Students awarded Dissertation Year Fellowships

Two graduate students at the Jacobs School of Engineering were selected by the UC San Diego Graduate Fellowship and Award Review Committee to receive UC President's Dissertation Year Fellowship awards. Alexander Chen, a chemical engineering PhD candidate, and Phoebe Valdes, a bioengineering PhD candidate, were among the five students honored with the fellowship this year. 

Alexander Chen and Phoebe Valdes
were awarded Dissertation Year Fellowships

The UC President's Dissertation Year Fellowship is awarded to promising students in the final stages of their doctoral work, who demonstrate strong potential for university teaching and research. Recipients receive a $23,500 stipend plus tuition and fees. 

Alexander Chen is advised by nanoengineering Professor Darren Lipomi. He studies a class of materials called semiconducting polymers, which are plastic materials that can conduct electricity.

"My research focuses on understanding and improving the mechanical properties of semiconducting polymers, particularly for enabling new applications in energy technologies," he said. "For example, one of my projects focuses on improving the mechanical robustness and survivability of organic solar cells to enable solar energy harvesting from human-transformed surfaces (e.g., rooftops, buildings, painted and coated surfaces)."

Outside of this research, Chen founded the Graduate Application Mentorship Program (GradAMP) at UC San Diego in 2019. The organization's goal is to help make the graduate education pathway more accessible by pairing undergraduate applicants with a PhD student mentor in their field of study to help guide them through the graduate application process.

With research interests in the fields of energy, materials and healthcare, Chen is leaving his future options open, but hopes to continue conducting research that interests and motivates him, and that has a positive impact on society. 

Phoebe Valdes is advised by bioengineering Professor Shankar Subramaniam and conducts research in his Systems Biology and Systems Medicine laboratory. She uses computational methods to study different forms of Alzheimer's Disease (AD) in order to better understand the mechanisms behind the disease. 

"I want to look into the full progression of early to late stages of AD development by assessing key mechanistic endotypes (i.e. disease substate characteristics) in patient-derived neurons and postmortem patient brain samples," she said. "To investigate what these endotypes could be and how to better formulate mechanisms responsible for AD, I want to analyze large multi-omics data sets at both the gene and chromatin levels (RNA-seq and ATAC-seq) using various computational methods." 

Valdes plans to travel and sightsee for a few months after completing her PhD, and then hopes to secure a post-doctoral research position in the biotech industry or academia to pursue a career as a data science or bioinformatics scientist. 

"I am a big fan of looking into analyzing big data generated from diseases (open to going beyond neurodegenerative diseases after my PhD)," she said. "Otherwise, we will see where life takes me after I complete my doctoral studies."

Valdes is a second-generation Filipino-American whose parents immigrated from the Philippines, and is the only bioengineer in her family. She hopes her research will help direct new avenues of treatment for patients with different forms of AD, as there is no cure yet. 

"I am completely thrilled and honored to be receiving this fellowship as it will help support my own research endeavors. Thank you Graduate Division for supporting me on my graduate school journey."

Bioengineering students create prototype lymph node for cancer patients

Yuxuan Zhou, Sonia Singh, Riyam Al-Msari and
 Arielle Hancko present their award-winning research. 

By Kiran Kumar

Four UC San Diego undergraduate bioengineering students designed a prototype of a decellularized lymph node for individuals who have had their original lymph nodes surgically removed during head and neck squamous cell carcinomas (HNSCCs) treatment. The students– Sonia Singh, Yuxuan Zhou, Riyam Al-Msari and Arielle Hancko – completed the project for their Jacobs School of Engineering bioengineering capstone senior design project. Their work was awarded the Best Overall Poster designation at the student-run Bioengineering Day 2022.

Ninety percent of head and neck cancers originate from squamous cells: cells in the surface of the skin, and the linings of many organs in the body. These are referred to as HNSCCs. Standard treatment of HNSCCs involves surgical removal of lymph nodes in the neck. However, these lymph nodes carry a host of immune cells, which can be vital to the success of several cancer therapies, including cancer immunotherapies and radiotherapies. Without these lymph nodes, these therapies can sometimes prove ineffective.

