Title :
MUPHY: A parallel high performance MUlti PHYsics/Scale code
Author :
Bernaschi, Massimo ; Succi, Sauro ; Fyta, Maria ; Kaxiras, Efthimios ; Melchionna, Simone ; Sircar, Jayanta K.
Author_Institution :
Ist. Applicazioni Calcolo, CNR, Rome
Abstract :
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.
Keywords :
biology computing; lattice Boltzmann methods; macromolecules; molecular biophysics; molecular dynamics method; parallel programming; polymers; BlueGene platform; MUPHY code; biopolymers translocation; mesoscopic Lattice Boltzmann method; microscopic molecular dynamics; nanometer size pores; parallel high performance multiphysics-scale code; parallel high-performance program; Biological information theory; Biological system modeling; Biological systems; Biology computing; Computational modeling; Concurrent computing; Fluid dynamics; Lattice Boltzmann methods; Physics; Solvents;
Conference_Titel :
Parallel and Distributed Processing, 2008. IPDPS 2008. IEEE International Symposium on
Conference_Location :
Miami, FL
Print_ISBN :
978-1-4244-1693-6
Electronic_ISBN :
1530-2075
DOI :
10.1109/IPDPS.2008.4536464
