Related papers: Permeation as a Diffusion Process
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…
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 more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or…
Channels are Catalysts for Diffusion and in that sense are Enzymes. This idea is useful for the design and interpretation of experiments.
The diffusion of particles in confining walls forming a tube is discussed. Such a transport phenomenon is observed in biological cells and porous media. We consider the case in which the tube is winding with curvature and torsion, and the…
In a recent paper [1] we developed a theoretical model to describe current transients arising during electrochemical deposition experiments performed at the bottom of sub-micrometric cylindrical vessels with permeable walls. In the present…
To simulate the transient enhanced diffusion near the surface or interface, a set of equations describing the impurity diffusion and quasichemical reactions of dopant atoms and point defects in ion-implanted layers is proposed and analyzed.…
Channel-mediated transport is ubiquitous in biology. A series of works by different theoreticians have sought to determine how the diffusive flux through a channel depends on (a) stochastic gating, (b) channel geometry, and (c)…
Membrane protein transporters alternate their substrate-binding sites between the extracellular and cytosolic side of the membrane according to the alternating access mechanism. Inspired by this intriguing mechanism devised by nature, we…
This paper studies the mechanisms of dispersion in the laminar flow through the pore space of a $3$-dimensional porous medium. We focus on pre-asymptotic transport prior to the asymptotic hydrodynamic dispersion regime, in which solute…
Ion transport through narrow water--filled channels is impeded by a high electrostatic barrier. The latter originates from the large ratio of the dielectric constants of the water and a surrounding media. We show that ``doping'', i.e.…
Point processes often have a natural interpretation with respect to a continuous process. We propose a point process construction that describes arrival time observations in terms of the state of a latent diffusion process. In this…
Ionic transport in nanopores is a fundamentally and technologically important problem in view of its occurrence in biological processes and its impact on novel DNA sequencing applications. Using microscopic calculations, here we show that…
Molecular Dynamics simulations of water molecules in nanometre sized cylindrical channels connecting two reservoirs show that the permeation of water is very sensitive to the channel radius and to electric polarization of the embedding…
Gas permeation through nanoscale pores is ubiquitous in nature and plays an important role in a plethora of technologies. Because the pore size is typically smaller than the mean free path of gas molecules, their flow is conventionally…
Using the advection-diffusion equation, we analytically study contaminant transport in a sharply contrasting medium with a diffusion barrier due to localization of a contaminant source in a low-permeability medium. Anomalous diffusion…
A simple model for the reaction-driven propulsion of a small device is proposed as a model for (part of) a molecular machine in aqueous media. Motion of the device is driven by an asymmetric distribution of reaction products. The propulsive…
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…
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…
The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…