Ion flux through membrane channels: an enhanced algorithm for the Poisson-Nernst-Planck model

Dyrka, Witold, Augousti, Andy T. and Kotulska, Malgorzata (2008) Ion flux through membrane channels: an enhanced algorithm for the Poisson-Nernst-Planck model. Journal of Computational Chemistry, 29(12), pp. 1876-1888. ISSN (print) 0192-8651

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Abstract

A novel algorithmic scheme for numerical solution of the 3D Poisson-Nernst-Planck model is proposed. The algorithmic improvements are universal and independent of the detailed physical model. They include three major steps: an adjustable gradient-based step value, an adjustable relaxation coefficient, and an optimized segmentation of the modeled space. The enhanced algorithm significantly accelerates the speed of computation and reduces the computational demands. The theoretical model was tested on a regular artificial channel and validated on a real protein channel-alpha-hemolysin, proving its efficiency.

Item Type: Article
Uncontrolled Keywords: PNP, nanopore, algorithm optimization, relaxation technique, electrodiffusion, alpha-hemolysin, Brownian dynamics, electrostatics, conductance, permeation, boltzmann
Research Area: Chemistry
Faculty, School or Research Centre: Faculty of Science (until 2011)
Faculty of Science (until 2011) > School of Life Sciences
Related URLs:
Depositing User: Katrina Clifford
Date Deposited: 29 May 2008
Last Modified: 17 Dec 2012 11:51
URI: http://eprints.kingston.ac.uk/id/eprint/3092

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