Current Members

Ozlem Demir is an Associate Project Scientist II in the Amaro Lab. She earned a PhD from the University of Florida's Department of Chemistry, and worked as a postdoctoral scholar in the Amaro Lab, initially at UC Irvine and now at UC San Diego. Ozlem has been working on various projects at molecular dynamics and quantum mechanics levels to aid drug discovery efforts for various diseases including cancer, African sleeping sickness, Chagas disease, and HIV. In these projects, she incorporates flexibility of active sites simulated by molecular dynamics into drug discovery efforts for biological targets working closely with various experimental collaborators. Outside work, Ozlem likes reading, listening to music, and hiking.

Daniel grew up near Chicago and was an undergraduate chemistry major at Hamilton College, in upstate New York. After college, he spent a year playing with mice in a lab at Columbia University before heading off to grad school in the University of Iowa’s Department of Chemistry. At Iowa Daniel worked in Amnon Kohen’s lab, where he measured enzyme kinetics—particularly isotope effects—as a probe for conformational dynamics during catalysis. During grad school he took an opportunity to visit Dan Major’s lab at Bar-Ilan University, in Israel, where he began to use molecular dynamics simulations to study enzymes. This led him to a post-doc in Qiang Cui’s lab at the University of Wisconsin-Madison, where he used hybrid quantum/classical simulations to study enzyme chemistry. Now that Daniel is at UCSD he is working with the Center for Aerosol Impacts on Chemistry of the Environment (CAICE) to determine if and how biomolecules that get incorporated into atmospheric aerosols affect the behavior of those aerosols. If he’s not simulating things, Daniel is probably playing rugby.

Martina completed her undergraduate education at University of Turin, where she studied quantum chemistry. After spending five years looking at static atomistic representation of crystals, she decided that it was time for something more dynamic in her scientific life and chose to pursue a PhD in the field of Molecular Dynamics at Ecole Politechnique de Lausanne (EPFL) under the Prof. Dal Peraro's supervision. Combing X-ray experiments and Molecular Dynamic simulations, Martina investigated the membrane-protein interplay in modeled physiological conditions. Her work highlighted the importance of applying a multilevel approach to achieve a comprehensive picture of biological systems and understanding the dynamic interactions and subsequent events that occur in cells. Currently, in collaboration with the Villa lab and the Taylor lab, Martina aims to investigate the LRRK2 familial mutations and their association with Parkinson Disease.

Lorenzo earned his M.Sc. in Pharmaceutical Chemistry and Technologies at University of Milan studying new peptide antagonists of a3b4 nicotinic receptor by combining solid-phase peptide synthesis experiments with Molecular Dynamics simulations. Afterwards, he started his PhD in Physics and Chemistry of Biological Systems at SISSA (International School for Advanced Studies, Trieste) under the supervision of Dr. Alessandra Magistrato. During his PhD he spent six months as visiting student at EPFL (École Polytechnique Fédérale de Lausanne) in the group headed by Prof. U. Rothlisberger. He graduated in 2017, after having worked on pre-mRNA splicing, studying the catalytic mechanism of group II intron ribozymes and the functional dynamics of the spliceosome by classical and QM/MM MD simulations. Lorenzo is currently a postdoctoral scholar in the Amaro Lab and his research will be focused on computer simulations and modelling of the Influenza virus.

Zied Gaieb earned his PhD in Bioengineering from the University of California, Riverside in 2016 where he worked with Dimitrios Morikis on the activation mechanism of G protein-coupled receptors using Molecular Dynamics simulations. Currently, Zied is a postdoctoral scholar with the Amaro Lab and Drug Design Data Resource (D3R), co-advised by both Rommie Amaro and Michael K. Gilson. His work focuses on advancing the technology of computer-aided drug discovery and understanding the "general" mechanics governing protein binding and dynamics.

