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  Home > JCE Print > Journal of Chemical Education > Issues > 2008  > May  >
On the Web
Modeling Ion Channels Using Poisson–Nernst–Planck Theory as an Integrated Approach To Introducing Nanotechnology Concepts: The PNP Cyclic Peptide Ion Channel Model
Brian Radak, Hyonseok Hwang, and George C. Schatz
Department of Chemistry, Northwestern University, Evanston, IL 60208-3113
Cover
May 2008
Vol. 85 No. 5
p. 744
Abstract
One of the most fundamental challenges in biochemistry and biophysics is describing the function of ion channels, proteins that control ion transport across cell membranes. One approach to this problem is the application of Poisson–Nernst–Planck (PNP) theory. In practice, applying PNP theory involves creating a computational model of the ion channel and generating a numerical solution of differential equations that describes ion transport and electrostatic interactions. The PNP Cyclic Peptide Ion Channel Model is a simulation tool designed to offer an integrated approach to this important problem in bionanotechnology by demonstrating and explaining the application of PNP theory in a way that is accessible to students at an upper undergraduate level. The program interface was made using the free Rapid Application Infrastructure (Rappture) software made available by the Network for Computational Nanotechnology (NCN). Rappture is designed specifically for Web-based applications. Here we introduce a free version of the PNP Cyclic Peptide Ion Channel Model for use in the simulation of ion transport properties for a model ion channel structure that has been the subject of recent experiments.
Supplement
Manual for using a free Web version of the PNP Cyclic Peptide Ion Channel Model
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Contents
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Citation
Radak, Brian; Hwang, Hyonseok; Schatz, George C. J. Chem. Educ. 2008, 85, 744.
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Keywords
Biochemistry; Biophysical Chemistry; Computational Chemistry; Computer-Based Learning; Interdisciplinary / Multidisciplinary; Internet / Web-Based Learning; Molecular Modeling; Nanotechnology; Proteins / Peptides; Theoretical Chemistry; Transport Properties; Upper-Division Undergraduate
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History
Created:
Last Updated:
3/25/2008
4/3/2008
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