Ion Channel Simulations Using the TR-PNP Model and the Excess Chemical Potential Approach

摘要

We describe a new method referred to as TR-PNP model to study general types of nanostructure ion channels. Our method extends the common continuum methods to include particle like properties, such as ion trapping and release effects. A previously known approach to deal with those effects is the excess chemical potential method. The Eyring rate theory is utilized to connect the two methodologies. We implement a toy channel model with single binding site in terms of both approaches, and demonstrate their equivalence under steady state conditions. Then we perform a time dependent simulation (timescale:μs) on another toy channel with two binding sites by using the TR-PNP model. Our results quantitatively illustrate the hopping process of ions from one site to the other. This method is therefore a good candidate to be integrated into a multi-scale simulation framework to provide a bridge between continuum and particle methods.