This team of bioengineering students wanted to help those individuals who have had their lymph nodes removed still experience the benefit of immunotherapies and radiotherapies. They used tissue engineering to design decellularized lymph nodes which can be surgically implanted in place of the removed lymph nodes. Ex vivo experiments were conducted on mouse models to establish that these engineered lymph nodes had an adaptive immune response, restoring immune function. The results were promising.

“We spent most of our time on the decellularization aspect of the lymph nodes since that is the foundational aspect of tissue engineering, removing the double stranded DNA” said the team. Decellularization is very important to maintain the morphology of the tissue. Non-decellularized tissue can lead to rejection of the lymph node.

To engineer these replacement lymph nodes,  cervical lymph nodes were harvested from mice, and then washed in a phosphate buffered saline solution.  Then, sodium dodecyl sulfate was used for decellularizing the mouse lymph nodes. The tissue was recellularized using dendritic cells from the bone marrow of mice. They also attached chemokine proteins to the lymph nodes.

The team is excited that this research will be taken to the next level with in vivo experiments in mice.

“It will be completed by a senior design team next year,” the students said. “We have now completed the handover work. They will test how the mice fare with our lymph nodes, and then test the immune function of the lymph nodes.”

Cheng Ye: ECE Best Undergraduate Research Award recipient

UC San Diego undergraduate computer engineering student Cheng Ye is the first author of a Bioinformatics paper describing a phylogenetic software tool that is capable of handling the vast amounts of SARS-CoV-2 data. Ye was awarded the Electrical and Computer Engineering Best Undergraduate Research Award for his work in Professor Yatish Turakhia's lab. 

Learn more about how Ye got involved in research and the project he worked on in this Q&A:

Ye, left, receives the ECE Best Undergraduate
Research Award from his advisor, Professor 
Turakhia, at right. 

How did you decide to get involved in research as an undergraduate?

I like open-ended questions, and to try new ideas, so I got involved in research.

You got involved in research thanks to the ECE Summer Research Internship Program (SRIP). How did SRIP help you personally?

One alternative way of finding a faculty to do research with without a wonderful program like SRIP is to read their publications and email them directly. However, (1) I won't know whether they have the time to mentor an undergrad, and (2) I won't know what project I will be working on. SRIP streamlines the search process by providing a directory of faculty seeking students and the available projects.

What year are you, and do you have any goals/plans for after you complete your undergrad?

I am a senior. I am not sure whether I want to be a research software engineer or a digital circuit designer building hardware accelerators, so I am going for the BS/MS program to have more experience with digital circuit design, and procrastinating the decision.

What were you working on before you were assigned the tree optimizer project?

I was initially assigned to work on accelerating sequence alignment on GPU, but I thought the SARS-COV-2 phylogeny project might be more exciting, and it indeed was. By the way, the pandemic is a rare opportunity to make some impact quickly, though I am not saying I want another pandemic. Actually, the SARS-COV-2 phylogeny project is the first project I worked on with Prof. Yatish Turakhia. I did some variant calling in my second year, and some neuroscience in my first year in other labs. 

How does the matOptimize parallel software work?

It can both scale up (multiple threads) and scale-out (multiple hosts). The state of art software for Tree Analysis using New Technology (TNT)  can only scale-out, so it has to duplicate the internal data structure on all processes, even on the same host, so it needs a beyond practical memory to CPU ratio. matOptimize exploits multi-core CPUs more effectively, by allowing all threads running on the same CPU to share the same immutable internal data structure, which is also more compact than the one used in TNT. Therefore, it has a more practical memory to CPU ratio. It can also leverage message passing interface (MPI) to scale-out.

What are some of the challenges you faced when creating this software?

