Related papers: From Brownian Dynamics to Markov Chain: an Ion Cha…
The diffusion equation is the primary tool to study the movement dynamics of a free Brownian particle, but when spatial heterogeneities in the form of permeable interfaces are present, no fundamental equation has been derived. Here we…
Many ion channels spontaneously switch between different levels of activity. Although this behaviour known as modal gating has been observed for a long time it is currently not well understood. Despite the fact that appropriately…
For ion channel gating, the appearance of two distinct conformational states and the discrete transitions between them is essential, and therefore of crucial importance to all living organisms. We show that the physical interplay between…
Ion channels are proteins with a hole down the middle embedded in cell membranes. Membranes form insulating structures and the channels through them allow and control the movement of charged particles, spherical ions, mostly Na+, K+, Ca++,…
We present a study on the dynamics of a system consisting of a pair of hardcore particles diffusing with different rates. We solved the drift-diffusion equation for this model in the case when one particle, labeled F, drifts and diffuses…
The flow of ions through permeable channels causes voltage drop in physiological nanodomains such as synapses, dendrites and dendritic spines, and other protrusions. How the voltage changes around channels in these nanodomains has remained…
The effect of fluctuations on the conductivity of ion channels is investigated. It is shown that modulation of the potential barrier at the selectivity site due to electrostatic amplification of charge fluctuations at the channel mouth…
Filtration, flow in narrow channels and traffic flow are examples of processes subject to blocking when the channel conveying the particles becomes too crowded. If the blockage is temporary, which means that after a finite time the channel…
We prove that under certain mild assumptions, the entropy rate of a hidden Markov chain, observed when passing a finite-state stationary Markov chain through a discrete-time continuous-output channel, is jointly analytic as a function of…
Based on the Langevin equation, a stochastic formulation is implemented to describe the dynamics of a trapped ion in a bath of ultracold atoms, including an excess of micromotion. The ion dynamics is described following a hybrid…
The large time dynamics of a periodically driven Fokker-Planck process possessing several metastable states is investigated. At weak noise transitions between the metastable states are rare. Their dynamics then represent a discrete…
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.…
A statistical test is presented to decide whether data are adequately described by probabilistic functions of finite state Markov chains (''hidden Markov models'') as applied in the analysis of ion channel data. Particularly, the test can…
For a network of discrete states with a periodically driven Markovian dynamics, we develop an inference scheme for an external observer who has access to some transitions. Based on waiting-time distributions between these transitions, the…
We consider random flights of point particles inside $n$-dimensional channels of the form $\mathbb{R}^{k} \times \mathbb{B}^{n-k}$, where $\mathbb{B}^{n-k}$ is a ball of radius $r$ in dimension $n-k$. The particle velocities immediately…
The phenomena that emerge from the interaction of the stochastic opening and closing of ion channels (channel noise) with the non-linear neural dynamics are essential to our understanding of the operation of the nervous system. The effects…
We consider a simple discrete-time Markov chain with values in $[0,\infty)^{Z^d}$. The Markov chain describes various interesting examples such as oriented percolation, directed polymers in random environment, time discretizations of binary…
It is quite clear from a wide range of experiments that gating phenomena of ion channels is inherently stochastic. It has been discussed using BD simulations in a recent paper that memory effects in ion transport is negligible, unless the…
Networks of channels conveying particles are often subject to blockages due to the limited carrying capacity of the individual channels. If the channels are coupled, blockage of one causes an increase in the flux entering the remaining open…
We study dynamical properties of confined, self-propelled Brownian particles in an inhomogeneous activity profile. Using Brownian dynamics simulations, we calculate the probability to reach a fixed target and the mean first passage time to…