2015 Cohort

Joshua Brake

Advisor: Changhuei Yang

Option: Electrical Engineering

LinkedIn: https://www.linkedin.com/in/joshbrake

Lab Website: http://www.biophot.caltech.edu/research/index.html

Current Research: Trying to see deep within the human body is like trying to peer through fog – visible light only penetrates so far into the body before it is scattered into a diffuse haze. Current medical imaging techniques like ultrasound and X-ray provide glimpses, but these have limited diagnostic and therapeutic utility. Josh aims to develop sophisticated imaging methods that will suppress seemingly-random light scattering in living biological tissues and enable deep tissue imaging and therapeutic applications. The Yang Lab has been exploiting the time-symmetric nature of light scattering, effectively undoing its effects by developing an efficient deep-tissue optical imaging method using a light field that propagates as if it were traveling backwards in time. Collaborating with neuroscientists and applying the Yang Lab's time-reversal optical focusing approach, Josh's research will use this technology to selectively activate optogenetically-modified neurons in the living brain. He uses a variety of state-of-the-art techniques in his work, including turbidity suppression via optical phase conjugation (TSOPC) and time-reversed ultrasound-encoded light (TRUE). Josh completed his undergraduate degree at LeTourneau University and has published a textbook that is used there to teach introductory circuit analysis to engineering undergraduates. He received an NIH F31 fellowship and won 2nd prize in the 2013 IEEE Region 5 Circuit Design Competition.

Selected Publications & Presentations:

D. Wang*, E.H. Zhou*, J. Brake, H. Ruan, M. Jang and C. Yang; Focusing through dynamic tissue with millisecond digital optical phase conjugation; Optica 2015, 2, pp. 728-735.
S. Cho, J. Brake, C. Joy, and S. Kim. "Refractive index measurement using an optical cavity based biosensor with a diﬀerential detection." BiOS SPIE Photonics West. San Francisco, CA, February 2015.
J. Brake and S. Kim. "An optical cavity based biosensor with chained diﬀerential detection to improve sensitivity and fabrication tolerance." BiOS SPIE Photonics West. San Francisco, CA, February 2014.
J. Brake . "Graduate School at LeTourneau University and Beyond." Presentation at LeTourneau University, Common Day of Learning. Longview, TX. April, 2014.
J. Brake . "The LeTourneau University Biosensors Lab." Presentation at LeTourneau University, Common Day of Learning. Longview, TX. April, 2014.
J. Brake . "What is Engineering?" Presentation at Christian Heritage School. Trumbull, CT. December 2012.

Get to know Josh: "One of my favorite things to do when I'm not in the lab is to hike. While I enjoy the hiking in the LA area, my favorite place to hike is in the Adirondack mountains of upstate New York. Over the past few summers I've been working on conquering the 46 High Peaks. I've finished 29 and I'm hoping to keep chipping away as I get the opportunity."

In Josh's words: "The access to powerful tools enables us to develop new technologies that never would have been possible even a few years ago. I am excited to push the boundaries of what we think is possible and try to solve some of the most pressing biomedical problems through the synergistic efforts of engineering and medical research."

Pradeep Ramesh

Advisor: Mikhail Shapiro

Option: Bioengineering

LinkedIn: https://www.linkedin.com/pub/pradeep-ramesh/1a/986/60a

Lab Website: http://shapirolab.caltech.edu

Current Research: Genetically-encoded magnetic nanomaterials, used as contrast agents in non-invasive medical imaging techniques (e.g. MRI), will enable unprecedented studies of biological function in living organisms. The primary limitation to adopting this technology for broad clinical use is that, to target specific tissues, these particles must be chemically synthesized and modified in vitro. Pradeep joined the Shapiro Lab as one of the founding members and quickly implemented a collaborative plan with UC Berkeley researchers to genetically program mammalian cells to synthesize these magnetic nanomaterials. Pradeep also leads a collaboration to fundamentally understand how magnetic fields interact with tissue using Nitrogen-Vacancy (NV) centers, which are a unique class of optical magnetometers that enable sensitive mapping of magnetic fields within biological specimens under ambient conditions. Pradeep completed his undergraduate degree at Caltech and has received a number of fellowships, including an NSF Graduate Fellowship, an IIE Fulbright Fellowship, and an Amgen Foundation Fellowship to perform summer undergraduate research. Pradeep has also received a Caltech Environmental Microbiology (CEMI) award to study bio-magnetism using nitrogen vacancy centers (2014) and won a Baxter Bioscience Award as an undergraduate (2007), among others.