Understanding why optimization is necessary. Thanks Prof. Yatish for providing several examples in the early stage of the project to unblock me. And the parallelization. Heuristic phylogenetic tree optimization is based on applying small changes to the tree, and the effect of a change may impact whether other changes are desirable, so it is difficult to parallelize. TNT can parallelize by either optimizing a small part of tree independently on the different processes (divide and conquer), which cannot discover all beneficial changes, or having each process explore the entire tree independently, and broadcast the best tree found to other processes, and continue the process on the best tree found, similar to an ant colony. I appreciate Prof. Yatish and Prof. Russell Corbett-Detig’s insight that beneficial changes are rare, the effect of a change is local and their suggestion of finding all beneficial moves simultaneously and independently, then apply all the non-conflicting changes simultaneously. Their help and inspiration from IQ-TREE, which is another tree optimization software, make parallelization possible.

Any advice to students who think they may want to try research as an undergraduate?

Unfortunately, I don't feel qualified to answer this question. However, I can talk about what I wish I had done. First, have an idea of what I wanted to get out of the research experience, and don't forget about it. In my case, I am getting more experience with designing hardware accelerators, but with the particular problem of phylogenetic inference at hand, improving the algorithm and parallelizing across conventional hardware is a more effective solution than optimizing the implementation to death on a particular hardware platform.

I chose to improve and parallelize the algorithm and learned how to use Intel TBB and MPI along the way (and got something that exceeds my expectation).  I wish I could have found a better way of accommodating both my goal and the most effective approach to the project at hand. However, it can be difficult to see what is the best approach to the project, before being significantly involved, and what is more difficult is to wrap up a project and move on.

Secondly, communicate. A few unnecessary initial iterations of matOptimize were redundant because I felt I understood what was needed, but I didn't, but I jumped right into implementation too soon.

One step closer to fire safe, recyclable lithium-metal batteries

High-energy density, improved safety, temperature resilience and sustainability are desirable properties for lithium-battery electrolytes, yet these metrics are rarely achieved simultaneously. Inspired by the compositions of clean fire-extinguishing agents, a team of nanoengineers from UC San Diego demonstrated inherently fire safe liquefied gas electrolytes, as well as a one-step solvent-recycling process which promises sustainable operation at scale, in a Nature Energy paper published on June 16.

Yijie Yin and Professor Shirley Meng working in
the lab to develop this lithium-battery electrolyte

This work provides a route to sustainable, temperature-resilient lithium-metal batteries with fire-extinguishing properties that maintain state-of-the-art electrochemical performance.

Yijie Yin, a nanoengineering PhD student and co-first author of the paper, shares how this work came about in the following paragraphs. Yin and co-first author Yangyuchen Yang are both graduate students in adjunct professor Shirley Meng’s Laboratory for Energy Storage and Conversation. Read the Nature Energy paper here.

“In 2017, a team of UC San Diego nanoengineers discovered hydrofluorocarbon molecules that are gasses at room temperature and will liquefy under a certain pressure. They then invented a new type of electrolyte, which is called "Liquefied Gas Electrolyte"(LGE). The related results were published in Science1.

Yijie Yin

The liquefied gas electrolyte greatly broadens the choice of electrolyte solvent molecules. The screened fluoromethane and difluoromethane 2 small molecules have a low melting point, fast kinetics, and wide voltage window. With the combination of co-solvents, these characteristics make these liquefied gas electrolytes exhibit excellent low temperature performance (< -60°C), Li metal Coulombic efficiency (>99.8%)3 and high performance of high-voltage cathodes4.

However, the LGE electrolyte is not yet "perfect", because the saturated vapor pressure of the molecules used is high, and like most electrolytes, it is still flammable, which makes the safety and environmental protection of the system irrational.

The idea of this work came from a chat between Yin and Yang, also a nanoengineering PhD student at UC San Diego. Yin mentioned that he wanted to try to replace the strong solvating power liquid co-solvents with the smallest ether molecule - methyl ether (Me2O) in follow-up work.

Yangyuchen Yang

‘"As a gas molecule, Me2O can only be used in liquefied gas,” said Yin. “It may only work under the pressurized system, and it may provide better lithium metal interface and stability while maintaining fast kinetics."’

