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

M. Bernaschi, S. Melchionna, S. Succi, M. Fyta, E. Kaxiras, J.K. Sircar
2009 Computer Physics Communications  
We demonstrate the excellent parallel scalability and global performance on the IBM Blue-Gene Supercomputer of MUPHY, a new multiscale/physics code. MUPHY provides a unique parallel multiphysics combination of microscopic Molecular Dynamics (MD) with a hydro-kinetic Lattice Boltzmann (LB) method, which permits to simulate a variety of bio-fluidic problems across a wide range of scales in a fully concurrent fashion. The features of MUPHY are hereby demonstrated for the case of translocation of
more » ... opolymers through nanometer-sized, multi-pore configurations, taking into account explicitly the hydrodynamic interactions of the translocating molecules 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 parallel applications, such as hemodynamics, targeted-drug delivery and others.
doi:10.1016/j.cpc.2009.04.001 fatcat:dexg5yewsjcrjpjt3ceyoduo5a