Veniamin Borin
Stillwater,OK
Summary
Accomplished computational scientist with over 15 years of expertise in computational chemistry and photochemistry, specializing in biological systems. Proficient in advanced computational chemistry software, methods, and techniques, with fluency in Python and Bash programming within GNU/Linux environments. Recognized for driving innovative research, leading multidisciplinary teams, and delivering impactful solutions in molecular dynamics, QM/MM simulations, and machine learning applications. Adept at translating complex scientific concepts into actionable insights, with a proven track record in project management, mentorship, and high-impact publications. Passionate about advancing drug discovery and artificial intelligence integration in computational research.
Overview
15
15
years of professional experience
Work History
Postdoctoral Research Associate
Oklahoma State University
03.2022 - Current
- Conduct large-scale molecular dynamics simulations to elucidate inter-residue interactions, driving advancements in enzymatic function prediction.
- Develop and train artificial neural networks to model enzymatic activity.
- Design Python-based tools for automated data analysis of molecular dynamics simulations, enhancing result reproducibility.
- Lead data interpretation and reporting for multidisciplinary teams, contributing to four peer-reviewed publications and three conference presentations.
- Establish training programs for new researchers and HPC cluster users, covering Bash, Python, parallel computing, and data analysis.
Postdoctoral Research Associate
Hebrew University of Jerusalem
12.2016 - 03.2022
- Run nonadiabatic QM/MM molecular dynamics simulations to investigate photoisomerization in bacteriorhodopsin and proteorhodopsins, uncovering key photochemical mechanisms.
- Supervised a group of 7 researchers (two undergraduates, three graduate students, and two postdocs) on spectral tuning projects, resulting in four high-impact publications.
- Developed and optimized protocols for conical intersection analysis in light-sensing proteins.
- Facilitated cross-group collaboration, coordinating with HPC administrators to streamline computational workflows.
Graduate Research Assistant
Bowling Green State University
08.2010 - 12.2016
- Directed computational studies on ultrafast photoinduced transformations of small molecules (e.g., diiodomethane, bromoform) using MS-CASPT2 nonadiabatic molecular dynamics, contributing to 4 peer-reviewed publications.
- Pioneered a CASPT2 QM/MM protocol for excited-state molecular dynamics in solvent environments, adopted by the research group for subsequent studies.
- Authored successful allocation proposals for the Ohio Supercomputer Center, securing over 1 million CPU hours for research projects.
- Mentored peers in quantum and computational chemistry methods, enhancing group productivity and research quality.
Education
Ph.D. - Photochemistry
Bowling Green State University
Bowling Green, OH12.2016
Master of Science - Physical Chemistry
St. Petersburg State University
Saint Petersburg, Russia07.2010
Bachelor of Science - Chemistry
St. Petersburg State University
Saint Petersburg, Russia06.2008
Skills
- Quantum Chemistry
- Molecular Dynamics
- QM/MM
- Ab Initio
- DFT
- Molecular Modeling
- Homology Modeling
- Enhanced Sampling
- FEP
- Deep Learning
- Statistical Analysis
- Amber
- MOE
- Chimera
- VMD
- MODELLER
- SWISS-MODEL
- AlphaFold
- Autodock
- HADDOCK
- TensorFlow
- PyTorch
- Scikit-learn
- Python
- Bash
- R
- C
- MATLAB
- GNU/Linux
- High-Performance Computing
Languages
English (fluent)
Russian (native)
Publications
- Contreras, M., Borin, V.A., Agarwal, P.K., et al., 2025, Modelling protein-protein interactions for vaccine chimeric antigen design., PLoS ONE, 20, 2, e0318439
- Borin, V.A., Wiebeler, C., Schapiro, I., 2018, A QM/MM Study of the Initial Excited State Dynamics of Green-Absorbing Proteorhodopsin., Faraday Discussions, 207, 137–152
- Welfer, G.A., Borin, V.A., Cortez, L.M., Opresko, P.L., Agarwal, P.K., Freudenthal, B.D., 2023, Altered Nucleotide Insertion Mechanisms of Disease-Associated TERT Variants., Genes, 14, 2, 281
Timeline
Postdoctoral Research Associate
Oklahoma State University
03.2022 - Current
Postdoctoral Research Associate
Hebrew University of Jerusalem
12.2016 - 03.2022
Graduate Research Assistant
Bowling Green State University
08.2010 - 12.2016
Ph.D. - Photochemistry
Bowling Green State University
Master of Science - Physical Chemistry
St. Petersburg State University
Bachelor of Science - Chemistry
St. Petersburg State University
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