MAE3 Robot Competition: Animal Crossing

The annual MAE3 robot competition— part of the mechanical and aerospace engineering Introduction to Engineering Graphics and Design course— was held on Zoom for the fall 2020 class. 

This quarter's project was inspired by the popular Animal Crossing game. Students worked in teams of two or three to design and build a robot that can pick up as many "fruits" as possible and deliver them to a basket within a minute. These robots were built with the materials in a hardware kit shipped to the students, including cardboard, foam core, precut acrylic components, motors and more.

Congratulations to Andrew Hallett, Jason Howard and Parker Knopf from the winning Team 28! 

Learn more about the course and this year's teams: https://sites.google.com/a/eng.ucsd.edu/mae3-robots/2020-fall

Graduate students honored as mentors, leaders

 

Two Jacobs School of Engineering graduate students were honored with Community Awards from the UC San Diego Graduate Student Association for their contributions to graduate student life. The Community Awards celebrate faculty, staff and students who go out of their way to make being a graduate student at UC San Diego a little bit easier.

Structural engineering PhD student Adrielly Hokama Razzini was selected as the Peer Mentorship award recipient, and computer science PhD student Maryam Pourebadi was recognized with the Graduate Student Leader award. Learn more about both students below.

Adrielly Hokama Razzini

Razzini, a structural engineering PhD student, was recognized with the Peer Mentorship award for her work with graduate, undergraduate and even high school students. In addition to her role as a teaching assistant, she’s volunteered as a mentor for the Jacobs Undergraduate Mentoring Program through the IDEA Center, and has also mentored students through summer programs including Research Experience for Undergraduates and Enlace. Razzini also mentors undergraduates and a masters student in her research lab.

“In an informal capacity, I try to help my peers navigate school bureaucracy, chat about their research projects, and advise them based on my previous experiences as an international grad student,” she said.

“I've had really good mentors during my undergraduate and graduate studies, and also in industry. They've shared their knowledge and skills and helped me become a better person and professional. Being a mentor is a way of sharing my knowledge and giving back to the community, in hopes of enhancing the experience of my colleagues at UC San Diego.”

Razzini’s PhD research is in the area of structural health monitoring—the process of implementing damage detection and a characterization strategy for various structures. Her goal is to be able to monitor the wings of an airplane and assess its structural integrity in real time, using an optimal sensor placement and data interrogation process. This involves a lot of finite element modeling, signal processing, and machine learning.

“This award honors a graduate student at UC San Diego for their outstanding peer mentorship, and I feel extremely grateful to receive it. It is very nice to know that I had a positive impact on other people's lives,” she said.

She encourages any student who wants to take a more active role as a mentor to get involved in the IDEA Center’s JUMP or TEAM programs, and ask about additional opportunities within their departments.

 

Maryam Pourebadi

Computer science PhD student Maryam Pourebadi received the Graduate Student Leader award, given to a graduate student who has tirelessly advocated on behalf of graduate students, significantly improving their lives at UC San Diego.

She served as a leader in both the Graduate Women In Computing (GradWIC) group, and the Computer Science andEngineering Department’s diversity, equity and inclusion community.

“For the past three years, I was actively involved in creating an inclusive community for masters and PhD students in the CSE department, and providing services to them.”

Pourebadi has been a member of the student admissions committee, helping review graduate student applications, and has also helped organize the PhD orientation panel for new CSE graduate students to help them get acclimated to life at UC San Diego. She also co-organized a workshop on Imposter Syndrome to make students aware of this phenomenon, and provide them with resources to combat it. Also at the department level, Pourebadi led several CSE social events, including the inaugural and second annual Waffle Social Hour, which drew more than 100 computer science students, faculty and staff.

 Through GradWIC, Pourebadi was elected as the coordinator of the group’s mentorship program, managing a group of mentors serving over 110 mentees. She also led GradWIC’s K-12 outreach program, which brought UC San Diego computer science students and staff to the Girls in STEAM Symposium at St. Margaret’s Episcopal School to share their research and experience in computer science.

 “I not only dedicated my time and energy to support my graduate fellows, but also worked toward identifying K-12 students from underrepresented minorities and encourage them to pursue their education in the STEM fields.”

 To that end, Pourebadi volunteers as an IEEE fellow judge for the SumoBot competition at UC San Diego, and as a judge for the VEX Robotics Competition; she helped open this opportunity up to other computer science graduate students as well.

 “It gives me great joy and happiness to help others and see them happy, to raise self-awareness and social-awareness, to significantly increase others' involvement in these activities, and to give back to the community by providing leadership and services in promoting equity, diversity, and inclusion in this department in a similar way that this community supported me once,” she said.

 Her PhD research focuses on building physical robots and virtual avatars that can realistically express human-like expressions and neurological impairments. This would enable platform-independent expression synthesis methods for robotic systems, and yields new modalities for interaction. Her work also has the potential to provide a realistic training tool for clinical students to better understand the expressions of patients and interact with them appropriately, which has the potential to significantly reduce the impact of patient harm.

 Her advice for students who want to take a more active leadership role?

“Think good, say good, and do good. Wherever you are and whatever your role is, do good deeds as little or as big as you can. And believe that putting all those good deeds together makes the world a better place.”

 

Home workspace tour: Ariane Nazemi

Electrical engineering undergraduate student Ariane Nazemi is a maker at heart. He enjoys designing, printing and painting miniature models; dabbles in printed circuit board modeling; and he even makes his own mechanical keyboards! 

As a student supervisor in the Electrical and Computer Engineering Makerspace, Nazemi had access to all the space and tools needed for these hobbies-- from 3D printers to laser cutters, soldering irons, and more. With the closure of this workspace and many campus spaces due to the COVID-19 pandemic, Nazemi decided to rearrange and spruce up his home work area.

