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Deep learning collective variables from transition path ensemble

The Journal of chemical physics, 2023-05, Vol.158 (20)

2023

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Distant residues modulate conformational opening in SARS-CoV-2 spike protein

Proceedings of the National Academy of Sciences - PNAS, 2021-10, Vol.118 (43)

2021

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Weighted ensemble milestoning (WEM): A combined approach for rare event simulations

The Journal of chemical physics, 2020-06, Vol.152 (23), p.234114-234114

2020

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Predicting residue cooperativity during protein folding: A combined, molecular dynamics and unsupervised learning approach

The Journal of chemical physics, 2023-04, Vol.158 (13), p.134108-134108

2023

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Micellization of Ionic Liquid Surfactants Induced by Sodium Polystyrenesulfonate in Aqueous Solutions

Journal of solution chemistry, 2019-12, Vol.48 (11-12), p.1576-1590

2019

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Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies

Chemical science (Cambridge), 2022-06, Vol.13 (24), p.7224-7239

2022

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Kinetics and free energy of ligand dissociation using weighted ensemble milestoning

The Journal of chemical physics, 2020-10, Vol.153 (15), p.154117-154117

2020

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Therapeutic opportunities of surface-active ionic liquids: a case study on acetylcholinesterase, citrate synthase and HeLa cell lines

New journal of chemistry, 2022-10, Vol.46 (42), p.2419-2432

2022

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Interfacial water and ion distribution determine ζ potential and binding affinity of nanoparticles to biomolecules

Nanoscale, 2020-09, Vol.12 (35), p.18106-18123

2020

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Kinetics from Metadynamics: Principles, Applications, and Outlook

Journal of chemical theory and computation, 2023-09, Vol.19 (17), p.5649-5670

2023

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Selective heteroaromatic nitrogen base promoted chromium(VI) oxidation of isomeric pentanols in aqueous micellar media at room temperature

Journal of Industrial and Engineering Chemistry, 2016, 42(0), , pp.53-62

2016

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Fluorescence based studies on the interaction and characterization of surface-active ionic liquids with polarity sensitive intramolecular charge transfer probe

Chemical physics impact, 2023-12, Vol.7, p.100368, Article 100368

2023

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Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA

Biophysical journal, 2020-10, Vol.119 (8), p.1568-1579

2020

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Hoogsteen Base Pairing in DNA vs RNA: Thermodynamics and Kinetics from Enhanced Sampling Simulation and Markov State Modeling

Biophysical journal, 2020-02, Vol.118 (3), p.299a-300a

2020

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Markovian Weighted Ensemble Milestoning (M-WEM): Long-Time Kinetics from Short Trajectories

Journal of chemical theory and computation, 2022-01, Vol.18 (1), p.79-95

2022

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Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations

Journal of chemical information and modeling, 2024-05, Vol.64 (9), p.3953-3958

2024

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Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA

Journal of chemical information and modeling, 2022-12, Vol.62 (24), p.6749-6761

2022

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Machine learning guided weighted ensemble for rare event simulation in biophysics

Biophysical journal, 2023-02, Vol.122 (3), p.423a-423a

2023

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Rare Event Kinetics from Adaptive Bias Enhanced Sampling

Journal of chemical theory and computation, 2022-11, Vol.18 (11), p.6500-6509

2022

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Hoogsteen Base Pairing in DNA: Effects of Force Field Models on Free Energy and Transition Pathways

Biophysical journal, 2021-02, Vol.120 (3), p.77a-77a

2021

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Effects of alloying on mode-selectivity in H 2 O dissociation on Cu/Ni bimetallic surfaces

The Journal of chemical physics, 2019-03, Vol.150 (11), p.114702

2019

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Controlling Heterogeneous Catalysis of Water Dissociation Using Cu–Ni Bimetallic Alloy Surfaces: A Quantum Dynamics Study

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2018-07, Vol.122 (26), p.5698-5709

2018

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Influence of sodium carboxymethylcellulose on the aggregation behavior of aqueous 1-hexadecyl-3-methylimidazolium chloride solutions

Carbohydrate polymers, 2014-11, Vol.113, p.208-216

2014

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Kinetics and Free Energy of Protein Ligand Interaction using Weighted Ensemble Milestoning (WEM)

Biophysical journal, 2021-02, Vol.120 (3), p.97a-97a

2021

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Controlling Electron Dynamics with Carrier-Envelope Phases of a Laser Pulse

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2019-06, Vol.123 (22), p.4702-4707

2019

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Deep learning collective variables from transition path ensemble

Distant residues modulate conformational opening in SARS-CoV-2 spike protein

Weighted ensemble milestoning (WEM): A combined approach for rare event simulations

Predicting residue cooperativity during protein folding: A combined, molecular dynamics and unsupervised learning approach

Micellization of Ionic Liquid Surfactants Induced by Sodium Polystyrenesulfonate in Aqueous Solutions

Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies

Kinetics and free energy of ligand dissociation using weighted ensemble milestoning

Therapeutic opportunities of surface-active ionic liquids: a case study on acetylcholinesterase, citrate synthase and HeLa cell lines

Interfacial water and ion distribution determine ζ potential and binding affinity of nanoparticles to biomolecules

Kinetics from Metadynamics: Principles, Applications, and Outlook

Selective heteroaromatic nitrogen base promoted chromium(VI) oxidation of isomeric pentanols in aqueous micellar media at room temperature

Fluorescence based studies on the interaction and characterization of surface-active ionic liquids with polarity sensitive intramolecular charge transfer probe

Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA

Hoogsteen Base Pairing in DNA vs RNA: Thermodynamics and Kinetics from Enhanced Sampling Simulation and Markov State Modeling

Markovian Weighted Ensemble Milestoning (M-WEM): Long-Time Kinetics from Short Trajectories

Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations

Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA

Machine learning guided weighted ensemble for rare event simulation in biophysics

Rare Event Kinetics from Adaptive Bias Enhanced Sampling

Hoogsteen Base Pairing in DNA: Effects of Force Field Models on Free Energy and Transition Pathways

Effects of alloying on mode-selectivity in H 2 O dissociation on Cu/Ni bimetallic surfaces

Controlling Heterogeneous Catalysis of Water Dissociation Using Cu–Ni Bimetallic Alloy Surfaces: A Quantum Dynamics Study

Influence of sodium carboxymethylcellulose on the aggregation behavior of aqueous 1-hexadecyl-3-methylimidazolium chloride solutions

Kinetics and Free Energy of Protein Ligand Interaction using Weighted Ensemble Milestoning (WEM)

Controlling Electron Dynamics with Carrier-Envelope Phases of a Laser Pulse

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