simulation of biological ionic channels by technology computer-aided design模拟生物离子通道技术的计算机辅助设计.pdfVIP

VLSI DESIGN (C) 2001 OPA (Overseas Publishers Association) N.V. 2001, Vol. 13, Nos. 1-4, pp. 179-187 Published by license under Reprints available directly from the publisher the Gordon and Breach Science Publishers imprint, Photocopying permitted by license only member of the Taylor Francis Group. Simulation of Biological Ionic Channels by Technology Computer-Aided Design K. HESSa, U. RAVAIOLIa’*, M. GUPTAa, N. ALURUa, T. VAN DER STRAATENb and R. S. EISENBERGb aBeckman Institute, University of Illinois at Urbana-Champaign Urbana, IL 61801, USA; bDepartment ofMolecular Biophysics, Rush Medical Center, Chicago, IL 60612, USA 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