Adaptive controlled Brownian dynamics approach for permeation in bio-nanotubes

Ion channels are biological nanotubes formed by large protein molecules. In this paper we address the permeation problem which deals with the propagation of individual ions in an ion channel at an Angstrom unit spatial scale and femtosecond time scale. We present an adaptive controlled Brownian dynamics simulation approach to predict the structure of an ion channel. The Brownian dynamics algorithm is coupled with a stochastic gradient algorithm to match the simulated current with experimentally determined currents.