Support Options

Submit a Support Ticket

Home Tools PNP Cyclic Peptide Ion Channel Model About

PNP Cyclic Peptide Ion Channel Model

By Brian Radak1, Hyonseok Hwang2, Mark Ratner1

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

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

Launch Tool

This tool version is unpublished and cannot be run. If you would like to have this version staged, you can put a request through HUB Support.

Archive Version 1.1
Published on 20 Jan 2009, unpublished on 12 Oct 2009
Latest version: 1.1.4. All versions

doi:10.4231/D3930NT8F cite this

This tool is closed source.



Published on


Poisson-Nernst-Planck (PNP) theory couples the Poisson (describing the electrostatic potential of a system of fixed charges) and Smoluchowski equations (describing the diffusion of charged particles) to describe ion flow. 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. Schatz, and M. Ratner. J. Phys. Chem. B Vol. 110, No. 13 p 6999-7008 (2006).
  • Cite this work

    Researchers should cite this work as follows:

    • H. Hwang, G. Schatz, and M. Ratner. J. Phys. Chem. B Vol. 110, No. 13 p 6999-7008 (2006).
    • Brian Radak; Hyonseok Hwang; Mark Ratner (2014), "PNP Cyclic Peptide Ion Channel Model," (DOI: 10.4231/D3930NT8F).

      BibTex | EndNote

    Tags, a resource for nanoscience and nanotechnology, is supported by the National Science Foundation and other funding agencies. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.