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PNP Cyclic Peptide Ion Channel Model
Simulate ion flow in a system modeled after cyclic peptide ion channels using Poisson-Nernst-Planck (PNP) theory.
Launch Tool
Archive Version 1.1
Published on 20 Jan 2009, unpublished on 12 Oct 2009 All versions
doi:10.4231/D3930NT8F cite this
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Abstract
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.
Credits
| 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.
References
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).