Sept. 30, 2024
The Molecular Engineering and Science Institute (MolES) is excited to introduce the newest cohort of Ph.D. candidates to the Molecular Engineering program. Their pioneering research, which spans diverse fields such as advanced drug delivery systems and sustainable material innovation, has the potential to revolutionize industries and tackle some of the most urgent global challenges. Get to know our 13 new students.
Rafael (Rafi) Brent is interested in developing deep-learning methods to facilitate protein design, including novel enzymes, targeted binders, and exciting nanostructures. He worked on machine learning models for binding affinity estimation and small-molecule library generation during his undergraduate studies. He has a B.S. in Molecular Biophysics & Biochemistry from Yale University.
Mia Giallorenzi is interested in designing synthetic biological circuits and their many applications. As an undergraduate, she researched transcription/translation circuits in E. Coli to better understand positive and negative feedback control within a bacterial system. She has a B.A. and B.E. in Biomedical Engineering from Dartmouth College.
Melissa Hopkins is interested in synthetic biology, genetic engineering, and HTP technology development. As an undergraduate, she worked with halophiles. After graduating, she worked to improve HTP COVID-19 sequencing and protein engineering in yeast. She has a B.S. in Biochemistry from the University of California San Diego.
Daniel Howell is interested in using synthetic biology to sequester atmospheric carbon and manufacture products currently produced from fossil fuels. As an undergraduate, he researched metabolic engineering to increase yields of natural products with potential as medicines. After his undergraduate studies, he spent a year studying mechanisms of pathogenesis and genetic tractability of an obligate intracellular bacterium. Then, he spent a year in Germany on a Fulbright Research grant studying engineered carbon-fixation metabolism. He has a B.S. in Biochemistry and Biophysics from Oregon State University.
Mariya Hryb is interested in computational protein engineering. She focuses on using deep learning and generative models to design novel protein structures, including DNA and RNA binders, and applications in immune engineering. As an undergraduate, she focused on using molecular dynamics simulations to uncover mechanisms in cancer therapeutics and vaccine development. She has a B.S. in Biological Sciences and Pharmaceutical Sciences from Rowan University.
Jordan Koehler is interested in researching novel drug-delivery methods and vaccine components, mainly targeting infectious diseases. She aims to develop more accessible, effective, and safe vaccine technologies. She has conducted immune engineering research that has contributed to creating a more effective, universal flu vaccine by investigating the structure and binding of influenza antibodies. She has a B.A. in Engineering Sciences and a B.Eng. in Biochemical Engineering from Dartmouth College.
Arnav Nagle is interested in applying machine learning to protein design. He has worked on classifying protein folds in AlphaFold predictions and developing graph neural network-based force fields. He has a B.S. in bioengineering from the University of California Berkeley.
Anika O’Brian is interested in working with proteins and using the newest developments in machine learning algorithms to accelerate discoveries in this field. She hopes to do research in synthetic biology, protein engineering, and collaborating across disciplines to develop novel solutions that address pressing challenges in healthcare and sustainability. She conducted research as an undergraduate on enhancing protein crystal stability through rational design and introducing disulfide bridges. She has a B.S. in Chemical and Biological Engineering and a B.S. in Biomedical Engineering.
Crystal Perez is a graduate student in Professor Sean Gibbon’s Lab at the Institute for Systems Biology. She is interested in studying how microbially produced metabolites from the human gut microbiome influence health outcomes (i.e., contributing to disease pathology or altering response to medications). Before graduating from UW, Crystal obtained a B.S. and M.S. in Biology from Stanford University.
Eshwa Sawant is excited to utilize computational approaches to accelerate the discovery of new treatments. She has worked on stem cell research, protein engineering, and therapeutic discovery. She has a B.S. in Bioengineering and Materials Science Engineering from the University of California Berkeley.
Alex Shida is a graduate student in the lab of David Baker , the Henrietta and Aubrey Davis Endowed Professor in Biochemistry, and a trainee in the University of Washington’s medical scientist training program He aims to utilize de novo protein design to elucidate the underpinnings of complex biological mechanisms. He holds a B.S. in Quantitative Biology and an M.S. in Quantitative and Computational Biology from the University of Southern California.
Jay Squire is interested in using protein engineering and computational techniques to develop novel protein therapeutics. As an undergraduate researcher, he explored the development of nanobodies that bind tau with conformational specificity and lytic enzymes that act against antibiotic-resistant pathogens. He has B.S. in chemical and biomolecular engineering from Georgia Tech.
Avery Yang is interested in coupling computational enzyme design with high-throughput microfluidic assays to understand the principles of engineering dynamics in proteins. She hopes to use these methods to improve enzymes that catalyze challenging reactions such as carbon capture, nitrogen fixation, and plastic degradation. She worked as an undergraduate research assistant in the Michelle Chang Lab, where she structurally characterized and engineered several Fe(II) aKG-dependent radical amino acid halogenases to understand their mechanism better and expand their substrate scope. She has a B.S. in Chemical Biology and a B.A. in music from the University of California Berkeley.