Toward Microscopic Simulations of Proteins in Cell-Like Environments

Abstract

The Lattice Boltzmann Molecular Dynamics methodology (LBMD) has been recently designed to challenge the problem of simulating proteins in cell-like environments [1]. This method is based on the integration of two techniques specialized to treat respectively the fluid and molecular motions. The LBMD approach handles the interactions between solute and solvent particles through an explicit representation of their local collisions. As consequence HI are naturally included in the simulations of water free molecular models. LBMD is intrinsically a multi-scale methodology since the resolution of the description of both its components, the fluid and the molecular system, can be changed at wish allowing to cover a large spectrum of conditions. As side advantage, because of the local nature of the LB equation, high scalability in parallel machines is achieved. We will showcase recent applications based on the very efficient coarse-grained model OPEP [2,3] and treating the problem of amyloid aggregation [4], shear-induced unfolding and cellular crowding [3].