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Dhiman Ray
Dhiman Ray
Postdoctoral Researcher, Italian Institute of Technology, Genoa, Italy
Verified email at iit.it - Homepage
Title
Cited by
Cited by
Year
Distant residues modulate conformational opening in SARS-CoV-2 spike protein
D Ray, L Le, I Andricioaei
Proceeding of the National Academy of Sciences 118 (43), e2100943118, 2021
772021
Weighted ensemble milestoning (WEM): A combined approach for rare event simulations
D Ray, I Andricioaei
The Journal of Chemical Physics 152 (23), 234114, 2020
252020
Markovian Weighted Ensemble Milestoning (M-WEM): Long-time Kinetics from Short Trajectories
D Ray, SE Stone, I Andricioaei
Journal of Chemical Theory and Computation 18 (1), 79-95, 2022
232022
Controlling heterogeneous catalysis of water dissociation using Cu–Ni bimetallic alloy surfaces: a quantum dynamics study
D Ray, S Ghosh, AK Tiwari
The Journal of Physical Chemistry A 122 (26), 5698-5709, 2018
222018
Effects of alloying on mode-selectivity in H2O dissociation on Cu/Ni bimetallic surfaces
S Ghosh, D Ray, AK Tiwari
Journal of Chemical Physics 150 (11), 114702, 2019
202019
Rare event kinetics from adaptive bias enhanced sampling
D Ray, N Ansari, V Rizzi, M Invernizzi, M Parrinello
Journal of Chemical Theory and Computation, 2022
192022
Deep learning collective variables from transition path ensemble
D Ray, E Trizio, M Parrinello
The Journal of Chemical Physics 158 (20), 2023
182023
Kinetics from metadynamics: Principles, applications, and outlook
D Ray, M Parrinello
Journal of Chemical Theory and Computation 19 (17), 5649-5670, 2023
152023
Interfacial water and ion distribution determine ζ potential and binding affinity of nanoparticles to biomolecules
D Liang, U Dahal, YK Zhang, C Lochbaum, D Ray, RJ Hamers, ...
Nanoscale 12 (35), 18106-18123, 2020
152020
Kinetics and free energy of ligand dissociation using weighted ensemble milestoning
D Ray, T Gokey, DL Mobley, I Andricioaei
The Journal of Chemical Physics 153 (15), 154117, 2020
132020
Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA
D Ray, I Andricioaei
Biophysical Journal 119 (8), 1568-1579, 2020
122020
Point Mutations in SARS-CoV-2 Variants Induce Long-Range Dynamical Perturbations in Neutralizing Antibodies
D Ray, RN Quijano, I Andricioaei
Chemical Science, 2022
112022
A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2. 0]
AT Bogetti, JMG Leung, JD Russo, S Zhang, JP Thompson, AS Saglam, ...
Living journal of computational molecular science 5 (1), 2023
7*2023
Controlling Electron Dynamics with Carrier Envelope Phases of a Laser Pulse
D Dey, D Ray, AK Tiwari
Journal of Physical Chemistry A, 2019
62019
Force Field Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA
SE Stone, D Ray, I Andricioaei
Journal of Chemical Information and Modeling, 2022
52022
Data Driven Classification of Ligand Unbinding Pathways
D Ray, M Parrinello
arXiv:2308.05752, 2023
12023
Path Sampling and Machine Learning Approaches to Biomolecular Simulation
D Ray
https://escholarship.org/uc/item/3mn9t9bt, 2022
12022
Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations
D Ray, S Das, U Raucci
Journal of Chemical Information and Modeling, 2024
2024
Predicting residue cooperativity during protein folding: A combined, molecular dynamics and unsupervised learning approach
PR Prabhakar, D Ray, I Andricioaei
The Journal of Chemical Physics 158 (13), 2023
2023
Machine learning guided weighted ensemble for rare event simulation in biophysics
PR Prabhakar, D Ray, I Andricioaei
Biophysical Journal 122 (3), 423a, 2023
2023
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