MUPHY: A parallel high performance multi physics/scale code

M Bernaschi and S Succi and M Fyta and E Kaxiras and S Melchionna and JK Sircar, 2008 IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, VOLS 1-8, 2937-+ (2008).

We present a parallel high-performance program that combines microscopic Molecular Dynamics (MD) with a mesoscopic Lattice Boltzmann (LB) method to simulate the translocation of biopolymers through nanometer size pores explicitly taking into account the interactions of the molecule with the surrounding fluid. The parallel implementation exhibits excellent scalability on the BlueGene platform and includes techniques which may improve the flexibility and efficiency of other complex multi- physics applications.

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