  We employ a multiscale approach to model the translocation of biopolymers
through nanometer size pores. Our computational scheme combines microscopic
Molecular Dynamics (MD) with a mesoscopic Lattice Boltzmann (LB) method for the
solvent dynamics, explicitly taking into account the interactions of the
molecule with the surrounding fluid. We describe an efficient parallel
implementation of the method which exhibits excellent scalability on the Blue
Gene platform. We investigate both dynamical and statistical aspects of the
translocation process by simulating polymers of various initial configurations
and lengths. For a representative molecule size, we explore the effects of
important parameters that enter in the simulation, paying particular attention
to the strength of the molecule-solvent coupling and of the external electric
field which drives the translocation process. Finally, we explore the
connection between the generic polymers modeled in the simulation and DNA, for
which interesting recent experimental results are available.
