A numerical solver of 3D Poisson Nernst Planck equations for functional studies of ion channels

Recent results of X-Ray crystallography have provided important information for functional studies of membrane ion channels based on computer simulations. Because of the large number of atoms that constitute the channel proteins, it is prohibitive to approach functional studies using molecular dynamic methods. To overcome the current computational limit we propose a novel approach based on the Poisson, Nernst, Planck electrodiffusion theory. The proposed numerical method allows the quick computation of ion flux through the channel, starting from its 3D structure. We applied the method to the KcsA potassium channel obtaining a good accordance with the experimental data.