Simulation of Biological Ionic Channels by Technology Computer-Aided Design. Issue 1 (2001)

• Record Type: Journal Article
• Authors: Hess, K.; Ravaioli, U.; Gupta, M.; Aluru, N.; van der Straaten, ; Eisenberg, R. S.
• Is Part Of: VLSI design. Volume 13:Issue 1/4(2001)
• Page Start: 179
• Page End: 187
• Publication Date: 2001
• Subjects: Ionic channels -- Transport simulation -- Nanotechnology; Integrated circuits -- Very large scale integration -- Periodicals; 621.395
• DOI: 10.1155/2001/25603
• Languages: English
• ISSNs: 1065-514X

Abstract

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.