Selected Publications & Presentations:

Ramesh, P. 2015. Invited speaker, "Emerging frontiers in biomedical imaging and bioengineering," Westlake High School
Ramesh, P. et al. FBAR Syndapin 1 recognizes and stabilizes highly curved tubular membranes in a concentration dependent manner. Sci. Rep. 3, 1565
Ramesh, P. et al. FBAR Syndapin 1 recognizes and stabilizes highly curved tubular membranes in a concentration dependent manner, poster presentation, 2014 Biophysical Society Meeting

Get to know Pradeep: Pradeep is an adventurer, saying "I grew up in four different countries and I've hiked in every single national park west of the Mississippi River."

In Pradeep's words: "If I could choose only one problem to potentially devote my career to, given the chance, it would be combatting antibiotic resistance in the developing world using gene-therapy."

Zach Zixuan Shao

Advisor: Julia Kornfield

Option: Bioengineering

LinkedIn: https://www.linkedin.com/in/zachshao

Lab Website: http://kornfield.caltech.edu

Current Research: To defeat diseases that rob people of their eyesight, including age-related macular degeneration and diabetic retinopathy, we must develop new classes of drugs that act in unique ways. Zach is working with industry collaborators to uncover the mechanism of action of a novel therapeutic oligopeptide using high-throughput genomic and proteomic analysis. Early clinical results indicate this drug may provide longer-lasting effects than those currently approved and on the market. Since drug effects and responses are often transient, Zach uses a unique combination of genomic (RNA-seq) and proteomic (BONCAT/pSILAC) tools in his research to reveal underlying patterns of regulation at the molecular level. Zach completed his undergraduate degree at UCSD and did an honors thesis where he used genetic screening to identify mutations in Arabidopsis, a model plant species. Zach also did an internship at Genencor and had the opportunity to present his results in a company-wide symposium. A member of the Caltech Entrepreneur Club, the Biotechnology Club and the Bioinformatics Journal Club, Zach also volunteered as Grand Awards Judge at the Intel ISEF Conference in 2014. He is bilingual in Mandarin and has received mentoring from the Hughes Scholar Program as well as funding from a Rosen Summer Research Fellowship.

Selected Publications & Presentations:

Shao, Z. (2010) RNA interference optimization in C. elegans using quantification methods. Undergraduate Scholastic Grants Journal of Research.
"Modeling T-helper Cells Mediated Immunity." Pasadena, CA, May 2015
''NADPH to Apoptosis." Pasadena, CA, June 2014
"A Better Protein Assay with Aptamers." Pasadena, CA, March 2014
"Genetic Screening for Arabidopsis Mutants that Enhance the Phenotype of npy 1 cuc 1 Double Mutants." Poster presented at the 25th Annual UCSD Undergraduate Research Conference, La Jolla, CA, April 2012
"High-throughput Antibody Library Screening via BiFC." La Jolla, CA, December 2011
"Genetic Screening for Arabidopsis Mutants that Enhance the Phenotype of npy 1 cucl Double Mutants." UCSD Biology Student Research Showcase 2011, La Jolla, CA
"Enhance Essential Amino Acid Content in Plants." La Jolla, CA, June 2010

Get to know Zach: "I'm actually an avid gardener ever since when I was young. I'm also very interested in plant biology and did my undergraduate thesis on Arabidopsis genetics. My parents instilled in me early a firm attitude of working hard. Before starting undergraduate at UCSD, I performed many odd jobs such as swimmer instructor and front desk receptionist and learned many things along the way through these unique experiences."

