoparticle designed to deliver dexamethasone to inflamed lungs. Credit: Zhang Lab

What’s special about these nanoparticles is that they are coated in a cell membrane that’s been genetically engineered to look for and bind to inflamed lung cells. They are the latest in the line of so-called cell membrane-coated nanoparticles that have been developed by the lab of UC San Diego nanoengineering professor Liangfang Zhang. His lab has previously used cell membrane-coated nanoparticles to absorb toxins produced by MRSA; treat sepsis; and train the immune system to fight cancer. But while these previous cell membranes were naturally derived from the body’s cells, the cell membranes used to coat this dexamethasone-filled nanoparticle were not.

Liangfang Zhang, a professor of nanoengineering at UC San Diego, has been developing cell membrane-coated nanoparticles for over a decade.

“In this paper, we used a genetic engineering approach to edit the surface proteins on the cells before we collected the membranes. This significantly advanced our technology by allowing us to precisely overexpress certain functional proteins on the membranes or knockout some undesirable proteins,” said Zhang, who is a senior author of the paper. 

Joon Ho Park, a graduate student in Zhang’s lab and first author of the paper, said the researchers noticed that when endothelial cells become inflamed, they overexpress a protein called VCAM1, whose purpose is to attract immune cells to the site of inflammation. In response, the immune cells express a protein called VLA4, which seeks out and binds to VCAM1. 

“We engineered cell membranes to express the full version of VLA4 all the time,” said Park. “These membranes constantly overexpress VLA4 in order to seek out VCAM1 and the site of inflammation. These engineered cell membranes allow the nanoparticle to find the inflamed sites, and then release the drug that’s inside the nanoparticle to treat the specific area of inflammation.”

While the nanoparticle won’t directly enhance the efficacy of the drug—dexamethasone in this case—concentrating it at the site of interest may mean a lower dosage is required. This study showed that the dexamethasone accumulated at the site of interest at higher levels, and faster, than standard drug delivery approaches. 

“We’re delivering the exact same drug used in the clinic, but the difference is we’re concentrating the drugs to the point of interest,” said Park. “By having these nanoparticles target the inflammation site, it means a larger portion of the medicine will wind up where it’s needed, and not be cleared out by the body before it can accumulate and be effective.”

The researchers note that this genetically engineered cell membrane approach is a platform technology that in theory can be used to target not only inflammation in other areas of the body— VCAM1 is a universal signal of inflammation—but much broader use cases as well.

“This is a versatile platform, not just for lung inflammation but any type of inflammation that upregulates VCAM1,” said Park. “This technology can be generalized; this engineered cell membrane-coated nanoparticle doesn’t have to overexpress VLA4, it could be swapped out to another protein that can target other areas of the body or accomplish other goals.”

Nanoengineering graduate student Joon Ho Park is first author of the study.
 

To engineer the cell membranes to overexpress the VLA4 protein, Park and the team start with packaging VLA4 genes into a viral vector. They then insert this reprogrammed viral vector into lab-grown host cells derived from mice. The cells incorporate the genes that the viral vector is carrying into their own genome and as a result, produce membranes that constantly overexpress VLA4. 

The researchers’ next step is to study the process using human cell membranes, instead of mice cell membranes, that are engineered to express the human version of VLA4. There are still many steps needed before the technology could be tested in human clinical trials, but the researchers say that these early results from the platform technology are encouraging. 

“By leveraging the established gene editing techniques, this study advances the cell membrane-coated nanoparticles to a new level and opens up new opportunities for targeted drug delivery and other medical applications”, concluded by Zhang.  

Paper: “Genetically engineered cell membrane–coated nanoparticles for targeted delivery of dexamethasone to inflamed lungs.” Co-authors include Yao Jiang, Jiarong Zhou, Hua Gong, Animesh Mohapatra, Jiyoung Heo, Weiwei Gao, and Ronnie H. Fang.

This work was supported by the National Institutes of Health (R01CA200574) and the Defense Threat Reduction Agency Joint Science and Technology Office for Chemical and Biological Defense (HDTRA1-18-1-0014).

Titans of industry, academia team up to advance engineering in medicine

Generosity of Shu and K.C. Chien and Peter Farrell to be recognized through named research collaboratory in Franklin Antonio Hall

June 10, 2021--When renowned UC San Diego bioengineer Shu Chien completed medical school in 1953, he wanted to find ways to make technological advancements in healthcare that would improve human lives. To do so, he had to find an engineer to collaborate with, since physicians and engineers were largely siloed professions at the time.

Peter Farrell, founder of sleep-disordered breathing medical device company ResMed, experienced something similar when completing his bioengineering Ph.D. research into treatments with the artificial kidney, working under the guidance of two advisors: one a nephrologist, and the other an engineer.

“Many years ago, if you talked to leaders in medical school about engineering, they’d say ‘Oh we’re not very interested in that,” said Chien. “But today, almost every major medical school leadership would like to have an engineering presence, and conversely leadership in engineering would like to have biomedical engineering complementation.”

Chien went on to earn a Ph.D. in physiology, and helped to create the engineering-meets-medicine world he was looking for as a young physician. The great success of his efforts are reflected in advances made by former students and colleagues around the world and right here at UC San Diego where the Bioengineering Department is ranked No. 3 in the nation according to U.S. News & World Report and No.1 according to the National Research Council of the U.S. National Academies.

Chien's research includes work critical to our understanding of how blood flows in the cardiovascular system. He is one of only a handful of individuals to be awarded the U.S. National Medal of Science and to be voted into all three National Academies (Science, Medicine and Engineering).

As founder of ResMed, Peter Farrell’s development of a machine that helps people with sleep apnea breathe better while asleep has transformed lives and led to greater understanding of the link between sleep-disordered breathing and chronic illnesses such as diabetes and hypertension. The concept of nasal CPAP (continuous positive airway pressure) was pioneered by Dr. Colin Sullivan at the University of Sydney Medical School to treat obstructive sleep apnea. Farrell came to the interface of engineering and medicine as an engineer. He is an elected member of the National Academy of Engineering, and served as founding director of biomedical engineering at the University of New South Wales, Sydney before becoming vice president of research and development at Baxter Healthcare, Japan.

Farrell was research and development vice president at Baxter for five years before founding ResMed, where he remains Chairman of the Board. ResMed sells 360,000 medical devices a month and 1.2 million masks of various types in more than 140 countries to treat sleep apnea, COPD and other respiratory conditions. ResMed is listed on the New York Stock Exchange (RMD) and employs 7,500 people.

Chien and Farrell agree that while the silos that once kept engineering and medicine as distinctly separate from one another have been breaking down, there is still room for improvement.

“Without engineering, medicine is just not going to advance at the level that it should,” said Farrell. “The participation of both fields is not only here to stay, it’s vital for healthcare in general. Engineers and physicians, pharmaceutical scientists and biologists all need to be working together, as a team. In the good programs, like UC San Diego, the silos have virtually disappeared.”

The UC San Diego Institute for Engineering in Medicine, which Chien founded, with Farrell sitting on the advisory board, is a prime example of how engineering and medicine have converged on campus. The Institute facilitates the integration of engineering principles and novel technologies with biomedical and translational research.

KC and Shu Chien

As the silos between engineering and medicine continue to dissolve, there is a growing need on campus for facilities where engineers, physicians and medical researchers can work in the same physical research ecosystems. Shu Chien and his wife, KC, recently joined forces with Peter Farrell to support this vision.

The Chiens and Farrell each recently donated $1.5 million to support programmatic expansion of engineering and medicine on campus. A large collaborative research facility for engineering and medicine in the Jacobs School’s newest building, Franklin Antonio Hall, will be named in recognition of their generosity.

The named Chien-Farrell Institute for Engineering in Medicine Collaboratory will serve as a hub for research at the interface of engineering and medicine. This collaborative research facility is one of 13 such "collaboratories" within the Jacobs School's newest building, Franklin Antonio Hall.

The Chien-Farrell Collaboratory will bring faculty, students, researchers and industry partners from different fields together in the same space, to facilitate the types of truly interdisciplinary, collaborative research required to solve society’s greatest challenges in medicine and healthcare.

“Today, one young person can get trained and have knowledge in all of these fields,” said Chien. “Nevertheless, one person cannot do as much as people collaborating together—we’re limited beings, so we still need a group to work together. That’s the beauty of interdisciplinary research: different people with different expertise mutually beneficial to each other. When we work together like this, the total of our efforts is much greater than the sum of each individual’s work.”

The Chien-Farrell Collaboratory in particular and Franklin Antonio Hall more generally will focus not only on collaborations among researchers from disparate fields, but among academic teams and industry partners as well.

“Entrepreneurship is not about risk taking, it’s about opportunity seeking,” said Farrell “Industry and academia all need to be part of the same ecosystem with the same goals. They support each other in a loop where the best ideas are fed into the marketplace to generate revenue, where a portion of the profit flows back to academia in research support coupled with potential equity. This new Collaboratory and Franklin Antonio Hall accelerate that loop, delivering good ideas which solve problems into the marketplace. Everybody benefits: it can help the campus, the students, society as a whole.”

“I'm really very honored to share the naming of the building with Peter,” said Chien. “He and his company Resmed have made tremendous contributions to the science and engineering of respiratory and sleep problems. I myself am a beneficiary of their product with sleep apnea, so I personally am grateful for that.”

“Shu is a pleasure to work with and a good guy to be involved with,” said Farrell. “He gets it. I have a lot of respect for him.”

Franklin Antonio Hall

In addition to the Chien-Farrell Collaboratory, 12 more of these large research facilities make up the heart of Franklin Antonio Hall. Each collaboratory will house a collection of professor-led research groups from different but related disciplines. Together, these complementary research teams will pursue grand-challenge research in areas like renewable energy technologies, smart cities and smart transportation, wearable and robotics innovations, and digital privacy and security. The building is designed to maximize the circulation and collaboration of UC San Diego faculty, students, professional research staff, and industry partners.

Franklin Antonio Hall will also serve as an important new facility for undergraduate and graduate-student learning, both inside and outside the classroom. The building will provide critical workspace for Jacobs School undergraduate student organizations that are participating in national design competitions. Teams of students will design, build and test their projects in this new collaborative environment. Teams will cycle through the space annually to best serve the growing number of nationally ranked student teams.

Franklin Antonio Hall is named after UC San Diego alumnus Franklin Antonio in recognition of his incredible $30 million gift to the UC San Diego Jacobs School of Engineering. The approximately 186,000 square foot university building is projected to be completed in early 2022.

Philanthropic gifts, like the gift from Shu and K.C. Chien and Peter Farrell, 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. Visit the Campaign for UC San Diego website to learn more.

World's largest outdoor earthquake simulator undergoes major upgrade

June 9, 2021-- A major upgrade to the world’s largest outdoor earthquake simulator reached a milestone mid-April when the facility’s floor--all 300,000 lbs of it--was put back into place. When completed this fall, the simulator will have the ability to reproduce multi-dimensional earthquake motions with unprecedented accuracy to make structures and their residents safer during strong shakes.

The simulator, or shake table,  will be able to test the world’s heaviest and tallest structures to gauge how well they would withstand various types of earthquakes. The shake table will be equipped with the ability to reproduce all the six possible movements of the ground, known as six degrees of freedom. The first test following the upgrade will feature a full-scale, 10-story, cross-laminated timber building. 

The shake table's platen, or floor, is put back into place by two cranes at the Englekirk Structural Engineering Center. 

“This facility will save a large number of human lives by making the places we live and work in safer during earthquakes,” said Joel Conte, the shake table’s principal investigator and a professor of structural engineering at the University of California San Diego. Conte and colleagues lay out the details of the upgrade in a paper published in January 2021 in Frontiers in Built Environment

In the paper, researchers also detail the impact that the shake table has had on building and design codes since it opened in 2004. 

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 was performed on the UC San Diego shake table in 2013. Professor John van de Lindt from Colorado State University, who led this project, played a key role in writing the guidelines for the retrofit of these buildings.

In 2008, a test led by Professors Robert Fleischman of the University of Arizona and Jose Restrepo of UC San Diego led to new recommendations on how precast concrete floors, known as diaphragms, should be built into parking garage structures to improve their seismic behavior.

In 2011 and 2012, during a series of landmark tests, a team tested elevators and stairs inside a full-size, six-story building. The findings led to new, better guidelines for the way these components should be connected to buildings’ structural frames so they don’t detach during a quake.

How it works
 

Principal investigator Joel Conte (right), who is also a professor of structural engineering at UC San Diego, and Koorosh Lotfizadeh, the table's operations manager, inspect the platen. 

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 that researchers have gathered from around the world.

The facility is transitioning from one degree of freedom--the ability to move structures backwards and forwards--to six degrees of freedom, adding the ability to move up and down, left to right, as well as pitch, roll and yaw motions. To understand these last three, think of an airplane in flight: pitch is when the nose of the airplane goes up and its tail goes down; roll is when one wing dips and the other lifts; and yaw is when the plane’s whole body slides from left to right. 

Two additional horizontal actuators were added to two existing ones in a new configuration in order to move the table horizontally forwards and backwards; left to right; and to make a yaw motion. The six existing actuators that move the table up and down were hooked up to a new, stronger hydraulic power source. 

Why do six degrees of freedom matter? 

Tests on a soft-story structure helped design guidelines to retrofit these buildings. 

Reproducing earthquake motions in six degrees of freedom is key because during a temblor, the ground might move in more than one 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.

Principal investigator Conte says he believes results of prior tests would have revealed additional ways to make buildings safer if they had been done in six degrees of freedom rather than one.

More power, better sensors

The upgrade will also add a new, state-of-the-art sensing and data collection system with a total of 768 channels to carry information coming from a wide range of sensors, including high-definition cameras, strain gauges, accelerometers and more. The software controlling the shake table also will be upgraded. 

In addition, the mechanism that powers the shake table also been expanded and connected to a hydraulic power system whose capacity has quadrupled. 
 

Students thrive in program focused on diversifying undergraduate engineering at UC San Diego

First cohort of ACES Scholars graduate after completing NSF-funded program supporting students from backgrounds traditionally underrepresented in engineering

Xavier Perez, Yoon Jung Choi and Armando Godoy-Velasquez are members of the first cohort of ACES Scholars.

June 9, 2021--Among the more than 1,400 undergraduate engineering and computer science students earning bachelor’s degrees from the University of California San Diego Jacobs School of Engineering this year, are Xavier Perez, Yoon Jung Choi, and Armando Godoy-Velasquez, who are all members of the first cohort of ACES Scholars. Students in the National Science Foundation-funded Academic Community for Engineering Success (ACES) Scholars program are highly motivated students from economically and educationally underserved backgrounds; nearly all are Pell grant eligible, many are the first in their family to attend college, and many are women or from underrepresented groups in engineering. 

Perez, Choi and Godoy-Velasquez say their participation in the ACES Scholars program was crucial in not only helping them make it to graduation, but to leave their undergraduate years with research experience, internships, and involvement in student organizations under their belts, and offers to attend graduate school and industry careers in hand.

ACES Scholars Program

UC San Diego is one of six universities in the NSF-funded Redshirt in Engineering Consortium, which aims to support low income students through an engineering degree by intervening in the crucial first two years on campus. The program was formed in 2016, and UC San Diego’s Redshirt-funded ACES Scholars program started in the fall of 2017. The Consortium takes its name from the practice of redshirting in college athletics, with the idea of providing extra support to help promising engineering students complete a bachelor’s degree.

“This NSF funding has boosted our ability to provide comprehensive support and improve undergraduate student success here at the Jacobs School," said Pamela Cosman, the UC San Diego PI for the NSF award and a professor in the Department of Electrical and Computer Engineering. Cosman served as Associate Dean for Students of the Jacobs School of Engineering from September 2013 to December 2016. "This NSF investment has allowed us to reach more students, and to engage with them on multiple levels, through programs administered through our IDEA Engineering Student Center."

