Related papers: Three-Dimensional Simulation of Biological Ion Cha…
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…
In this article we address the study of ion charge transport in the biological channels separating the intra and extracellular regions of a cell. The focus of the investigation is devoted to including thermal driving forces in the…
The behaviour of a system of ion channels formed across the cell membrane is presented. The infinite number of channels with an infinite coupling is introduced first as a reference point for the detailed derivation of the…
Recent advance in nanotechnology has led to rapid advances in nanofluidics, which has been established as a reliable means for a wide variety of applications, including molecular separation, detection, crystallization and biosynthesis.…
We study dynamics and thermodynamics of ion channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and lipids,…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Three-dimensional numerical model is developed and applied for studies of physical processes in Electron Cyclotron Resonance Ion Source. The model includes separate modules that simulate the electron and ion dynamics in the source plasma in…
We consider an anisotropically two-dimensional diffusion of a charged molecule (particle) through a large biological channel under an external voltage. The channel is modeled as a cylinder of three structure parameters: radius, length, and…
The movement of ionic solutions is an essential part of biology and technology. Fluidics, from nano- to micro- to microfluidics, is a burgeoning area of technology which is all about the movement of ionic solutions, on various scales. Many…
A simple theory of ion permeation through a channel is presented, in which diffusion occurs according to Fick's law and drift according to Ohm's law, in the electric field determined by all the charges present. This theory accounts for…
In this paper we find an analytical solution of the equilibrium ion distribution for a toroidal model of a ionic channel, using the Perfect Screening Theorem (PST). The ions are charged hard spheres, and are treated using a variational Mean…
Ion channels are important proteins for physiological information transfer and functional control. To predict the microscopic origins of their voltage-conductance characteristics, we here applied dissipation-corrected targeted Molecular…
Ions in water are the liquid of life. Life occurs almost entirely in 'salt water'. Water itself (without ions) is lethal to animal cells and damaging for most proteins. Water must contain the right ions in the right amounts if it is to…
A macroscopic model to describe the dynamics of ion transport in ion channels is the Poisson-Nernst-Planck(PNP) equations. In this paper, we develop a finite-difference method for solving PNP equations, which is second-order accurate in…
We study compressible fluid flow in narrow two-dimensional channels using a novel molecular dynamics simulation method. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream…
In the present study, the ionic transport and selectivity of electrokinetically-driven flow of power-law fluids in a long pH-regulated rectangular nanochannel are analyzed. The electrical potential and momentum equations are numerically…
The transport of fluids at the nanoscale is fundamental to manifold biological and industrial processes, ranging from neurotransmission to ultrafiltration. Yet, it is only recently that well-controlled channels with cross-sections as small…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
By performing an ensemble of molecular dynamics simulations, the model-dependent ionisation state is computed for strongly interacting systems self-consistently. This is accomplished through a free energy minimisation framework based on the…
We present a hydrodynamic theory describing pair diffusion in systems with periodic boundary conditions, thereby generalizing earlier work on self-diffusion [D\"unweg and Kremer, J. Chem. Phys. 1993, 99, 6983-6997; Yeh and Hummer, J. Phys.…