Zach chose Caltech because: "Caltech is a world-class research institute and I'm excited to study alongside with other like-minded students and researchers. The close-knitted community really solidified my decision as I am interested in establishing strong relationships with a diverse group of people."

Bradley Silverman

Advisor: David Tirrell

Option: Chemical Engineering

LinkedIn: https://www.linkedin.com/pub/bradley-silverman/62/659/299

Lab Website: https://tirrell-lab.caltech.edu

Current Research: Novel biomaterials have properties that will make them uniquely suited to solving some of mankind's toughest challenges, performing in environments and under conditions where other materials have failed. Bradley is currently investigating methods to control diffusion through engineered protein hydrogels. The complex dynamics underlying how molecules, like therapeutic drugs, diffuse into and out of engineered biomaterials will dictate how these materials may be used in a clinical setting to treat disease. As part of a large, collaborative project, Bradley is also exploring how engineered proteins may be used to control spatial organization in complex microbial communities. Results from this research will help guide the development of biomaterials that can withstand harsh environmental conditions, like those found in the human gastrointestinal tract. Bradley has done two summer internships with Merck, working on sterile operations for vaccine production and lab-scale production of a bioengineered pharmaceutical ingredient. Bradley completed his undergraduate degree at Georgia Tech, where he took first place in the Senior Design Competition in 2013. He has also received three industry-supported fellowships and scholarships from Air Products, Merck and Chevron.

Selected Publications & Presentations:

Silverman, B. R. and J. A. Champion (2014). "Presentation of fibronectin fragments using affinity protein interactions for enhanced retention and function." Acta Biomaterialia 10(12): 4956-4960
Bradley R. Silverman, Julie A. Champion, "SH3-Domain Affinity Based Fibronectin Biomaterials for Wound Healing," AICHE Student Conference, 2013, San Francisco, CA
Bradley R. Silverman, Julie A. Champion, "SH3-Domain Affinity Based Fibronectin Biomaterials for Wound Healing," Air Products Undergraduate Research Symposium, 2013, Atlanta, GA.

Get to know Bradley: "I'm a huge college football fan. Growing up in the South that's maybe not surprising, but you definitely aren't going to be finding me in the lab on Saturday late morning/early afternoons in the fall! My two favorite teams are Georgia Tech and whoever is playing the University of Georgia. I competed in the 2008 Jeopardy! Teen Tournament, and got second place, losing (badly) in the finals. It was a lot of fun, and I still keep in touch with the other participants. I also may have predicted (a bit) of my future, even back then... (http://www.j-archive.com/showplayer.php?player_id=5567)"

If Bradley could have lunch with any scientist (living or dead), he'd choose: "...Frederick Sanger, as he truly revolutionized (several times) the field of molecular biology, and we'd likely be at a truly different place had he not done the work he did. As well, he was known for being an exceptionally nice and humble man."

Kevin Yang

Advisor: Frances Arnold

Option: Chemical Engineering

LinkedIn: https://www.linkedin.com/in/kevinkyang/

Lab Website: http://www.che.caltech.edu/groups/fha/Projects.htm

Current Research: Machine learning is the science of getting computers to learn from data instead of being explicitly programmed. In the past decade, machine learning has given us machine translation, self-driving cars, and effective web search. As DNA-sequencing and synthesis technology improves, humanity is amassing a vast collection of biological sequence data. Machine learning will be a vital approach for understanding and using this data. Kevin's research uses machine learning to attack challenges in protein engineering that are otherwise intractable because they are both too complex to be designed from first principles and not amenable to the high-throughput screens used in directed evolution. He is currently collaborating with scientists both in the Arnold lab and in other groups to design enzymes and light-sensitive proteins with unique properties. As science becomes more complex and data-driven, many of the interesting problems will be at the borders between disciplines, and working with people with different backgrounds provides a fuller perspective on what problems are interesting and how to approach them. Kevin completed his undergraduate degree at The Ohio State University, where he studied chemical engineering with a minor in piano performance. Between Ohio State and graduate school, he taught math and physics for three years at a high school in Inglewood, California through Teach for America. In those three years, he transformed from a struggling first-year teacher into an effective instructor and robotics coach with the help of the amazing staff at Animo Inglewood Charter High School and Green Dot Public Schools. Kevin has received a number of awards, including the 2017 Chemistry and Chemical Engineering Teaching Assistantship Award for outstanding teaching, an NSF Research Experience for Teachers scholarship and two Green Dot Public Schools awards. Kevin also received an NSF Graduate Research Fellowship in 2011 and a fellowship to conduct summer research at Ohio State in 2009.

