MathWorks supports expanded use of computer modeling tools with MicroGrant Program

The Jacobs School of Engineering at UC San Diego is home to nearly 10,000 students, making it the largest engineering school in California. Every single one of these students has access to computer modeling software including MATLAB and Simulink, produced by MathWorks. 

MathWorks has donated $60,000 for small grants up to $15,000 to be awarded to student and faculty projects for use in curriculum and research development that involve MathWorks tools in some way. This could be student organizations using MATLAB to design a new race car, faculty research projects incorporating Simulink in their multidisciplinary simulation models or graduate student research projects that make use of MathWorks tools. The grant can also be used to support the development of curriculum materials for undergraduate teaching and labs, assessment tools, interactive tool development, research education and training tools. 

Along with funding, each selected project will be co-advised by a MathWorks engineer, who can provide technical support and guidance. 

In addition to establishing the MicroGrant Program, MathWorks has joined the Corporate Affiliates Program of the Jacobs School of Engineering, as well as the Scripps Institution of Oceanography’s Corporate Alliance and the Halıcıoğlu Data Science Institute’s Industry Partner Alliance Program. 

Students and faculty of the Jacobs School of Engineering, Scripps Institution of Oceanography and Halıcıoğlu Data Science Institute had a chance to apply for the first round of grants with submissions due August 1. Awards will be announced by September 2. More information on the program, and following application rounds, is available here. 

Alex Mosser: from chemical engineering student to Naval Reactors Engineer

Meet Alex Mosser, a chemical engineering alumnus who graduated from the Jacobs School of Engineering in 2022, and is now commissioning into the Navy as an officer. Mosser plans to serve as a Naval Reactors Engineer, where he'll be involved in research, design, maintenance, operations and regulation of Navy nuclear reactors and power plants. Learn more about his time on campus, career trajectory, and role in the Navy, in this Q&A:

1) What did you study at UC San Diego, and why?

Originally, I wanted to study nuclear engineering in college. I've always considered it an underrated and highly misrepresented energy source, and want to do the most I can to change that. That being said, nuclear engineering isn't offered at many undergraduate colleges, while chemical engineering covers a lot of the same fundamental concepts while offering a much broader curriculum and application. So, I chose to major in chemical engineering.

2) Were you involved in any groups on campus that were meaningful during your time here?

I joined a number of groups at UC San Diego, but the one that had the greatest impact on my future and career was AIChE, or the American Institute of Chemical Engineers. In AIChE, I was able to participate in a team which worked on cryodesalination, or the freezing (and thereby separation) of fresh water out of a salty brine. Though a large part of our time in this group was impacted by the COVID-19 pandemic, we were still able to research new ideas for the automation of our (successful) prototype, which involved learning new programming languages and reading many research papers. Overall, this opportunity gave me a lot of real-world research and design experience, and helped me learn to effectively communicate ideas through presentations and papers.

3) Why did you decide to join the Navy, and do you know what your particular role will be yet?

I chose to join the Navy because it was the best job opportunity available to me. My particular role will be as a Naval Reactors Engineer. The benefit of this, aside from being a stable job, is that pay begins while still in college, allowing me to pursue my studies without needing part-time work. Moreover, there is access to military benefits and (for my position) no stress of deployment. Overall, these benefits outweighed those offered by other nuclear or chemical engineering jobs.

4) Has your engineering degree helped you at all in your role as an officer yet? Or might it in the future?

My role as an officer has not yet begun. At the time of writing, I am still enjoying my final summer break. That being said, my engineering degree will absolutely come in handy in future assignments and responsibilities. Aside from it being necessary to even apply for the job, the Navy will also send me through a post-graduate education equivalent to a master's degree in nuclear engineering. As a chemical engineering major from UC San Diego, where I was able to take classes on nuclear energy for credit, I am uniquely equipped to excel in this post-grad education where other majors from other schools may have a more steep learning curve.

5) Any advice for students looking to follow a similar career trajectory, or considering it as an option?

For any students looking to get into nuclear engineering, the Navy is an excellent option. They offer a diverse array of opportunities, each with drastically different requirements and responsibilities. For those who want to travel around the world, you can become a nuclear engineer on an aircraft carrier or nuclear submarine. For those who want to be educators, the Navy also offers positions as an instructor in nuclear power school or at a hands-on prototype school. The Navy has many opportunities that the private sector doesn't, but the opposite is also true, and the private sector tends to have less physically strenuous training requirements. Overall, for those looking into a similar trajectory, my strongest advice would be to stay well-informed.

Jacobs School staff receive Exemplary Employee awards

Several Jacobs School of Engineering staff members were recognized for their outstanding performance and dedication with Exemplary Staff Employee of the Year awards. Carol Kling, program administration support in the Department of Bioengineering, and Andrea Willis, student services advisor in the Computer Science and Engineering Department, were honored with the award. Willis shares more about her role, and what she enjoys about working at UC San Diego, below. 

Andrea Willis, student services advisor

Q: What does your job entail?

A: Academic Advisors work directly with students to connect them with the information they need to succeed.  This includes: course and graduation requirements, experiential learning opportunities (like internships, research, study abroad, etc.), support resources that are available to them on campus, connecting with student organizations, and so much more!

Q: How does your role support the overall mission of the university?

A: UC San Diego has committed to being a student-centered organization, and I use this as a guidepost in my day-to-day work. I always aim to advocate for our students, making sure that the CSE department places our students, and their experience, at the center of any policy or curriculum changes that we make.  

Q: What is the best part of the job?

A: I love working one-on-one with the students in our department, helping them to take full advantage of all that UC San Diego has to offer during the time that they're here. I feel lucky to be a part of their growth, from their first day of orientation, to graduation!

Q: Any other ways you've been involved on campus?

A: I've been involved with a number of different Student Affairs staff groups at UC San Diego, which has been a great way to connect and collaborate with colleagues who share the same goals.

All members of the UC San Diego community are invited to help us celebrate these outstanding staff members at the virtual Exemplary Staff of the Year award program on Thursday, August 25, 2022, at 3 p.m. Registration is not required. Use this link to join the event https://ucsd.zoom.us/j/92205469196

Senior Assistant Dean honored by YWCA

Tana Troke Campana, Senior Assistant Dean and Chief of Staff at the Jacobs School of Engineering, has been honored by YWCA San Diego County with the Tribute to Women & Industry (TWIN) Award. This award recognizes the extraordinary achievements of women in managerial, executive or leadership roles. 

In her current role, Troke Campana works directly with Dean Albert P. Pisano and academic and administrative senior leaders on strategic planning, implementation of the dean's vision, and oversight of the school’s finances and administrative operations. In 2015, she developed and implemented a schoolwide Lean Six Sigma-based administrative best practices initiative, which has been expanded across the campus with 19 new tools to date.

Troke Campana is a UC San Diego LEAD Fellow, STRIVE mentor, Academic Affairs Best Practices Co-Chair, and member of many campus-wide committees. Her prior roles at UC San Diego include Administrative Vice Chair for the Department of Family Medicine and Public Health and Assistant Dean for Medical Education. She held multiple management roles at UC Irvine and UC San Francisco and served as the chief administrative officer and IT director at a K-12 public school in New York. She is also a founding Board member of the Drums Along the Waterfront organization. Troke Campana earned her MBA and BS in Information Systems from the University of Redlands.

Troke Campana and other women colleagues throughout the San Diego area were honored at a citywide ceremony in June. Please join us in applauding her dedication, service and leadership.

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.