相关论文: TransPath: A Computational Method to Study the Ion…

ClC chloride channels possess a homodimeric structure in which each monomer contains an independent chloride ion pathway. ClC channel gating is regulated by chloride ion concentration, pH, and voltage. Based on structural and physiological…

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 transport of biomolecules across a cell membrane is an important phenomena that plays a pivotal role in the functioning of biological cells. In this paper, we investigate such processes by modeling the translocation of polymers through…

We introduce an implicit solvent Molecular Dynamics approach for calculating ionic fluxes through narrow nano-pores and transmembrane channels. The method relies on a dual-control- volume grand-canonical molecular dynamics (DCV-GCMD)…

This paper discusses an optimization method called Modified Bee Colony algorithm (MBC) based on a particular intelligent behavior of honeybee swarms. The algorithm was checked in a few benchmarks like Shekel, Rozenbroke, Himmelblau and…

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…

We consider an anisotropically two-dimensional diffusion of a charged molecule (particle) through a large biological channel under an external voltage. The channel is modeled as a cylinder of three structure parameters: radius, length, and…

Ion channels are membrane proteins responsible for an enormous range of biological functions. Ion selectivity and permeation are based on simple laws of physics and chemistry. Ion channels are therefore ideal candidates for physical…

Modulating ion transport through nanoporous membranes is critical to many important chemical and biological separation processes. The corresponding transport timescales, however, are often too long to capture accurately using conventional…

Transport of molecules across membrane channels is investigated theoretically using exactly solvable discrete stochastic site-binding models. It is shown that the interaction potential between molecules and the channel has a strong effect…

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…

Ions transiting biomembranes might pass readily from water through ion-specific membrane proteins if those protein channels provide environments similar to the aqueous solution hydration environment. Indeed, bulk aqueous solution is an…

In this work, a generic rigorous Bayesian formalism is introduced to predict the most likely path of any ion crossing a medium between two detection points. The path is predicted based on a combination of the particle scattering in the…

Classical molecular dynamics and electro-diffusion theories have achieved profound success in elucidating ion selectivity and gating mechanisms. However, reconciling strict selectivity with high flux permeation in Angstrom-scaled biological…

Dynamic Monte Carlo simulations are used to study coupled transport (co-transport) through sub-nanometer-diameter pores. In this classic Hodgkin-Keynes mechanism, an ion species uses the large flux of an abundant ion species to move against…

Membrane proteins move in heterogeneous environments with spatially (sometimes temporally) varying friction and with biochemical interactions with various partners. It is important to reliably distinguish different modes of motion to…

The study of selection and gating in potassium channels is a very important issue in modern biology. Indeed such structures are known in all types of cells in all organisms where they play many important functional roles. The mechanism of…

We combine quantum-chemical calculations and molecular dynamics simulations to consider aqueous ion flow across non-axisymmetric nanopores in monolayer graphene and MoS$_2$. When the pore-containing membrane is subject to uniaxial tensile…

To accelerate the development of novel ion-conducting materials, we present a general graph-theoretic analysis framework for ion migration in any crystalline structure. The nodes of the graph represent metastable sites of the migrating ion…

In this work, Transition Probability Matrix (TPM) is proposed as a new method for extracting the features of nodes in the graph. The proposed method uses random walks to capture the connectivity structure of a node's close neighborhood. The…