Selected Publications & Presentations:

"Machine learning to predict eukaryotic expression and plasma membrane localization of engineered integral membrane proteins." Bedbrook, C. N., Yang, K. K., Rice, A. J., Gradinaru, V., Arnold, F.H. (2017). In preparation.
"Structure-Guided SCHEMA Recombination Generates Diverse Chimeric Channelrhodopsins" C. N. Bedbrook, A. J. Rice, K. K. Yang, X. Ding, S. Chen, E. M. LeProust, V. Gradinaru, F. H. Arnold. *Proceedings of the National Academy of Sciences* 114, E2624-E2633 (2017). [doi/10.1073/pnas.170026911](http://www.pnas.org/content/early/2017/03/09/1700269114.abstract)
"Machine Learning to Predict Eukaryotic Expression and Plasma Membrane Localization of an Integral Membrane Protein." Proteins Gordon Research Seminar. 18 June 2017.

Get to know Kevin: "After years of playing pick-up off and on, I'm joining Caltech's club ultimate team, Aftermath. I'm also a pianist and played 3 solo recitals at Ohio State."

In Kevin's words: "Bioengineering is the culmination of centuries of work in biology, chemistry, physics, and other fields. I believe that its effect on the 21st century will be as transformative as the effects of applied physics, electronics, or petroleum engineering on the 20th century."

Ruijie (Kelly) Zhang

Advisor: Frances Arnold

Option: Chemistry

LinkedIn: https://www.linkedin.com/pub/ruijie-kelly-zhang/104/214/b60

Lab Website: http://www.che.caltech.edu/groups/fha/Projects.htm

Current Research: The pharmaceutical industry is keenly interested in the development of new classes of therapeutic drugs to treat diseases incurred by the world's ever-growing, ever-aging population. At the same time, engineered enzymes that allow "green chemistry" and sustainability are gaining utility in various industrial production processes. Kelly leads a group within the Arnold Lab that is addressing these challenges by engineering P450s to catalyze fundamentally-important reactions that have no natural counterparts. Her current project aims to design a P450 that can perform direct intermolecular C-H amination using non-biological reagents. This would represent a radical departure from current methods that often require harsh conditions, heavy metal catalysts and designer ligands. Depending upon the starting molecules, the resulting amine-containing products may serve as raw materials in other green chemistry processes, or they may find applications as therapeutic drugs. Kelly received her undergraduate degree from the University of Chicago where she had a merit-based, full-tuition scholarship provided by Argonne. She has received an NSF Graduate Research Fellowship and an NSF Green Chemistry Scholarship to attend the 2015 American Chemical Society's Green Chemistry and Engineering Conference.

Selected Publications & Presentations:

Farwell, C. C. *; Zhang, R. K. *; Mcintosh, J. A.; Hyster, T. K.; Arnold, F. 11. "Enantioselective enzymecatalyzed aziridination enabled by active-site evolution of a cytochrome P450." ACS Central Science 2015, I, 89-93.*both authors contributed equally

Get to know Kelly: "Before I came to Caltech, I traveled for 6-weeks in Asia. My friend and I covered seven countries on a moderate budget and no cell phone service. We climbed Mt. Fuji (well, we almost made it to the top) and watched the sunrise at Angkor Wat."

In Kelly's words: "Bioengineering excites me because it hasn't been well defined yet! So far it is emerging as a collaborative field that includes research spanning from electrical engineering to chemistry. Recently at a Caltech alumni event, I met someone who is currently working at USC on a collaborative project to grow an artificial kidney!"