Publications

Google Scholar

At University of Oregon

  1. Acceleration with Interpretability: Surrogate Model Based Collective Variable for Enhanced Sampling. Sompriya Chatterjee and Dhiman Ray. ChemRxiv (2024)

  2. Enhanced Sampling with Sub-optimal Collective Variables: Reconciling Accuracy and Convergence Speed. Dhiman Ray and Valerio Rizzi. Journal of Chemical Theory and Computation (2024)

  3. Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics. Dhiman Ray. The Journal of Chemical Physics (2023)

Before University of Oregon

  1. A Stochastic Landscape Approach for Protein Folding State Classification. Michael Faran, Dhiman Ray, Shubhadeep Nag, Umberto Raucci, Michele Parrinello, and Gili Bisker. Journal of Chemical Theory and Computation (2024)

  2. Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations. Dhiman Ray, Sudip Das, and Umberto Raucci. Journal of Chemical Information and Modeling (2024)

  3. Data-Driven Classification of Ligand Unbinding Pathways. Dhiman Ray and Michele Parrinello. Proceedings of the National Academy of Sciences (2024) Preprint Link

  4. Kinetics from Metadynamics: Principles, Applications, and Outlook. Dhiman Ray and Michele Parrinello.  Journal of Chemical Theory and Computation (2023)

  5. Deep Learning Collective Variables from Transition Path Ensemble. Dhiman Ray, Enrico Trizio, and Michele Parrinello.  The Journal of Chemical Physics (2023) (Editor’s Pick)

  6. Predicting residue cooperativity during protein folding: A combined, molecular dynamics and unsupervised learning approach. Praveen Ranganath Prabhakar, Dhiman Ray, and Ioan Andricioaei.  The Journal of Chemical Physics (2023)

  7. A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software Anthony T. Bogetti*, Jeremy M. G. Leung*, Dhiman Ray*, John D. Russo*, Ali S. Saglam*, Jeff P. Thompson*, She Zhang*, Junchao Xia*, Ioan Andricioaei, David N. LeBard, James R. Faeder, Daniel M. Zuckerman, Matthew C. Zwier, and Lillian T. Chong. (*=co-first author) Living Journal of Computational Molecular Science (2022)

  8. Rare Event Kinetics from Adaptive Bias Enhanced Sampling. Dhiman Ray, Narjes Ansari, Valerio Rizzi, Michele Invernizzi, and Michele Parrinello.  Journal of Chemical Theory and Computation (2022)

  9. Force Field Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA. Sharon E. Stone, Dhiman Ray, Ioan Andricioaei, Journal of Chemical Information and Modeling (2022)

  10. Point Mutations in SARS-CoV-2 Variants Induce Long-Range Dynamical Perturbations in Neutralizing Antibodies. Dhiman Ray, Riley N. Quijano, Ioan Andricioaei, Chemical Science (2022)

  11. Studying the Association and Dissociation of a Trypsin-Benzamidine Complex with Enhanced Sampling Molecular Dynamics. Sharon E. Stone, Dhiman Ray, Ioan Andricioaei. Revue Roumaine De Chimie (2022)

  12. Markovian Weighted Ensemble Milestoning (M-WEM): Long-Time Kinetics from Short Trajectories. Dhiman Ray, Sharon E. Stone, Ioan Andricioaei, Journal of Chemical Theory and Computation (2022)

  13. Distant Residues Modulate the Conformational Opening in SARS-CoV-2 Spike Protein. Dhiman Ray, Ly Le, Ioan Andricioaei, Proceedings of the National Academy of Sciences (2021)

  14. Kinetics and Free Energy of Ligand Dissociation Using Weighted Ensemble Milestoning. Dhiman Ray, Trevor Gokey, David L. Mobley, Ioan Andricioaei, The Journal of Chemical Physics (2020)

  15. Free Energy Landscape and Conformational Kinetics of Hoogsteen Base-Pairing in DNA vs RNA.  Dhiman Ray, Ioan Andricioaei, Biophysical Journal (2020)

  16. Interfacial water and ion distribution determine ζ potential and binding affinity of nanoparticles to biomolecules. Dongyue Liang, Udaya Dahal, Yongqian Kelly Zhang, Christian Lochbaum, Dhiman Ray, Robert J Hamers, Joel A Pedersen, Qiang Cui, Nanoscale (2020)

  17. Weighted ensemble milestoning (WEM): A combined approach for rare event simulations. Dhiman Ray, Ioan Andricioaei, The Journal of Chemical Physics (2020) (Editor’s Pick)

  18. Controlling Electron Dynamics with Carrier Envelope Phases of a Laser Pulse. Diptesh Dey, Dhiman Ray, Ashwani K Tiwari, Journal of Physical Chemistry A (2019)

  19. Effects of alloying on mode-selectivity in H2O dissociation on Cu/Ni bimetallic surfaces. Smita Ghosh, Dhiman Ray, and Ashwani Kumar Tiwari, Journal of Chemical Physics (2019)

  20. Controlling Heterogeneous Catalysis of Water Dissociation Using Cu-Ni Bimetallic Alloy Surfaces: A Quantum Dynamics Study. Dhiman Ray, Smita Ghosh, and Ashwani Kumar Tiwari,  Journal of Physical Chemistry A (2018)