Ion fluxes through nano-pores and transmembrane channels

TL;DR

This paper presents a novel implicit solvent molecular dynamics method combining DCV-GCMD and analytical electrostatic solutions to accurately compute ionic fluxes through nano-pores and channels, matching experimental data.

Contribution

The paper introduces a new computational approach that integrates analytical electrostatics with molecular dynamics to model ionic fluxes in nano-pores.

Findings

The method accurately reproduces current-voltage and current-concentration relations.

Results show two binding sites and saturation effects similar to real gramicidin A channels.

The approach is validated against experimental characteristics of artificial channels.

Abstract

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) simulation and the analytical solution for the electrostatic potential inside a cylindrical nano-pore recently obtained by Levin [Europhys. Lett., 76, 163 (2006)]. The theory is used to calculate the ionic fluxes through an artificial trans-membrane c hannel which mimics the antibacterial gramicidin A channel. Both current-voltage and current-concentration relations are calculated under various experimental conditions. We show that our results are comparable to the characteristics associated to the gramicidin A pore, specially the existence of two binding sites inside the pore and the observed saturation in the current-concentration profiles.