Here's a tour of his space, featuring some of his creations. 

Digitizing the genome

by Cam Lamoureux, UC San Diego bioengineering PhD candidate 

The genome has historically been known as life’s instruction manual. Indeed, the genome sequence of any organism contains all of the information needed to specify its form and function, from the simplest single-celled bacterium to complex organisms such as humans. But with rapidly developing sequencing technology, the genome is taking the stage as a new type of hard drive, nature’s way of storing information.

Understanding exactly how the genome represents an organism’s information remains a challenge for scientists. Any given DNA base (A, T, C or G) in the genome sequence can be involved in multiple different functions. As part of a gene, for example, a DNA base codes for a particular building block, known as an amino acid, of the protein that the gene specifies. That amino acid, in turn, may be part of a particular shape in the final protein. The DNA base may also be part of a sequence on the opposite side of the DNA double helix that is involved in controlling another gene’s activity. With so many different functions, information encoded by the genome sequence is convoluted and overlapping, yet it is critical to understanding an organism’s behavior.

Our work in bioengineering professor Bernhard Palsson’s Systems Biology Research Group at UC San Diego addresses this challenge. We introduce a completely new way of representing this information. For every DNA base, we can answer a simple yes/no question about every type of information the sequence can encode: does this DNA base encode that information? Borrowing from computer science, we realized that the answer to this question can be thought of as a “bit,” a binary digit. By doing so, we can scan across the entire genome of any organism, ask this question, and tabulate the answer as 1 for “yes” and 0 for “no.”

With this approach, we can construct a clean, quantitative record of the bits of information that an entire genome encodes. We call this method of genome annotation the “Bitome.”

We envision that the Bitome will serve as a key foundational tool for genome engineering, with applications in the sustainable production of industrial and medical compounds. For example, bioprocess engineers who reprogram bacterial genomes to sustainably produce chemical compounds can use our method to quickly assess which parts of an organism’s genome sequence are important for their application, and which are less important. They can make predictions about how proposed changes to the genome sequence will affect the organism.

While the Bitome’s capability mirrors traditional genome browsers, our approach provides far more utility and flexibility. Because we have digitized genome information, we can perform computations on those bits of information.

As a test case, we studied the E. coli genome and showed that DNA bases that contain fewer bits of information are more likely to be mutated during adaptive evolution. Because this observation is based on information that can be encoded by any genome sequence—not just E. coli—it could be used to predict genes that are more likely to mutate in cancerous tissues, for example.

The Bitome’s digitized representation facilitates prediction with machine learning. In part of our study, we applied machine learning to pinpoint the use of a particular stop codon as a predictor of mutability. This result is significant because it provides a deeper understanding of how genes mutated during adaptive evolution, a key tool for genome engineering. We also used machine learning to predict gene essentiality directly from the genome, another key capability for engineering genomes.

We are excited by the potential future applications of the Bitome as a way of analyzing genome sequences. This concept is inherently extensible to any organism’s genome and will undoubtedly serve useful both for deeply understanding the information encoded in a genome and for predicting behavior based on that information. With this work, we hope to further bridge the gap between the genome sequence information and the complex, critical functions that it encodes.

Publication: Lamoureux, C. et al (2020) The Bitome: digitized genomic features reveal fundamental genome organization. Nucleic Acids Res. https://doi.org/10.1093/nar/gkaa774

Summer 2020: a virtual NASA internship

The summer of 2020 was a far-out one for many people, but for Ferrill Rushton, a 2020 electrical engineering alumnus of the Jacobs School, it was really, really far-out; to deep space, to be exact. Rushton, who is returning to UC San Diego this fall to work towards his master’s degree in photonics, was an intern at NASA’s Space Communication and Navigation (SCaN) Internship Project, analyzing photon counting methods that affect deep space communications.

The internship was designed to be an in-person research experience, but Rushton and the NASA team quickly transitioned to create a meaningful remote internship when the COVID-19 pandemic forced many plans to change.

Rushton's at-home setup for his remote
NASA internship

When electromagnetic radiation from certain deep space communications or low-power systems in low-Earth orbit gets to a receiver on Earth, there is so little incoming light that the photons actually need to be counted. Rushton’s job this summer was to quantify the inefficiency in photon counting methods in situations where a ground station is detecting incoming light from these photon-depraved situations. The results from his project—Finding the Modes of Arbitrary 2D Geometries Using Finite Difference Techniques—will be incorporated into existing NASA frameworks.

“I don’t feel like I was given work just so there could be an internship, they had all this real work for us,” Rushton said.

The internship allows students to perform hands-on training with real mission scenarios, gain exposure and analyze powerful space communication systems, utilize networks software tools and effectively communicate their findings in a final presentation to NASA management. Each student is paired with an experienced and multidisciplinary mentor who counsels the student with his/her work, and also engages with career planning.

Rushton speaking with former NASA astronaut
Alvin Drew during his virtual 2020 NASA internship. 

At UC San Diego, Rushton was involved with SPIE—the International Society of Optics and Photonics—serving as treasurer of the UC San Diego branch last year. He is also involved in Engineers for Exploration, on the Maya Archaeology team.

His advice to current and future students?

“If there's something that you want, there's no reason not to apply for it. Never be afraid to put yourself out there.”

Evolutionary assimilation of foreign DNA in a new host

 

We know from decades of biological study that all living beings share many similar genes. We also know that these genes are subject to evolution, from mutations that change the DNA sequence of an organism’s offspring, or through horizontal gene transfer (HGT), the acquisition of DNA from a creature other than a parent, and even of a different species.