Summer Engineering Institute at the Jacobs School

ACES Scholars receive a scholarship to participate in the IDEA Engineering Student Center's five-week Summer Engineering Institute before the fall quarter of their first year even begins. The goal of this summer program for incoming Jacobs School undergraduates is to strengthen students' technical preparation and study skills while also offering community building activities to help the students develop a supportive peer network and a familiarity with campus life. As part of the program, students take an academic enrichment course such as ENG 15 "Engineer your Success" as well as a foundational technical engineering course. 

"The Summer Engineering Institute is about building community, making friends, and focusing on the skills and strategies that set our students up for academic and personal success at the Jacobs School of Engineering," said Mechanical and Aerospace Engineering professor Olivia Graeve, who is wrapping up her service as Faculty Director of the IDEA Engineering Student Center this summer. "It's quite gratifying to see so many incoming Jacobs School students coming together through the Summer Engineering Institute. I wish this program had existed when I was an engineering undergraduate here at UC San Diego."

Faculty and Peer Mentorship

Another key component of the ACES program is mentorship. ACES Scholars are paired with a faculty mentor and peer mentor to help answer questions, direct the students to useful contacts, and provide another layer to the support network. ACES Scholars also attend weekly discussions with ACES Program advisor Jessica Baldis and their whole cohort during fall quarter, and monthly or quarterly meetings for the rest of the program.

ACES Scholars have access to professional and technical development workshops, including resume preparation help, which is particularly important because the internship cycle in engineering starts early in the year and many students have never gone through the steps needed to land an engineering internship. ACES Scholars also have access to many additional resources provided by the IDEA Center, including coding workshops, guest speakers, and scholarships. 

Below are snapshots of how the three students have thrived at the Jacobs School thanks in part to the ACES Program. 

"In different ways, each of these students made the most of, and benefited greatly from, early access to community building; research; and peer, staff and faculty mentorship," said UC San Diego nanoengineering professor Darren Lipiomi, the incoming Faculty Director of the IDEA Engineering Student Center. "The ACES Scholars program is a powerful example of how a little extra support and guidance to students at the start of their undergraduate careers can transform careers and lives."

Xavier Perez

Electrical engineering student Xavier Perez has been involved in so much on and off campus it’s hard to keep track of it all. He’s been active in groups ranging from the Society of Hispanic Professional Engineers to intramural soccer; was selected as one of five UC San Diego students for the UC LEADS research program; and conducted award-winning research in Professor Vikash Gilja’s Translational Neuroengineering Lab. He credits his willingness to make these connections and seek out these opportunities to the ACES Scholars program, which helped him get his footing before school even started. 

“The Summer Engineering Institute was amazing,” Perez said. “It opened all these doors as they introduced me to the world of engineering at UC San Diego. With the two classes we got the chance to take--I took ECE5 as well as ENG10--I met the professor I have done research with up until today.”

After meeting Gilja through ECE5, Perez jumped at the opportunity to do research in his lab through the STARS and UC LEADS programs. After fielding offers from Columbia University and UC Irvine, Perez chose to pursue his PhD at UC San Diego, in none other than Gilja’s lab. He’ll be earning his doctorate in electrical engineering with a focus on medical devices and systems. 

His current research has contributed to a neurally-driven speech prosthesis, based on studying the neural activities of song birds. Perez designed a custom recording studio to record the birds’ songs that is 10 times less expensive than the existing professional installation system being used.

Aside from the SEI and meetings with his faculty mentor, Perez said the friends he made through ACES were crucial to his success.

“That’s the other part -- the ACES Scholar community helped me come to UC San Diego with a  group of friends already, which was very helpful. I still talk to all my ACES friends; I even lived with two of them off campus. Another part of the ACES program I really enjoyed was the cohort meetings we had. That was impactful in the sense that it brought us all together once a month or once a quarter such that we could see everyone all together.”
 

Yoon Jung Choi

For chemical engineering student Yoon Jung Choi, the ACES Scholars program was all about making connections. For example, her peer mentor when she first arrived at UC San Diego was an active member of Engineers for a Sustainable World. This introduction to the group and a couple of its members convinced the sustainability-focused Choi to get involved as well. She was an active member of ESW all four years, and served in leadership roles. 

Similarly, her ACES faculty mentors gave her the encouragement and know-how to reach out to her professors. She has been conducting research for the last two years in Professor Ping Liu’s lab, focused on developing new battery technologies.

“I worked on multiple research projects and I also got my name on two publications from that. From this research group I got exposure to the fundamentals of lithium ion batteries, and different experimental techniques to make them and characterize them.”

Choi also appreciated the ACES Scholars regular cohort meetings and discussions. 

“That was very helpful because it provides space for people to mingle and form a community. They also allow people to help each other, clarify concepts in classes, and just hang out with your peers. I think the Jacobs School of Engineering does a great job of forming community; ACES is a great example of that.”

Choi will intern at the NASA Glenn Research Center this summer, before heading to UC Berkeley to earn her master’s degree.

Armando Godoy-Velasquez

Armando Godoy-Velasquez was introduced to structural engineering in a rather unusual way.

“I heard about structural engineering when I was watching a Netflix show called Prison Break,’ he said. “The main character is a structural engineer so I looked it up and started researching about structural engineering, and it really interested me. I liked building things and designing things, and a couple of my family members work in construction so it’s always intrigued me.”

After learning that UC San Diego is the only school in the nation with an undergraduate structural engineering degree, his mind was made up.

It’s all come full circle for Godoy-Velasquez, who accepted a full time position as a field engineer with Turner Construction, after having interned for the company for the past year.  His current project involves, you guessed it, renovating and upgrading the electrical, mechanical, and plumbing systems in a local prison. He’s also worked on commercial office renovations, and may get the opportunity to work on the new San Diego Airport terminal.

Godoy-Velasquez is more than qualified for the job. Thanks to his ACES faculty mentor, he started conducting research in the Powell Laboratory during his first year on campus.

“I worked on a project for the California Earthquake Agency, researching how homes built before the 1980s were prone to more damage during earthquakes,” Godoy-Velasquez said. “So we built walls inside the Powell Lab, then tested them against earthquakes and studied their performance. Then we rebuilt them reinforced with plywood sheeting and compared the differences in performance with reinforcement and without reinforcement.”

During his time at UC San Diego, Godoy-Velasquez played on the men’s club soccer team, was a member of the Tau Kappa Epsilon fraternity, was a member of SHPE, and also joined the Associated Schools of Construction Design-Build project team. Their project was sponsored by Clarke Construction company, which was building the new Sixth College at UC San Diego, so a lot of their homework was based off those real, current, plans. 

In addition to his ACES faculty mentor providing an early research opportunity, Godoy-Velasquez said the Summer Engineering Institute was also critical to his success. 

“SEI was a really crucial program for me. I’m still friends with everyone I met in SEI; that’s pretty much been my main study group in college. When I started off my first quarter after SEI, I felt like I wasn’t a freshman. That was thanks to SEI, all the workshops we had, I felt like I’d been there for a year already.”

He had such a positive experience that he returned the following year as a peer facilitator to help incoming students get the same jump start that he did. 

“The peer mentors during my SEI year were really cool, and I still keep in touch with them. They helped me out even after SEI. Being able to give that back to incoming students was really great.”

Super productive 3D bioprinter could help speed up drug development

ALT TEXT
The high-throughput 3D bioprinting setup performing prints on a standard 96-well plate. Images adapted from Biofabrication

June 8, 2021 -- A 3D printer that rapidly produces large batches of custom biological tissues could help make drug development faster and less costly. Nanoengineers at the University of California San Diego developed the high-throughput bioprinting technology, which 3D prints with record speed—it can produce a 96-well array of living human tissue samples within 30 minutes. Having the ability to rapidly produce such samples could accelerate high-throughput preclinical drug screening and disease modeling, the researchers said.

The process for a pharmaceutical company to develop a new drug can take up to 15 years and cost up to $2.6 billion. It generally begins with screening tens of thousands of drug candidates in test tubes. Successful candidates then get tested in animals, and any that pass this stage move on to clinical trials. With any luck, one of these candidates will make it into the market as an FDA approved drug.

The high-throughput 3D bioprinting technology developed at UC San Diego could accelerate the first steps of this process. It would enable drug developers to rapidly build up large quantities of human tissues on which they could test and weed out drug candidates much earlier.

“With human tissues, you can get better data—real human data—on how a drug will work,” said Shaochen Chen, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering. “Our technology can create these tissues with high-throughput capability, high reproducibility and high precision. This could really help the pharmaceutical industry quickly identify and focus on the most promising drugs.”

The work was published in the journal Biofabrication.

The researchers note that while their technology might not eliminate animal testing, it could minimize failures encountered during that stage.

“What we are developing here are complex 3D cell culture systems that will more closely mimic actual human tissues, and that can hopefully improve the success rate of drug development,” said Shangting You, a postdoctoral researcher in Chen’s lab and co-first author of the study.

ALT TEXT
Examples of the geometries that the high-throughput 3D bioprinter can rapidly produce.

 

The technology rivals other 3D bioprinting methods not only in terms of resolution—it prints lifelike structures with intricate, microscopic features, such as human liver cancer tissues containing blood vessel networks—but also speed. Printing one of these tissue samples takes about 10 seconds with Chen’s technology; printing the same sample would take hours with traditional methods. Also, it has the added benefit of automatically printing samples directly in industrial well plates. This means that samples no longer have to be manually transferred one at a time from the printing platform to the well plates for screening.

“When you’re scaling this up to a 96-well plate, you’re talking about a world of difference in time savings—at least 96 hours using a traditional method plus sample transfer time, versus around 30 minutes total with our technology,” said Chen.

Reproducibility is another key feature of this work. The tissues that Chen’s technology produces are highly organized structures, so they can be easily replicated for industrial scale screening. It’s a different approach than growing organoids for drug screening, explained Chen. “With organoids, you’re mixing different types of cells and letting them to self-organize to form a 3D structure that is not well controlled and can vary from one experiment to another. Thus, they are not reproducible for the same property, structure and function. But with our 3D bioprinting approach, we can specify exactly where to print different cell types, the amounts and the micro-architecture.”

How it works

To print their tissue samples, the researchers first design 3D models of biological structures on a computer. These designs can even come from medical scans, so they can be personalized for a patient’s tissues. The computer then slices the model into 2D snapshots and transfers them to millions of microscopic-sized mirrors. Each mirror is digitally controlled to project patterns of violet light—405 nanometers in wavelength, which is safe for cells—in the form of these snapshots. The light patterns are shined onto a solution containing live cell cultures and light-sensitive polymers that solidify upon exposure to light. The structure is rapidly printed one layer at a time in a continuous fashion, creating a 3D solid polymer scaffold encapsulating live cells that will grow and become biological tissue.

The digitally controlled micromirror array is key to the printer’s high speed. Because it projects entire 2D patterns onto the substrate as it prints layer by layer, it produces 3D structures much faster than other printing methods, which scans each layer line by line using either a nozzle or laser.

“An analogy would be comparing the difference between drawing a shape using a pencil versus a stamp,” said Henry Hwang, a nanoengineering Ph.D. student in Chen’s lab who is also co-first author of the study. “With a pencil, you’d have to draw every single line until you complete the shape. But with a stamp, you mark that entire shape all at once. That’s what the digital micromirror device does in our technology. It’s orders of magnitude difference in speed.”

This recent work builds on the 3D bioprinting technology that Chen’s team invented in 2013. It started out as a platform for creating living biological tissues for regenerative medicine. Past projects include 3D printing liver tissues, blood vessel networks, heart tissues and spinal cord implants, to name a few. In recent years, Chen’s lab has expanded the use of their technology to print coral-inspired structures that marine scientists can use for studying algae growth and for aiding coral reef restoration projects.

Now, the researchers have automated the technology in order to do high-throughput tissue printing. Allegro 3D, Inc., a UC San Diego spin-off company co-founded by Chen and a nanoengineering Ph.D. alumnus from his lab, Wei Zhu, has licensed the technology and recently launched a commercial product.

Paper: “High throughput direct 3D bioprinting in multiwell plates.” Co-authors include Xuanyi Ma, Leilani Kwe, Grace Victorine, Natalie Lawrence, Xueyi Wan, Haixu Shen and Wei Zhu.

This work was supported in part by the National Institutes of Health (R01EB021857, R21AR074763, R21HD100132, R33HD090662) and the National Science Foundation (1903933, 1937653).

Class of 2021 students honored at Ring Ceremony

The recipients of the 2021 Jacobs School of Engineering Awards of Excellence

June 8, 2021-- In addition to UC San Diego’s commencement ceremonies, the Jacobs School of Engineering will honor the class of 2021 at its annual Ring Ceremony on Saturday, June 12. During the Ceremony, graduating engineering and computer science students will receive their class ring, and recite together the Jacobs School of Engineering oath, vowing to practice engineering with integrity and high ethical standards. 

Six students who have made significant contributions to their department and the Jacobs School community, will also be honored with Awards of Excellence. 

Watch the Ring Ceremony live here: https://jacobsschool.ucsd.edu/idea/programs/ring-ceremony  And learn more about these impressive graduates below. 


Bioengineering: Aoife O’Farrell

 Aoife O’Farrell was drawn to bioengineering because of the excitement of the field; there is still so much to discover about how our bodies work, and how we can treat disease. She wanted to find ways to transfer medical discoveries from the lab to patients that need them, and had the opportunity to do so as an undergraduate researcher at the UC San Diego Moores Cancer Center.

“I am most excited by the opportunities in the field of immunoengineering - designing novel therapeutics to modulate the immune system to treat cancer and autoimmune disease. I currently work at the Moores Cancer Center, studying how immune checkpoint blockade inhibitors can best be used to treat certain types of cancer, and hope to continue similar work in the future to aid patients currently unresponsive to standard of care.”

After graduating, she’s pursuing a PhD in bioengineering at the University of Pennsylvania, with funding from the NSF Graduate Research Fellowship Program. She plans to continue her immunoengineering and immo-oncology research, and hopes to eventually become a professor at a public university. 

Aside from coursework and hands-on research with Dr. Robert Saddawi-Konefka in the Gutkind Lab at Moores, O’Farrell was involved in several organizations that helped shape her time on campus: she worked as a Campus Ambassador (tour guide) for three years; and served as an officer in both Engineers without Borders and the Biomedical Engineering Society (BMES).

As the project lead for Engineers Without Borders’  Project FogCatchers, O'Farrell led a team of 15 students to develop technology to aid those without access to clear water, and authored two successful research grants to fund this work. As BMES’ Vice President External, she helped run Bioengineering Day in 2020, including a quick pivot to a virtual event, and planned the Bioengineering Career Fair in 2021. 

Her advice to students is to be willing to try things that make you uncomfortable.

“It sounds cliche, but I think the best advice I can give is to say “yes” to things,” O’Farrell said. “There were a lot of times where I felt uncomfortable about jumping into something (like leading an engineering-based project team, or writing a research grant to ask for funding) but being willing to try anyways opened so many doors that I never would have experienced otherwise. There’s a lot of support on campus at UC San Diego to help with  whatever it is you want to learn.”

 

Computer Science and Engineering: Priyal Suneja

Priyal Suneja’s favorite class was always math, until a basic programming class in high school got her curious about how the words she was typing could make the computer perform certain functions. 

“In order to learn exactly how that pipeline worked, I decided to pursue CS as a major,” Suneja said.

After graduating with the Department’s Award of Excellence, Suneja is heading to the University of Washington, Seattle, for a PhD in Systems and Networking. 

While at UC San Diego, she served as a computer science tutor, conducted research in operating systems, and was involved in the Women in Computing student organization, serving as president this year.

“I started out as a member of WIC and then proceeded to serve as a board member. I had the privilege to serve as WIC’s president over this last year.”

Her advice for students is to get to know your peers and professors.

“My journey at UC San Diego would have been starkly different had I not met the friends and mentors that I met. They made me realize the importance of enjoying what I do, and helped me believe that I could do anything that I set my mind to. I owe all the fun parts of my four years at UC San Diego to the people that I met here.”

 

Electrical and Computer Engineering: Geeling Chau

To computer engineering student Geeling Chau, electrical and computer engineering is magic. 

