Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel

Functional stability of water wire–carbonyl interactions in an ion channel

(2020) Joana Paulino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field

(2020) Jigneshkumar Dahyabhai Prajapati et al.   Journal of Chemical Information and Modeling

Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian

(2020) Chetan Rupakheti et al.   JOURNAL OF CHEMICAL PHYSICS

Benchmarking polarizable and non-polarizable force fields for Ca2+–peptides against a comprehensive QM dataset

(2020) Kazi S. Amin et al.   JOURNAL OF CHEMICAL PHYSICS

Temperature Induced Dynamical Transition of Biomolecules in Polarizable and Nonpolarizable TIP3P Water

(2019) Arup Kumar Pathak et al.   Journal of Chemical Theory and Computation

Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications

(2019) Zhifeng Jing et al.   Annual Review of Biophysics

Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation

(2019) Emelie Flood et al.   CHEMICAL REVIEWS

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator

(2018) Fang-Yu Lin et al.   Journal of Chemical Information and Modeling

Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields

(2018) Anthony J. Hazel et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks

(2018) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg2+

(2018) Francesco Villa et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels

(2018) Wojciech Kopec et al.   Nature Chemistry

Unbinding of fluorinated oxime drug from the AChE gorge in polarizable water: a well-tempered metadynamics study

(2017) Arup Kumar Pathak et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

(2016) Justin A. Lemkul et al.   CHEMICAL REVIEWS

Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections

(2016) Xiangda Peng et al.   Journal of Chemical Theory and Computation

Instantaneous ion configurations in the K+ion channel selectivity filter revealed by 2D IR spectroscopy

(2016) Huong T. Kratochvil et al.   SCIENCE

Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins

(2015) Van Ngo et al.   Journal of Chemical Theory and Computation

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

(2015) Hui Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein–Drug Interactions with Effective Polarization in Polarizable Water: Oxime Unbinding from AChE Gorge

(2015) Arup K. Pathak et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ion-Induced Defect Permeation of Lipid Membranes

(2014) Igor Vorobyov et al.   BIOPHYSICAL JOURNAL

Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models

(2014) Igor V. Leontyev et al.   JOURNAL OF CHEMICAL PHYSICS

Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model

(2014) Jing Huang et al.   Journal of Physical Chemistry Letters

Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization

(2014) Miriam Kohagen et al.   Journal of Physical Chemistry Letters

Ion permeation in K+ channels occurs by direct Coulomb knock-on

(2014) D. A. Kopfer et al.   SCIENCE

Ion channel stability of Gramicidin A in lipid bilayers: Effect of hydrophobic mismatch

(2013) Ipsita Basu et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Six-site polarizable model of water based on the classical Drude oscillator

(2013) Wenbo Yu et al.   JOURNAL OF CHEMICAL PHYSICS

Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data

(2013) Lei Huang et al.   Journal of Chemical Theory and Computation

Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator

(2013) Pedro E. M. Lopes et al.   Journal of Chemical Theory and Computation

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

An Entropic Mechanism of Generating Selective Ion Binding in Macromolecules

(2013) Michael Thomas et al.   PLoS Computational Biology

Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field

(2012) Yun Luo et al.   FARADAY DISCUSSIONS

Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer

(2012) Wei Jiang et al.   Journal of Chemical Theory and Computation

Polarizable Mean-Field Model of Water for Biological Simulations with AMBER and CHARMM Force Fields

(2012) Igor V. Leontyev et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

New materials for biological fuel cells

(2012) Shelley D. Minteer et al.   Materials Today

Selective Artificial Transmembrane Channels for Protons by Formation of Water Wires

(2011) Wen Si et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

(2011) Pengyu Ren et al.   Journal of Chemical Theory and Computation

Ion selectivity in channels and transporters

(2011) Benoît Roux et al.   JOURNAL OF GENERAL PHYSIOLOGY

Gramicidin A Backbone and Side Chain Dynamics Evaluated by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Experiments. I: Molecular Dynamics Simulations

(2011) Helgi I. Ingólfsson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantum Confinement Effects in Nanoscale-Thickness InAs Membranes

(2011) Kuniharu Takei et al.   NANO LETTERS

Vibrational excitons in ionophores: experimental probes for quantum coherence-assisted ion transport and selectivity in ion channels

(2011) Ziad Ganim et al.   NEW JOURNAL OF PHYSICS

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

(2010) Haibo Yu et al.   Journal of Chemical Theory and Computation

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD

(2010) Wei Jiang et al.   Journal of Physical Chemistry Letters

Two mechanisms of ion selectivity in protein binding sites

(2010) H. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Orientational constraints as three-dimensional structural constraints from chemical shift anisotropy: The polypeptide backbone of gramicidin A in a lipid bilayer

(2010) W. Mai et al.   PROTEIN SCIENCE

Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics

(2009) Wei Jiang et al.   Journal of Chemical Theory and Computation

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Hydration Number, Topological Control, and Ion Selectivity

(2009) Haibo Yu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions

(2009) Yun Luo et al.   Journal of Physical Chemistry Letters

Exploring Ion Permeation Energetics in Gramicidin A Using Polarizable Charge Equilibration Force Fields

(2009) Sandeep Patel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Transition Path Theory for Markov Jump Processes

(2009) Philipp Metzner et al.   MULTISCALE MODELING & SIMULATION

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

The Selectivity of K+ Ion Channels: Testing the Hypotheses

(2008) Philip W. Fowler et al.   BIOPHYSICAL JOURNAL

Comment on “Free energy simulations of single and double ion occupancy in gramicidin A” [J. Chem. Phys. 126, 105103 (2007)]

(2008) Benoît Roux et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Control of Ion Selectivity in LeuT: Two Na+ Binding Sites with Two Different Mechanisms

(2008) Sergei Y. Noskov et al.   JOURNAL OF MOLECULAR BIOLOGY