Simulation of ion conduction in the ompF porin channel using BioMOCA

In this paper, we present a full three-dimensional simulation of the ompF porin channel using BioMOCA, a self-consistent particle-based ion channel simulation tool, based on the Boltzmann Transport Monte Carlo methodology widely used to simulate conduction in the solid-state device. Significant computational speed-up over atomistic Molecular Dynamics simulations is achieved by treating protein, membrane and water as continuum dielectric background media and computing only the trajectories of mobile ions in solution. A realistic channel structure with permanent fixed charges is mapped onto a finite mesh using the Cloud-in-Cell scheme. Electrostatic forces, computed by solving Poisson equation at regular intervals, are added to a pair-wise ion-ion interaction, which is necessary to prevent the unphysical coalescence of finite-sized ions. The interaction between ions and water is modeled as a random scattering process that thermalizes the ion. Using this tool we computed the complete current-voltage characteristic of the porin channel in approximately one week using ten IBM p690 processors. We also present steady-state ion channel occupancies and compare them with results obtained from recent drift-diffusion based simulations.