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.