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Volumn 19, Issue 6, 2008, Pages 764-778

Accelerating molecular dynamics simulations with reconfigurable computers

Author keywords

Chemistry; Distributed architectures; Physics; Reconfigurable hardware

Indexed keywords

COMPUTER ARCHITECTURE; COMPUTER SIMULATION; INTERCONNECTION NETWORKS; MOLECULAR DYNAMICS; NATURAL SCIENCES COMPUTING; PROGRAM PROCESSORS; SCALABILITY;

EID: 44049100960     PISSN: 10459219     EISSN: None     Source Type: Journal    
DOI: 10.1109/TPDS.2007.70777     Document Type: Article
Times cited : (31)

References (52)
  • 8
    • 44049085792 scopus 로고    scopus 로고
    • IBM to Build World's First Cell Broadband Engine Based Supercomputer, Sept. 2006
    • IBM to Build World's First Cell Broadband Engine Based Supercomputer http://www-03.ibm.com/press/us/en/pressrelease/ 20210.wss, Sept. 2006.
  • 15
    • 44049103671 scopus 로고    scopus 로고
    • SRC Computers
    • SRC Computers, http://www.srccomputers.com, 2007.
    • (2007)
  • 16
    • 44049102731 scopus 로고    scopus 로고
    • Cray, http://www.cray.com, 2005.
    • (2005) Cray
  • 18
    • 34548223233 scopus 로고    scopus 로고
    • Preliminary Investigation of Advanced Electrostatics in Molecular Dynamics on Reconfigurable Computers
    • R. Scrofano and V.K. Prasanna, "Preliminary Investigation of Advanced Electrostatics in Molecular Dynamics on Reconfigurable Computers," SC '06: Proc. ACM/IEEE Conf. Supercomputing, 2006.
    • (2006) SC '06: Proc. ACM/IEEE Conf. Supercomputing
    • Scrofano, R.1    Prasanna, V.K.2
  • 21
    • 0038440700 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions
    • M. Patra, M. Karttunen, M.T. Hyvönen, E. Falck, P. Lindqvist, and I. Vattulainen, "Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions," Biophysics J., vol. 84, pp. 3636-3645, 2003.
    • (2003) Biophysics J , vol.84 , pp. 3636-3645
    • Patra, M.1    Karttunen, M.2    Hyvönen, M.T.3    Falck, E.4    Lindqvist, P.5    Vattulainen, I.6
  • 22
    • 0346844966 scopus 로고    scopus 로고
    • AMBER 8 User's Manual, http://amber.scripps.edu/doc8/amber8.pdf, 2004.
    • (2004) AMBER 8 User's Manual
  • 23
    • 44049089307 scopus 로고    scopus 로고
    • PDB Format Guide, http://www.rcsb.org/pdb/file_formats/pdb/ pdbguide2.2/guide2.2_frame.htm, 1996.
    • (1996) Guide
    • Format, P.D.B.1
  • 24
    • 44049094638 scopus 로고    scopus 로고
    • Intel, http://www.intel.com, 2006.
    • (2006)
  • 25
    • 44049106554 scopus 로고    scopus 로고
    • OProfile, http://oprofile.sourceforge.net/about/, 2007.
    • (2007) OProfile
  • 27
    • 0347801414 scopus 로고
    • The Interaction of Shocks and Defects in Lennard-Jones Crystals
    • Aug
    • L. Phillips, R. Sinkovits, E. Oran, and J. Boris, "The Interaction of Shocks and Defects in Lennard-Jones Crystals," J. Physics: Condensed Matter, vol. 5, no. 35, pp. 6357-6376, Aug. 1993.
    • (1993) J. Physics: Condensed Matter , vol.5 , Issue.35 , pp. 6357-6376
    • Phillips, L.1    Sinkovits, R.2    Oran, E.3    Boris, J.4
  • 31
    • 0002467378 scopus 로고
    • Fast Parallel Algorithms for Short-Range Molecular Dynamics
    • Mar
    • S. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics," J. Computational Physics, vol. 117, no. 1, pp. 1-19, Mar. 1995.
    • (1995) J. Computational Physics , vol.117 , Issue.1 , pp. 1-19
    • Plimpton, S.1
  • 32
    • 44049091765 scopus 로고    scopus 로고
    • A. Nakano, Class Notes for CSCI 599: High-Performance Scientific Computing. Univ. of Southern California, Fall Semester, 2003.
    • A. Nakano, Class Notes for CSCI 599: High-Performance Scientific Computing. Univ. of Southern California, Fall Semester, 2003.
  • 33
    • 57649241435 scopus 로고
    • MPI: A Message Passing Interface, http://www.mpi-forum.org/docs/ mpi-11-html/mpi-report.html, 1995.
    • (1995) Message Passing Interface
  • 34
  • 40
    • 34147177681 scopus 로고    scopus 로고
    • Using FPGA Devices to Accelerate Biomolecular Simulations
    • Mar
    • S.R. Alam, P.K. Agarwal, M.C. Smith, J.S. Vetter, and D. Caliga, "Using FPGA Devices to Accelerate Biomolecular Simulations," Computer, vol. 40, no. 3, pp. 66-73, Mar. 2007.
    • (2007) Computer , vol.40 , Issue.3 , pp. 66-73
    • Alam, S.R.1    Agarwal, P.K.2    Smith, M.C.3    Vetter, J.S.4    Caliga, D.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.