“Electrical engineering is the magic that has enabled the life changing technological advancements we've seen in the past few decades. Through doing robotics in high school and taking a hands-on interactive device design course, I was fortunate to see first hand the utility of studying this field and gain the confidence that I could take a step into understanding this magic.”

At UC San Diego, she’s applied this magic to brain computer interface work, through research in Professor Vikash Gilja’s Translational Neuroengineering Lab. She specifically worked on a project trying to detect emotional signals from a user playing video games. Chau also conducted research in the Voytek Lab on a data science project on parameterizing power spectral features on working memory neural signals, and with the de Sa Lab on building real-time BCIs for detecting focus levels.

In addition to research, Chau has been involved in the IEEE Honor Society, Eta Kappa Nu (HKN), serving as an officer for three years. While president of HKN, she co-founded the NeuroTech club, which has grown to span more than seven departments at UC San Diego. As a computer engineering student, she also worked as a tutor in the Computer Science and Engineering Department. 

After graduating with the ECE Award for Excellence, Chau is heading to CalTech to pursue a PhD in Computation and Neural Systems. She hopes to contribute to the field of neural engineering, and the next generation of brain computer interface technologies.

Her advice to students?

“There's a lot you can do as an engineering student at UC San Diego - be strategic in what opportunities you choose, and remember why you chose it -- this really helped me get through times that felt tough. You will be pushed to your limits, but remember that being in that uncomfortable state is how you will grow the fastest.”

 

Mechanical and Aerospace Engineering: Luca Scotzniovsky

Luca Scotzniovsky was amazed by planes as a child, and was intrigued by how an object so large and heavy could even get off the ground. This translated into a serious interest in physics in high school, and eventually to aerospace engineering. After being involved in aerospace engineering organizations and conducting research in two different labs at the Jacobs School, he found his calling.

“Upon working in the Large-Scale Design Optimization Lab, I found the path I wanted to follow once I finished my undergraduate career,” Scotzniovsky said.

He will return to UC San Diego next year to pursue a Ph.D. in mechanical and aerospace engineering, working in Professor John Hwang’s Large-Scale Design Optimization Lab, conducting fluid mechanics-based optimization and modeling for urban air mobility vehicles.

During his undergraduate years, Scotzniovsky played on the Men’s Club Soccer Team, including two years as president and captain. He was also a member of Design-Build-Fly, and conducted research in Hwang’s lab, as well in Professor David Saintillan’s lab, where he focused on data analysis of a DNA Loop Extrusion model. 

Scotzniovsky makes no bones about it--engineering is challenging. But focusing on the basics and having a support network will make the journey possible, and enjoyable.

“You can ask anyone in the Jacobs School of Engineering and they will agree that engineering is plain hard, and everyone has had a tough time with it at some point. My experiences have shown me that you really get out what you put into it and that the basic concepts are crucial to really understand the more complex subtopics within engineering. Another thing, which I wish I knew earlier, is that the experience of joining major-related organizations is not only interesting but just as important when it comes to learning and gaining relevant expertise. The one thing that shouldn't stop you from applying for a club, lab, or internship is your course-related experience, especially since the opportunity will provide the proper tools to succeed.”

 

Nanoengineering: Zoe Li

Chemical engineering student Zoe Li came to campus with a career plan in place: she wanted to be a teacher. Working as a teaching assistant in the nanoengineering and math departments, as well as working as a physics tutor in the PATHS program, helped her decide she would specialize in science and STEM education.

 After graduating with the Department of Nanoengineering’s Award of Excellence, Li, who double majored in psychology with a minor in education, will return to UC San Diego for the one-year master’s of education plus teaching credential program, before shaping the next generation of scientists and engineers as a secondary science teacher. 

“I’ve had a lot of jobs in education; I’ve taught pretty much everything from theater when I was younger, and writing, and now I’m teaching more of the STEM subjects like math, science and computer science,” she said. “So it’s been a shift for me. I thought I was going to be an English teacher when I was in high school, but now I’m like ‘Science is cool too’!”

In addition to these teaching roles, on campus Li also worked as a Resident Assistant for three years in Marshall and Revelle colleges, and is an EcoNaut for Housing, Dining and Hospitality, educating students on their latest sustainability goals and calls to action. This year, that included educating students about HDH’s new reusable to-go containers. 

Her advice for students is to find a group of friends you can commiserate with--which can include professors! 

“What got me through these years was having a good group of friends in all my classes. Every time I felt like I could just drop out of chemical engineering and just be a psychology major, my friends would say ‘No, we need to take these classes together!’ In chemical engineering we take almost all our classes with the same cohort so you get to know thm super well. That’s what got me through it, getting to know friends. My other advice is be friends with your professors. They get you through it too.”
 

Structural Engineering: Janelle Coleen Dela Cueva

In high school, Janelle Coleen Dela Cueva was involved in extracurriculars including auto mechanics and woodshop, where she got to work on cars and build birdhouses. 

“ I had so much fun working on these projects that I felt pursuing a degree in structural engineering would allow me to continue designing and creating throughout my entire life. When it comes to coursework, I found that solving problems with a practical application of theory solidified my love for engineering.”

After graduating with the Award of Excellence, Dela Cueva will return to UC San Diego to pursue a PhD in structural engineering, researching advanced aerospace composites.

As an undergraduate, Dela Cueva was involved with the Society of Civil and Structural Engineers (SCSE), serving as Social Chair and VP Internal, and also conducted research as a UC Leadership Excellence through Advanced Degrees (UC LEADS) undergraduate fellowship, having the opportunity to be first author on a paper characterizing fracture in carbon fiber composites. 

Through her roles with SCSE, Dela Cueva had a particular focus on outreach to younger students, and creating a supportive environment for all students at UC San Diego. 

“I found that plan and action go hand in hand to push forward solutions for issues affecting students of color.  In my many roles, I led a team of 5 students to create and promote professional development opportunities for students in my department. Transforming ideas into many initiatives, I created opportunities for young engineers through general body meetings, scientific writing workshops, and industry panels. Through SCSE, I started out teaching local middle schoolers about seismic engineering with our Seismic Outreach initiative and moved onto building houses in Tijuana. I experienced firsthand the integral role engineering plays in impacting the community and I wanted to continue being a part of that throughout my career.”

Her advice to students is to take advantage of every opportunity available, but not at the expense of your own well-being. 

“Over the four years that I have spent studying at UC San Diego, I learned that taking the time to rest will really let your work shine. I also believe that it’s important to not be disheartened by failures, but rather take the chance to learn from them. There will inevitably be times that you don’t succeed at first, but with great effort and support from the people around you things will always work out in the end.”

Doing this allowed her to not only survive her undergraduate years, but enjoy the process too.

“I had a lot of fun. The Jacobs School of Engineering has one the most diverse set of opportunities to grow in engineering. The hands-on experience and education that I received on advanced aerospace composite manufacturing was a rare opportunity that is seldom found at other schools. I feel genuinely lucky and grateful to be able to complete my undergraduate at this institution."

Stabilizing gassy electrolytes could make ultra-low temperature batteries safer

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Artistic rendering of a battery separator that condenses gas electrolytes into liquid at a much lower pressure. The new separator improves battery performance in the extreme cold by keeping more electrolyte, as well as lithium ions, flowing in the battery. Credit: Chen group

 

June 7, 2021 -- A new technology could dramatically improve the safety of lithium-ion batteries that operate with gas electrolytes at ultra-low temperatures. Nanoengineers at the University of California San Diego developed a separator—the part of the battery that serves as a barrier between the anode and cathode—that keeps the gas-based electrolytes in these batteries from vaporizing. This new separator could, in turn, help prevent the buildup of pressure inside the battery that leads to swelling and explosions.

“By trapping gas molecules, this separator can function as a stabilizer for volatile electrolytes,” said Zheng Chen, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering who led the study.

The new separator also boosted battery performance at ultra-low temperatures. Battery cells built with the new separator operated with a high capacity of 500 milliamp-hours per gram at -40 C, whereas those built with a commercial separator exhibited almost no capacity. The battery cells still exhibited high capacity even after sitting unused for two months—a promising sign that the new separator could also prolong shelf life, the researchers said.

The team published their findings June 7 in Nature Communications.

The advance brings researchers a step closer to building lithium-ion batteries that can power vehicles in the extreme cold, such as spacecraft, satellites and deep-sea vessels.

This work builds on a previous study published in Science by the lab of UC San Diego nanoengineering professor Ying Shirley Meng, which was the first to report the development of lithium-ion batteries that perform well at temperatures as low as -60 C. What makes these batteries especially cold hardy is that they use a special type of electrolyte called a liquefied gas electrolyte, which is a gas that is liquefied by applying pressure. It is far more resistant to freezing than a conventional liquid electrolyte.

But there’s a downside. Liquefied gas electrolytes have a high tendency to go from liquid to gas. “This is the biggest safety issue with these electrolytes,” said Chen. In order to use them, a lot of pressure must be applied to condense the gas molecules and keep the electrolyte in liquid form.

To combat this issue, Chen’s lab teamed up with Meng and UC San Diego nanoengineering professor Tod Pascal to develop a way to liquefy these gassy electrolytes easily without having to apply so much pressure. The advance was made possible by combining the expertise of computational experts like Pascal with experimentalists like Chen and Meng, who are all part of the UC San Diego Materials Research Science and Engineering Center (MRSEC).

Their approach makes use of a physical phenomenon in which gas molecules spontaneously condense when trapped inside tiny, nanometer-sized spaces. This phenomenon, known as capillary condensation, enables a gas to become liquid at a much lower pressure.

The team leveraged this phenomenon to build a battery separator that would stabilize the electrolyte in their ultra-low temperature battery—a liquefied gas electrolyte made of fluoromethane gas. The researchers built the separator out of a porous, crystalline material called a metal-organic framework (MOF). What’s special about the MOF is that it is filled with tiny pores that are able to trap fluoromethane gas molecules and condense them at relatively low pressures. For example, fluoromethane typically condenses under a pressure of 118 psi at -30 C; but with the MOF, it condenses at just 11 psi at the same temperature.

“This MOF significantly reduces the pressure needed to make the electrolyte work,” said Chen. “As a result, our battery cells deliver a significant amount of capacity at low temperature and show no degradation.”

The researchers tested the MOF-based separator in lithium-ion battery cells—built with a carbon fluoride cathode and lithium metal anode—filled with fluoromethane gas electrolyte under an internal pressure of 70 psi, which is well below the pressure needed to liquefy fluoromethane. The cells retained 57% of their room temperature capacity at -40 C. By contrast, cells with a commercial separator exhibited almost no capacity with fluoromethane gas electrolyte at the same temperature and pressure.

The tiny pores of the MOF-based separator are key because they keep more electrolyte flowing in the battery, even under reduced pressure. The commercial separator, on the other hand, has large pores and cannot retain the gas electrolyte molecules under reduced pressure.

But tiny pores are not the only reason the separator works so well in these conditions. The researchers engineered the separator so that the pores form continuous paths from one end to the other. This ensures that lithium ions can still flow freely through the separator. In tests, battery cells with the new separator had 10 times higher ionic conductivity at -40 C than cells with the commercial separator.

Chen’s team is now testing the MOF-based separator on other electrolytes. “We are seeing similar effects. We can use this MOF as a stabilizer to adsorb various kinds of electrolyte molecules and improve the safety even in traditional lithium batteries, which also have volatile electrolytes.”

Paper: “Sub-Nanometer Confinement Enables Facile Condensation of Gas Electrolyte for Low-Temperature Batteries.” Co-authors include Guorui Cai*, Yijie Yin*, Dawei Xia*, Amanda A. Chen, John Holoubek, Jonathan Scharf, Yangyuchen Yang, Ki Kwan Koh, Mingqian Li, Daniel M. Davies and Matthew Mayer, UC San Diego; and Tae Hee Han, Hanyang University, Seoul, Korea.

*These authors contributed equally to this work

This work was supported by NASA’s Space Technology Research Grants Program (ECF 80NSSC18K1512), the National Science Foundation through the UC San Diego Materials Research Science and Engineering Center (MRSEC, grant DMR-2011924) and startup funds from the Jacobs School of Engineering at UC San Diego. This work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) at UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which is supported by the National Science Foundation (grant ECCS-1542148). This research used resources of the National

Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This work also used the Extreme Science and Engineering Discovery Environment (XSEDE), and the Comet and Expanse supercomputers at the San Diego Supercomputing Center, which is supported by National Science Foundation (grant ACI-1548562).

NASA's Perseverance inspires UC San Diego's Yonder Dynamics

Several members of the Yonder Dynamics team, with their rover Apathy

By Melissa Hernandez

June 3, 2021--NASA’s latest feat, the landing of its rover Perseverance on Mars this past February, inspired the nation and world, as people were able to watch in near real-time as the autonomous robot touched down on Mars. Perseverance has an important job: gathering soil samples and other intel on the red planet to answer the age-old question: Is there life on Mars? This accomplishment was particularly exciting for the Yonder Dynamics student robotics team at the Jacobs School of Engineering at UC San Diego, which builds a Mars rover of their own each year in a bid to compete in the international University Rover Challenge (URC) hosted by The Mars Society.

 Rovers that are accepted to the competition are tasked with tackling challenges similar to what Perseverance faces, including autonomously collecting soil samples, traversing difficult terrain to deliver a payload, repairing broken equipment on a mock lander, and autonomously navigating to a set site. Though the in-person URC competition was cancelled in 2020 and 2021 due to COVID-19, the Yonder Dynamics team and their rover, Apathy, were one of 36 teams from around the world that qualified for a pared down remote competition in June 2021, with teams competing at their own campuses. Watch footage of their rover here.

Fourth-year biophysics student and Yonder Dynamics Project Manager and Science Team Lead Luke Piszkin, said watching the Perseverance’s landing was inspirational. 

“The NASA rovers have been a huge inspiration for us at Yonder, especially the students on the science sub-team. The goal of the science team is to develop ways for our rover to look for signs of life in the environment to find out if there is life on other planets,” Piszkin said. “We’ve mimicked the Perseverance’s way of detecting life on our rover by using a high-powered spectroscopy laser to use light scattering to detect organic molecules in the soil, which would give us clues of past life."

Yonder’s 2020 rover, Apathy, was one of 36 from around the world that qualified for the University Rover Challenge competition before it was cancelled due to COVID-19 restrictions. This wasn’t the only setback the team would face in 2020. Yonder Dynamics also had to make changes to the way they functioned as a robotics team, as the pandemic forced them into a fully remote workflow, which is especially challenging for a team building a physical robot. Despite not having access to their rover or being able to work in-person, the team was able to not only complete a submission to the virtual 2021 competition, but they were even able to make improvements to Apathy, including a complete revamp of the electronics of the rover, an improvement to the code underpinning its autonomous tasks, and mechanical improvements to Apathy’s robotic arm.

Electrical team lead and second-year electrical engineering student Karl Johnson, notes the changes the electrical team has been able to make. 

“We changed a lot of the wiring on our rover from a breadboard, which is not optimal and very complicated. This year we decided to learn more about printed circuit board design, and we’ve designed and printed our own PCBs to put on the rover,” Johnson said. “Even without access to the rover we can design the boards to then replace the existing breadboards once we have physical access to the rover. It provides an opportunity for all the electronics team members to contribute to the rover.”

 The country-wide shutdown not only affected the Yonder team in terms of the way they work on the rover, but it affected their approach to planning their future as an organization on campus. Their entire recruitment process was completed online.

Fourth-year computer science student and Software co-lead Cyrus Cowley explained that the software team was able to create a simulated version of Apathy, which allowed them to work on the autonomous tasks, without accessing the actual robot.

“Because of COVID-19, we have been focusing a lot on simulation. We’ve gone through and taken our entire software stack and simulated it. It can run on any member of the software team’s computer,” Cowley said. “We can launch the simulation with just two commands. We rethought our approach to our autonomous traversal task entirely, and things have gone pretty well.”

On the mechanical side of things, Johnson highlighted that not having physical access to their hardware was a blow to the mechanical team. To deal with this, they created CAD replicas of the mechanics of the robot, using these simulated versions of their hardware to test out changes and new additions. Through this form of remote designing, the mechanics team has been able to visualize the future physical changes that will be done to the rover. 

