Current Members

Ozlem Demir is an Assistant Project Scientist in the Amaro lab. She obtained her PhD from the University of Florida Department of Chemistry, and worked as a postdoctoral scholar in the Amaro lab first in UC Irvine and then in 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 incorporated 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.

Martina did her undergraduate at University of Turin, where she studied quantum chemistry. After five years spent looking at static atomistic representation of crystals, she decided that it was time for something more dynamic in her scientific life. Therefore, she decided 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.

Zied Gaieb obtained 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.

Conor did his undergraduate 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. During his PhD, conor worked on the problem of polymorph prediction. Specifically, Conor studied 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 upstream in the pharmaceutical pipeline, and is using in silico methods to assist in drug discovery.

Jamie received a B.S. in biochemistry and a minor in mathematics and biology from Boston University in the spring of 2012. While at Boston University, Jamie played Division I soccer and pursued scientific research. She worked in the synthetic organic laboratory of John Porco for a brief period before realizing her love for neurobiology and moved to the laboratory of Xue Han where she studied optogenetics. Jamie's scientific interests encompass defining how the atoms of a protein dance through time in molecular dynamics simulations, and how this dance confers function to various proteins. She is mostly interested in large systems like E3 ligases and the IKK signalosome, but is also fascinated with long time scale dynamics of well-studied protein systems.

Pek Ieong is a newly graduated alumnus of UCSD with a Bachelor's degree in Pharmacological Chemistry. She has resigned herself to the fact that because Ieong is such an unusual last name, most of the time people will assume her surname to be Leong when they first see it. Pek enjoys sleeping so much that her biggest dream in life is to hibernate in wintertime. When she is not daydreaming about hibernation, she can be found working in the lab or in class.

Abby received her A.B. in Chemistry and 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.

Alexandra "Sasha" Heyneman's insatiable curiosity in science and mathematics yielded with a B.S. in chemistry from the University of Montana in 2014. In the summer 2013, Sasha became an alumna of the Amaro Lab's BioChemCoRe program. This introduction created a lasting impression, uprooting this Northwesterner to sunny SoCal. During her 1st year as a graduate student, she joined Dr. Amaro's lab with intent to develop biochemistry software, simulate intersting biophysical systems, and conduct great research. In undergrad, she received multiple awards through the UM chemistry department for her aid in undergraduate chemistry classes. (She founded and led the UM Undergraduate Chemistry Association as president, researched year-round in Dr. Bowler's biophysics lab, and TAed three of her peers' courses.) Sasha enjoys talking about science, teaching, snowboarding, puzzles, calculus problems, the Argentine tango, napping in the sun, scuba diving, and making lists.

Sophia Hirakis started graduate summer research with the Amaro Lab in of 2012 as part of the CompChemBio program. She joined the lab as a first-year graduate student in 2013. She also works jointly with Dr. Terry Sejnowski at the Salk Institute of Biological Sciences. Before coming to graduate school, Sophie attended Manhattan College in Riverdale, NY. There, she worked in the organic chemistry research lab of Dr. James McCullagh. She received her Bachelors of Science degree in Biochemistry in 2011. Her primary research interests include brownian dynamics simulations, and sub-cellular modeling of calcium dynamics in cardiac myocytes. Her favorite protein is the ryanodine receptor 2 (RyR2). Sophie's hobbies involve singing, dancing, and listening to New York Yankees games on her radio.

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 received his B.S in chemistry from Duquesne University in 2015. He did 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. When he’s not doing science, Ben is an avid fencer, where he has a national rating and is also a referee and coach.

Christopher Lee received a B.Sc. in Chemistry and B.A. in Computer Science from the University of Virginia (UVA) in 2011. He also received 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 Ph.D. student 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.

Tavina obtained her Bachelor of Science in Chemistry from Spelman College in 2010. She then participated in the MIT B-cubed Post-baccalaureate Program, where she took biology courses at MIT, and performed research at Novartis Institute for Biomedical Research. During her time at Novartis, Tavina became involved in Computational Chemistry research, and developed a passion for drug design and development. She is currently a fourth year graduate student who works in Rommie Amaro's lab. Upon receiving her PhD from UCSD, Tavina plans to pursue a career in rational drug design. Some of her hobbies include dancing, watching movies, and traveling.

Emília Pécora de Barros did her undergraduate 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 when participating in the Amaro Lab first BioChemCoRe program and fell in love with the field and the group, so much so that she returned for her PhD. Emília loves traveling, sightseeing, eating and reading. Upon moving to California she bought a U.S. scratch map and hopes to have all the states scratched out by the time she completes her PhD (which may not be very feasible, but she dreams about it anyway!).

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 be in the Amgen Scholars Program in 2015, allowing him to spend a formative summer in the lab of William A. Goddard III at Caltech. Starting in the lab of Rommie Amaro and J. Andrew McCammon in 2017, Christian is working to combine multiple computational programs to simulate large scale biological events, such as cell signaling, to better understand influenza. 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 received her BS in biological sciences at UC San Diego and is currently pursuing her PhD in biomedical sciences, 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.

Jeffrey graduated from Claremont McKenna College in 2011 with a bachelor's degree in Chemistry and Physics. In school, he played NCAA football and was president of the Chemistry Club. Over the summers he worked with Dr. Abhi Jain at JPL to develop an MD simulation package, and after graduation he worked in the Vaidehi Lab at City of Hope on a variety of modelling projects. Jeff started graduate school at UCSD and joined the Amaro lab in 2013. His research interests are in drug design and the application of modelling in support of experimental science. Outside of lab, Jeff enjoys teaching, travelling, reading, and a good beer.

Ben is a senior at UC San Diego studying Biochemistry & Cell Biology with a Minor in Education Studies. He teaches, researches and runs a national nonprofit that designs science education programs for underserved K-12 schools. He also serves on the UCSD Changemaker Steering Committee and helps boost entrepreneurship initiatives in San Diego. Ben researches in the laboratories of Rommie Amaro and Pieter Dorrestein (and spent the past summer working with Debora Marks of Harvard Medical School). Ben is interested in using computational methods to both simulate and build molecular machines that can address pressing issues in structural biology and drug discovery. Ben is currently applying to PhD programs in order to further study Systems Biology or Bioinformatics. In his free time, he likes to play basketball.

Egbert is currently pursuing a bachelor's degree in Pharmacological Chemistry with a minor in Mathematics. In the future, he plans on becoming a researcher to continue studying novel ways of drug activity prediction. His interest in drug discovery comes from his fascination with the field's interdisciplinary nature, which he sees as an opportunity for scientific creativity. In the Amaro lab, Egbert is working under Ben on the lab's SEEKR project. Outside of the lab, Egbert enjoys hiking, reading, learning about cryptography, and music.

Thuy Tien Nguyen pursues her love for Chemistry at University of California, San Diego as a Pharmacological Chemistry major. She wants to become a research pharmacist to find a better cancer treatment. In Pharmacology class, she met Dr. Amaro; mutual interest sparked; and she joined the lab. She is studying protein IKK2, an important drug target for cancer, under Jamie. On the side, Thuy Tien is a volunteer at Cross-Cultural Center, a short distance bicyclist, and a karateka.

Nazare Simas

Nazare Simas

Nazaré Simas is a Alumni from Point Loma Nazarene University majoring in Applied Health Science. She plans to attend 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. Nazaré works part time as a photographer, elementary and middle school tutor, and as a clerk for a local psychologist. 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.