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VLSI Design
Volume 13 (2001), Issue 1-4, Pages 179-187
http://dx.doi.org/10.1155/2001/25603

Simulation of Biological Ionic Channels by Technology Computer-Aided Design

1Beckman Institute, University of Illinois at Urbana-Champaign, Urbana 61801, IL, USA
2Department of Molecular Biophysics, Rush Medical Center, Chicago 60612, IL, USA
3255 Beckman Institute 3, University of Illinois, 405 N. Mathews Avenue, Urbana 61801, IL, USA

Copyright © 2001 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

This paper discusses the use of established Technology Computer-Aided Design (TCAD) tools and methodologies for the study of charge transport in molecular biology systems, like ionic channels, that display a behavior analogous to electronic devices. Continuum drift-diffusion and Monte Carlo methods can be applied to analyze steady-state and transient behavior of ionic channels over time scales that cannot be resolved practically by detailed molecular dynamics or quantum approaches. The difficult ion-water interaction can be lumped phenomenologically into mobility or scattering rate parameters, while the solution of Poisson equation over the complete domain provides a simple way to include external boundary conditions and image force effects at dielectric discontinuities. We present here some recent results of 3-D simulations for a gramicidin ion channel, obtained using the rapid prototyping computational platform PROPHET.