 “We have been able to improve a lot of aspects that have been flaws in our design through our CAD models,” Johnson said. “When we get back to physically working on it, these  will help us improve the mechanics of our rover.”

“We promoted recruitment events normally as we would before and much like we would’ve done in person we had a general body meeting for potential new members,” Johnson said. “This year we had a pretty good turnout for interviews, fortunately, but with things being virtual it is difficult to keep retention with new members.”

The new robotic arm that the Yonder team designed for Apathy.

Despite the circumstances, the Yonder Team was able to submit the System Acceptance Review documents required to earn a spot in the University Rover Challenge; these consist of a five-minute video and a seven-page report detailing the ins and outs of their rover. Their hard work paid off when they found out that Apathy was one of only 36 from around the world to score highly enough to qualify for the pared down version of the competition being held remotely in 2021. Unfortunately, since each competing team needs to setup their own course on their own campus this year due to COVID considerations, the Yonder Dynamics team made the tough decision to not compete.

“Unfortunately, we will not be participating in the virtual competition this year because we do not have the time or resources to set up the courses for ourselves,” said Piszkin. “But seeing Apathy score so well was a really great feeling, knowing that all the time and effort we put in during the last year made a difference. Although we have to miss this year's virtual competition, we are looking forward to competing for the presumably in-person URC 2022.”

The team first qualified for the competition in 2017, and has since qualified in 2018 and 2020. Their latest rover, Apathy, is a nod to the team’s culture.

“We just thought it was funny,” said Piszkin. “It sort of represents the style of Yonder: we don't take ourselves too seriously.”

Light-shrinking material lets ordinary microscope see in super resolution

Square, semi-transparent material held against light.
This light-shrinking material turns a conventional light microscope into a super-resolution microscope. Credit: Junxiang Zhao

June 1, 2021 -- Electrical engineers at the University of California San Diego developed a technology that improves the resolution of an ordinary light microscope so that it can be used to directly observe finer structures and details in living cells.

The technology turns a conventional light microscope into what’s called a super-resolution microscope. It involves a specially engineered material that shortens the wavelength of light as it illuminates the sample—this shrunken light is what essentially enables the microscope to image in higher resolution.

“This material converts low resolution light to high resolution light,” said Zhaowei Liu, a professor of electrical and computer engineering at UC San Diego.

Closeup of a microscope stage.
The material mounted on the stage of an inverted microscope. Credit: Junxiang Zhao

“It’s very simple and easy to use. Just place a sample on the material, then put the whole thing under a normal microscope—no fancy modification needed.”

The work, which was published in Nature Communications, overcomes a big limitation of conventional light microscopes: low resolution. Light microscopes are useful for imaging live cells, but they cannot be used to see anything smaller. Conventional light microscopes have a resolution limit of 200 nanometers, meaning that any objects closer than this distance will not be observed as separate objects. And while there are more powerful tools out there such as electron microscopes, which have the resolution to see subcellular structures, they cannot be used to image living cells because the samples need to be placed inside a vacuum chamber.

“The major challenge is finding one technology that has very high resolution and is also safe for live cells,” said Liu.

The technology that Liu’s team developed combines both features. With it, a conventional light microscope can be used to image live subcellular structures with a resolution of up to 40 nanometers.

Image
Artistic rendering of the new super resolution microscopy technology. Animal cells (red) are mounted on a slide coated with the multilayer hyperbolic metamaterial. Nanoscale structured light (blue) is generated by the metamaterial and then illuminates the animal cells. Image credit: Yeon Ui Lee

 

The technology consists of a microscope slide that’s coated with a type of light-shrinking material called a hyperbolic metamaterial. It is made up of nanometers-thin alternating layers of silver and silica glass. As light passes through, its wavelengths shorten and scatter to generate a series of random high-resolution speckled patterns. When a sample is mounted on the slide, it gets illuminated in different ways by this series of speckled light patterns. This creates a series of low resolution images, which are all captured and then pieced together by a reconstruction algorithm to produce a high resolution image.

Microscope images displayed in orange against a black background.
Comparison of images taken by a light microscope without the hyperbolic metamaterial (left column) and with the hyperbolic metamaterial (right column): two close fluorescent beads (top row), quantum dots (middle row), and actin filaments in Cos-7 cells (bottom row). Adapted from Nature Communications

The researchers tested their technology with a commercial inverted microscope. They were able to image fine features, such as actin filaments, in fluorescently labeled Cos-7 cells—features that are not clearly discernible using just the microscope itself. The technology also enabled the researchers to clearly distinguish tiny fluorescent beads and quantum dots that were spaced 40 to 80 nanometers apart.

The super resolution technology has great potential for high speed operation, the researchers said.  Their goal is to incorporate high speed, super resolution and low phototoxicity in one system for live cell imaging.

Liu’s team is now expanding the technology to do high resolution imaging in three-dimensional space. This current paper shows that the technology can produce high resolution images in a two-dimensional plane. Liu’s team previously published a paper showing that this technology is also capable of imaging with ultra-high axial resolution (about 2 nanometers). They are now working on combining the two together.

Paper title: “Metamaterial assisted illumination nanoscopy via random super-resolution speckles.” Co-authors include: Yeon Ui Lee*, Junxiang Zhao*, Qian Ma*, Larousse Khosravi Khorashad, Clara Posner, Guangru Li, G. Bimananda M. Wisna, Zachary Burns and Jin Zhang, UC San Diego.

*These authors contributed equally to this work

This work was supported by the Gordon and Betty Moore Foundation and the National Institutes of Health (R35 CA197622). This work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) at UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which is supported by the National Science Foundation (grant ECCS-1542148).

A 'self-stirring' pill enhances drug bioavailability

Self-propelling microparticles enhance the dissolution of drugs in the stomach, achieving better bioavailability without the side effects of high dosing.

May 28, 2021 -- The majority of drugs we take are administered orally, and while this route is easy for patients, safe, and effective, there are many hurdles to overcome before a drug molecule can be delivered to a desired organ or location in the body. This is not always a bad thing and your body does a fairly good job at keeping foreign molecules and parasites out. However, ensuring drugs are absorbed at levels high enough to elicit a desired therapeutic outcome can be challenging.

One of the main parameters to assess drug performance is bioavailability, which is defined as the fraction of dosed drug that reaches systemic circulation. Achieving high bioavailability depends strongly on drug solubility, stability in the stomach, and its absorption in the GI tract, among other factors. One way around this is high dosing, but this can be dangerous and result in undesired side effects. Needless to say, efficient absorption through this route is often difficult to achieve.

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Top row: Images of aspirin-loaded static (white) and microstirring pills (black). Bottom row: The tube used to perform the pill administration by oral gavage. Images courtesy of Advanced Science

From modifying the structure of drug molecules to developing sophisticated formulation systems, researchers are exploring new and innovative ways to safely enhance drug bioavailability. In a recent study published in Advanced Science, researchers at the University of California San Diego report the development of a microstirring pill platform with built-in mixing capability to enhance drug uptake and bioavailability.

“For over a decade we have been working on using micromotor-based active transport to improve the delivery of drugs,” said Joseph Wang, a professor of nanoengineering at UC San Diego and co-corresponding author of the study. “Our recent efforts have been aimed at bridging the field of microrobots with the pharmaceutical industry. Our goal has been to greatly increase the bioavailability of oral drugs by incorporating a built-in stirring capability into traditional drug tablets.”

To accomplish this, Wang, an expert in the field of microrobotics, reached out to UC San Diego nanoengineering professor Liangfang Zhang, who is himself an expert in drug design and delivery and the study's other corresponding author. They hypothesize that including chemically-powered microstirrers into a pharmaceutical pill could enhance the drug dissolution and dispersion in the stomach, leading to faster absorption and increased bioavailability.

The researchers note that their “smart pill” platform is safe. “Similar to conventional oral pills, the self-stirring pills cause no damage to the stomach,” said Wang.

Zhang and Wang’s pill contains embedded “microengines” called Janus microparticles made from magnesium microparticles that are partially coated with a thin layer of titanium dioxide. The fabrication process leaves a small opening in the particle’s structure through which microbubbles generated via an internal chemical reaction can exit and shoot the microparticle around.

“Embedding microscopic stirrers into a pill matrix offers significantly faster pill disintegration and dissolution,” explained Wang. “Since the encapsulated drugs and microstirrers are decoupled, the drug loading is not affected or compromised by the microstirrer.”

In vivo studies using animal models demonstrated that the enhanced pills greatly improved the absorption and bioavailability of aspirin, both immediately post administration and at longer time scales. “Considering [these] encouraging results, we anticipate a high likelihood of clinical translation of the microstirring pill technology,” said Wang.

“In principal, the microstirrer pill can be broadly applicable for numerous types of oral drugs. The concept thus has a very high translation potential: adding only one excipient material (the synthetic microstirrers) into the pill formulation without changing anything else.”

Source: Advanced Science News

Thin, large-area device converts infrared light into images

May 27, 2021 -- Seeing through smog and fog. Mapping out a person’s blood vessels while monitoring heart rate at the same time—without touching the person’s skin. Seeing through silicon wafers to inspect the quality and composition of electronic boards. These are just some of the capabilities of a new infrared imager developed by a team of researchers led by electrical engineers at the University of California San Diego.

The imager detects a part of the infrared spectrum called shortwave infrared light (wavelengths from 1000 to 1400 nanometers), which is right outside of the visible spectrum (400 to 700 nanometers). Shortwave infrared imaging is not to be confused with thermal imaging, which detects much longer infrared wavelengths given off by the body.

The imager works by shining shortwave infrared light on an object or area of interest, and then converting the low energy infrared light that’s reflected back to the device into shorter, higher-energy wavelengths that the human eye can see.

“It makes invisible light visible,” said Tina Ng, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering.

While infrared imaging technology has been around for decades, most systems are expensive, bulky and complex, often requiring a separate camera and display. They are also typically made using inorganic semiconductors, which are costly, rigid and consist of toxic elements such as arsenic and lead.

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The new infrared imager is thin and compact with a large-area display. Credit: Ning Li

The infrared imager that Ng’s team developed overcomes these issues. It combines the sensors and the display into one thin device, making it compact and simple. It is built using organic semiconductors, so it is low cost, flexible and safe to use in biomedical applications. It also provides better image resolution than some of its inorganic counterparts.

The new imager, published recently in Advanced Functional Materials, offers additional advantages. It sees more of the shortwave infrared spectrum, from 1000 to 1400 nanometers—existing similar systems often only see below 1200 nanometers. It also has one of the largest display sizes of infrared imagers to date: 2 square centimeters in area. And because the imager is fabricated using thin film processes, it is easy and inexpensive to scale up to make even larger displays.

Energizing infrared photons to visible photons

The imager is made up of multiple semiconducting layers, each hundreds of nanometers thin, stacked on top of one another. Three of these layers, each made of a different organic polymer, are the imager’s key players: a photodetector layer, an organic light-emitting diode (OLED) display layer, and an electron-blocking layer in between.

The photodetector layer absorbs shortwave infrared light (low energy photons) and then generates an electric current. This current flows to the OLED display layer, where it gets converted into a visible image (high energy photons). An intermediate layer, called the electron-blocking layer, keeps the OLED display layer from losing any current. This is what enables the device to produce a clearer image.

This process of converting low energy photons to higher energy photos is known as upconversion. What’s special here is that the upconversion process is electronic. “The advantage of this is it allows direct infrared-to-visible conversion in one thin and compact system,” said first author Ning Li, a postdoctoral researcher in Ng’s lab. “In a typical IR imaging system where upconversion is not electronic, you need a detector array to collect data, a computer to process that data, and a separate screen to display that data. This is why most existing systems are bulky and expensive.”

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The imager sees the word "EXIT" concealed by smog (left). An image of the setup without smog (right). Courtesy of Ning Li/Advanced Functional Materials 

Another special feature is that the imager is efficient at providing both optical and electronic readouts. “This makes it multifunctional,” said Li. For example, when the researchers shined infrared light on the back of a subject’s hand, the imager provided a clear picture of the subject’s blood vessels while recording the subject’s heart rate.

The researchers also used their infrared imager to see through smog and a silicon wafer. In one demonstration, they placed a photomask patterned with “EXIT” in a small chamber filled with smog. In another, they placed a photomask patterned with “UCSD” behind a silicon wafer. Infrared light penetrates through both smog and silicon, making it possible for the imager to see the letters in these demonstrations. This would be useful for applications such as helping autonomous cars see in bad weather and inspecting silicon chips for defects.

The researchers are now working on improving the imager’s efficiency.

Paper title: “Organic Upconversion Imager with Dual Electronic and Optical Readouts for Shortwave Infrared Light Detection.” Co-authors include Naresh Eedugurala and Jason D. Azoulay, University of Southern Mississippi; and Dong-Seok Leem, Samsung Electronics Co., Ltd.

This work was supported by the National Science Foundation (ECCS-1839361) and Samsung Advanced Institute of Technology. The work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) at UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which is supported by the National Science Foundation (grant ECCS-1542148). 

Sustainable method to 3D print steel wins big at Triton Innovation Challenge

May 26, 2021--Engineers, physicians, biologists and business students at UC San Diego showcased their environmentally focused technologies at the ninth annual Triton Innovation Challenge business competition. A startup developing a 3D printing technique that can manufacture steel cheaper than existing methods, with no carbon emissions and minimal wasted scrap metal, earned the $7,000 Grand Prize.

The Triton Innovation Challenge is a business competition focused on fostering creativity and bringing to the spotlight commercially promising, environmentally focused technologies generated by students, staff and faculty from across UC San Diego. The competition is hosted by the Jacobs School of Engineering, Rady School of Management and Scripps Institution of Oceanography, and showcases startups or technologies that come from, are inspired by, or directly impact nature. The competition is funded by the William and Kathryn Scripps Family Foundation.

Jacobs School of Engineering materials science Ph.D. students Andy Zhao and Olivia Dippo are the founders of Green Steel Printing, which won Grand Prize at the Triton Innovation Challenge.

On May 21, five teams presented their ventures virtually to a panel of five judges and an audience, with $12,500 worth of prizes on the line: a Grand Prize of $7,000; Runner Up earning $4,000; and an Audience Choice award of $1,500. All the competing teams participated in a pitch-prep workshop and received other training and networking opportunities as part of the Challenge program. 

Green Steel Printing, a venture founded by Jacobs School of Engineering materials science Ph.D. students Olivia Dippo and Andy Zhao, earned the Grand Prize for their solution to reducing carbon emissions and metal waste in the steel manufacturing industry. Current steel manufacturing processes take iron oxide ore, and burn coal or natural gas to reduce the ore into iron, which is then converted to steel. This accounts for 7 percent of global carbon dioxide emissions. 

“For every ton of steel produced, 1.8 tons of carbon dioxide is emitted,” said Zhao. “There’s an inherent carbon price you have to pay to produce steel; there are fossil fuels embedded in the steel supply chain.” 

The traditional process of manufacturing steel parts is subtractive, meaning companies purchase large blocks of steel, and then remove material until they reach the desired shape and size of the part they’re building, resulting in a lot of scrap metal waste.

Green Steel aims to solve both of these problems by combining metal 3D printing, with green hydrogen technology, to generate steel with no carbon emissions, and significantly less scrap metal waste. Their patent pending 3D printing process is also projected to be cheaper than existing methods.

“Inspired by metal 3D printing and inspired by using green hydrogen as a replacement for fossil fuels, we have come up with our Green Steel printer,” said Dippo. “The two inputs are iron oxide ore—which is how the material comes out of the earth—and green hydrogen. These two things are mixed together in a reaction zone that forms iron powder. We can add additional alloying elements such as carbon in order to make steel, and at the very bottom of the machine we have our print head, where we can print the desired shapes.”

In the future, they plan to partner with aerospace or automotive companies to produce steel parts.

Dippo and Zhao are securing additional funding and lab space to further develop their steel 3D printing machine, and hope to have a prototype complete in about a year. 

