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Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

The Journal of chemical physics, 2017-03, Vol.146 (9)

2017

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Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics

Journal of computational chemistry, 2016-06, Vol.37 (16), p.1413-1424

2016

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Mean force based temperature accelerated sliced sampling: Efficient reconstruction of high dimensional free energy landscapes

Journal of computational chemistry, 2021-10, Vol.42 (28), p.1996-2003

2021

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Exploring high‐dimensional free energy landscapes of chemical reactions

Wiley interdisciplinary reviews. Computational molecular science, 2019-05, Vol.9 (3), p.e1398-n/a

2019

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Phase space and collective variable based simulation methods for studies of rare events

Molecular simulation, 2019-10, Vol.45 (14-15), p.1273-1284

2019

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Ligand Exchanges and Hydroxypalladation Reactions of the Wacker Process in Aqueous Solution at High Cl− Concentration

The journal of physical chemistry. B, 2011-03, Vol.115 (10), p.2312-2321

Nair, Nisanth N

2011

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A Comprehensive Study of Factors Affecting the Prediction of the p K a Shift of Asp 26 in Thioredoxin Protein

The journal of physical chemistry. B, 2024-08, Vol.128 (30), p.7304-7312

2024

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Glycine at the Pyrite−Water Interface: The Role of Surface Defects

Journal of the American Chemical Society, 2006-10, Vol.128 (42), p.13815-13826

2006

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Excited State Relaxation Dynamics of Model Green Fluorescent Protein Chromophore Analogs: Evidence for Cis–Trans Isomerism

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2011-12, Vol.115 (47), p.13733-13742

2011

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Mechanistic Insights into the Brønsted Acid-Catalyzed Dehydration of β‑d‑Glucose to 5‑Hydroxymethylfurfural under Ambient and Subcritical Conditions

ACS catalysis, 2019-08, Vol.9 (8), p.7250-7263

2019

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Achieving an Order of Magnitude Speedup in Hybrid-Functional- and Plane-Wave-Based Ab Initio Molecular Dynamics: Applications to Proton-Transfer Reactions in Enzymes and in Solution

Journal of chemical theory and computation, 2021-04, Vol.17 (4), p.2244-2255

2021

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Speeding-up ab initio molecular dynamics with hybrid functionals using adaptively compressed exchange operator based multiple timestepping

The Journal of chemical physics, 2019-10, Vol.151 (15), p.151102-151102

2019

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Interfacing the Core-Shell or the Drude Polarizable Force Field With Car-Parrinello Molecular Dynamics for QM/MM Simulations

Frontiers in chemistry, 2018-07, Vol.6, p.275-275

2018

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Efficient computation of free energy surfaces of chemical reactions using ab initio molecular dynamics with hybrid functionals and plane waves

Journal of computational chemistry, 2020-07, Vol.41 (19), p.1790-1797

2020

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Temperature Accelerated Sliced Sampling to Probe Ligand Dissociation from Protein

Journal of chemical information and modeling, 2023-08, Vol.63 (16), p.5182-5191

2023

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Aggregation-Induced Chemical Reactions: Acid Dissociation in Growing Water Clusters

Journal of the American Chemical Society, 2011-03, Vol.133 (11), p.4062-4072

2011

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High Proton Conductivity by a Metal–Organic Framework Incorporating Zn8O Clusters with Aligned Imidazolium Groups Decorating the Channels

Journal of the American Chemical Society, 2012-11, Vol.134 (47), p.19432-19437

2012

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Hydrolysis of cephalexin and meropenem by New Delhi metallo-β-lactamase: the substrate protonation mechanism is drug dependent

Physical chemistry chemical physics : PCCP, 2017-05, Vol.19 (20), p.13111-13121

2017

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Methanol synthesis on ZnO(000 $\mathbf {\overline{1}}$ 1 ¯ ). III. Free energy landscapes, reaction pathways, and mechanistic insights

