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

fYear

2008

Firstpage

1

Lastpage

8

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;

fLanguage

English

Publisher

ieee

Conference_Titel

Parallel and Distributed Processing, 2008. IPDPS 2008. IEEE International Symposium on

Conference_Location

Miami, FL

ISSN

1530-2075

Print_ISBN

978-1-4244-1693-6

Electronic_ISBN

1530-2075

Type

conf

DOI

10.1109/IPDPS.2008.4536464

Filename

4536464