The judges selected Lichen Lab as the Triton Innovation Challenge Runner Up. Lichen Lab, founded by biology alumnus Will Landry, developed and sells an alarm to help lab users keep their fume hoods closed, not only improving lab safety, but reducing energy consumption and saving money as well. When these fume hoods are left open when not in use, they waste upwards of $1,000 in energy per hood annually.

The Audience Choice award went to SynBioEnergy, founded by bioengineering PhD student Tyler Myers. SynBioEnergy uses a bioreactor to treat wastewater and desalinate water, using the components filtered out of the water as a biofuel to power the device. They plan to market the small-scale device to wineries and agricultural industries needing to meet state wastewater treatment regulations. 

Other Triton Innovation Challenge finalists include Algeon Materials, founded by Rady School of Management students, which leverages ocean derived materials like kelp to create plastic alternatives, initially in the retail space for items like hangers; and Kryos Cooling, led by a UC San Diego physician and faculty in the School of Public Health, which is developing a cooling vest for the increasing number of people living in hot climates, or who work outside in the summer. 

In addition to the Triton Innovation Challenge, Scripps Oceanography and Rady School of Management are now launching another innovation program, startBlue, on campus this fall. The startBlue accelerator program is currently accepting applications from San Diego-based innovators, engineers, and scientists who are working to solve ocean-related challenges. The deadline to apply for the fall cohort is July 2, 2021. Visit the startBlue website to learn more.

Improved maps for self-driving vehicles win Research Expo 2021

May 25, 2021-- From monitoring the structural integrity of airplane wings, to improving lithographic 3D printing processes, to creating better maps for self-driving cars, this year’s Research Expo symposium showcased the depth and breadth of work done by graduate engineering and computer science students at the University of California San Diego Jacobs School of Engineering.

Computer science Ph.D. students David Paz-Ruiz and Hengyuan Zhang took the top prize, the Lea Rudee Outstanding Poster Award, in addition to the Best Poster Award for the Department of Computer Science and Engineering. Their work focuses on improving the maps that self-driving vehicles use to navigate the world. They worked under the direction of Henrik Christensen, director of UC San Diego’s Contextual Robotics Institute and a professor in the computer science department.

David Paz-Ruiz Hengyuan Zhang

Paz-Ruiz and Zhang are tackling a problem that makes it hard for self-driving cars to scale up: most rely on high-definition (HD) maps, with resolution as small as one centimeter, which are manually labeled.

The computer scientists instead created what is known as semantic maps--2D data based on camera images overlapping with point cloud maps. The maps contain information about drivable areas, crosswalks, sidewalks, and lane markings. 

“Unlike HD maps, our maps do not include centimeter level annotations for the trajectories that the vehicle can follow,” Paz-Ruiz said. “Instead, we seek to generate these in real time.” 

“Our semantic maps are generated without human labeling effort and can be continuously updated if the environment was to change in the future,” Zhang added. 

Researchers can build a semantic map of campus in just a few hours. By contrast, an HD map would take weeks. In addition, the researchers’ maps can be used across different robots and different vehicles. 

“At UCSD we are studying how smart vehicles can be used in urban areas such the university campus or a parking lot at the airport to assist people with daily tasks” adds Prof. Christensen 

This year, the 39th annual Research Expo event was held virtually, with students submitting video presentations ahead of time, and answering questions about their work during the live event from judges, alumni and industry representatives. In all, 250 people attended the event. 

In addition to Paz-Ruiz and Zhang, one research project from each of the Jacobs School’s six departments was recognized. They are listed below, with links to their video presentations: 

Bioengineering

Sandhya Sihra

"A Heart-to-Heart Worth Having"

Computer Science and Engineering

David Paz and Hengyuan Zhang

"Towards Autonomous Vehicle Navigation without HD Maps"

Electrical and Computer Engineering

Ross Greer

“Trajectory Prediction in Autonomous Driving with a Lane Heading Auxiliary Loss”

Mechanical and Aerospace Engineering

Jessica Medrado

"Fundamentals of water-evaporation processes for renewable energy application"

NanoEngineering

David Wirth and Justin Hochberg

"A Highly Expandable Foam for Lithographic 3D Printing"

Structural Engineering

Adrielly Hokama Razzini

"Structural Health Monitoring of an Airplane’s Wings Using Gaussian Process Regressors"


 

Zexiang Xu wins Chancellor's Dissertation Medal

Undergraduate researchers earn Goldwater Scholarship

May 13, 2021-- Three UC San Diego undergraduate students with impressive academic and research credentials were selected to receive the Goldwater Scholarship, designed to foster and encourage outstanding students to pursue research careers in the fields of the natural sciences, engineering and mathematics. The Goldwater Scholarship, which provides students up to $7,500 toward tuition, books and fees, is the preeminent undergraduate award of its type in these fields.

The scholarship is named in honor of Senator Barry Goldwater, and this year was administered in partnership with the Department of Defense National Defense Education Programs.

Bioengineering students Aditi Gnanasekar and Claire Zhang, and physics student Mara Casebeer, received the scholarship in recognition of their research contributions and plans to pursue careers in research.

Aditi Gnanasekar

Aditi Gnanasekar was interested in biology, computer science and technology from an early age, but was not sure how to combine all three fields until she discovered the Bioengineering: Biotechnology major at UC San Diego.

“There is definitely a lot of computation within the biotech track, but it also has a focus on chemical engineering concepts and biomolecular techniques as well, so it’s the perfect blend of those disciplines,” said Gnanasekar.

She has applied her bioengineering know-how as an undergraduate researcher in the lab of Professor Weg Ongkeko at the UC San Diego School of Medicine, analyzing RNA sequences to extract information on immune cell expression, ultimately working toward characterizing cancers on the molecular level.

“Recently, I’ve been working on research into the intratumor microbiome, and specific microbes that are characterized in specific tumors,” Gnanasekar said. “We think it’s pretty interesting that there are microbes that are only present in certain tumors, and think they could play a critical role in determining the clinical outcome of cancer.”

After earning her bachelor’s degree, Gnanasekar plans to pursue an M.D./Ph.D., enabling her to continue this type of research while also working hands-on with patients.

In addition to earning the Goldwater Scholarship, Gnanasekar is also one of just 11 Jacobs School of Engineering students in the class of 2022 to receive the prestigious Jacobs School Scholar award, supported by school namesakes Dr. Irwin and Joan Jacobs. Jacobs Scholars are selected for demonstrated academic achievement, leadership, commitment to community, and innovative potential, and become a close community of scholars during their undergraduate years.

Outside of the classroom, Gnanasekar played intramural sports, sung in a capella groups, and volunteered with UC San Diego StRIVE, assisting adults with disabilities. But research was her main passion.

“My lab is really important—they’re like a second family to me.”

She advises students interested in research to stick with it, even when the going gets tough.

“One of the biggest lessons I’ve learned from doing scientific research and being part of a lab is being really patient,” she said. “Research is hard and you need to be persistent—you can't expect to get published right away or for your experiments to work out your way. A lot of times experiments will fail; that's totally expected and fine. And even if they do fail, that doesn't mean the research was useless or you didn't get anything out of it. That information is still very important.”

Claire Zhang 

As a young student, Claire Zhang was intrigued by both patient-facing clinical medicine and the technical innovations required to better manage disease. An early hands-on introduction to biomedical research solidified her desire to do both, and helped her see a path to do so.

Now a bioengineering student at UC San Diego, Zhang plans to earn an M.D./Ph.D. after graduation, with a goal of improving computational precision medicine by unifying molecular, cellular and physiological data as a physician scientist. She got a taste for what this can look like as an undergraduate researcher in the lab of Dr. Kevin King, from the Departments of Medicine and Bioengineering. Zhang used tools like single-cell RNA sequencing to study diseases in which the immune system becomes activated even though there is no infection, including heart attacks.

“Dr. King has been an incredible role model and crucial source of support and mentorship over the past two years, and inspired my interest in pursuing a physician-scientist career myself,” said Zhang.

She hopes to put the medical and computational skills she’s learning to use to synthesize all the various data points we can learn about an individual‒ from genetics to heart rate to sleep habits‒into actionable information.

“We’ve gotten quite good at drawing conclusions from each of these types of data on their own, but synthesizing information from all of these diverse sources to make holistic personalized predictions about one’s risk for disease, or what drugs will be most effective for someone, could truly revolutionize clinical medicine.”

Like Gnanasekar, Zhang is also a Jacobs School Scholar, one of the 11 Jacobs School of Engineering students in the class of 2022 to receive the prestigious full-ride scholarship award that is supported by school namesakes Dr. Irwin and Joan Jacobs.

In addition to the Jacobs Scholars community and her research, Zhang is involved in the International Health Collective, a student-run nonprofit that operates a monthly free clinic in Tijuana, Mexico, and is a member of the Theta Tau professional engineering fraternity.

Her advice for current and future students?

“Take advantage of opportunities to grow, even (and sometimes especially) if they make you uncomfortable. Apply to that internship that you don’t think you’ll get into, email that professor whose research sounded interesting, try out a few student orgs!”

Mara Casebeer

Mara Casebeer, a biological physics student with a minor in chemistry, has been captivated by the power of physics since high school.

“My junior year of high school I had an amazing physics teacher who showed me everything that physics could do,” she said. “We had one lab where we had to calculate the angle we needed to release a ball in order to get it to land in a basket. On the first try, based off our calculations, we got it right in the basket, nothing but net. And that blew my mind, that simple physics equations can predict what’s happening in the natural world so easily.”

As an undergraduate researcher at the Scripps Institution of Oceanography, Casebeer now harnesses the power of physics to study how radio frequency cell-to-cell communications and high-frequency electromagnetic waves interact with biological systems. She models how DNA behaves and changes in these high-frequency environments.

After graduating in 2022, Casebeer plans to earn a doctorate in biological physics, and continue conducting research in experimental and computational biophysics. At UC San Diego, Casebeer is also a supplemental physics instructor through the Teaching and Learning Commons, an experience which has affirmed her goal of becoming a professor one day, combining her love of research and teaching.

Outside of research, coursework and teaching, Casebeer is also co-president of the Warren Honor Society, plays intramural soccer and clarinet in the chamber ensemble and is part of the Undergraduate Women in Physics organization.

Her advice to current and future students?

“Don’t be afraid to put yourself out there in terms of research‒it can never hurt to talk to a professor after class about their research, or email them. It can be really intimidating but if it’s something you’re passionate about it’ll be worth it.”

Bioengineering student earns Strauss Scholarship

May 13, 2021--UC San Diego bioengineering undergraduate Zina Patel was selected to receive the $15,000 Strauss Scholarship, awarded to outstanding students developing social change or public service projects. Patel is one of only 14 students to receive the scholarship, which aims to prepare future leaders by encouraging them to undertake a high-impact venture and providing the funds to get started.

Patel’s project, called This Able, is a free online platform that connects college students with disabilities interested in joining the workforce, to mentors with disabilities already in the workforce. The goal is to not only provide mentorship, but to also provide these students with tailored expertise to bolster their job applications by assisting with resumes, interview preparation and more.

“The goal of this effort is to guide the next generation of those with disabilities and empower them by providing mentorship and networking opportunities,” said Patel. “I hope that This Able will serve as an avenue to increase employment rates for the special needs community and help cultivate a diverse and inclusive workforce, setting a precedent for the post-COVID world. My long-term and ultimate goal is to hand This Able off to web developers with disabilities who can run the platform, making it uniquely for those with disabilities by those with disabilities.”

Patel was inspired to create This Able as a volunteer at TRACE Alternative School in San Diego, where she witnessed talented job applicants being passed over for jobs they seemed to be qualified for. According to the Bureau of Labor and Statistics, only 18 percent of people with disabilities were employed in 2020. 

“As a volunteer at TRACE, I have heard countless stories from students about unsuccessful job applications,” Patel said. “ More often than not, it’s because of their disability and stigmas/stereotypes surrounding that. They are often seen as a liability rather than an asset, who will bring a fresh perspective to the table. And I wanted to do something about this because I personally knew those students who were the faces behind the rejection letters. I knew their potential that many companies didn’t recognize. That’s my motivation for This Able — to help the students I’ve worked with and others like them secure a job and secure their independence.”

Patel said her engineering courses have prepared her well for not only the technical skills required to build out a platform like This Able, but also in the critical thinking and problem solving skills necessary for undertaking a project of this scale. 

“Another key component that I really love about engineering and entrepreneurship is customer development — going out in the community to talk to the people who will be using the technologies I create and getting their perspectives to drive the development of my projects,” she said.

Patel is doing that now for This Able, working with the UC San Diego Office for Students with Disabilities to conduct user testing. She hopes to launch the platform in the fall. 

On campus, Patel has been active in the Student-run Intercommunicative and Vocational Education (StRIVE) group, which aims to assist adults with disabilities in the critical age range of 18-22 with their transition to independent living; that’s how she taught and interacted with young adults with disabilities at TRACE, and is also part of the reason she’s studying engineering. Patel entered UC San Diego as a molecular and cellular biology student, but an experience during her freshman year convinced her that bioengineering was a better fit. 

“While volunteering at an autism center in India during my freshman year, I noticed that many of the students had no access to or could not afford assistive technology,” she said. “In fact, the school itself did not have an elevator for those in wheelchairs. Back in the US, I was a volunteer for an alternative school where all students had at least one form of assistive technology. Seeing the gap between students with disabilities and assistive technology in the country my ancestors come from, I decided to pursue a career in bioengineering to better understand the creation of medical devices so that I could one day give back to those students in need.”

Personalized sweat sensor reliably monitors blood glucose without finger pricks

ALT TEXT
A handheld device combined with a touch sweat sensor (strip at right) measures glucose in sweat, while a personalized algorithm converts that data into a blood glucose level. Image courtesy of ACS Sensors

May 10, 2021 -- Many people with diabetes endure multiple, painful finger pricks each day to measure their blood glucose. Now, engineers at the University of California San Diego have developed a device that can measure glucose in sweat with the touch of a fingertip, and then a personalized algorithm provides an accurate estimate of blood glucose levels.

The work was published recently in ACS Sensors.

According to the American Diabetes Association, more than 34 million children and adults in the U.S. have diabetes. Although self-monitoring of blood glucose is a critical part of diabetes management, the pain and inconvenience caused by finger-stick blood sampling can keep people from testing as often as they should. And while scientists have developed ways to measure glucose in sweat, levels of the sugar are much lower than in blood, and they can vary with a person’s sweat rate and skin properties. As a result, the glucose level in sweat usually doesn’t accurately reflect the value in blood.

To obtain a more reliable estimate of blood sugar from sweat, a team led by UC San Diego nanoengineering professor Joseph Wang and Juliane Sempionatto, a nanoengineering Ph.D. student in Wang’s lab, devised a system that could collect sweat from a fingertip, measure glucose and then correct for individual variability.

The researchers made a touch-based sweat glucose sensor with a polyvinyl alcohol hydrogel on top of an electrochemical sensor, which was screen-printed onto a flexible plastic strip. When volunteers placed their fingertip on the sensor surface for one minute, the hydrogel absorbed tiny amounts of sweat. Inside the sensor, glucose in the sweat underwent an enzymatic reaction that resulted in a small electrical current that was detected by a handheld device.

The researchers also measured the volunteers’ blood sugar through a standard finger prick test, and they developed a personalized algorithm that could translate each person’s sweat glucose to their blood glucose levels. In tests, the algorithm was more than 95% accurate in predicting blood glucose levels before and after meals. To calibrate the device, a person with diabetes would need a finger prick only once or twice per month. But before the sweat diagnostic can be used to manage diabetes, a large-scale study must be conducted, the researchers say.

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

Paper title: “Touch-Based Fingertip Blood-Free Reliable Glucose Monitoring: Personalized Data Processing for Predicting Blood Glucose Concentrations.”

This system helps robots better navigate emergency rooms

May 10, 2021-- Computer scientists at the University of California San Diego have developed a more accurate navigation system that will allow robots to better negotiate busy clinical environments in general and emergency departments more specifically.  The researchers have also developed a dataset of open source videos to help train robotic navigation systems in the future. 