Sophia P. Hirakis (aka Sophie) is a post-doctoral scholar in the Amaro Lab. She began working with Dr. Amaro in 2012 as the first-ever participant of the BioChemCoRe program. Her doctoral work is centered on Multi-scale Biophysics and Biochemistry. Specifically, she focuses on cardiac systems at atomistic, molecular, and sub-cellular levels. Using Molecular Dynamics (MD), Brownian Dynamics (BD), Ordinary Differential Equations (ODE) and Monte Carlo (MC) Markos Models (MM) she transcends spatiotemporal scales to understand the sub-cellular level effects of atomistic alterations. Dr. Hirakis is a professional national anthem singer and owner of a Philanthropic Non-Profit Organization named Works of Wisdom. Her passion is centered on making science more accessible to underprivileged and disabled youth

Christopher Lee received a B.Sc. in Chemistry and B.A. in Computer Science from the University of Virginia (UVA) in 2011. He also earned a M.Sc. degree in Chemistry from UVA in 2013, under the supervision of Professors Linda Columbus and Cameron Mura, studying enzyme kinetics. He is currently a postdoc in the labs of Rommie Amaro and J. Andrew McCammon. His research is focused on diffusional processes, membrane permeability and building models of sub-cellular electron tomographic data.

Conor completed his undergraduate education at the University of Michigan, where he studied chemical engineering and mathematics. Conor went on to obtain his PhD in chemical engineering from Purdue University, where he studied under Professor Doraiswami Ramkrishna. While pursuing his PhD, Conor worked on the problems associated with polymorph prediction, specifically, studying the ability to use molecular dynamics to predict temperature and solvent dependent accessibility of crystal structures through polymorph specific nucleation rate calculations. Conor has now moved up the pharmaceutical pipeline, and is using in silico methods to assist in drug discovery.

Teri Simas earned her Bachelor's degree in Sociology and Spanish from Central Washington University in 1983. She she began her career on the UC San Diego campus in 1992 at the San Diego Supercomputer Center and is now with the Chem/Biochem Department, serving as the Lab and Project Manager for the very awesome Amaro Lab. She also serves as an analyst with the National Biomedical Computation Resource and is the former Program Manager for the Pacific Rim Applications and Grid Assembly (PRAGMA) and the Pacific Rim Experiences for Undergraduates (PRIME). In her spare time she enjoys spending time with her family and five dogs, photography, gardening and bird watching. In 2012 she and her husband served as Presidents for San Diego's oldest ethnic festival, the "Festa do Espirito Santo" in Point Loma, with their daughters serving as the 2012 Festa Queens. Teri volunteers with mulitiple organizations and basically never sits still.

Philip graduated from Boise State University (BSU) in May 2018 with a B.S. in physics with an emphasis in biophysics and a minor in applied mathematics. While at BSU he taught as an adjunct lab instructor for the physics department, hosted and volunteered at numerous STEM educational outreach events, and worked on various projects in Dr. Daniel Fologea’s Biophysics lab studying lysenin, a membrane toxin, and its properties and potential applications. He also focused on mechanical engineering as a team lead on the Boise State Micro-g NExT NASA Undergraduate Research Team, and Heliophysics research for two summers at NASA Goddard Space Flight Center. He recently joined the Amaro and Komives Labs to be co-advised on a project studying an ASB-containing ubiquitin E3 ligase by utilizing biochemical and computational techniques. Outside of lab he spends his time outdoors hiking, skiing/snowboarding, mountain biking, etc., and has caught the surfing bug since moving to SD.

Abby earned her A.B. in Chemistry with a minor in Greek Language and Literature from Washington University in St. Louis. She then began a Ph.D. program at UCSD, where she fell in love with atmospheric chemistry after working on sea spray aerosol generation, collection and characterization methods. Before joining the Amaro Lab, Abby took two years off to teach chemistry at the high school and junior college level. It was during this brief hiatus that she discovered her passion for teaching science to students and to the public. In the lab, Abby is interested in investigating the molecular dynamics of lipid monolayers found at the surface of nascent sea spray aerosols. In her free time, she runs a blog focused on communicating science through creative medias. She also enjoys developing innovative chemical education technology that she hopes will make chemistry more accessible to all students. If she is not in the office, she is probably doing yoga or snuggling her cats.

