Related papers: From Brownian Dynamics to Markov Chain: an Ion Cha…
A position-dependent stochastic diffusion model of gating in ion channels is developed by considering the spatial variation of the diffusion coefficient between the closed and open states. It is assumed that a sensor which regulates the…
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…
The dynamics of the open or closed state region of an ion channel may be described by a probability density $p(x,t)$ which satisfies a Fokker-Planck equation. The closed state dwell-time distribution $f_c(t)$ derived from the Fokker-Planck…
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…
Kinetic equations for the stationary state distribution function of ions moving through narrow pores are solved for a number of one-dimensional models of single ion transport. Ions move through pores of length $L$, under the action of a…
A model of mobile, charged ion channels in a fluid membrane is studied. The channels may switch between an open and a closed state according to a simple two-state kinetics with constant rates. The effective electrophoretic charge and the…
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 discuss various models of ion transport through cell membrane channels. Recent experimental data shows that sizes of ion channels are compared to those of ions and that only few ions may be simultaneously in any single channel.…
Aim of this note is to analyse branching Brownian motion within the class of models introduced in the recent paper [4] and called chemical diffusion master equations. These models provide a description for the probabilistic evolution of…
The physiology of voltage gated ion channels is complex and insights into their gating mechanism is incomplete. Their function is best represented by Markov models with relatively large number of distinct states that are connected by…
Stochastic Resonance in single voltage-dependent ion channels is investigated within a three state non-Markovian modeling of the ion channel conformational dynamics. In contrast to a two-state description one assumes the presence of an…
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…
A model of mobile, charged ion channels embedded in a biomembrane is investigated. The ion channels fluctuate between an opened and a closed state according to a simple two-state reaction scheme whereas the total number of ion channels is a…
We present a class of stochastic processes in which the large deviation functions of time-integrated observables exhibit singularities that relate to dynamical phase transitions of trajectories. These illustrative examples include Brownian…
Stochastic transitions between discrete microscopic states play an important role in many physical and biological systems. Often, these transitions lead to fluctuations on a macroscopic scale. A classic example from neuroscience is the…
Aggregated Markov models provide a flexible framework for stochastic dynamics that develops on multiple timescales. For example, Markov models for ion channels often consist of multiple open and closed state to account for "slow" and "fast"…
We investigate out of equilibrium stationary distributions induced by a stochastic dichotomous noise on double and multi-well models for ion channels. Ion-channel dynamics is analyzed both through over-damped Langevin equations and master…
The reduction of a continuous Markov process with multiple metastable states to a discrete rate process is investigated in the presence of slow time dependent parameters such as periodic external forces or slowly fluctuating barrier…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
The first arrivals among $N$ Brownian particles is ubiquitous in the life sciences, as it often trigger cellular processes from the molecular level. We study here the case where stochastic particles, which represent molecules, proteins or…