The team, led by Professor Laurel Riek and Ph.D. student Angelique Taylor, detail their findings in a paper for the International Conference on Robotics and Automation taking place May 30 to June 5 in Xi’an, China.  

The project stemmed from conversations with clinicians over several years. The consensus was that robots would best help physicians, nurses and staff in the emergency department by delivering supplies and materials. But this means robots have to know how to avoid situations where clinicians are busy tending to a patient in critical or serious condition. 

“To perform these tasks, robots must understand the context of complex hospital environments and the people working around them,” said Riek, who holds appointments both in computer science and emergency medicine at UC San Diego. 

Taylor and colleagues built the navigation system, the Safety Critical Deep Q-Network (SafeDQN), around an algorithm that takes into account how many people are clustered together in a space and how quickly and abruptly these people are moving. This is based on observations of clinicians’ behavior in the emergency department. When a patient’s condition worsens, a team immediately gathers around them to render aid. Clinicians’ movements are quick, alert and precise. The navigation system directs the robots to move around these clustered groups of people, staying out of the way.

“Our system was designed to deal with the worst case scenarios that can happen in the ED,” said Taylor, who is part of Riek’s Healthcare Robotics lab at the UC San Diego Department of Computer Science and Engineering. 

The team trained the algorithm on videos from YouTube, mostly coming from documentaries and reality shows, such as “Trauma: Life in the ER” and “Boston EMS.”  The set of more than 700 videos is available for other research teams to train other algorithms and robots.

Researchers tested their algorithm in a simulation environment, and compared its performance to other state-of-the-art robotic navigation systems. The SafeDQN system generated the most efficient and safest paths in all cases. 

Next steps include testing the system on a physical robot in a realistic environment. Riek and colleagues plan to partner with UC San Diego Health researchers who operate the campus’ healthcare training and simulation center. 

The algorithms could also be used outside of the emergency department, for example during search and rescue missions. 

Ph.D. student Sachiko Matsumoto and undergraduate student Wesley Xiao also contributed to the paper. 

Social Navigation for Mobile Robots in the Emergency Department

Angelique M. Taylor, Sachiko Mastumoto, Wesley Xiao and Laurel Riek, University of California San Diego
http://cseweb.ucsd.edu/~lriek/papers/taylor-icra-2021.pdf


 

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May 8, 2021

Programs help Jacobs School undergraduates make the most of research experiences

GEAR and ERSP set engineering and computer science students up for success as researchers

May 6, 2021 -- As a first year bioengineering major at UC San Diego, Kanksha Patel had heard that there were opportunities to do research in professors’ labs as an undergraduate, but she didn't know how to get started or what lab to join.

Emily Tang liked physics but, as a first year, wasn't clear what her nanoengineering major was all about or if it was really for her. 

These two University of California San Diego engineering undergraduates broadened their understanding of what it means to study engineering -- and transformed their college experiences -- by getting involved in engineering research through a Jacobs School of Engineering program called GEAR

GEAR stands for Guided Engineering Apprenticeship in Research, and it's run by the IDEA Engineering Student Center here at the UC San Diego Jacobs School of Engineering. The program is modeled off a similar program for computer science undergraduates at the Jacobs School of Engineering called the Early Research Scholars Program (ERSP)

ERSP was launched by Christine Alvarado, who is a professor in the Department of Computer Science and Engineering and also Associate Dean for Students for the Jacobs School of Engineering. 

Both GEAR and ERSP bring second-year undergraduates into university research labs where they work on team projects that contribute to the actual research mission of the lab. In both programs, in addition to mentorship from people within the research lab, students get outside guidance, mentorship and community building opportunities. Students with no previous research experience and students from traditionally underrepresented groups in engineering and computer science are particularly encouraged to apply. Applications are due in the spring, and the programs run from fall through the spring of the following academic year. 

One of the unique aspects of these programs is that the students are systematically required to discover and truly understand the big picture "Why" of the research lab they have joined. 

"Challenging undergraduate students to understand the big picture 'Why' of the research laboratory they are working in gives them the ability to understand why their contribution matters, why the intermediate step they are responsible for is important," said Ekaterina (Katya) Evdokimenko, Ph.D.

Evdokimenko teaches the two-credit ENG 20 "Introduction to Engineering Research" course which all GEAR students take during the first-quarter of their three-quarter GEAR experience. The students cover a lot of ground in ENG 20, all of it tied to making the most of their first research experience in a lab and building on the experience in order to open more opportunities and eventually a fulfilling career. 

The final ENG 20 project is a customized research proposal which the students use as a roadmap for their research project which continues for the next two quarters. 

"Each week you log something different," said Patel, the bioengineering major who was embedded in Karsten Zengler's microbiology lab which is part of the Center for Microbiome Innovation at UC San Diego. The students learn how to communicate effectively within a research lab environment, including teasing out the big-picture goals of the lab and learning how to communicate with the professor who leads the lab as well as graduate students, research scientists and other lab group members to keep them updated.

Emily Tang felt intimidated by the prospect of joining nanoengineering professor Zheng Chen's battery lab, but she found a supportive environment and developed a research project to test the efficiency of lithium ion batteries with varying electrolyte concentrations. 

"GEAR gave me more direction in what nanoengineering even is," said Tang. "I'm a nanoengineering major with an environmental studies minor. Renewable energy is something that bridges these interests."

Building on the momentum from her research experience, Tang enrolled in a graduate-level nano-scale energy course taught by world-renowned battery pioneer and nanoengineering professor Shiley Meng

GEAR and ERSP are specifically designed for undergraduates who have never worked in a professor's research lab and aim to give all students, no matter their past experiences, the tools and support necessary for success. 

"The biggest thing about the GEAR program for me is that it's introductory. I didn't know what research was like," said Tang. 

Patel learned about herself through the experience. "I wasn't sure if I would like research and the lab environment." After going through GEAR, she said, "I decided I really like research. I want to pursue research after graduation."

Both Patel and Tang were in the first cohort of GEAR students during the 2019-2020 school year. They both thrived and went on to serve as tutors for the Fall 2020 GEAR class, ENG 20, taught by Evdokimenko. 

"I think the GEAR experience helps students understand if they WANT to be an engineer or if they WANT to be in an engineering research lab," said Evdokimenko. "Students need to understand what it means to be an engineer."

"I think the GEAR experience helps students to understand what it means to be an engineer, what exactly engineers do, and what the word 'research' implies," said Evdokimenko. 

The ERSP and GEAR programs give Jacobs School of Engineering students opportunities to answer these questions. 

"This idea of engaging sophomores in research is a little bit out there," said Alvarado in a video showcasing ERSP. "People take time to warm up to the idea that sophomores can do something meaningful in a research project." 

In addition to inspiring the Jacobs-School-wide program, ERSP has also inspired similar programs at a handful of universities including UC Santa Barbara. 

ERSP was originally supported with funding from the National Science Foundation and is currently funded through the Department of Computer Science and Engineering here at UC San Diego. GEAR is supported through the Jacobs School of Engineering, and the pilot year was partially funded through support from the Office for Equity, Diversity, and Inclusion (EDI) at UC San Diego.

UC San Diego runs a wide range of programs that help undergraduate students get involved in research. There is a Student Research portal on TritonLink and also a campus-wide Undergraduate Research website.

We need to build more EV fast-charging stations, researchers say

The campus is home to one of the largest, most diverse range of electric vehicle charging stations at any university in the world.

May 5, 2021-- A team of engineers recommends expanding fast-charging stations for electric vehicles as campuses and businesses start planning for a post-pandemic world. 

The recommendation is based on a study of charging patterns for electric vehicles on the University of California San Diego campus from early January to late May of 2020, after the university moved most of its operations online. Researchers say the findings can be applied to a broader range of settings. 

“Workplace charging is a critical enabler of carbon-free transportation as the electrons consumed primarily come from solar power plants, as opposed to at-home charging, which occurs at night and relies more on fossil fuel power plants,” said Jan Kleissl, the paper’s senior author and a professor of environmental engineering at UC San Diego.

It’s the first time that a research team gathered information on workplace charging patterns for electric vehicles during the COVID-19 pandemic. As expected, charging declined dramatically once most campus operations became remote. Also as expected, charging at the campus’ medical center was less impacted as medical facilities continued most in-person operations and healthcare workers and patients kept using those charging stations. 

This reflects nationwide trends. Vehicle travel in the United States declined by about 40 percent from mid-March to mid-April 2020, according to the National Bureau of Economic Research.

But DC fast chargers that provide a full charge in about half an hour were less affected than what is known as Level 2 chargers, which provide a full charge over eight hours. Energy dispatched at Level 2 chargers on the main UC San Diego campus decreased by 84 percent. DC fast charging initially dropped by 67 percent. These stations quickly returned to near-normal usage in a short period of time, unlike Level 2 charging stations. 

“This finding reinforces ongoing efforts to deploy at least an additional 20 DCFCs primarily on the perimeter of campus in order to serve both UC San Diego commuters as well as the general public in need of recharging,” said Byron Washom, the UC San Diego director of strategic energy initiatives and one of the paper’s coauthors.

The team details their findings in the March 23 issue of the Journal of Renewable and Sustainable Energy. 

Only four out of 100 stations in the study were fast-charging. More broadly, in the United States, only a tiny fraction of charging stations are fast-charging, and most of those only serve Tesla vehicles. For example, California has about 31,800 EV charging stations. Of those, almost 3000 are Tesla supercharging stations, only available to Tesla vehicles. An additional 470 are DCFC stations managed by California-based Chargepoint. 

The study looked at 100 charging stations in 28 parking structures. Specifically, researchers found that from March 11 to May 20, 2020: 

  • Charging on the main campus dropped by 84 percent from pre-pandemic levels
  • Charging dropped by 50 percent at the parking structures at the UC San Diego medical center locations
  • Charging at DC fast charging stations initally dropped by 67 percent before going back up to near pre-pandemic levels 

Charging will likely not resume back to normal even  after the pandemic ends, researchers say. 

“Commuting patterns based on five days a week in the office are unlikely to  resume, however, as employers may allow more telecommuting even after the end of the pandemic,” Kleissl said. . 

That may be good news as the anticipated dramatic increase in EV adoption over the coming years would otherwise strain the existing charging infrastructure, he  added.

Impact of the Coronavirus Pandemic on Electric Vehicle Workplace Charging

Graham McClone, Jan Kleissl, Byron Washom, Sushil Silwal, University of California San Diego


 

The Wave Beneath Their Wings

The intricate dance between waves, wind, and gliding pelicans is worked out for the first time

April 21, 2021-- It’s a common sight: pelicans gliding along the waves, right by the shore. These birds make this kind of surfing look effortless, but actually the physics involved that give them a big boost are not simple. 

Researchers at the University of California San Diego have recently developed a theoretical model that describes how the ocean, the wind and the birds in flight interact in a recent paper in Movement Ecology.

This cartoon illustrates the equation that describes the physics of wave slope-soaring. 

UC San Diego mechanical engineering PhD student Ian Stokes and adviser Professor Drew Lucas of UC San Diego’s Department of Mechanical and Aerospace Engineering and Scripps Institution of Oceanography found that pelicans can completely offset the energy they expend in flight by exploiting wind updrafts generated by waves through what is known as wave-slope soaring. In short, by practicing this behavior, seabirds take advantage of winds generated by breaking waves to stay aloft.

The model could be used to develop better algorithms to control drones that need to fly over water for long periods of time, the researchers said. Potential uses do not stop there.

“There’s a community of biologists and ornithologists that studies the metabolic cost of flight in birds that can use this and see how their research connects to our estimates from theory. Likewise, our model generates a basic prediction for the winds generated by passing swell, which is important to physicists who study how the ocean and atmosphere interact in order to improve weather forecasting,” Stokes said. 

“This is an interesting project because it shows how the waves are actually moving the air around, making wind. If you're a savvy bird, you can optimize how you move to track waves and to take advantage of these updrafts. Since seabirds travel long distances to find food, the benefits may be significant,” Lucas said. 

Stokes and Lucas are, of course, not the first scientists to study the physics of the atmosphere that pelicans and other birds are hardwired to intuit so they can conserve energy for other activities. For centuries, humans have been inspired by the sight of birds harnessing the power and patterns of the winds for soaring flight.

That’s how it started with Stokes, who is now in the second year of his PhD at UC San Diego. As a UC Santa Barbara undergraduate, Stokes, a surfer and windsurfer in his off hours, needed a project for his senior physics class and thought of the birds that would accompany him on the waves. When he looked closer, he appreciated the connection between their flight dynamics and the study of environmental fluid dynamics, a speciality of scientists at UC San Diego. The project ultimately turned into a master’s thesis with Lucas, drawing inspiration from oceanographers at Scripps who seek to understand the interactions between the ocean and atmosphere.

Wave-slope soaring is just one of the many behaviors in seabirds that take advantage of the energy in their environment. By tapping into these predictable patterns, the birds are able to forage, travel, and find mates more effectively. 

“As we appreciate their mastery of the fluid, ever-changing ocean environment, we gain insight into the fundamental physics that shape our world,” said Lucas.

Pelicans glide above the waves, a behavior known as wave-slope soaring.
Photo: Simone Staff

 

Computer Scientists Discover Vulnerability Affecting Computers Globally

From left, clockwise: Dean Tullsen, professor, and Ph.D. student Mohammadkazen Taram at UC San Diego, teamed up with UC San Diego alumnus and UVA professor Ashish Venkat. 

April 30, 2021--Computer scientists at the University of California San Diego with researchrs at the University of Virginia School of Engineering to uncover a line of attack that breaks current defenses against Spectre, a devastating hardware flaw in computers eqwuipped with Intel and AMD processors. This means that billions of computers and other devices across the globe are just as vulnerable today as they were when Spectre was first announced.

The team reported its discovery to international chip makers in April and will present the new challenge at a worldwide computing architecture conference, the International Symposium on Computer Architecture, or ISCA, in June.

Led by Ashish Venkat, a UVA professor and UC San Diego alumni, with Dean Tullsen, a professor in the Department of Computer Science and Engineering at UC San Diego, the researchers found a new way for hackers to exploit something called a “micro-op cache,” which speeds up computing by storing simple commands and allowing the processor to fetch them quickly and early in the speculative execution process. Micro-op caches have been built into Intel computers manufactured since 2011.

The UC San Diego/UVA team reverse-engineered certain undocumented features in Intel and AMD processors. They have detailed the findings in their paper: “I See Dead µops: Leaking Secrets via Intel/AMD Micro-Op Caches.”

These two UC San Diego and UVA teams have collaborated before, including on a paper UC San Diego Ph.D. student Mohammadkazem Taram presented at the ACM International Conference on Architectural Support for Programming Languages and Operating Systems in April 2019. The paper, “Context-Sensitive Fencing: Securing Speculative Execution via Microcode Customization,” which introduced one of just a handful more targeted microcode-based defenses developed to stop Spectre in its tracks, was recently selected as a Top Pick in Hardware and Embedded Security among papers published in the six-year period between 2014 and 2019.

Read the full story from UVA about their research and its impact here.

CAREER awards for three researchers at UC San Diego Contextual Robotics Institute

May 15, 2021--Three researchers at the Contextual Robotics Institute at UC San Diego have received CAREER awards from the National Science Foundation in 2021. Their work ranges from robot mapping, to invertebrate locomotion, to autonomous robotic surgery. 

The projects’ descriptions are below.