The Journal of chemical physics, 2011-02, Vol.134 (6), p.064710-064710-14

2011

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Elucidating the Molecular Basis of Avibactam‐Mediated Inhibition of Class A β‐Lactamases

Chemistry : a European journal, 2020-08, Vol.26 (43), p.9639-9651

2020

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Synthesis of a highly thermostable insulin by phenylalanine conjugation at B29 Lysine

Communications chemistry, 2024-07, Vol.7 (1), p.161-10, Article 161

2024

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Mechanism of Nucleotidyltransfer Reaction and Role of Mg2+ Ion in Sugar Nucleotidyltransferases

Biophysical journal, 2020-08, Vol.119 (3), p.619-627

2020

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Buckets Instead of Umbrellas for Enhanced Sampling and Free Energy Calculations

Journal of chemical theory and computation, 2024-09

2024

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Peptide Synthesis in Aqueous Environments: The Role of Extreme Conditions on Peptide Bond Formation and Peptide Hydrolysis

Journal of the American Chemical Society, 2009-09, Vol.131 (38), p.13668-13675

2009

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Enhanced sampling and free energy calculations with hybrid functionals and plane waves for chemical reactions

The Journal of chemical physics, 2018-10, Vol.149 (14), p.144113-144113

2018

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Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics

Mean force based temperature accelerated sliced sampling: Efficient reconstruction of high dimensional free energy landscapes

Exploring high‐dimensional free energy landscapes of chemical reactions

Phase space and collective variable based simulation methods for studies of rare events

Ligand Exchanges and Hydroxypalladation Reactions of the Wacker Process in Aqueous Solution at High Cl− Concentration

A Comprehensive Study of Factors Affecting the Prediction of the p K a Shift of Asp 26 in Thioredoxin Protein

Glycine at the Pyrite−Water Interface: The Role of Surface Defects

Excited State Relaxation Dynamics of Model Green Fluorescent Protein Chromophore Analogs: Evidence for Cis–Trans Isomerism

Mechanistic Insights into the Brønsted Acid-Catalyzed Dehydration of β‑d‑Glucose to 5‑Hydroxymethylfurfural under Ambient and Subcritical Conditions

Achieving an Order of Magnitude Speedup in Hybrid-Functional- and Plane-Wave-Based Ab Initio Molecular Dynamics: Applications to Proton-Transfer Reactions in Enzymes and in Solution

Speeding-up ab initio molecular dynamics with hybrid functionals using adaptively compressed exchange operator based multiple timestepping

Interfacing the Core-Shell or the Drude Polarizable Force Field With Car-Parrinello Molecular Dynamics for QM/MM Simulations

Efficient computation of free energy surfaces of chemical reactions using ab initio molecular dynamics with hybrid functionals and plane waves

Temperature Accelerated Sliced Sampling to Probe Ligand Dissociation from Protein

Aggregation-Induced Chemical Reactions: Acid Dissociation in Growing Water Clusters

High Proton Conductivity by a Metal–Organic Framework Incorporating Zn8O Clusters with Aligned Imidazolium Groups Decorating the Channels

Hydrolysis of cephalexin and meropenem by New Delhi metallo-β-lactamase: the substrate protonation mechanism is drug dependent

Methanol synthesis on ZnO(000 $\mathbf {\overline{1}}$ 1 ¯ ). III. Free energy landscapes, reaction pathways, and mechanistic insights

Elucidating the Molecular Basis of Avibactam‐Mediated Inhibition of Class A β‐Lactamases

Synthesis of a highly thermostable insulin by phenylalanine conjugation at B29 Lysine

Mechanism of Nucleotidyltransfer Reaction and Role of Mg2+ Ion in Sugar Nucleotidyltransferases

Buckets Instead of Umbrellas for Enhanced Sampling and Free Energy Calculations

Peptide Synthesis in Aqueous Environments: The Role of Extreme Conditions on Peptide Bond Formation and Peptide Hydrolysis

Enhanced sampling and free energy calculations with hybrid functionals and plane waves for chemical reactions

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