A computational algorithm based on Grand Canonical Monte Carlo (GCMC) and Brownian Dynamics (BD) is described to simulate the movement of ions in membrane channels. The proposed algorithm, GCMC/BD, allows the simulation of ion channels with a realistic implementation of boundary conditions of concentration and transmembrane potential. The method is consistent with a statistical mechanical formu...

Adsorption of carbon dioxide in slit-shaped carbon micropores at 273 K has been studied by means of the grand canonical Monte Carlo (GCMC) simulations and the nonlocal density functional theory (NLDFT). Three molecular models of CO2 have been used. Long-run GCMC simulations were performed with the three-center model of Harris and Yung (J. Phys. Chem. 1995, 99, 12021). For NLDFT calculations, we...

The ability of grand canonical Monte Carlo (GCMC) to create and annihilate molecules in a given region greatly aids the identification of water sites and water binding free energies in protein cavities. However, acceptance rates without the application of biased moves can be low, resulting in large variations in the observed water occupancies. Here, we show that replica-exchange of the chemical...

Solute sampling of explicit bulk-phase aqueous environments in grand canonical (GC) ensemble simulations suffer from poor convergence due to low insertion probabilities of the solutes. To address this, we developed an iterative procedure involving Grand Canonical-like Monte Carlo (GCMC) and molecular dynamics (MD) simulations. Each iteration involves GCMC of both the solutes and water followed ...

It is important to gain a physical understanding of ion transport through the voltage-dependent anion channel (VDAC) because this channel provides primary permeation pathways for metabolites and electrolytes between the cytosol and mitochondria. We performed grand canonical Monte Carlo/Brownian dynamics (GCMC/BD) simulations to explore the ion transport properties of human VDAC isoform 1 (hVDAC...

Identification of the molecular interaction governing ion conduction through biological pores is one of the most important goals of modern electrophysiology. Grand canonical Monte Carlo Brownian dynamics (GCMC/BD) and three-dimensional Poisson-Nernst-Plank (3d-PNP) electrodiffusion algorithms offer powerful and general approaches to study of ion permeation through wide molecular pores. A detail...

A multiscale approach based on ab initio and grand canonical Monte Carlo (GCMC) simulations is used to report the H2, N2, and CH4 uptake behaviors of two zeolitic imidazolate frameworks (ZIFs), ZIF-95 and -100, with exceptionally large and complex colossal cages. The force fields describing the weak interactions between the gas molecules and ZIFs in GCMC simulations are based on ab initio MP2 l...

Because of the increasing interest in studying the phenomenon exhibited by charge-stabilized colloidal suspensions in confining geometry, we present a density functional theory (DFT) for a hard-core multi-Yukawa fluid. The excess Helmholtz free-energy functional is constructed by using the modified fundamental measure theory and Rosenfeld's perturbative method, in which the bulk direct correlat...

This study aimed to evaluate the effects of two ginsenoside Rb1 (G-Rb1) loaded films on oral wound healing. Two types G-Rb1 films, carboxymethyl cellulose (GCMC) film and hyaluronic acid (GHA) film, were developed. A total 36 Sprague-Dawley rats divided into 3 groups: control, GCMC, GHA. After formation midpalate, control group was left without treatment, whereas experimental groups had attache...

Grand canonical Monte Carlo (GCMC) simulation was used for the systematic investigation of the supercritical methane adsorption at 273 K on an open graphite surface and in slit-like micropores of different sizes. For both considered adsorption systems the calculated excess adsorption isotherms exhibit a maximum. The effect of the pore size on the maximum surface excess and isosteric enthalpy of...