Modeling and simulation of ion channels
C Maffeo, S Bhattacharya, J Yoo, D Wells… - Chemical …, 2012 - ACS Publications
Transport of ions through pores in membranes is a process of fundamental importance to
cell biology. In living organisms, such transport is facilitated by ion channels that utilize the …
cell biology. In living organisms, such transport is facilitated by ion channels that utilize the …
Simulating monovalent and divalent ions in aqueous solution using a Drude polarizable force field
An accurate representation of ion solvation in aqueous solution is critical for meaningful
computer simulations of a broad range of physical and biological processes. Polarizable …
computer simulations of a broad range of physical and biological processes. Polarizable …
Dissociation of NaCl in water from ab initio molecular dynamics simulations
We perform ab initio molecular dynamics simulations to study the dissociation of NaCl in
water. The potential of mean force (PMF) between the two ions is determined using the …
water. The potential of mean force (PMF) between the two ions is determined using the …
Optimal transport and colossal ionic mechano-conductance in graphene crown ethers
Biological ion channels balance electrostatic and dehydration effects to yield large ion
selectivity alongside high transport rates. These macromolecular systems are often …
selectivity alongside high transport rates. These macromolecular systems are often …
QM and QM/MM simulations of proteins
T Steinbrecher, M Elstner - Biomolecular Simulations: Methods and …, 2013 - Springer
Molecular dynamics simulations of biomolecules have matured into powerful tools of
structural biology. In addition to the commonly used empirical force field potentials, quantum …
structural biology. In addition to the commonly used empirical force field potentials, quantum …
Coordination numbers of K+ and Na+ ions inside the selectivity filter of the KcsA potassium channel: Insights from first principles molecular dynamics
Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were
performed to estimate the coordination numbers of K+ and Na+ ions in the selectivity filter of …
performed to estimate the coordination numbers of K+ and Na+ ions in the selectivity filter of …
Molecular simulations of ion channels: a quantum chemist's perspective
D Bucher, U Rothlisberger - Journal of General Physiology, 2010 - rupress.org
Molecular dynamics (MD) has become a popular method to study ion channels by
theoretical means and to provide new insights into their fundamental properties, such as fast …
theoretical means and to provide new insights into their fundamental properties, such as fast …
Polarizable intermolecular potentials for water and benzene interacting with halide and metal ions
A complete derivation of polarizable intermolecular potentials based on high-level, gas-
phase quantum-mechanical calculations is proposed. The importance of appreciable …
phase quantum-mechanical calculations is proposed. The importance of appreciable …
A guide to QM/MM methodology and applications
A guide to QM/MM methodology and applications Page 370 CHAPTER 10 A Guide to QM/MM
Methodology and Applications Rui Zhanga, c, e, Bogdan Levb, c, e, Sergei Yu Noskovb, c and …
Methodology and Applications Rui Zhanga, c, e, Bogdan Levb, c, e, Sergei Yu Noskovb, c and …
Simulation studies of ion permeation and selectivity in voltage-gated sodium channels
C Ing, R Pomes - Current Topics in Membranes, 2016 - Elsevier
Voltage-gated ion channels are responsible for the generation and propagation of action
potentials in electrically excitable cells. Molecular dynamics simulations have become a …
potentials in electrically excitable cells. Molecular dynamics simulations have become a …