This got a team of bioengineers at UC San Diego wondering: could a human gene function in other organisms? And if it does function, what evolutionary changes are happening to the DNA to allow it to work properly in a new host species?

Bioengineers in Professor Bernhard Palsson’s Systems BiologyResearch Group used genetic engineering and laboratory evolution to test the functionality of DNA placed into a new species and study how it can mutate to become functional if given sufficient evolutionary time. They published their results on August 10 in Nature Ecology and Evolution.

Schematic of the experimental workflow. Native E. coli glycolytic isomerases pgi and tpiA were replaced with the coding sequence of foreign orthologues and subjected to laboratory evolution for improved exponential phase growth rate. Ma, million years ago.

The researchers used the bacteria E.coli to answer these questions. They took two common genes from the human genome involved in sugar metabolism, and used CRISPR to swap them into a commonly used laboratory strain of E. coli.

The two genes used—pgi and tpiA-- cripple E. coli when removed, causing the bacteria to grow about 5 times slower. Initially, following the gene swap, E. coli’s growth rate did drop, signaling that the genes weren’t functioning properly. But then, the researchers subjected the transformed E. coli strain to a laboratory “evolution machine”—a robotic system used to study how engineered bacteria adapt to changes. After thousands of generations of evolution, the new genes started to function properly. The human genes could serve just the same function in the bacterium as its own genes.

The automated evolution system enabled a large-scale study, generating hundreds of mutant strains evolved for more than 50,000 cumulative generations, something that would take decades rather than months if performed manually.

How was it possible that the human genes were fulfilling the same role in E.coli?  The researchers sequenced the genomes of the evolved strains to find out.

For every strain that successfully evolved, the critical factor was one or more mutations increasing gene expression level. Most of these mutations did not occur within the foreign gene, but rather in regions of E. coli’s DNA controlling regulation of the gene, with their nature depending sensitively on the gene’s specific DNA sequence and location in the chromosome. Some of these mutations occurred with shocking regularity, including one observed independently more than 20 times, demonstrating that evolutionary outcomes can be (probabilistically) predicted to the single DNA basepair.

“This result shows the importance of systems biology,” said Professor Bernhard Palsson, principal investigator of the study. “Namely, biological function, in this case, is not so much about the parts of the cell, but how they come together to function as a system.”

The original motivation for the study was to determine ’self’ versus ’non-self’ at the molecular biology level. The surprising answer is that even if human enzymes are foreign entities to the E. coli bacterium, they are not recognized as such, and the bacterium adopts their function by simply adjusting their abundance to achieve balanced phenotypic state.

This study establishes the influence of various DNA and protein features on cross-species genetic interchangeability and evolutionary outcomes, with implications for both natural horizontal gene transfer and strain design via genetic engineering.

NanoEngineer earns Dissertation Year Fellowship

Jacobs School of Engineering nanoengineering PhD student Qiaowan Chang has been awarded a Dissertation Year Fellowship funded by the Marye Anne Fox Endowed Fellowship Fund. This fellowship is awarded to students who demonstrate highly distinguished academic records, and provides recipients with a $22,000 stipend for their dissertation year, plus tuition and fees.

Qiaowan Chang

We spoke with Chang about her research, her accomplishments at UC San Diego, and her future goals.

Q: How did it feel to receive this award?

A: I feel very excited and lucky to receive this award. It's not only a recognition of my current research, but also encouragement for my future work. And thanks to my supervisor, Professor Zheng Chen, for the instruction, the help during my PhD studies, and for offering lots of opportunities to collaborate with other groups.

Q: Tell us about the research you’ve been conducting in Professor Zheng Chen's lab.

A: My research is mainly focused on designing electrocatalysts at atomic scale through fundamental understanding of their elementary processes in several key electrocatalytic applications and reactions, including decentralized hydrogen peroxide (H2O2) production (2-electron oxygen reduction reaction), direct liquid fuel cells (ethanol oxidation reaction), and carbon dioxide (CO2) conversion (carbon dioxide reduction reaction).

Q:  What are some of the applications of your research?

A: For the decentralized hydrogen peroxide (H2O2) production (2-electron oxygen reduction reaction), H2O2 is one of the most useful chemicals across the entire chemical industry. For the traditional production method, the transportation and storage of H2O2 are unresolved problems due to its chemical instability. Only a dilute H2O2 solution is needed for most applications. For example, 3% H2O2 solution is used as the disinfectant to fight the COVID-19 virus. My research is to develop a green and user-friendly method to produce H2O2 on-site from the two-electron oxygen reduction reaction.

For the direct ethanol fuel cells (ethanol oxidation reaction), it could be used in electric vehicles. In direct ethanol fuel cells, ethanol is oxidized by oxygen to generate electricity. Ethanol is a green and sustainable fuel that can be produced from agriculture feedstocks. Thus, direct ethanol fuel cells are environmentally-friendly techniques for powering vehicles.

For the carbon dioxide (CO2) conversion (carbon dioxide reduction reaction), electrochemical technology could reutilize and convert CO2 to other important chemicals to mitigate climate change and ocean acidification caused by the increased CO2 level. 

Q: Tell us about your dissertation topic.

A: My dissertation topic is to explore novel strategies to design electrocatalysts at atomic scale through fundamental understanding of their elementary processes in the above applications and reactions. The key to make such electrochemical reactions happen is the electrocatalysts. The thesis mainly discusses several strategies, including to tune the local chemical coordination between atomic catalyst clusters (metal) and their support materials (defect carbons) using a composite approach to achieve the synergistic effect of “1+1>2” (that is, Pd clusters deposited on the oxidized carbon nanotubes) for decentralized hydrogen peroxide (H2O2) production (2-electron oxygen reduction reaction), and to control the morphology and structure of the electrocatalyst (that is, the core-shell cubic-shaped electrocatalysts: 10 nm of platinum (Pt) nanocubes as a core and a ~0.2 nm thick of iridium (Ir) layer as a shell) in direct ethanol fuel cells (DEFCs).

