MUPHY: A parallel MUlti PHYsics/scale code for high performance bio- fluidic simulations

M Bernaschi and S Melchionna and S Succi and M Fyta and E Kaxiras and JK Sircar, COMPUTER PHYSICS COMMUNICATIONS, 180, 1495-1502 (2009).

DOI: 10.1016/j.cpc.2009.04.001

We present a parallel version of MUPHY, a multi-physics/scale code based upon the combination of microscopic Molecular Dynamics (MD) with a hydro-kinetic Lattice Boltzmann (LB) method. The features of the parallel version of MUPHY are hereby demonstrated for the case of translocation of biopolymers through nanometer-sized, multi-pore configurations, taking into explicit account the hydrodynamic interactions of the translocating molecules with the surrounding fluid. The parallel implementation exhibits excellent scalability on the IBM BlueGene platform and includes techniques which may improve the flexibility and efficiency of other complex multi-physics parallel applications, such as hemodynamics, targeted-drug delivery and others. (C) 2009 Elsevier B.V. All rights reserved.

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