Related papers: Predicting ion channel conductance via dissipation…
Protein-ligand (un)binding simulations are a recent focus of biased molecular dynamics simulations. Such binding and unbinding can occur via different pathways in and out of a binding site. We here present a theoretical framework how to…
Ion channels are of major interest and form an area of intensive research in the fields of biophysics and medicine since they control many vital physiological functions. The aim of this work is on one hand to propose a fully stochastic and…
Ion channels are specific proteins present in the membranes of living cells. They control the flow of specific ions through a cell, initiated by an ion channel's electrochemical gradient. In doing so, they control important physiological…
Ion channels are proteins with holes down their middle that control the flow of ions and electric current across otherwise impermeable biological membranes. The flow of sodium, potassium, calcium (divalent), and chloride ions have been…
Steered molecular dynamics (SMD) simulations for the calculation of free energies are well suited for high-throughput molecular simulations on a distributed infrastructure due to the simplicity of the setup and parallel granularity of the…
In this article we address the three-dimensional modeling and simulation of biological ion channels using a continuum-based approach. Our multi-physics formulation self-consistently combines, to the best of our knowledge for the first time,…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
We have studied the dynamics of chloride and potassium ions in the interior of the OmpF porin under the influence of an external electric field. From the results of extensive all-atom molecular dynamics simulations of the system we computed…
We introduce an implicit solvent Molecular Dynamics approach for calculating ionic fluxes through narrow nano-pores and transmembrane channels. The method relies on a dual-control- volume grand-canonical molecular dynamics (DCV-GCMD)…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
Computational prediction of protein structures is a difficult task, which involves fast and accurate evaluation of candidate model structures. We propose to enhance single model quality assessment with a functionality evaluation phase for…
Ionic conductivity is a critical property of solid ionic conductors, directly influencing the performance of energy storage devices such as batteries. However, accurately calculating ionic conductivity or diffusion coefficient remains…
The interpretation electrical phenomena in biomembranes is usually based on the assumption that the experimentally found discrete ion conduction events are due to a particular class of proteins called ion channels while the lipid membrane…
In dilute gases, transport properties such as the thermal conductivity, self-diffusion, and viscosity are significantly affected by interatomic collisions, which are determined by the potential form. This study explores these transport…
A discrete rate theory for general multi-ion channels is presented, in which the continuous dynamics of ion diffusion is reduced to transitions between Markovian discrete states. In an open channel, the ion permeation process involves three…
Experiments on single ionic channels have contributed to a large extent to our current view on the function of cell membrane. In these experiments the main observables are the physical quantities: ionic concentration, membrane electrostatic…
We address the problem of constructing accurate mathematical models of the dynamics of molecular systems projected on a collective variable. To this aim we introduce an algorithm optimizing the parameters of a standard or generalized…
Ion channels are membrane proteins responsible for an enormous range of biological functions. Ion selectivity and permeation are based on simple laws of physics and chemistry. Ion channels are therefore ideal candidates for physical…
The process of ion transport through a locust potassium channel is described by means of the Fokker-Planck equation (FPE). The deterministic and stochastic components of the process of switching between various conducting states of the…
We introduce a scheme for deriving an optimally-parametrised Langevin dynamics of few collective variables from data generated in molecular dynamics simulations. The drift and the position-dependent diffusion profiles governing the Langevin…