BioMOCA—a Boltzmann transport Monte Carlo model for ion channel simulation

摘要: With the recent availability of high-resolution structural information for several key ion channel proteins and large-scale computational resources, Molecular Dynamics has become an increasingly popular tool simulation. However, CPU requirements simulating transport on time scales relevant to conduction still exceed resources presently available. To address this problem, we have developed Biology Monte Carlo (BioMOCA), a three-dimensional (3D) coarsegrained particle simulator based Boltzmann Transport (BTMC) methodology. Although approach is widely employed in engineering community study charge electron devices, its application molecular biology electrolytes general new hence must be validated. The pair correlation function, which measure microscopic structure matter, provides suitable benchmark compare BTMC method against well-established Equilibrium (EMC) approach. For validation purposes BioMOCA used simulate simple homogeneous equilibrium at concentrations physiological interest. – functions computed from these simulations very well with those obtained EMC simulations. We also demonstrate performance-improving techniques that result several-fold speed-up without compromising function. then perform full 3D gramicidin A situ membrane environment, as link between electrostatic dielectric properties protein channel’s selectivity.