Q: What are your future goals once you earn your PhD?

A: I will do a postdoc first to finish my remaining projects. Then, I will try to pursue a faculty position in academia, or a researcher/scientist position in industry.

Using nanotechnology for more targeted, safer pesticide delivery

Nanoengineers at UC San Diego will develop more targeted ways to apply pesticides to food crops using plant virus nanocarriers, thanks to a $490,000 grant from the Department of Agriculture’s National Institute of Food and Agriculture. This could lead to a reduction in the amount of pesticide used, and therefore less chemical accumulation from pesticides in our food, drinking water and environment.

Engineers are using a plant virus as a nanocarrier
for more targeted pesticide delivery to protect crops
like tomatoes from root-eating nematodes. 

Pesticides are used extensively in food production to ensure crop health and yield. While these toxic chemicals can keep bugs, weeds, parasites, fungi and rodents from damaging crops, they also accumulate in the environment, in the crops themselves, and even in drinking water supplies, leading to adverse health effects for humans.

Nanoengineers led by Professor Nicole Steinmetz at the Jacobs School of Engineering plan to use a plant virus as a nanocarrier to more precisely deliver pesticide payloads when and where needed, resulting in less pesticide required, and less bioaccumulation. The team will study and use the tobacco mild green mosaic virus (TMGMV), which they’ve previously shown can carry cargo down to 30 centimeters below the soil surface, much deeper than traditional synthetic nanoparticles which travel 8 to 12 centimeters deep.

Their first target for these nanoparticles is a type of roundworm called a nematode, which eats plant roots, destroying the plant in the process. By being able to deliver the pesticide deeper into the plant’s root system, the researchers believe their plant virus nanoparticles will be more effective in stopping nematodes than synthetic pesticide delivery particles.

“In this project we focus on pesticides to target roundworms that infect the roots of crops, using our plant virus nanotechnology,” said Steinmetz.  “More specifically we will produce a library of nanoparticles derived from harmless plant viruses to answer how size, shape, and materials properties affect the nanocarriers interactions with soil and plants. Understanding these fundamental questions is expected to make an impact on next-generation pesticides, literally attacking the problem at its roots.”

Since plant viruses like TMGMV can be engineered to a custom size and certain physical properties, the researchers will study the effectiveness of plant virus nanocarriers of different sizes, shapes, and surface chemistries.  They’ll create a library of nanomaterials derived from TMGMV, detailing the nanocarriers’ pesticide delivery efficacy.

“We’ve seen that in medicine, changing the shape of a nanoparticle delivering a specific drug can lead to advantages such as enhanced diffusion and tissue penetration,” Steinmetz said. “We hypothesize that this is true for pesticide delivery as well, and will investigate the effect of nanocarrier size and shape on pesticide application effectiveness.”

The tobacco mild green mosaic virus is non-infectious to most plants, but the researchers will also create inactivation protocols to ensure it’s safe to use with any desired plant.  The virus is non-infectious in humans.

Steinmetz will collaborate with researchers Erin Rosskopf and Jason Hong at the USDA Agricultural Research Service, who will test candidate materials on nematode-infested crops.

Comic-Con@Home features UC San Diego scientists

Saura Naderi, outreach director at the Halıcıoğlu Data
Science Institute

Comic-Con 2020 may look a little different this year, coming to you from the comfort of your own home. The annual San Diego comic and pop culture convention is going virtual due to COVID-19, but the good news is more than 350 panels will be available for free online, no waiting overnight in line required.

Comic-Con@Home will feature seven UC San Diego speakers during the five-day virtual event running from July 22 to July 26.

Tune in on Thursday, July 23 from 3-4pm for The Science of Back to the Future, where the creative teams from "Back to the Future" and "Transformers" talk to local scientists about how they came up with their vision for each storyline and how science would play a part in these movies. UC San Diego panelists include engineer and roboticist Saura Naderi, the outreach director at the Halıcıoğlu Data Science Institute and an alumna of the Jacobs School of Engineering.

Marine biologist Ben Frable will speak on
the More Science in Your Fiction panel.

Up next is The League of Extraordinary Scientists and Engineers: More Science in Your Fiction on Thursday, July 23 from 6-7pm. Scientists and engineers will discuss how both comic books and science fiction push them to dive deeper into the unknown. UC San Diego panelists include Ben Frable, a marine biologist at Scripps Institution of Oceanography, and Angela Zoumplis, an extremophile explorer at Scripps Institution of Oceanography.

You can catch Sinless, Fearless, Ruthless - A look at science and social science in a YA sci-fi book Friday, July 25 at 4pm. Learn about the social sciences and the idea of morality behind Eye of the Beholder by author Sarah Tarkoff. UC San Diego panelists include Samantha Russman, a PhD student at the Jacobs School of Engineering.

Cognitive Science Professor Virgina De Sa

The Fleet Science Center Celebrates: Agents of S.H.I.E.L.D. - The Stories and Science of Androids, Space Travel and Aliens will air on Saturday, July 25 from 3-4pm. Celebrate the seven seasons of Marvel's Agents of S.H.I.E.L.D. and hear executive producers, actors, and writers discuss how accurate the science in the series was with local scientists. UC San Diego panelists include Virginia De Sa, a professor in the Cognitive Science Department and associate director of the Halıcıoğlu Data Science Institute ; Troy Sandberg, a bioengineering PhD alumnus; and Melissa Miller, a scientist and science writer at the Scripps Institution of Oceanography. 