During the discussion, Yang also agreed with this idea and hoped that this system could be further improved. He said, "If we continue to use the current FM and DFM weakly solvated solvents, the existing high-pressure and flammability shortcomings will not be changed, instead we should work on the searching for molecules with increased fluorinated carbon bonding".

Next, the two referred to the structure of fluoromethane to search for fluorinated molecules with longer carbon chains, while maintaining the inherent advantages of liquefied gasses, such as low melting point, low viscosity, and maintaining a certain polarity. Considering all the above requirements, 1,1,1,2 tetrafluoroethane (TFE) and pentafluoroethane pentafluoroethane(PFE) came to mind.

What's even more surprising is that these two molecules are the main components in some fire extinguishers, which means that the molecules are not only non-flammable, but also have excellent fire-extinguishing properties.

1             Rustomji, C. S. et al. Liquefied gas electrolytes for electrochemical energy storage devices. Science, doi:10.1126/science.aal4263 (2017). 

2             Davies, D. M. et al. A Safer, Wide-Temperature Liquefied Gas Electrolyte Based on Difluoromethane. Journal of Power Sources 493, 229668 (2021). 

3             Yang, Y. et al. High-Efficiency Lithium-Metal Anode Enabled by Liquefied Gas Electrolytes. Joule 3, 1986-2000, doi:https://doi.org/10.1016/j.joule.2019.06.008 (2019). 

4             Yang, Y. et al. Liquefied gas electrolytes for wide-temperature lithium metal batteries. Energy & Environmental Science 13, 2209-2219, doi:10.1039/D0EE01446J (2020).

ACM Dissertation Honorable Mention awarded to Pratul Srinivasan and Ben Mildenhall

The ACM Dissertation Honorable Mention has been awarded to Pratul Srinivasan and Ben Mildenhall for their work on Neural Radiance Fields (NeRFs). Srinivasan is the last of UC San Diego Computer Science & Engineering professor Ravi Ramamoorthi's graduate students to graduate from UC Berkeley. Professor Ramamoorthi moved from UC Berkeley to UC San Diego in 2014. At UC San Diego, Ramamoorthi Directs the UC San Diego Center for Visual Computing.

Pratul Srinivasan and Benjamin Mildenhall were jointly awarded an Honorable Mention for their co-invention of the Neural Radiance Field (NeRF) representation, associated algorithms and theory, and their successful application to the view synthesis problem.

From the ACM citation: Srinivasan’s dissertation, "Scene Representations for View Synthesis with Deep Learning," and Mildenhall’s dissertation, “Neural Scene Representations for View Synthesis,” addressed a long-standing open problem in computer vision and computer graphics. That problem, called “view synthesis” in vision and “unstructured light field rendering” in graphics, involves taking just a handful of photographs of a scene and predicting new images from any intermediate viewpoint.

NeRF has already inspired a remarkable volume of follow-on research, and the associated publications have received some of the fastest rates of citation in computer graphics literature—hundreds in the first year of post-publication.

2022 Bioengineering Award of Excellence: Kendra Worthington

Every year, six outstanding undergraduate students who made significant contributions to their academic department and the Jacobs School of Engineering community are celebrated with department Awards of Excellence at the Ring Ceremony event for graduating undergraduates.

The 2022 Bioengineering Award of Excellence was awarded to Kendra Worthington. Learn more about her background and future plans in this Q&A.

What do you enjoy about bioengineering, and why did you decide to pursue this field?

I love that bioengineering is a diverse field, both in research and in its community. What initially drew me towards bioengineering was knowing that I would always be learning something new throughout my entire career, which means that I will never be bored in bioengineering. I also love that as a bioengineer I can serve my community through the creation of next generation therapeutics, and it's this desire to help others that fuels me to work hard and be the best bioengineer that I can be.

Were you involved in any activities/groups/clubs/research labs on campus that were impactful during your time at UC San Diego?

