Modeling ion channels using Poisson-Nernst-Planck theory as an integrated approach to introducing nanotechnology concepts: The PNP cyclic peptide ion channel model

Describing the function of ion channels poses a big challenged in biochemistry and biophysics. 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, a graphical user interface designed specifically for Web-based applications, made available by the Network for Computational Nanotechnology (NCN). 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 has been introduced.