Nanotech 2001 Vol. 2
Nanotech 2001 Vol. 2
Technical Proceedings of the 2001 International Conference on Computational Nanoscience and Nanotechnology

Bioinformatics/Mathematical Biology Chapter 2

Three-Dimensional Continuum Simulation of Biological Ion Channels

Authors: T.A. van der Straaten, J. Tang, R.S. Eisenberg, U. Ravaioli and N. Aluru

Affilation: Rush Medical College, United States

Pages: 39 - 42

Keywords: ion channels, Poisson-Nernst-Planck, transport simulation, ompF Porin, nanotechnology

We present a self-consistent continuum 3-D simulation of ion permeation through the ompF porin channel, a protein found in the membrane of the e-coli bacterium. The model is based on the simultaneous solution of Poisson's equation, which captures Coulomb interactions and a continuity equation for each ion species, describing permeation down an electrochemical gradient. Water is treated as a uniform background medium with a specific dielectric constant and macroscopic current flow is resolved by assigning an appropriate mobility/diffusivity to each ionic species. Using this model with a single diffusivity for each ion species we predict the current-voltage relations for ompF porin for a wide range of experimental conditions. Agreement with experimental measurements is remarkably good given that the model uses the same two adjustable parameters (diffusivity for each ion species) for the entire set of experimental conditions.

ISBN: 0-9708275-3-9
Pages: 218