Related papers: From Brownian Dynamics to Markov Chain: an Ion Cha…
We present an equilibrium statistical-mechanical theory of selectivity in biological ion channels. In doing so, we introduce a grand canonical ensemble for ions in a channel's selectivity filter coupled to internal and external bath…
We study a generalization of the Brownian bridge as a stochastic process that models the position and velocity of inertial particles between the two end-points of a time interval. The particles experience random acceleration and are assumed…
We study the dynamics of an asymmetric simple exclusion process with open boundaries and local interactions using a pair approximation which generalizes the 2-node cluster mean field theory and the Markov chain approach to kinetics and…
In this paper, based on geometric singular perturbation analysis of a quasi-one dimensional Poisson-Nernst-Planck model for ionic flows, we study the problem of zero current condition for ionic flows through membrane channels with a simple…
We have studied the general aspects of the dynamics of an ion trapped in an ideal multipolar radiofrequency trap while interacting with a dense cold atomic gas. In particular, we have explored the dynamical stability, the energy relaxation…
We investigate a system of Brownian particles weakly bound by attractive parity-symmetric potentials that grow at large distances as $V(x) \sim |x|^\alpha$, with $0 < \alpha < 1$. The probability density function $P(x,t)$ at long times…
The physical mechanism underlying the voltage-dependent gating of K channels is usually addressed theoretically using molecular dynamics simulations.However, besides being computationally very expensive, this approach is presently unable to…
Fluids confined to quasi-one-dimensional channels exhibit a dynamic crossover from single file diffusion to normal diffusion as the channel becomes wide enough for particles to hop past each other. In the crossover regime, where hopping…
We investigate the outflux of ions through the channels in a cell membrane. The channels undergo an open/close cycle according to a periodic schedule. Our study is based both on theoretical considerations relying on homogenization theory,…
The mathematical formulation of the model for molecular movement of single motor proteins driven by cyclic biochemical reactions in an aqueous environment leads to a drifted Brownian motion characterized by coupled diffusion equations. In…
Physical notions of stochastic resonance for potential diffusions in periodically changing double-well potentials such as the spectral power amplification have proved to be defective. They are not robust for the passage to their effective…
We investigate the effects of the relative dielectric coefficient on ionic flows in open ion channels, using mathematical analysis of reasonably general Poisson-Nernst-Planck type models that can include the finite sizes of ions. The value…
Splitting probabilities quantify the likelihood of particular outcomes out of a set of mutually-exclusive possibilities for stochastic processes and play a central role in first-passage problems. For two-dimensional Markov processes…
Filtering theory gives an explicit models for the flow of information and thereby quantifies the rates of change of information supplied to and dissipated from the filter's memory. Here we extend the analysis of Mitter and Newton from…
In a recent article, Krapivsky and Redner (J. Stat. Mech. 093208 (2018)) established that the distribution of the first hitting times for a diffusing particle subject to hitting an absorber is independent of the direction of the external…
We develop two-dimensional Brownian dynamics simulations to examine the motion of disks under thermal fluctuations and Hookean forces. Our simulations are designed to be experimental-like, since the experimental conditions define the…
In line with Pomeau's conjecture about the relevance of directed percolation (DP) to turbulence onset/decay in wall-bounded flows, we propose a minimal stochastic model dedicated to the interpretation of the spatially intermittent regimes…
We investigate the properties of a class of mode-coupling equations for the glass transition where the density mode decays into multiple relaxation channels. We prove the existence and uniqueness of the solutions for Newtonian as well as…
In this work, the dependence of reversal potentials and zero-current fluxes on diffusion coefficients are examined for ionic flows through membrane channels. The study is conducted for the setup of a simple structure defined by the profile…
We consider a class of discrete time Markov chains with state space [0,1] and the following dynamics. At each time step, first the direction of the next transition is chosen at random with probability depending on the current location. Then…