PNP Cyclic Peptide Ion Channel Model

By Brian Radak1, Hyonseok Hwang2, George C. Schatz1, Mark Ratner1

1. Northwestern University 2. Kangwon National University, Kangwon-do, Rep. of Korea

This tool simulates ion flow in a system modeled after cyclic peptide ion channels using Poisson-Nernst-Planck (PNP) theory.

Launch Tool

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Archive Version 1.1.2
Published on 13 May 2011 All versions

doi:10.4231/D3J678W75 cite this



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Poisson-Nernst-Planck (PNP) theory describes ion flow by coupling the Poisson equation, which describes the electrostatic potential of a system of fixed charges, and the Smoluchowski equation, which describes the diffusion of charged particles. Using complex boundary conditions, these equations can be used to model an ion channel. This model approximates proteins as cylindrical tubes embedded in a lipid membrane. The ions, lipids, protein, and water molecules are all described as dielectric continuums, exchanging the electronic and nuclear polarizations of molecules for dielectric constants and the ion distributions for number density functions. The system of equations in PNP theory is solved simultaneously and self-consistently via the finite difference method, whereby continuous functions are mapped onto a discrete grid. Using several different input parameters, the electrostatic potential, ion concentrations, ion flux, and ion current of the system can be found.


Brian Radak... GUI development/parallel processing
Hyonseok Hwang... original application programmer

This work was suppored by the Network for Computational Nanotechnology through a grant from the National Science Foundation.


  • H. Hwang, G. C. Schatz, and M. Ratner. J. Phys. Chem. B Vol. 110, No. 13 p 6999-7008 (2006).
  • Publications

  • B. Radak, H. Hwang, G. C. Schatz, J. Chem. Ed. Vol. 85 p 744-48 (2008).
  • Cite this work

    Researchers should cite this work as follows:

    • H. Hwang, G. C. Schatz, and M. Ratner. J. Phys. Chem. B Vol. 110, No. 13 p 6999-7008 (2006).
    • Brian Radak; Hyonseok Hwang; George C. Schatz; Mark Ratner (2014), "PNP Cyclic Peptide Ion Channel Model," (DOI: 10.4231/D3J678W75).

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