Sarah graduated from Duquesne University in May 2015 with a B.S. in Chemistry and a minor in Mathematics. At Duquesne, Sarah worked in the lab of Dr. Jeffrey Evanseck where she conducted quantum mechanics studies of intramolecular hydrogen bonds. In recognition of her academic achievements as well as her research and leadership skills, Sarah was awarded the 2014 Barry M. Goldwater Scholarship. In 2015 Sarah joined the Amaro Lab as a first year graduate student. Her current research interests include drug design and simulation of biologically relevant systems. In her free time, Sarah enjoys do-it-yourself projects, gardening, and visiting local farmers’ markets.

Ben earned his B.S. in Chemistry from Duquesne University in 2015. He performed his undergraduate research under the supervision of Dr. Ralph Wheeler and was named a Goldwater Scholar for his research and academic accomplishments. As a member of the Amaro Lab, Ben’s interests include brownian dynamics, molecular dynamics and milestoning. He is also interested in the development of new computational tools, particularly those that bridge multiple scales. In his spare time, Ben is an avid fencer, where he has a national rating and is also a referee and coach.

Emília Pécora de Barros earned her undergraduate degree in Chemistry and Master's in Physical Chemistry at the University of Campinas, Brazil. In her junior year she studied abroad at Columbia University with a scholarship from the Brazilian program Science Without Borders. During that time she had her first contact with Computational Chemistry, while participating in the Amaro Lab's first BioChemCoRe program. She fell in love with the field and the group, so much so that she returned to UC San Diego to pursue her PhD. Emília loves traveling, sightseeing, eating and reading. Upon moving to California she bought a U.S. scratch map and hopes to visit all 50 US states by the time she completes her PhD (which may not be very feasible, but she dreams about it anyway!).

Mia received her BS in Chemistry and BA in Mathematics from the University of North Carolina Wilmington. There she conducted biophysical research on peptide-membrane binding kinetics under Dr. Antje Almeida and Dr. Paulo Almeida and completed an Honors Thesis entitled “Are leucine and isoleucine equivalent in binding of amphipathic peptides to membranes?” She served as a research fellow at the National Institutes of Health in the Laboratory of Human Carcinogenesis under Dr. Curtis Harris and in the Laboratory of Biochemistry and Molecular Biology under Dr. Alexander Kelly. Mia joined the Amaro lab as a first-year PhD candidate in 2019 with joint mentorship from Dr. Rommie Amaro and Dr. Elizabeth Komives. Her research interests include Markov state modeling, p53, drug design, and carcinogenesis. In her free time, she enjoys going to live music events, hosting Shabbats for her fellow graduate students, and bicycling by beach.

Christian graduated from Elon University in 2016 with a B.S. in Chemistry and a minor in French. He completed an REU in Germany at RWTH Aachen University in 2014 and was selected to participate in the Amgen Scholars Program in 2015, allowing him to spend a formative summer in the lab of William A. Goddard III at Caltech. In 2017 Christian joined Rommie Amaro and J. Andrew McCammon's labs. In 2018 he was awarded an NSF GRFP to use molecular dynamics and Brownian dynamics to study chemical and biological effects that modulate influenza's seasonal transmissibility variances. In the rare times he's not playing sports or fantasizing about becoming a math theorist, he enjoys West Coast swing dancing, playing classical violin, going to museums, drinking milk, and exploring nature from a mom-approved height. He maintains that the best career advice he ever received was from a Russian genius who told him that "Every great computational chemist was once a hacker."

Bryn earned her BS in Biological Sciences at UC San Diego and is currently pursuing her PhD, co-advised by both Rommie Amaro and Rob Knight. She uses computational chemistry and biophysics tools to investigate microbial proteomes and elucidate the function of human and environmental microbiomes. When she’s not at the computer, Bryn can be found in the ocean, on a bike, eating burritos, camping off a trail somewhere, or searching for the best cheese & cracker combo.