To learn more about Comic-Con 2020 events, visit their website.

Olivia Graeve's team is "crystal clear" about quantifying crystallinity

UC San Diego engineering professor and materials science pioneer Olivia Graeve’s research team has a new paper out that reports on work that will be used to help materials scientists develop higher quality materials for use in many applications including super-durable solar cells, ultra-hard metals for space exploration, better infrared optical fibers for carrying digital information, and materials for new kinds of biomedical devices like self-expanding stents.

The paper was published by PLOS ONE on June 22, 2020.

A schematic representation of the team’s DSC-based methodology

 for determination of the change of crystallinity and 

crystallinity percentage as a function of temperature.

In this particular paper, the researchers present a new method for calculating the initial crystallinity, change of crystallinity and crystallinity percentage of amorphous metal alloys as a function of temperature. The first author on the paper is Arash Yazdani who is finishing his PhD at UC San Diego in Professor Graeve's lab.

"This is exciting materials science work that will have an impact in the field," said Graeve. “We all live in this world in which materials science plays a role in nearly everything we do. We all benefit from the materials science breakthroughs yet to be developed. If you think you're interested in this kind of work, pursue it. Don't leave it up to others to do the work. There is a place for everyone in materials science.”

The methods presented in this paper are particularly interesting because the behavior of amorphous materials for use in exciting applications often depends on the partial crystalline nature of the materials. Creating materials with properties such as ultra-hardness or super-resistance to corroding often depends on being able to characterize and control crystallinity, and that's what this research is working toward.

Paper info

"A Method to Quantify Crystallinity in Amorphous Metal Alloys:  A Differential Scanning Calorimetry Study," in PLOS.

Authors: Arash Yazdani (1), Günther W.H. Höhne (2), Scott T. Misture (3), Olivia A. Graeve (4)

1  Department of Mechanical and Aerospace Engineering

University of California, San Diego

9500 Gilman Drive – MC 0411

La Jolla, CA 92093-0411, USA

2  University of Ulm

Helmholtzstraße 16, 89081 Ulm, Germany

3  Kazuo Inamori School of Engineering

Alfred University

2 Pine Street, Alfred, NY 14802, USA

Alumna combines engineering, medical expertise to alleviate PPE shortage

By Daniel Li

Dr. Aditi Sharma, a UC San Diego bioengineering alumna and resident physician at the UC Irvine dermatology department, is combining her engineering skills and medical expertise to solve one of the ongoing challenges of the COVID-19 pandemic: a shortage of protective masks for healthcare workers. 

Sharma and several colleagues developed a method to fabricate face masks out of discarded surgical tool sterilization wraps, and launched a project that aims to create 10,000 of these masks for healthcare workers. Their project was featured in the Los Angeles Times.

Their mask is made from recycled Halyard H600, a material used for surgical equipment sterilization, with straps made of recycled Gemini surgical wrap material. 

Their repurposed sterilization wrap mask has up to 86.5 percent filtration rate; this is lower than the 95 percent of N95 masks, but more than three times more effective than ordinary cloth masks, which many health care workers have been forced to use due to insufficient personal protective quipment (PPE). Their goal is to be able to reserve N95 masks for medical personnel working directly with known COVID-19 patients.

In just two months, Sharma and her team have made over 2,000 face masks, and are looking to expand the project to the entire state of California and hopefully the rest of the country. 

“We're hoping that ultimately not only will healthcare providers have the masks, but maybe even people in the community can have access to them as well,” Sharma said. “In terms of getting towards that 10,000 goal, I think probably in the next couple of weeks we should be there, between manufacturers in the local community who are willing to help us and volunteer groups who are willing to help.”

Sharma graduated from UC San Diego in 2009 with a degree in biomedical engineering, and then received her medical degree at the Medical College of Virginia. During her time at UC San Diego, Sharma had the opportunity to work at Pfizer as a research assistant and participate in the Amgen Scholars Program over the summer. These two experiences sparked her curiosity in immunology and inspired her to conduct research on biological warfare and bioterrorism under Dr. Anthony Fauci at the National Institutes of Health.

Sharma's masks, made from repurposed sterilization wrap.

After a one-year stint at the NIH, Sharma shifted gears and worked as an engineer at the World Health Organization to improve access to medical devices for low income individuals. She explained that her background in engineering has given her a unique approach to medicine. 

“I think something that is kind of fundamental to engineering is asking, “Is this the most efficient process and how can we improve it?” Sharma said. “I think sometimes in medicine, we accept what is told to us-- that this is how it is. And I find that that engineering side of me is constantly saying, ‘What can we do better?’”

When Sharma came back into the medical field, her main goal was to find a way to integrate the fields of public health, engineering, and medicine in her work; this project has allowed her to do so and help contribute to the fight against COVID-19. Sharma encourages students to take advantage of all the resources that UC San Diego offers and to dream big.  

“What I loved about UC San Diego is there are so many resources,” Sharma said. “I used to go to the Teaching and Learning Commons...and I remember really learning linear algebra very well because I had that extra support system. I am also grateful for applying for those job opportunities that I never thought I would get. I think it set me up for the rest of my career.”

Dispatches from a pandemic: graduate students create COVID virus simulations

By Daniel Li

As it became clear in late February that COVID-19 was not going anywhere, four UC San Diego graduate students were planning their final project for the Numerical Analysis for Multiscale Biology course, which uses math to simulate biological processes.

The mechanical engineering and bioengineering students—Parker Dow, Cathleen Nguyen, Clara Posner, and Patrick Wall—decided to put their skills to a new use, and build a predictive model analysis that could bridge from the molecular biology of the SARS-CoV-2 virus to the epidemiology of the spread of infection through the population. The team started the three-week project in early March.

