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.