Nicholas graduated from Cal Poly San Luis Obispo in 2018 with a B.S. in Biochemistry. He conducted his undergraduate research on the bioengineering of a bacterial natural product gene cluster under Dr. Katharine Watts. Nicholas started a Ph.D. program in the fall of 2018 at UCSD and joined the Amaro lab as a first-year graduate student after falling in love with computational techniques while rotating. Outside the lab, he typically spends his time rock climbing, playing volleyball, or just relaxing with friends and family.

Nazaré Simas

Nazare Simas

Nazaré Simas is an alumni from Point Loma Nazarene University where she earned a B.S. in Applied Health Science. Her long term goals include eventually attending graduate school to earn an MS in Genetic Counseling, specializing in pediatric medical genetics. Nazaré served as an Atlantis Project Pre-Health Intern in Faial, Azores, Portugal during the summer of 2013. In her spare time she dances with the Portuguese American Dancers, plays clarinet with the Filarmónica União Portuguesa de San Diego, and volunteers with many local ethnic and military organizations. She’s a lifetime member of Girl Scouts and earned her Gold Award in 2011.

Teresa Jackson

Teresa Jackson

Teresa (Terry) Jackson is a 4th year undergraduate studying at UCSD in Eleanor Roosevelt College majoring in Biochemistry/Chemistry and minoring in Japanese Studies. She attended Mission Bay High School and is a San Diego native. She is currently studying neuraminidase inhibitors under Christian Seitz in Professor Amaro's lab. In 2018 she was awarded the Ledell family research scholarship to do work on Azurin in professor Judy Kim's lab. She works as a math and chemistry tutor for the Teaching and Learning Commons at UCSD, and as an independent contractor. She hopes to graduate this Summer. In her spare time she likes to do art and play table top rpgs and board games. If you ask her to elaborate further, prepare to have your ears talked off.

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Andy Mitchell

Andy Mitchell

Originally from Irvine, CA, Andy Mitchell is a 3rd year undergraduate double-majoring in Chemistry and Applied Mathematics. He joined the Amaro Lab during his freshman year in 2015 as a part of the Regents Scholar Research Initiative and has since worked on several projects associated with protein dynamics. Currently, he is part of a study on lipid monolayer dynamics with the Center for Aerosol Impacts on Chemistry of the Environment (CAICE). He aspires to eventually earn a doctorate and to help develop more sophisticated computational methods for molecular simulation and drug discovery. Outside of his own academic endeavors, Andy develops his passion for teaching by tutoring high school students in math, science, and test prep. He spends his free time playing/listening to music, watching Dodger baseball, indulging in video games, and hanging out with his wonderful family (and dog) on the weekends.

Andrew Tao

Andrew Tao

Andrew Tao is a graduating 3rd year undergraduate majoring in biochemistry and minoring in business. He hopes to take a gap year doing research on protein engineering before applying to graduate school. He is an officer of the American Chemical Society - Student Affiliate on campus and enjoys hiking around San Diego in his free time.

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Rob Swift

Rob Swift

Rob began his academic trajectory at Santa Barbara City College, where he earned associates degrees in chemistry, physics, mathematics, and liberal arts, all with honors. He went on to earn a bachelor’s degree in Biochemistry, with highest honors, from UCSB before relocating to San Diego, where he completed his PhD at UCSD in the laboratory of Professor J. Andrew McCammon. He was the first member of the Amaro lab, where completed post-doctoral research and also worked as an assistant project scientist. He has consulted in the pharmaceutical industry and was an active participant in the Drug Design Data Resource. In addition to research, Rob has a long-standing interest in teaching, and he left full-time academic research to pursue a career as a high school science teacher. He is currently a full-time physics instructor at Carlsbad High School and moonlights as a researcher in the Amaro group. Besides NGSS-aligned, phenomenon driven lessons, Dr. Swift is primarily interested in atomistic free energy simulations and the interrelationship between structure, dynamics and function.