“A lot of times, when working on basic cell biology research, it can seem kind of removed from the bigger picture of what’s happening in the world,” Posner said. “But working on this coronavirus project is a lot more motivating since it can help with this current crisis that’s affecting us all.”

The idea to focus the project on COVID-19 was first brought up by Dow. According to Dow, he had started to see new scientific literature related to the novel coronavirus come out and it became increasingly apparent that some of the data could be used for computer modeling.

“I floated the idea to the group because I’d seen in a paper that they got a new structure of the coronavirus binding protein,” Dow said. “Our group started to do a bit more research on it and discovered that the scientific community had been publishing things daily, so we all wanted to take a stab at it.”

Each student focused on a different level of the project: cellular, molecular, and population scale. Wall created an alveolus in the lung with the MCell modeling tool to figure out the virus's rate of spread. Dow analyzed viral binding kinetics using BrownDye software. Posner used Virtual Cell (VCell) to create a transforming growth factor (TGF)-beta signaling induced lung fibrosis model. Nguyen focused on creating a population infection model using Vcell at the population level.

Two of the tools—Browndye and MCell—that the team used to model their systems were developed in-house at UC San Diego. Several local scientists, including UC San Diego Project Scientist Gary Huber and Salk Institute Staff Scientist Tom Bartol, were actively involved and helped guide them through the project. 

“The course instructors went above and beyond,” Wall said. “It was really helpful to reach out to them and ask for their expert knowledge. They also were instrumental in getting our models to run properly.”

This hands-on course is one of seven lab courses offered by the Interfaces Graduate Training Program in Multi-scale Biology that involves students from 11 graduate programs at UC San Diego and is directed by Professor Andrew McCulloch from the Department of Bioengineering.

 “The scientific challenges of addressing the COVID-19 pandemic are so daunting because they span from the scale of the spike protein on the virus, to the cellular and pathophysiological responses of the infected human to the population of the globe. Problems like these require the kinds of novel multi-scale approaches and interdisciplinary teamwork that the Interfaces program was designed to teach and encourage.

According to Wall, one of the challenges when they first started was that the data surrounding COVID-19 was sparse. To tackle this, the team looked at similar viruses, such as SARS, and used data from that to generate initial models. 

“The 2002 SARS virus was also a coronavirus outbreak. These viruses are so similar,” Wall said, “we were able to use a lot of the data that was generated in the mid 2000s to early 2010s on the SARS coronavirus and extrapolate our modeling based off of that.”

Nguyen added that because the coronavirus was evolving in real time, there were a lot of unknowns and the team was forced to make assumptions throughout the project. 

“Everyday you’re receiving new information about the pandemic and want to apply it to the models,” Nguyen said. “You make a lot of assumptions and those assumptions are changing based on new information. You're changing your inputs, your process, and with every simplification you make, you lose some accuracy in the models.”

Nguyen enjoyed how she was able to work together with students of different engineering backgrounds.

“I’m more of a mechanical engineering background, but the rest of my team members have more of a bioengineering background,” Nguyen said. “And the novelty comes when you’re trying to work on a multiscale project with people who have different expertise and skills.”

Discovery of High-Entropy Ceramics via Machine Learning

by Kevin Kaufmann and Prof. Kenneth Vecchio

Materials are an essential part of our world; they have enabled us to build cities, treat disease, and communicate across the world in real time. For centuries, material scientists have been working to build our material library and to discover new materials with greater performance and better property trade-offs. Over the past few decades, however, the rate at which new materials are being discovered has been slowing continuously. This is due to several factors including increasingly stricter regulations, more challenging performance metrics, and increasingly more expensive empirical development strategies.

The reduced rate of material discovery is also in part because many of the simplest combinations have been investigated, and the number of remaining possible combinations is quite extensive. For example, if random combinations of five elements from the periodic table are combined in equal amounts, there would be 1078 possible combinations to choose from. This example ignores the fact that different numbers of elements can be combined, not just five, and that they do not have to be combined in equal ratios. For perspective, there are estimated to be 1066 atoms in the Milky Way galaxy. So, in terms of a “big data” challenge, materials development of complex composition alloys represents perhaps the biggest big data paradigm. There is a clear need for a method to narrow the search space to only the most promising candidates for a given application. Intuition and expensive trial and error strategies will not be sufficient for investigating this immense chemical space, and more informed computational methods must be developed and employed.

Our team of nanoengineers in Professor Kenneth Vecchio’s lab at UC San Diego is developing tools for screening large numbers of materials in a rapid fashion. The first step in our work is creating unique identifiers for each material, akin to a fingerprint of the material. In the same way no two fingerprints are alike, every individual material possible can be reduced to a simple but unique set of attributes. These identifiers describe the material composition in a way that supports computation work leveraging a subset of artificial intelligence called machine learning. The machine learning tools learn the underlying science that relates these attributes to various material properties. Typically, machine learning requires enormous initial datasets to learn from before it becomes a useful tool.

However, the method that our team developed is designed around the fact that material development problems frequently have less than 100 data points at the outset. After learning about the initial dataset, the machine learning algorithm suggests new materials with the goal of maximizing performance. Each time the materials suggested by the algorithm are fabricated and tested, this new information is made available to the algorithm, creating a learning loop.

The data-driven method that our team has developed was recently demonstrated for predicting the synthesizability of single crystal structure (e.g. rock-salt structured) carbide ceramic materials containing five metal cations, also known as high entropy carbides. High entropy carbides constitute a subset of the complex concentrated alloys class of materials described previously, as they have the added uniqueness of becoming more stable at increasing temperatures, which is unlike most engineering materials. The researchers focused their study on what are called non-intuitive compositions, in which three of the five metal cations are chromium, molybdenum, and tungsten, none of which form a rock-salt structure at room temperature in a one metal atom to one carbon atom ratio.