I was involved in the Biomedical Engineering Society (BMES) during my time at UC San Diego. BMES is one of the single most impactful factors of my time here. It is a community full of people who support one another and a place where every individual can grow and become who they want to be. BMES is also an org whose core mission is to serve our community, and as a bioengineer whose goal it is to make an impact in the world, I loved that I was surrounded by so many other people who have that same drive to help others. Due to this strong sense of community, I served as an officer three times for the org: as Freshman Representative my first year, as Bioengineering Day Chair in the 2019-2020 school year, and as Vice President Internal in my final year.

I was also involved in the Christman Lab on campus for all four years. What I loved about that environment was not only the opportunity to engage in top-tier research, but also the mentorship I received there. Dr. Christman and all of the grad students in the lab have always encouraged me to believe in myself and it was the guidance of them and most especially my graduate student mentor, Holly Sullivan, that has inspired me to pursue my own career in research.

Do you have any advice for current or future engineering students?

My advice for any current, and especially future, engineering students is that anyone can be an engineer. I think many people get stuck in the idea that because they are not a top student, they can't be a good engineer. However, it isn't the best grades in the class or the top spot in a student organization that makes a person a good engineer. It's the passion they have for their field that makes them the best engineer. So, don't worry over the small things like that one midterm in your class you didn't do well on. Instead, focus on the big picture and focus on what you are learning and if you will be able to apply it to real-world engineering solutions. At the end of the day, if you want it and are willing to put in the work for it, then you can and will become an engineer.

What will you do next year?

I am heading off to the University of Colorado Boulder to get my PhD in Biological Engineering with funding by the NSF Graduate Research Fellowship Program. I hope to continue to do research in biomaterials and one day become a researcher who helps bring the next-generation therapeutics to those who need them most.

Anything else that's important to know about your time and experience at the Jacobs School?

Many students get caught up in the "what if's", especially when choosing a college. However, the thought of "what if I chose this other school for undergrad" never crossed my mind, and that was because UC San Diego and Jacobs School has always been the right place for me. It is a phenomenal school with so many resources available to you that if you look, you will find the opportunity that you want. UC San Diego has been a great launching pad for my future career, and better yet, the Jacobs School is full of some of the most hard-working, inspiring students that I have been honored to learn alongside. I think you would be hard pressed to find a place with people who have a greater sense of comradery and more enthusiasm for science than there is here at UC San Diego.

2022 Computer Science and Engineering Award of Excellence: Eman Sherif

 

Every year, six outstanding undergraduate students who made significant contributions to their academic department and the Jacobs School of Engineering community are celebrated with department Awards of Excellence at the Ring Ceremony event for graduating undergraduates. 

The 2022 Computer Science and Engineering Award of Excellence was awarded to Eman Sherif. Learn more about her background and future plans in this Q&A.

What do you enjoy about computer science and engineering, and why did you decide to pursue this field?

 What I enjoyed most about CSE is how flexible the degree is. The responsibility of choosing a major when you are 17 years old that will dictate what you can do for the rest of your life is really daunting. So I wanted to make sure I chose something with the most amount of options. With a computer science degree I knew I could enter basically any field whether it is education, government, healthcare, etc.  

Were you involved in any activities/groups/clubs/research labs on campus that were impactful during your time at UC San Diego?

 I was involved in the Early Research Scholars Program (ERSP) during my second year which was really important in giving me experience outside the classroom and helped me discover my love for research. Without participating in ERSP I probably would never have continued doing research in computer science education and would not have decided to pursue a PhD in computer science. I was also involved in the National Society of Black Engineers (NSBE) which helped me feel more comfortable in engineering and gave me the ability to connect with my peers who look like me and share a common interest in engineering. 

 Do you have any advice for current or future engineering students?

 My biggest piece of advice for future computer science students is to explore all the different career options computer science can bring to you. A lot of times students only focus on software engineering, which can be great for a lot of students, but a computer science degree can bring you so many other careers as well. 

 What will you do next year?

 Next year I plan on starting my PhD program in computer science at the University of Washington, Seattle. I will be advised by Dr. Amy Ko and my research focus is on computer science education. 

 Anything else that's important to know about your time and experience at the Jacobs School?

I really loved my experience at the Jacob’s school! The faculty and staff are amazing and really made my time here memorable.