Group
Tiwary group photo, spring 2023
We are an interdisciplinary research group with backgrounds in Chemistry, Physics, Biophysics, Mathematics, Materials Science, Metallurgical Engineering and others. We share a common passion for understanding - and predicting - dynamics in complex molecular systems using statistical mechanics, information theory and machine learning.
We are looking for a Postdoctoral Fellow in RNA and Protein Bioinformatics - see full advertisement.
We also have openings for undergraduate researchers. You should be well-grounded in at least one subject (physical chemistry, biochemistry, biophysics, physics, maths or computing) and have an interest in learning the others. Prerequisites: You must have done well in both (1) Calc3 (MATH241) and (2) Pchem1 (CHEM481) (or equivalent courses for both). Additionally you must have some programming experience in C, C++, Python or similar language.
We are not looking for PhD students at the moment.
Principal Investigator
Pratyush Tiwary
Millard and Lee Alexander Professor (Curriculum Vitae)
Department of Chemistry and Biochemistry; Institute for Physical Science and Technology; Institute for Health Computing
Affiliate faculty in: UMD - Applied Mathematics & Statistics, and Scientific Computation (AMSC) program, Biophysics program, Chemical Physics program, Department of Materials Science and Engineering, Department of Physics; UMB School of Medicine - Department of Biochemistry and Molecular Biology
Postdoctoral researchers
Ruiyu Wang (Ph.D., Temple University)
Research areas: Enhanced sampling in solvated systems with interfaces, rare event methods
Xinyu Gu (Ph.D., Rice University)
Research areas: Protein conformational prediction, conformational-selective drug discovery, Generative AI for molecular dynamics
Da Teng (Ph.D., University of Chicago)
Research areas: Protein conformational prediction and antibody-antigen interactions
Personal webpage
Yunrui Qiu (Ph.D., University of Wisconsin-Madison)
Research areas: Diffusion models, representation learning, RNA structure prediction
Personal webpage
Graduate students
Shams Mehdi, 4th year Ph.D. student, Biophysics (M.S. Physics, University of Texas Rio Grande Valley)
Research areas: AI-integrated enhanced sampling simulations for RNA, Interpretable AI
Lukas Herron, 3rd year Ph.D. student, Biophysics (B.S. Physics, University of Florida).
Research areas: Denoising diffusion probabilistic models, RNA ensemble prediction
Personal webpage
Akashnathan Aranganathan, 3rd year Ph.D. student, Biophysics (B.S.+M.S. Biological Sciences, Indian Institute of Technology Madras).
Research areas: Protein conformation prediction, T-cells.
Personal webpage
Suemin Lee, 2nd year Ph.D. student, Biophysics (B.S. Physics, Simon Fraser University. M.S. Physics, University of Waterloo).
Research areas: Protein kinases, enhanced sampling of kinetics, diffusion models
Vanessa Meraz, 2nd year Ph.D. student, Chemical Physics (B.S. + M.S. Physics, University of Texas at El Paso).
Research areas: graph based learning and sampling for crystal nucleation, protein conformational transitions
Personal webpage
Anjali Verma, 1st year Ph.D. student, Biophysics (B.S. Applied Physics, Columbia University).
Research areas: time-series predictions from representation learning, RNA binding proteins
Personal webpage
Richard John, 1st year Ph.D. student, Physics (B.S. Physics, Case Western Reserve University).
Research areas: flow models and representation learning for glassy systems
Personal webpage
Venkata Sai Sreyas Adury, 1st year Ph.D. student, Chemical Physics (B.S. + M.S. Chemistry, IISER Pune, India).
Research areas: RNA tertiary structure prediction, ultra-large library screening
Personal webpage
Mariadelia Argüello-Acuña, 1st year Ph.D. student, Biophysics (B.S. Chemistry, Universidad de Costa Rica, M.S. Rutgers University-Camden).
Research areas: AlphaFold2-RAVE, conformation selective drug discovery
Personal webpage
Pakora, Wise beyond his (y)ears
Research areas: Skateboards, motorcycles and trains. Also belly rubs. And making the world free and safe from UPS/USPS/Amazon/GrubHub/UberEats delivery
Undergraduate students
Disha Sanwal, Junior, UMD (Chemistry and Applied Math)
Research areas: RNA structure prediction and diffusion models and avoid getting bitten by Pakora the Dog
Our alumni and where are they now
Postdocs
4. Eric Beyerle, Post-doc 2021-2024, now Post-doc researcher with Kresten Lindorff-Larsen at University of Copenhagen
3. Bodhi Vani, Post-doc 2021-2023, now Machine Learning Scientist at Prescient Design, San Franscisco
2. João Marcelo Ribeiro, Post-doc 2017-2018, now Assistant Professor at St. Joseph's College New York
1. Debabrata Pramanik, Post-doc 2018-2019, now Assistant Professor at SRM University, Amravati, India
PhD students
6. Dedi Wang, PhD (Biophysics, 2024) now Post-doc at Genentech, San Francisco
5. Ziyue Zou, PhD (Chemistry, 2024) now Post-doc with James Fraser, UCSF
4. Zachary Smith, PhD (Biophysics, 2023) now Senior Scientist I at Schrodinger Inc., NYC
3. Luke Evans, PhD (Applied Math, Statistics and Scientific Computation, 2023) now Flatiron Research Fellow at Flatiron Institute, NYC
2. Yihang Wang, PhD (Biophysics, 2022) now Center for Theoretical Chemistry Research Fellow, University of Chicago
1. Sun-Ting Tsai, PhD (Physics, 2022) now Postdoctoral Researcher with Prof. Sharon Glotzer, University of Michigan