The initial dataset contained all available data: 56 high entropy carbide materials with synthesizability calculated by computationally expensive density functional theory (DFT). None of the 56 known compositions contained chromium, one of the three metal cations of interest. While DFT can compute a few compositions per month, the machine learning model was able to learn from the 56 materials and make predictions on 70 new materials in less than one day.

Seven materials, four predicted to succeed and three predicted to fail, were experimentally fabricated and analyzed to assess the validity of the predictions. Rather surprisingly, several five-cation metal carbide compositions were discovered, wherein three of the five cations were chromium, molybdenum, and tungsten—the elements that don’t form the rocksalt monocarbide structure—and yet these compositions were experimentally shown to successfully form the rock-salt structure. Furthermore, all seven experimentally studied compositions resulted in single or multi-crystal structure materials in exact agreement with the machine learning predictions. The ability for the machine learning model to perform exceedingly well in such a non-intuitive chemical space, a composition space which contained no prior data to learn from, further demonstrates the unique strength of this approach. Our team expects the machine learning framework to be a useful tool in the development of other materials such as alloys, battery components, or pharmaceuticals.

This work is published in Nature Partner Journals (npj) Computational Materials, May 1, 2020.

Read the paper here: https://rdcu.be/b3UdG

DOI: 10.1038/s41524-020-0317-6

Jessica Sandoval: graduate student, ROV pilot, researcher

Filming: Erin Ranney. Editing: Daniel Sosa-Cobo

When Jessica Sandoval isn’t building robot components and microplastic detectors at the University of California San Diego, she drives a remotely operated underwater vehicle for an organization founded by Robert Ballard--the man who discovered the Titanic’s wreck.

This spring, Sandoval was part of a team of scientists working to understand plastic degradation in the ocean whose research was featured in The New York Times. The team of engineers and marine biologists at the UC San Diego Scripps Institution of Oceanography is studying how microplastics and microfibers enter and spread in the environment, particularly the ocean. Sandoval developed an instrument called the Automated Microplastics Identifier that gets these microfibers to fluoresce, making it easier to detect them and study them. She also developed software to quantify the amount of plastic in each sample and generate information on the features of the plastics using image recognition.

“It is an exciting first step, using automation technologies to assist with the monitoring of this prevalent marine pollutant,” said Sandoval, who began developing this technology as an undergraduate student at MIT. “With such technologies, we can more easily process samples from across the globe and generate a better understanding of microplastic distribution.”

Sandoval is also a PhD student in the Bioinspired Robotics and Design Lab of Professor Mike Tolley, developing new robotic technologies inspired by insects, animals and nature. In October, she was part of a team that developed a better suction cup inspired by a fish with extraordinary gripping capabilities, called a clingfish. By studying how the clingfish is able to strongly yet gently stick to both smooth and rough surfaces, Sandoval and other engineers in Tolley’s lab were able to develop an innovative suctioncup capable of delicately lifting objects like eggs or shells. Sandoval was the first author of the paper published in the journal Bioinspiration and Biomimetics.

Because she pilots an ROV on the research ship Exploration Vessel Nautilus, she got to test a prototype of her suction cup in the field during one of the ship’s missions. The job is an ideal combination for Sandoval.

“I am fascinated by marine biology and the technology that allows us to observe and measure it,” she said in an interview on the Nautilus’ website. “The ocean provides an imagination’s playground in which there is much to be explored and discovered. This excitement of the not yet known definitely sparked my interest in ocean exploration. That and the incredible plethora of marine biodiversity that exists in our oceans.”

Mechanical engineer recognized by Society for Industrial and Applied Mathematics

Jorge Cortes, a professor in the Department of Mechanical and Aerospace Engineering has been inducted as a 2020 Fellow by the Society for Industrial and Applied Mechanics.
Cortes is being recognized for contributions to the control and optimization of network systems.

The fellows were nominated for their exemplary research as well as outstanding service to the community. Through their contributions, SIAM Fellows help advance the fields of applied mathematics and computational science.

Cortés' research interests are on distributed coordination algorithms, autonomous robotic networks, adversarial networked systems, mathematical control theory, geometric mechanics and geometric integration. The recent emergence of low-cost, highly-autonomous vehicles with control, communication, sensing, and computing capabilities has paved the way for the deployment of robotic sensor networks in a wide range of applications. Controlled motion coordination of these networks will have far-reaching implications in the monitoring of natural phenomena and the enhancement of human capabilities in hazardous and unknown environments. Motivated by these scenarios, Professor Cortes' research program is developing systematic methodologies to control autonomous, reliable, and adaptive mobile networks capable of operating in unknown and dynamic environments.

Ruth J. Williams, from the UC San Diego Department of Mathematics, is also being recognized for contributions to the study of stochastic processes and their applications.

Full SIAM release here: https://sinews.siam.org/Details-Page/siam-announces-class-of-2020-fellows

Metabolic and genetic basis for auxotrophies in Gram-negative species

By Yara Seif

While some bacteria survive independently, others reduce their metabolic expenditures by utilizing the nutrients available to them in their environment. These bacteria choose to adapt the concept of simple living or “less is more,” meaning one can survive on minimal requirements (we could definitely learn from them). Auxotrophy, a.k.a nutritional dependencies, are a characteristic of host adaptation. They are hard to characterize experimentally because there are too many nutrients to choose from, and also because they differ from one strain to another.

