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Ion flux through membrane channels—An enhanced algorithm for the Poisson‐Nernst‐Planck model
Author(s) -
Dyrka Witold,
Augousti Andy T.,
Kotulska Malgorzata
Publication year - 2008
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20947
Subject(s) - nernst equation , planck , computation , algorithm , discretization , relaxation (psychology) , poisson distribution , channel (broadcasting) , flux (metallurgy) , poisson's equation , space (punctuation) , statistical physics , computer science , mathematics , physics , mathematical analysis , materials science , quantum mechanics , statistics , psychology , social psychology , computer network , electrode , metallurgy , operating system
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—α‐hemolysin, proving its efficiency. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008