Nikolai Atanasov

Atanasov’s project, “Active Bayesian Inference for Collaborative Robot Mapping" is an integrated research and education career development effort. It aims to design motion planning algorithms that enable robots to actively reduce uncertainty about their environment. Theoretically, this is an active Bayesian inference problem, aiming to achieve optimal control of a sensing and probabilistic estimation process. Practically, this is the goal of reproducing the curiosity that humans and animals exhibit when exploring an unknown environment on a robot system. The project considers collaboration among multiple robots to collaboratively explore and build a map of their environment. Applications include environmental monitoring, disaster response, and security and surveillance.
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2045945

Nicholas Gravish

Gravish's NSF CAREER award is entitled "The exceptional biomechanics of legged locomotion in the microcosmos". When viewed in relative terms, the fastest legged animals on the planet are the smallest of invertebrates.  These remarkable feats of movement are enabled by strong limbs, robust foot attachment mechanics, and resilient exoskeleton structures and these feats are unmatched in current insect-scale robotics. In this proposal we will study the legged movement performance in small invertebrates to reveal a set of radically different locomotor constraints and opportunities, enabled by favorable geometric and dynamic scaling laws. By elucidating principles of legged movement in small animals we seek to extrapolate these concepts to the insect-scale robots built in the Gravish lab. Overall the goal of this proposal is to better understand the rules of mobility and locomotion for scientific and engineering gain. 
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2048235&HistoricalAwards=false

 Michael Yip

Yip's NSF CAREER award, entitled "Contextually Informed Autonomous Robotic Surgery", will investigate how doctors use an understanding of the geometry and mechanics of human anatomy to guide their actions in surgery, and imbue surgical robots with this knowledge. By defining anatomical context for surgical robots, robots will be able to evaluate and optimize safe plans and trajectories in autonomous procedures, particularly those that involve stabilizing patients during first response. Yip's NIH Trailblazer award, entitled "Robotically controlled intraluminal instruments for flexible endoscopic intervention", investigates the design of handheld robotic catheters that may be used with flexible bronchoscopes for biopsying lung cancer. The work hypothesizes that handheld robotics may potentially offer a low-cost and more accessible solution today's expensive robot-assisted surgical diagnoses and interventional procedures and a potentially more complete diagnosis than with passive, manually controlled instruments.
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2045803&HistoricalAwards=false


 

Building a voice assistant for older adults

April 28, 2021-- Computer scientists at the University of California San Diego received an Amazon Research Award to develop a voice assistant to better communicate with older adults. Their initial goal is to create a system capable of understanding and answering the medical questions of adults over age 65.

The way the elderly sometimes struggle to use voice assistants like Alexa or Siri may often be joked about, but the problem is real: data show that adults over 65—a demographic expected to double between 2010 and 2050—tend to give up on using these tools after several unsuccessful attempts at getting their questions answered. 

The problem is that existing natural language processing (NLP) systems—the artificial intelligence models used to train computers to understand spoken and written human language—are trained to understand short, formal questions. This is fine for people who grew up with computer technology and know how to phrase their questions to be understood by the device. But older adults are used to speaking to people, not machines, and often struggle to pare down longer or conversational  questions to a sentence the artificial intelligence underpinning the voice assistants can understand.   

“Our job is to bridge that gap,” said Khalil Mrini, the UC San Diego computer science PhD student who will be supported by the Amazon Research Award to work on the project. “We’re working on technology that will flip the burden: instead of having older adults change or reformulate their question, we want the AI to be able to learn and understand the older adult.”

Computer science PhD student Khalil Mrini is working to make human language technology accessible to more populations.

To accomplish this, Mrini, a graduate student in UC San Diego computer science Professor Ndapa Nakashole’s lab, is working to create an end-to-end question answering system that can: 1) shorten the user’s question down to its key components, 2) match the shortened medical question to a frequently asked question from a database of 17,000 medical questions sourced from the National Institutes of Health; and 3) select the relevant portions of the corresponding longer answer to share with the user. 

Mrini has already completed the first step—training the AI to summarize a long question into a shorter one—which he did by training the NLP model jointly on summarizing questions and a classification task called question entailment, in which the model learns to tell if by answering a short question, the initial longer question has been addressed. 

“We found that if you’re training on both summarization—which is basically feeding longer user questions and the model learns to generate the short question—and at the same time training on question entailment, that classification task, then you’re able to generate better results,” said Mrini.

This question summarization AI model can be implemented as a standalone feature into existing voice assistants like Alexa, or integrated as a first step into any question answering system, where it can shorten user questions.

The team is still working on getting the tool to match the question with one in a pool of FAQs—in this case provided by the NIH—and then have the AI select the relevant pieces of a longer answer to read back to the user. 

Computer science Professor Ndapa Nakashole’s research focuses on developing algorithms that enable computers to understand and generate human language.

"The potential impact of this work is substantial because it aims to broaden the population of people who can benefit from conversational agents, by targeting an important segment of the population, older adults,” said Nakashole.

Making AI more inclusive

Why did this segment of the population need an add-on feature after the fact? Why were their user needs not considered in initial voice assistant testing? It’s a problem Mrini says is pervasive in AI systems and training, and one that he and researchers in the VOLI team are trying to rectify.

“Among users of existing question answering systems, older adults are underrepresented,” he said. “It stems from a lack of representation among internet users, which escalates into not having a lot of data about this particular demographic and so on. You have a problem that escalates into a lack of data, and if there’s no data, you can’t train an algorithm to meet their specific needs.”

Mrini is intimately familiar with this problem. As a native of Morocco, he noticed that virtually no AI models worked for his native language, Darija, a form of Arabic spoken in Morocco. 

“I realized there were—and still are—close to no NLP models or AI models that work well for my native language. So my first ever project was making data so that AI can be trained for my native language,” Mrini said.

He’s interned at Adobe Research and the Alexa group at Amazon, working to make AI models that can predict the syntax of a sentence in an interpretable way, and summarize the important takeaways of longer articles, respectively. 

“The global goal of my research is to make human language technology more interpretable and more accessible to wider audiences,” Mrini said. “Now I’m mainly working on English-language technology, but to make it more accessible for marginalized or underrepresented audiences, so older adults in this case.”

This project is part of the larger VOLI effort, (Voice Assistant for Quality of Life and Healthcare Improvement in Aging Populations) led by natural language processing researchers including Nakashole, along with geriatric physicians, and human computer interaction researchers at UC San Diego. One of the key goals of this NIH-funded project is to develop a personalized and context-aware voice-based digital assistant to improve the quality of life and the healthcare of older adults. Ultimately, the researchers hope the device will enable older adults to remain independent and optimize interactions with healthcare and service providers.

The principal investigators on the NIH grant are:
Qualcomm Institute Research Scientist Emilia Farcas; computer science Professors Ndapa Nakashole and Nadir Weibel; geriatric physician Dr. Alison Moore; and internal medicine physician and biomedical informatician Dr. Michael Hogarth.

UC San Diego joins Bytecode alliance to build safer software foundations for the Internet

The nonprofit is focused on building an ecosystem to advance the unique advantages of WebAssembly

April 28, 2021 -- The University of California San Diego has joined The Bytecode Alliance, a nonprofit organization dedicated to creating new software foundations and building on standards such as WebAssembly and WebAssembly System Interface (WASI). UC San Diego is part of a cross-industry collaboration alongside other new members Arm, DFINITY Foundation, Embark Studios, Google and Shopify to support the alliance, which was incorporated by Fastly, Intel, Mozilla and Microsoft.  

These organizations share a vision of a WebAssembly ecosystem that fixes cracks in today’s software foundations that are holding the industry and its software supply chains back from a secure, performant, cross-platform and cross-device future. 

Computer science professor Deian Stefan says, "they will contribute tools and techniques for a more secure software ecosystem"

“WebAssembly is quickly becoming the de facto intermediate representation for building secure systems. WebAssembly takes a principled approach to security and gives us just the right building blocks to build the next generation secure and high-assurance systems,” said Deian Stefan, an assistant professor in the Department of Computer Science and Engineering at the UC San Diego Jacobs School of Engineering. “It’s a core part of the sandboxing and high-assurance security toolkits we are developing at UC San Diego.”  

UC San Diego researchers and collaborators have developed the RLBox framework that uses WebAssembly to sandbox libraries, the CT-Wasm language extension for writing secure crypto code in WebAssembly, the Swivel compiler that mitigates Spectre attacks and the VeriWasm tool that verifies the safety of native compiled WebAssembly.

 “As members of the Bytecode Alliance we hope to help shape the direction of WebAssembly and contribute tools and techniques that will amplify the alliance’s vision towards a more secure software ecosystem,” Stefan said.

The Bytecode Alliance, founded in 2019, has helped bring attention to the inherent weaknesses in predominant models for building software, which rely heavily on composing up to thousands of third-party modules without security boundaries between them. These weaknesses in the software supply chain have historically been instrumental in breaching government systems, critical infrastructure services, and a large number of companies, as well as in stealing personal information of hundreds of millions, perhaps even billions of people. 

Neural implant monitors multiple brain areas at once, provides new neuroscience insights

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SEM images of the neural implant’s microelectrode array. Images courtesy of Nature Neuroscience

April 27, 2021 -- How do different parts of the brain communicate with each other during learning and memory formation? A new study by researchers at the University of California San Diego takes a first step at answering this fundamental neuroscience question.

The study was made possible by developing a neural implant that monitors the activity of different parts of the brain at the same time, from the surface to deep structures—a first in the field. Using this new technology, the researchers show that diverse patterns of two-way communication occur between two brain regions known to play a role in learning and memory formation—the hippocampus and the cerebral cortex. The researchers also show that these different patterns of communication are tied to events called sharp-wave ripples, which occur in the hippocampus during sleep and rest.

The researchers published their findings Apr. 19 in Nature Neuroscience.

“This technology has been developed particularly for studying interactions and communications between different brain regions simultaneously,” said co-corresponding author Duygu Kuzum, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering. “Our neural implant is versatile; it can be applied to any area of the brain and can enable study of other cortical and subcortical brain regions, not just the hippocampus and cerebral cortex.”

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The neural implant connected to a customized printed circuit board.

“Little is known about how various brain regions work together to generate cognition and behavior,” said Takaki Komiyama, a professor of neurobiology and neurosciences at UC San Diego School of Medicine and Division of Biological Sciences, who is the study’s other co-corresponding author. “In contrast to the traditional approach of studying one brain area at a time, the new technology introduced in this study will begin to allow us to learn how the brain as a whole works to control behaviors and how the process might be compromised in neurological disorders.”

The neural implant is made up of a thin, transparent, flexible polymer strip fabricated with an array of micrometer-sized gold electrodes, onto which platinum nanoparticles have been deposited. Each electrode is connected by a micrometers-thin wire to a custom-printed circuit board. Kuzum’s lab developed the implant. They worked with Komiyama’s lab to perform brain imaging studies in transgenic mice.

Engineering a multi-use neural probe

What makes this neural implant unique is that it can be used to monitor activity in multiple brain regions at the same time. It can record electrical signals from single neurons deep inside the brain, like in the hippocampus, while imaging large areas like the cerebral cortex.

“Our probe enables us to combine these modalities in the same experiment seamlessly. This cannot be done with current technologies,” said Xin Liu, an electrical and computer engineering Ph.D. student in Kuzum’s lab. Liu is a co-first author of the study along with Chi Ren, a recent UC San Diego biological sciences Ph.D. graduate who is now a postdoctoral researcher in Komiyama’s lab, and Yichen Lu, an electrical and computer engineering Ph.D. student in Kuzum’s lab.

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The flexible neural probe allows the working distance of the microscope to be close to the surface (top), while a conventional probe with rigid parts makes the working distance (red arrows) much farther (bottom).

Several design features make multi-region monitoring possible. One is that this probe is flexible. When it is inserted deep into the brain to monitor a region like the hippocampus, the part that sticks out of the brain can be bent down and make room for a microscope to be lowered close to the surface to do imaging of the cerebral cortex at the same time. Conventional neural probes are rigid, so they get in the microscope’s way; as a result, they cannot be used to monitor deep brain structures while imaging the brain’s surface. And even though the UC San Diego team’s neural probe is soft and flexible, it is engineered to withstand buckling under pressure during insertion.

Another important feature is that this probe is transparent, so it gives the microscope a clear field of view. It also does not generate any shadows or additional noise during imaging.

Exploring fundamental neuroscience questions

The motivation for this study was getting to the root of how different cognitive processes, such as learning and memory formation, occur in the brain. Such processes involve communication between the hippocampus and cerebral cortex. But how exactly does this communication happen? And which brain region initiates this communication: the hippocampus or the cerebral cortex? These types of questions have been left unanswered because it is very difficult to study these two brain regions simultaneously, said Kuzum.

“We were interested in investigating the nature of cortical-hippocampal interactions, so we built a technology to explore this neuroscience problem,” she said.

The researchers used their probe to monitor the activity of the hippocampus and the cerebral cortex in transgenic mice. Specifically, they monitored activity before, during and after oscillations that occur in the hippocampus called sharp-wave ripples.

Their experiments revealed that communication between the hippocampus and cerebral cortex is two-sided: sometimes the cortex initiates communication, other times it’s the hippocampus. This is an important first clue for understanding inter-region communication in the brain, the researchers said.

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L-R: Co-first authors Xin Liu, Chi Ren and Yichen Lu.

“The hippocampal-cortical interaction is important in memory consolidation and retrieval,” said Ren. “The two-sided communication we reported here is different from the conventional notion that the cortex passively receives the information from the hippocampus. Instead, the cortex is actively involved in encoding information into the brain and may play an instructive role during memory consolidation and retrieval.”

“We can now begin new studies to unlock how processes like learning and memory happen,” said Kuzum. “For example, when the brain acquires new information, how does the hippocampus transfer the memory to the cortex for storage, or does the cortex send a cue to transfer the memory? Our findings show that communication can be initiated by either, but to go beyond that we’d need to do behavioral studies.”

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Examples of different cortical activity patterns during sharp-wave ripples.

This study also reveals that there are diverse and distinct modes of communication between the hippocampus and the cerebral cortex. The researchers found that the hippocampus communicates with at least eight different parts of the cerebral cortex every time sharp-wave ripples occur. Further, each of these eight cortical activity patterns is tied to a different population of neurons in the hippocampus.

“These findings suggest that the interactions between brain regions, not only between cortex and hippocampus, can be fundamentally diverse and flexible. Therefore, multiple brain regions can efficiently work together to generate cognition and behavior that rapidly adapt to changing environments,” said Ren.

Paper title: “Multimodal neural recordings with Neuro-FITM uncover diverse patterns of cortical-hippocampal interactions.” Co-authors of the study include Yixiu Liu, Jeong-Hoon Kim and Stefan Leutgeb, all at UC San Diego.

This research was supported by the Office of Naval Research (N000142012405 and N00014162531), the National Science Foundation (ECCS-2024776, ECCS-1752241 and ECCS-1734940), and the National Institutes of Health (R21 EY029466, R21 EB026180, DP2 EB030992, R01 NS091010A, R01 EY025349, R01 DC014690, R21 NS109722 and P30 EY022589).

From self-driving cars, to drones, to healthcare robotics: UC San Diego at ICRA 2021 preview

April 26, 2021-- A record number of papers from robotics faculty at the University of California San Diego were accepted to the 2021 International Conference on Robotics and Automation taking place in Xi’an.China, May 30 to June 5. 

From helping robots navigate the ER, to making it easier for autonomous drones to fly around obstacles, to teaching robots how to suture wounds, the papers demonstrate the breath and depths of robotics research taking place at the UC San Diego Contextual Robotics Institute. 

“It is encouraging to see the strong growth in submissions in all areas of robotics research,” said Henrik Christensen, director of the robotics institute, which includes more than 50 faculty and more than 100 graduate students. “In spite of COVID-19 and all the challenges it presents, our research work continues in full force.”

Below is a list of papers accepted to the conference, in alphabetical order by department, with summaries and links. 