In a study published Mar. 5 in PNAS, we develop a computational workflow that uses both flux balance analysis and comparative genomics to predict nutrient requirements de novo and from sequences alone.

In our workflow, we compare the gene content across several strains of bacteria, and build metabolic networks tailored to each genetic background. Next, we simulate for growth on a minimal medium, and when that cannot be achieved, we run our algorithm called AuxoFind, to search for possible nutrients that would restore growth in silico.

Metabolic networks were tailored to the gene content of different bacteria and nutrient dependencies were predicted and validated experimentally. Image courtesy of Systems Biology Research Group

We find that when the same gene is missing, the nutrient requirements change across species, because they have different metabolic networks and combinations of alternative pathways. We also observed that the absences are manifested as a result of a large range of genetic modifications going from simple and small mutations (like single nucleotide polymorphisms) to large and complex genetic changes (whole genome rearrangements and multi-gene deletions).

The significance of this work is as follows:

Patients with certain diseases (such as Crohn’s disease or cystic fibrosis) tend to be chronically infected with bacteria. Over time, these bugs become more vicious because they slowly adapt to the in vivo environment. Understanding how these adaptations occur is a first step towards devising therapeutic solutions.

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Yara Seif is a UC San Diego bioengineering Ph.D. student. As a member of Bernhard Palsson's Systems Biology Research Group, she studies the metabolism of bacterial strains as well as the evolution of metabolic traits across strains especially in relation to their lifestyle. Her research so far has included multi-strain genomic and metabolic analysis of gram-negative strains using a combination of constraint-based metabolic modeling, comparative genomics and machine learning.

Barrett Romasko: structural engineer

 By Daniel Li

Barrett Romasko’s path in college has been full of exploration. Romasko, a senior majoring in structural engineering with a focus on aerospace structures, applied to UC San Diego without knowing much about the different applications of structural engineering, assuming it only involved civil engineering structures. His willingness to seek out new opportunities — through on-campus activities, classes, and internships — has been a contributing factor in helping him figure out his interests and goals for the future. 

On campus, Romasko is heavily involved in the UC San Diego Society of Civil and Structural Engineers (SCSE), which has three technical project teams that students can join to get hands-on structural engineering experience: steel bridge, concrete canoe, and seismic design. Romasko has been part of the steel bridge project team since his sophomore year –he was the team’s welding lead his junior year and is currently the project manager. 

The steel bridge project challenges students to design, fabricate, and construct a scaled model bridge that stays competitive in terms of the lightest weight, greatest stiffness, and fastest construction speed. The students start preparing their bridge each fall and bring it to the annual Pacific Southwest Conference each year to see how it stacks up to the competition.

The steel bridge team with their bridge.

“We start the design process in fall quarter, which generally consists of using a lot of design software and analysis,” Romasko said. “Winter quarter is dedicated to fabrication, so the team takes the design to a machining space and manufactures each component of the bridge. The last stage is construction, which is when we practice assembling each member of the bridge according to the regulations that we received in preparation for the competition.”

According to Romasko, the hardest part of the competition is getting all the components fabricated by the competition in April. That was compounded this year, as the team had to find a new location to fabricate their bridge, as the location they’d been using for 18 years was no longer available. Romasko and his co-project manager got to work and were able to come up with a solution.

Despite unexpected challenges, Romasko has enjoyed working on the steel bridge project the past three years. His favorite parts about steel bridge: the teamwork and hands-on learning aspect.

“I really like steel bridge because you get to apply what you learn in class to a real project and work with so many cool, motivated people,” Romasko said. “You also start to understand important industry concepts such as fabrication and tolerancing.”

Romasko encourages students to get involved in student groups as early as possible, and stresses the importance of finding organizations that are not only career focused, but also fun. 

“Joining the steel bridge project has introduced me to so many new people that I wouldn’t have met otherwise,” he said. “It has been a good way for me to make friends who share like-minded interests.”

In addition to their hands-on technical projects, SCSE organizes two main community outreach events each year: Seismic Outreach and Esperanza International. 

Members of the steel bridge team.

“Seismic outreach consists of us going to schools to teach elementary and middle school students about how to design for seismic safety and teach them about earthquakes,” Romasko said. “The goal is to get these students more interested in STEM fields. We also have another event where we go down to Rosarito in Mexico with an organization called Esperanza International, and put our engineering skills to use as we help build houses for the less fortunate.”

In addition to his involvement in SCSE, Romasko is a research assistant in Professor Machel Morrison’s lab, where he works on projects related to metallography and mechanics of materials. He’s also nabbed several internships over the summers, working at the Naval Surface Warfare Center in 2018 and General Atomics in 2019. 

“Internships are valuable because you can get direct experience in the industry,” Romasko said. “The internships that I have done really allowed me to see what I could do with my major and what I don’t want to do with my major. For example, at General Atomics, I was a manufacturing engineering intern; after the summer, I realized that although it was a great learning experience, I wouldn’t want to do it as a career. I feel that it is important for everyone to explore different areas to find what they’re most passionate about, and even more importantly, to find what they aren’t passionate about.”

Romasko came to UC San Diego thinking that he was going to follow the civil structures route in the structural engineering department, but during his internship at the Naval Surface Warfare Center, he realized that aerospace structures were more interesting to him. Without that internship, Romasko said he fears he would never have changed to the aerospace structures focus.

Romasko is returning to UC San Diego to complete a master’s degree in structural engineering this fall. In the future, he hopes to work abroad for a couple years, either in Australia, Europe, or New Zealand.

“I would love to work outside of the United States for two to three years doing something related to aerospace structures,” Romasko said. “One of my dream companies to work at is Virgin Galactic, which specializes in developing commercial spacecraft.”