Simulating Ion Permeation Through the ompF Porin Ion Channel Using Three-Dimensional Drift-Diffusion Theory

Abstract

Ionic channels, natural nanotubes found in biological cells, are interesting to the electronics community because they display a range of device-like functions. The purpose of this paper is to illustrate how the solution methodology, developed for 3-D drift-diffusion models of semiconductor devices, can be applied to ion permeation in ionic channels. For this study we select the ompF porin channel, found in the membrane of the E. coli bacterium. The self-consistent 3-D model is based on the simultaneous solution of Poisson's equation, which captures Coulomb interactions, and a current 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. For demonstration, a simple model is assumed for the mobility/diffusivity of each ionic species and we compute the current-voltage relations for ompF porin in a wide range of conditions. Agreement with experimental measurements is surprisingly good given that the model uses the ion diffusivity as the only calibrated parameter.