Group photo, circa 2019
Principal Investigator
Graduate Students
Shannon McElhenney
(Joint with Prof. Jin Yu)
Research Interest: MD Simulations of RNA polymerases. Master equations / Markov state models. Data science. Directionally-enhanced sampling methods.
smcelhen@uci.edu
Timothy Mai
BS, San Diego State University (2025)
Research Interest: Enhanced sampling methods development for kinetics, Allostery and relaxation in biomolecules.
timotm2@uci.edu
Praveen Ranganath Prabhakar
Research Interest: Enhanced sampling methodology. Machine learning methods for collective variables. RNA dynamics. Membrane simulations
prprabha@uci.edu
Undergraduate Students
Paaras Ajit Shah
BS: University of California Irvine (Class of 2026) (Theoretical and Computational Chemistry track)
Research Interest: Constant-pH simulations of RNA
paarass@uci.edu
Zachary Michael Chambers
BS: University of California Irvine (Class of 2026) (Theoretical and Computational Chemistry track)
Research Interest: Constant-pH simulations of RNA
zchamber@uci.edu
Hailey Khoury
BS: University of California Irvine (Class of 2028) (Pharmaceutical Sciences)
Research Interest: Protein-ligand binding simulations
hkhoury2@uci.edu
Cynthia Zhang
BS: University of California Irvine (Class of 2028) (Biological Sciences)
Research Interest: Bacteriophage simulations
cynthiz6@uci.edu
Group Alumni
| Name | Position in Group | Current Affiliation |
|---|---|---|
| Trevor Gokey | PhD (2019-2025) Joint with Prof. David Mobley |
Software Developer, Open Force Field |
| Dhiman Ray | PhD (2018-2022) | Assistant Professor, University of Oregon |
| Moises Ernesto Romero | PhD (2018-2022) Joint with Prof. Jin Yu |
Assistant Professor, Sierra College |
| Ly Le | Research Scientist (2020-2021) | Principal Research Scientist, Sandbox AQ |
| Anupam Chatterjee | PhD (2014-2019) | Manager - Institutional Outreach, PrashantAdvait Foundation, Uttar Pradesh |
| James McSally | PhD (2014-2019) | Computational Chemist at Variational AI |
| Gianmarc Grazioli | PhD (2011-2016) | Assistant Professor of Chemistry, San Jose State University |
| Emel Ficici | PhD (2010-2015) | Senior Scientist, Computational Chemistry and Drug Design, Nurix Therapeutics |
| Jason Deckman | Post-Doc (2011-2014) | Lead Engineer, DeepCure |
| Gavin Bascom | PhD (2010-2014) | Senior Scientist at Terray Therapeutics |
| Ahmet Mentes | PhD (2009-2013) | Computational Biophysicist at Black Diamond Therapeutics |
| Maryna Taranova | PhD (2009-2014) | Principal Data Scientist/ Group Leader in Bioinformatics at Roche Sequencing Solution |
| Nicholas K Preketes | PhD (2008-2013) Joint with Prof. Shaul Mukamel |
Director, Commercial Strategy & Analytics, Amgen |
| Mahua Roy | PhD (2008-2014) | Senior Scientist at Pfizer |
| Daun Jeong | Post-Doc (2012-2014) | Research Scientist at Samsung Research, Korea |
| Prasanth P Jose | Post-Doc (2008-2010) | Associate Professor of Physics, Indian Institute of Technology, Mandi, India |
| Eunae Kim | Post-Doc (2008-2010) | Associate Professor of Pharmacy, Chosun University, South Korea |
| Aaron T. Frank | PhD (2006-2011) | Assistant Professor of Chemistry, University of Michigan, Ann Arbor |
| K. Maria Mills | PhD (2005-2010) Joint with Mark M. Banaszak Holl |
Assistant Professor of Physics, University of Missouri, Columbia |
| Jeff Wereszczynski | PhD (2004-2008) | Professor of Physics and Biology, Illinois Institute of Technology, Chicago |
| Catherine Musselman | PhD (2004-2007) Joint with Hashim M. Al-Hashimi |
Associate Professor of Biochemistry, University of Colorado, Anschutz Medical Campus |
| Faten Yassin | Post-Doc (2005-2007) University of Michigan |
Professor at Hobart and William Smith College |
| Chenyue Xing | MS (2003-2005) University of Michigan |
Co-Founder & Chief scientist, Myst Labs |
| Levent Sari | Post-Doc (2003-2005) | Senior Research Scientist, University of Texas, Southwestern Medical Center |
| Pu Tian | Post-Doc (2003-2005) University of Michigan |
Professor, Jilin University |