Molecular Dynamics
Protein conformational landscapes and long-timescale dynamics.
Purdue University · Postdoctoral Research Associate
Rajarshi Roy, PhDComputational
Biophysicist
Decoding biomolecular motion through molecular simulation, enhanced sampling, and structural biology.
Illustrative placeholder · research imagery will replace this visual
01
Research philosophy
I study how biomolecules move, communicate, and change shape.
Molecular function is encoded not only by structure, but by motion. My research combines molecular dynamics, enhanced sampling, and computational structural biology to uncover mechanisms that are difficult to observe directly.
Read the research overview ↗Enhanced Sampling
Methods for capturing rare molecular transitions.
Structural Biology
Mechanistic understanding of molecular recognition and regulation.
Computational biophysics · Purdue UniversityProfile
About
I connect molecular motion with biological mechanism.
I am a computational biophysicist and Postdoctoral Research Associate at Purdue University. My work uses molecular dynamics, enhanced sampling, and structural analysis to investigate protein regulation, conformational transitions, molecular recognition, and glycobiological systems.
At Purdue, I work with Prof. Carol Beth Post in the Department of Medicinal Chemistry & Molecular Pharmacology, studying conformational path sampling, kinase dynamics, and the structural consequences of post-translational modification.
03
Research impact
A growing body of work across computation and structure.
Current approximate research metrics supplied for this site. Values can be updated as the research record grows.
30Peer-reviewed publications
15+First-author publications
530+Citations
12h-index
16i10-index
04
Selected publications
Defining contributions,
carefully selected.
Six representative papers trace a research program across glycobiology, enhanced sampling, molecular recognition, and host–pathogen systems.
01↗02↗03↗04↗05↗06↗
View all 30 publications ↗ 2023 · Journal of Biomolecular Structure and Dynamics
Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: insights from 20 μs long atomistic molecular dynamic simulations
Roy, R., Poddar, S., Sk, M. F. and Kar, P.2022 · The Journal of Physical Chemistry B
Effect of sulfation on the conformational dynamics of dermatan sulfate glycosaminoglycan: a Gaussian accelerated molecular dynamics study
Roy, R., Jonniya, N. A. and Kar, P.2022 · Frontiers in Molecular Biosciences
Comparative structural dynamics of isoforms of Helicobacter pylori adhesin BabA bound to Lewis b hexasaccharide via multiple-replica molecular dynamics simulations
Roy, R., Jonniya, N. A., Sk, M. F. and Kar, P.2022 · Journal of Biomolecular Structure and Dynamics
Investigating the mechanism of recognition and structural dynamics of nucleoprotein–RNA complex from Peste des petits ruminants virus via Gaussian accelerated molecular dynamics simulations
Roy, R.#, Mishra, A.#, Poddar, S., Nayak, D. and Kar, P.2021 · Journal of Chemical Information and Modeling
Unraveling the molecular mechanism of recognition of human interferon-stimulated gene product 15 by coronavirus papain-like proteases: a multiscale simulation study
Roy, R., Jonniya, N. A., Poddar, S., Sk, M. F. and Kar, P.2020 · ACS Omega
Investigating conformational dynamics of Lewis Y oligosaccharides and elucidating blood group dependency of cholera using molecular dynamics
Roy, R., Ghosh, B. and Kar, P.05
Software & methods
Building tools to understand molecular motion.
Enhanced-sampling methodology
Computational strategies for reaching rare transitions and mapping conformational pathways.
Simulation workflows
Reproducible molecular-dynamics workflows spanning system preparation, sampling, and analysis.
Computational ecosystem
Work involving OpenMM, CHARMM, MDAnalysis, and GPU molecular simulation, without presenting unreleased work as public software.
Verified software names, repositories, documentation, and publication links will be added when supplied.
Explore software & methods ↗06
Academic journey
From physics to biomolecular motion.
A research path shaped across physics, biophysics, biomedical engineering, and computational molecular science.
- 12011–2014
University of Calcutta
BSc · Physics (Hons.)
- 22014–2016
University of Kalyani
MSc · Biophysics
- 32017–2022
IIT Indore
PhD · Biosciences & Biomedical Engineering
- 4Current
Purdue University
Postdoctoral Research
07
Current position
Purdue University
Postdoctoral Research Associate
Working with Prof. Carol Beth Post in the Department of Medicinal Chemistry & Molecular Pharmacology, I bring molecular simulation, enhanced sampling, and structural biology together to investigate conformational path sampling, kinase dynamics, and biomolecular mechanisms.
08
Teaching & mentoring
Sharing computational science through practice.
Molecular Docking & MD Simulations
Two-day hands-on workshop at Woxsen University for postgraduate students, doctoral researchers, postdoctoral researchers, and early-career faculty.
Bioinformatics: Theory & Laboratory
Three semesters of teaching assistantship for postgraduate students at IIT Indore.
3
MSc dissertation students
5
Summer trainees
09
Professional service
Contributing to the scientific community.
Peer review for four journals, volunteer conference organization, research mentoring, and selected scientific presentations form a growing record of academic contribution.
View professional service ↗Research collaboration · Scientific discussion · Method development