The simulation of ion transport in biological ion channels presents numerous interesting challenges. Since there are accurate structures for only a handful of channel proteins it is difficult to predict solely from the conformation how internal and external structure of the molecule will affect it's ionic transport characteristics. This problem is compounded by the fact that the electrostatics and dynamic behaviour of these molecules is, only now, beginning to be understood. We present an ion transport simulation methodology based on a self-consistent Brownian/Poisson technique, that is capable of resolving ion transport on ps-μs timescales including the effect of long range electric fields in complex dielectric structures. The results of the self-consistent Brownian simulation are compared against the commercial drift diffusion simulation package Taurus and experimental measurements of the ion conduction for the Kcsa bacterial ion channel protein.
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