Brownian dynamics simulation of charge transport in ion channels

In this work, we study the suitability of a P³M force field scheme coupled with a Brownian dynamics simulation engine for the accurate modelling of charge transport in ion channels. The proposed simulation algorithm (Aboud et al 2004 J.Comput.Electron.3 117-33) is briefly discussed, and its validation for the electrodynamic description of aqueous solutions (Marreiro et al 2005 J.Comput.Electron.4 179-83; 2006 J.Comput.Electron.atpress) is presented. The algorithm is applied to the simulation of ion channel systems where the influence of the dielectric representation and the diffusion coefficients are computed and compared to experimental (Van Der Straaten et al 2003 J.Comput.Electron.2 29-47) and simulated (Van Der Straaten et al 2003 J.Comput.Electron.2 29-47; Miedema et al 2004 Biophys.J.87 3137-47) data. The results show that while the bulk parameters do not correctly apply to the channel, the model can be refined by a careful choice of parameters in order to yield accurate charge transport properties while remaining extremely effective from the computational viewpoint.