Department of Computer Science and Engineering

Looking Farther in Parametric Scene Parsing with Ground and Aerial Imagery

 

Raghava Modhugu, Harish Rithish Sethuram, Manmohan Chandraker, C.V. Jawahar

In this paper, researchers demonstrate the effectiveness of using aerial imagery as an additional modality to overcome challenges in road scene understanding. We propose a novel architecture, Unified, that combines features from both aerial and ground imagery to infer scene attributes. 

http://cdn.iiit.ac.in/cdn/cvit.iiit.ac.in/images/ConferencePapers/2021/Scene_attributes___ICRA_2021.pdf

Auto-calibration Method Using Stop Signs for Urban Autonomous Driving Applications

 

Yunhai Han, Yuhan Liu, David Paz, Henrik Christensen
Researchers developed an approach to calibrate sensors for self-driving cars using recognition of traffic signs, such as stop signs. The approach is based on detection, geometry estimation, calibration, and recursive updating. Results from natural environments are presented that clearly show convergence and improved performance.

https://arxiv.org/abs/2010.07441

Social Navigation for Mobile Robots in the Emergency Department

 

Angelique Taylor, Sachiko Mastumoto, Wesley Xiao, and Laurel D. Riek
In this paper, we introduce the Safety-Critical Deep Q-Network (SafeDQN) system, a new acuity-aware navigation system for mobile robots.

http://cseweb.ucsd.edu/~lriek/papers/taylor-icra-2021.pdf

Temporal Anticipation and Adaptation Methods for Fluent Human-Robot Teaming

 

Tariq Iqbal and Laurel D. Riek
In this paper, we introduce TANDEM: Temporal Anticipa- tion and Adaptation for Machines, a series of neurobiologically- inspired algorithms that enable robots to fluently coordinate with people. TANDEM leverages a human-like understanding of external and internal temporal changes to facilitate coordination.

http://cseweb.ucsd.edu/~lriek/papers/iqbal-riek-icra-2021.pdf

 

Department of Electrical and Computer Engineering

Mesh Reconstruction from Aerial Images for Outdoor Terrain Mapping Using Joint 2D-3D Learning

 

Q. Feng, N. Atanasov
This paper develops a joint 2D-3D learning approach to reconstruct local meshes at each camera keyframe, which can be assembled into a global environment model. Each local mesh is initialized from sparse depth measurements.
https://arxiv.org/abs/2101.01844

Coding for Distributed Multi-Agent Reinforcement Learning

 

B. Wang, J. Xie, N. Atanasov
We propose a coded distributed learning framework, which speeds up the training of MARL algorithms in the presence of stragglers, while maintaining the same accuracy as the centralized approach. As an illustration, a coded distributed version of the multi-agent deep deterministic policy gradient(MADDPG) algorithm is developed and evaluated
https://arxiv.org/abs/2101.02308

Non-Monotone Energy-Aware Information Gathering for Heterogeneous Robot Teams

X. Cai, B. Schlotfeldt, K. Khosoussi, N. Atanasov, G. J. Pappas, J. How
This work proposes a distributed planning approach based on local search, and shows how to reduce its computation and communication requirements without sacrificing algorithm performance.
https://arxiv.org/abs/2101.11093

Active Bayesian Multi-class Mapping from Range and Semantic Segmentation Observations

 

A. Asgharivaskasi, N. Atanasov
This work develops a Bayesian multi-class mapping algorithm utilizing range-category measurements. We derive a closed-form efficiently computable lower bound for the Shannon mutual information between the multi-class map and the measurements.
https://arxiv.org/abs/2101.01831

Learning Barrier Functions with Memory for Robust Safe Navigation

 

K. Long, C. Qian, J. Cortes, N. Atanasov
This paper investigates safe navigation in unknown environments, using onboard range sensing to construct control barrier functions online. To represent different objects in the environment, we use the distance measurements to train neural network approximations of the signed distance functions incrementally with replay memory. This allows us to formulate a novel robust control barrier safety constraint which takes into account the error in the estimated distance fields and its gradient.
https://arxiv.org/abs/2011.01899

Generalization in reinforcement learning by soft data augmentation

 

Nicklas Hansen, Xiaolong Wang
Instead of learning policies directly from augmented data, we propose SOft Data Augmentation (SODA), a method that decouples augmentation from policy learning. Specifically, SODA imposes a soft constraint on the encoder that aims to maximize the mutual information between latent representations of augmented and non-augmented data, while the RL optimization process uses strictly non-augmented data.
https://nicklashansen.github.io/SODA/

Bimanual Regrasping for Suture Needles using Reinforcement Learning for Rapid Motion Planning

 

Z.Y. Chiu, F. Richter, E.K. Funk, R.K. Orosco, M.C. Yip
In this work, we present rapid trajectory generation for bimanual needle regrasping via reinforcement learning (RL). Demonstrations from a sampling-based motion planning algorithm is incorporated to speed up the learning. In addition, we propose the ego-centric state and action spaces for this bimanual planning problem, where the reference frames are on the end-effectors instead of some fixed frame.
https://arxiv.org/pdf/2011.04813.pdf

Real-to-Sim Registration of Deformable Soft-Tissue with Position-Based Dynamics for Surgical Robot Autonomy

 

F. Liu, Z. Li, Y. Han, J. Lu, F. Richter, M.C. Yip
In this work, we propose an online, continuous, real-to-sim registration method to bridge from 3D visual perception to position-based dynamics(PBD) modeling of tissues. The PBD method is employed to simulate soft tissue dynamics as well as rigid tool interactions for model-based control.
https://arxiv.org/abs/2011.00800

Model-Predictive Control of Blood Suction for Surgical Hemostasis using Differentiable Fluid Simulations

 

J. Huang*, F. Liu*, F. Richter, M.C. Yip
We investigate the integration of differentiable fluid dynamics to optimizing a suction tool's trajectory to clear the surgical field from blood as fast as possible. The fully differentiable fluid dynamics is integrated with a novel suction model for effective model predictive control of the tool.
https://arxiv.org/abs/2102.01436

SuPer Deep: A Surgical Perception Framework for Robotic Tissue Manipulation using Deep Learning for Feature Extraction

 

J. Lu, A. Jayakumari, F. Richter, Y. Li, M.C. Yip
In this work, we overcome the challenge by exploiting deep learning methods for surgical perception. We integrated deep neural networks, capable of efficient feature extraction, into the tissue reconstruction and instrument pose estimation processes.
https://arxiv.org/pdf/2003.03472.pdf

Data-driven Actuator Selection for Artificial Muscle-Powered Robots

 

T. Henderson, Y. Zhi, A. Liu, M.C. Yip
To accelerate the development of artificial muscle applications, researchers developed a data driven approach for robot muscle actuator selection using Support Vector Machines (SVM). This first-of-its-kind method gives users insight into which actuators fit their specific needs and actuation performance criteria, making it possible for researchers and engineers with little to no prior knowledge of artificial muscles to focus on application design. It also provides a platform to benchmark existing, new, or yet-to-be-discovered artificial muscle technologies.
https://arxiv.org/abs/2104.07168

Optimal Multi-Manipulator Arm Placement for Maximal Dexterity during Robotics Surgery

 

J. Di, M. Xu, N. Das, M.C. Yip
Engineers created a method to generate the optimal manipulator base positions for the multi-port da Vinci surgical system that minimizes self-collision and environment-collision, and maximizes the surgeon's reachability inside the patient. The metrics and optimization strategy are generalizable to other surgical robotic platforms so that patient-side manipulator positioning may be optimized and solved.
J. Di, M. Xu, N. Das, M.C. Yip
https://arxiv.org/abs/2104.06348

MPC-MPNet: Model-Predictive Motion Planning Networks for Fast, Near-Optimal Planning under Kinodynamic Constraints

 

L. Li, Y.L. Miao, A.H. Qureshi, M.C. Yip
We present a scalable, imitation learning-based, Model-Predictive Motion Planning Networks framework that quickly finds near-optimal path solutions with worst-case theoretical guarantees under kinodynamic constraints for practical underactuated systems. Our framework introduces two algorithms built on a neural generator, discriminator, and a parallelizable Model Predictive Controller (MPC).
https://arxiv.org/pdf/2101.06798.pdf

Autonomous Robotic Suction to Clear the Surgical Field for Hemostasis using Image-based Blood Flow Detection

 

F. Richter, S. Shen, F. Liu, J. Huang, E.K. Funk, R.K. Orosco, M.C. Yip
In this work, we present the first, automated solution for hemostasis through development of a novel probabilistic blood flow detection algorithm and a trajectory generation technique that guides autonomous suction tools towards pooling blood. The blood flow detection algorithm is tested in both simulated scenes and in a real-life trauma scenario involving a hemorrhage that occurred during thyroidectomy.
https://arxiv.org/abs/2010.08441

Department of Mechanical and Aerospace Engineering

Scalable Learning of Safety Guarantees for Autonomous Systems using Hamilton-Jacobi Reachability

 

Sylvia Herbert, Jason J. Choi, Suvansh Qazi, Marsalis Gibson, Koushil Sreenath, Claire J. Tomlin
In this paper we synthesize several techniques to speed up computation: decomposition, warm-starting, and adaptive grids. Using this new framework we can update safe sets by one or more orders of magnitude faster than prior work, making this technique practical for many realistic systems.
https://arxiv.org/abs/2101.05916

Planning under non-rational perception of uncertain spatial costs

 

Aamodh Suresh and Sonia Martinez
This work investigates the design of risk- perception-aware motion-planning strategies that incorporate non-rational perception of risks associated with uncertain spatial costs. Our proposed method employs the Cumulative Prospect Theory (CPT) to generate a perceived risk map over a given environment.
https://arxiv.org/pdf/1904.02851.pdf


 

Three from UC San Diego Elected to American Academy of Arts and Sciences

From left: Ananda Goldrath, Eileen Myles and Stefan Savage

April 23, 2021, San Diego, CA -- Three members of the University of California San Diego community, including two professors and one professor emeritus, have been elected to the American Academy of Arts and Sciences—one of the oldest and most esteemed honorary societies in the nation.

Ananda Goldrath, Eileen Myles and Stefan Savage are among the Academy’s 2021 class of 252 members. They join fellow 2021 classmates who are artists, scholars, scientists and leaders in the public, non-profit and private sectors, including: civil rights lawyer and scholar Kimberlé Crenshaw; computer scientist Fei-Fei Li; composer, songwriter, and performer Robbie Robertson; and media entrepreneur and philanthropist Oprah Winfrey. 

The American Academy of Arts and Sciences has honored exceptionally accomplished individuals and engaged them in advancing the public good for more than 240 years. Professor Walter Munk was the first UC San Diego faculty member elected to the Academy. Since then, more than 80 faculty from disciplines that span the entire campus have received this prestigious honor. 

"This year, our faculty are being recognized for three vastly different fields of study: immunology, literature, and cybersecurity,” said UC San Diego Chancellor Pradeep K. Khosla. “Having the oldest and most distinguished American national academy honor the career accomplishments of these prestigious faculty both honors their individual successes and spotlights the breadth of expertise and influence of our Triton faculty. UC San Diego’s well-established prowess in science, technology and art offers a truly well-rounded experience for our students, our researchers and our collaborative faculty.”

In the statement announcing this year's new Academy members, David Oxtoby, President of the American Academy said, “The past year has been replete with evidence of how things can get worse; this is an opportunity to illuminate the importance of art, ideas, knowledge, and leadership that can make a better world.”

Following is more information about each of UC San Diego’s newest Academy members:

Ananda Goldrath
Goldrath is a Tata Chancellor’s Professor in the Division of Biological Sciences and former chair of the Molecular Biology Section. Her work as an immunologist has contributed to the understanding of transcriptional networks that govern the formation and maintenance of long-lived protective immunity. Goldrath’s research explores the mechanistic basis underlying memory T cell differentiation as a strategy to program the immune system to meet pathogens or malignancies in the tissues where they first pose a threat. This information has made it possible to beneficially manipulate the immune system to eliminate infection and malignancies. Goldrath is a Pew Scholar and Leukemia and Lymphoma Society Fellow and a member of the Immunological Genome Project, the Leadership Council of the Program in Immunology and Scientific Advisory Committee of the San Diego Center for Precision Immunotherapy at UC San Diego.

Eileen Myles
Myles, professor emeritus of fiction writing in the Department of Literature, began their career in New York City in 1974 as a poet, novelist, public talker and art journalist. While at UC San Diego from 2002 to 2007, they taught courses in poetry writing, short fiction, writing between genres and the libretto, among others. Also during this time, they wrote the libretto for the opera “Hell,” composed by Michael Webster with productions in 2004 and 2006. Myles is the recipient of a Guggenheim Fellowship, a Creative Capital/Andy Warhol Foundation Arts Writers grant, four Lambda Literary Awards, the Shelley Award from the Poetry Society of America, and a 2014 artist grant from the Foundation for Contemporary Arts. In 2016 they received a Creative Capital grant and the Clark Prize for Excellence in Art Writing and, in 2019, a poetry award from the American Academy of Arts and Letters. The Publishing Triangle honored Myles with the Bill Whitehead Award for Lifetime Achievement in 2020, recognizing writers in the LGBT community. Their 22 books include “For Now” (2020), “evolution” (2018), “Afterglow” (2017), “I Must Be Living Twice/new & selected poems” (2015) and “Chelsea Girls” (1994).

Stefan Savage
Savage is a cybersecurity researcher who holds an expansive view of the field. He and colleagues bring together computer science and the social sciences in their work by taking into account economics, policy and regulations, not just technology. His team has been instrumental in pointing out security vulnerabilities in cars, which have been addressed by the automotive industry’s regulatory bodies and manufacturers. They have tracked the financial transactions responsible for funding email spam campaigns and botnets around the world. The data has been used by government agencies and credit card companies to block these transactions. Savage and colleagues also have designed ways to measure and pinpoint the source of attacks that cripple the internet and large websites, known as distributed denial of service attacks. Savage has received numerous awards for his work, including a McArthur fellowship in 2017, the ACM Prize in Computing in 2015, and three test of time awards from leading academic computer security organizations. He holds the Irwin and Joan Jacobs Chair at the Jacobs School of Engineering and is a professor in the UC San Diego Department of Computer Science and Engineering.

In addition to these three faculty members, alumna Angela Davis is also part of this year’s class of fellows. A well known activist who is now on faculty at the University of California Santa Cruz, Davis earned a master’s degree from the Department of Philosophy at UC San Diego in 1969. She worked closely with philosopher Herbert Marcuse. Her likeness is now part of the Price Center’s Black Legacy Mural, and she is also portrayed on the walls of the Che Cafe. 

The American Academy of Arts & Sciences was founded in 1780 by John Adams, John Hancock and others who believed the new republic should honor exceptionally accomplished individuals and engage them in advancing the public good. The 2021 members join the company of those elected before them, including Benjamin Franklin and Alexander Hamilton in the eighteenth century; Ralph Waldo Emerson and Maria Mitchell in the nineteenth; Robert Frost, Martha Graham, Margaret Mead, Milton Friedman and Martin Luther King, Jr. in the twentieth; and more recently Joan C. Baez, Judy Woodruff, John Lithgow, and Bryan Stevenson. International Honorary Members include Charles Darwin, Albert Einstein, Winston Churchill, Laurence Olivier, Mary Leakey, John Maynard Keynes, Akira Kurosawa and Nelson Mandela.

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.

An aspect of this project that is near and dear to Vazquez-Mena is mentoring and training the next generation of nanoengineers. He will be developing hands-on nanoengineering fabrication workshops for pre-college students, particularly underrepresented students at schools that may have limited resources and laboratory equipment.

This builds on Vazquez-Mena’s ongoing work promoting STEM education and research among migrant communities and children of deported parents, as well as UC San Diego transfer students. In recognition of his outreach work, Vazquez-Mena has been named an Emerging Scholar in 2020 by Diverse: Issues in Higher Education magazine. He was also recently named an Outstanding Engineering Educator by San Diego County Engineering Council.

“In my career, I had plenty of support and opportunities, so for me it is very important to provide these two things to students who come from underserved communities and have a strong desire to make discoveries and contribute to our society through science and technology,” said Vazquez-Mena.

At the start of 2020, Vazquez-Mena started a pilot program to help new Latinx/Chicanx transfer students at UC San Diego get involved in research activities. The program, called Research Paths for LatinX Students, is supported by the university’s Latinx/Chicanx Academic Excellence Initiative. Students attend Saturday sessions where they learn about the importance of research, different research opportunities on campus and strategies to join a lab. During the pandemic, the program shifted to offering virtual workshops on Coding, Arduino controllers and Machine Learning for students to continue learning at home.

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,” said Vazquez-Mena.

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.