MUPHY

MUPHY: A parallel multi physics/scale code for high performance bio-fluidic simulations. 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


References in zbMATH (referenced in 9 articles )

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  1. Tang, Yu-Hang; Kudo, Shuhei; Bian, Xin; Li, Zhen; Karniadakis, George Em: Multiscale universal interface: a concurrent framework for coupling heterogeneous solvers (2015)
  2. Vergnault, E.; Sagaut, P.: An adjoint-based lattice Boltzmann method for noise control problems (2014)
  3. Schlauch, Eva; Ernst, Martin; Seto, Ryohei; Briesen, Heiko; Sommerfeld, Martin; Behr, Marek: Comparison of three simulation methods for colloidal aggregates in Stokes flow: finite elements, lattice Boltzmann and Stokesian dynamics (2013)
  4. Vergnault, E.; Malaspinas, O.; Sagaut, P.: A lattice Boltzmann method for nonlinear disturbances around an arbitrary base flow (2012)
  5. Bisson, Mauro; Bernaschi, Massimo; Melchionna, Simone: Parallel molecular dynamics with irregular domain decomposition (2011)
  6. Falcucci, Giacomo; Ubertini, Stefano; Biscarini, Chiara; Di Francesco, Silvia; Chiappini, Daniele; Palpacelli, Silvia; De Maio, Alessandro; Succi, Sauro: Lattice Boltzmann methods for multiphase flow simulations across scales (2011)
  7. Spencer, Timothy J.; Halliday, Ian; Care, Chris M.: A local lattice Boltzmann method for multiple immiscible fluids and dense suspensions of drops (2011)
  8. Vergnault, E.; Malaspinas, O.; Sagaut, P.: A time-reversal lattice Boltzmann method (2011)
  9. Clausen, Jonathan R.; Reasor, Daniel A.jun.; Aidun, Cyrus K.: Parallel performance of a lattice-Boltzmann/finite element cellular blood flow solver on the IBM blue gene/P architecture (2010)