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Journal of Computational Electronics

, Volume 2, Issue 1, pp 29–47 | Cite as

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

  • T.A. van der Straaten
  • J.M. Tang
  • U. Ravaioli
  • R.S. Eisenberg
  • N.R. Aluru
Article

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.

drift-diffusion simulation numerical methods ionic channels bioelectronics ompF porin 

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Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • T.A. van der Straaten
    • 1
    • 2
  • J.M. Tang
    • 2
  • U. Ravaioli
    • 1
  • R.S. Eisenberg
    • 2
  • N.R. Aluru
    • 1
  1. 1.Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  2. 2.Department of Molecular Biophysics and PhysiologyRush Medical CollegeChicagoUSA

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