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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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Advances in milestoning. I. Enhanced sampling via wind-assisted reweighted milestoning (WARM)

The Journal of chemical physics, 2018-08, Vol.149 (8), p.084103-084103

2018

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Modulation of Hoogsteen dynamics on DNA recognition

Nature communications, 2018-04, Vol.9 (1), p.1473-10, Article 1473

2018

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A General Method for Constructing Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Interhelical Motions Revealed

Journal of the American Chemical Society, 2013-04, Vol.135 (14), p.5457-5466

2013

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On the calculation of entropy from covariance matrices of the atomic fluctuations

The Journal of chemical physics, 2001-10, Vol.115 (14), p.6289-6292

2001

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Rate turnover in mechano-catalytic coupling: A model and its microscopic origin

The Journal of chemical physics, 2015-07, Vol.143 (4), p.045105-045105

2015

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Automated placement of interfaces in conformational kinetics calculations using machine learning

The Journal of chemical physics, 2017-10, Vol.147 (15), p.152727-152727

2017

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Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble

Nature chemical biology, 2011-06, Vol.7 (8), p.553

2011

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On Structural Transitions, Thermodynamic Equilibrium, and the Phase Diagram of DNA and RNA Duplexes under Torque and Tension

Proceedings of the National Academy of Sciences - PNAS, 2006-10, Vol.103 (44), p.16200-16205

2006

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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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Probing Sequence-Specific DNA Flexibility in A‑Tracts and Pyrimidine-Purine Steps by Nuclear Magnetic Resonance 13C Relaxation and Molecular Dynamics Simulations

Biochemistry (Easton), 2012-10, Vol.51 (43), p.8654-8664

2012

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Surface Orientation of Magainin 2: Molecular Dynamics Simulation and Sum Frequency Generation Vibrational Spectroscopic Studies

Langmuir, 2010-10, Vol.26 (20), p.16031-16036

2010

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Conformational and Solvent Entropy Contributions to the Thermal Response of Nucleic Acid-Based Nanothermometers

The journal of physical chemistry. B, 2010-02, Vol.114 (5), p.2076-2082

2010

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Interfacial Orientation and Secondary Structure Change in Tachyplesin I: Molecular Dynamics and Sum Frequency Generation Spectroscopy Studies

Langmuir, 2011-12, Vol.27 (23), p.14343-14351

2011

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Dynamic Distance Disorder in Proteins Is Caused by Trapping

The journal of physical chemistry. B, 2006-05, Vol.110 (19), p.9363-9367

2006

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Advances in milestoning. II. Calculating time-correlation functions from milestoning using stochastic path integrals

The Journal of chemical physics, 2018-08, Vol.149 (8), p.084104-084104

2018

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The Role of Entropy in Explaining Tightly Bend DNA Propensity and Kinetic Barriers to Base Pair Unzipping

Biophysical journal, 2016-02, Vol.110 (3), p.566a-566a

Andricioaei, Ioan

2016

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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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Advances in milestoning. II. Calculating time-correlation functions frommilestoning using stochastic path integrals

The Journal of chemical physics, 2018-08, Vol.149 (8)

2018

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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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Probing the Conformational Change of Contractile Tails using Coarse-Grained Normal Mode Analysis

Biophysical journal, 2020-02, Vol.118 (3), p.142a-142a

2020

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Directionally negative friction: a method for enhanced sampling of rare event kinetics

The Journal of chemical physics, 2008-03, Vol.128 (11), p.114112-114112

2008

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Estimation of free energies of FKBP-12-ligand systems using enhanced sampling methods

Biophysical journal, 2024-02, Vol.123 (3), p.137a-137a

2024

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

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

Advances in milestoning. I. Enhanced sampling via wind-assisted reweighted milestoning (WARM)

Modulation of Hoogsteen dynamics on DNA recognition

A General Method for Constructing Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Interhelical Motions Revealed

On the calculation of entropy from covariance matrices of the atomic fluctuations

Rate turnover in mechano-catalytic coupling: A model and its microscopic origin

Automated placement of interfaces in conformational kinetics calculations using machine learning

Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble

On Structural Transitions, Thermodynamic Equilibrium, and the Phase Diagram of DNA and RNA Duplexes under Torque and Tension

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

Probing Sequence-Specific DNA Flexibility in A‑Tracts and Pyrimidine-Purine Steps by Nuclear Magnetic Resonance 13C Relaxation and Molecular Dynamics Simulations

Surface Orientation of Magainin 2: Molecular Dynamics Simulation and Sum Frequency Generation Vibrational Spectroscopic Studies

Conformational and Solvent Entropy Contributions to the Thermal Response of Nucleic Acid-Based Nanothermometers

Interfacial Orientation and Secondary Structure Change in Tachyplesin I: Molecular Dynamics and Sum Frequency Generation Spectroscopy Studies

Dynamic Distance Disorder in Proteins Is Caused by Trapping

Advances in milestoning. II. Calculating time-correlation functions from milestoning using stochastic path integrals

The Role of Entropy in Explaining Tightly Bend DNA Propensity and Kinetic Barriers to Base Pair Unzipping

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

Advances in milestoning. II. Calculating time-correlation functions frommilestoning using stochastic path integrals

Machine learning guided weighted ensemble for rare event simulation in biophysics

Probing the Conformational Change of Contractile Tails using Coarse-Grained Normal Mode Analysis

Directionally negative friction: a method for enhanced sampling of rare event kinetics

Estimation of free energies of FKBP-12-ligand systems using enhanced sampling methods

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