Related papers: Translocation through conical pores: A direction-d…
We examine pressure-driven non-equilibrium transport of linear, circular and star polymers through a nanochannel containing a rectangular pit with full hydrodynamic interactions and thermal fluctuations. We demonstrate that with…
I did off-lattice 3D Monte Carlo simulations for polymer translocation through a narrow pore at low external field, trying to be as close to a direct approach as possible. The process was found non equilibrium globally, but dynamics of the…
We study different types of microswimmers moving in channels with varying cross section and thereby interacting hydrodynamically with the channel walls. Starting from the Smoluchowski equation for a dilute suspension, for which interactions…
We consider the escape of a flexible, self-avoiding polymer chain out of a confined geometry. By means of simulations, we demonstrate that the translocation time can be described by a simple scaling law that exhibits a nonlinear dependence…
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,…
We investigate the translocation of stiff polymers in the presence of binding particles through a nanopore by two-dimensional Langevin dynamics simulations. We find that the mean translocation time shows a minimum as a function of the…
A hydrophobic constriction site can act as an efficient barrier to ion and water permeation if its diameter is less than the diameter of an ion's first hydration shell. This hydrophobic gating mechanism is thought to operate in a number of…
Chaperone-assisted translocation through a nanopore embedded in membrane holds a prominent role in the transport of biopolymers. Inspired by classical Brownian ratchet, we develop a theoretical framework characterizing such translocation…
We investigate the dynamics of polymer translocation through a nanopore under an externally applied field using the 2D fluctuating bond model with single-segment Monte Carlo moves. We concentrate on the influence of the field strength $E$,…
Equations for dislocation evolution bridge the gap between dislocation properties and continuum descriptions of plastic behavior of crystalline materials. Computer simulations can help us verify these evolution equations and find their…
Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and…
Blockage of pores by particles is found in many processes, including filtration and oil extraction. We present filtration experiments through a linear array of ten channels with one dimension which is sub-micron, through which a dilute…
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.…
We develop a correlation-corrected transport theory in order to predict ionic and polymer transport properties of membrane nanopores in physical conditions where mean-field electrostatics breaks down. The experimentally observed low KCl…
In the popular solution-diffusion picture, the membrane permeability is defined as the product of the partition ratio and the diffusivity of penetrating solutes inside the membrane in the linear response regime, i.e., in equilibrium.…
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…
Bacterial cellulose biofilms are complex networks of strong interwoven nanofibers that control transport and protect bacterial colonies in the film. Design of diverse applications of bacterial cellulose films also relies on understanding…
We study the effect of a gradient of solvent quality on the coil-globule transition for a polymer in a narrow pore. A simple self-attracting self-avoiding walk model of a polymer in solution shows that the variation in the strength of…
Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations…
In this work we study the noise induced effects on the dynamics of short polymers crossing a potential barrier, in the presence of a metastable state. An improved version of the Rouse model for a flexible polymer has been adopted to mimic…