Anton, a Special-Purpose Machine for Molecular Dynamics Simulation.
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macro-molecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry, and medicine. A wide range of biolog...
| Publicado en: | Communications of the ACM Vol. 51; no. 7; pp. 91 - 98 |
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| Autores principales: | , , , , , , , , , , , , , , , , , , , |
| Formato: | Artículo |
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Association for Computing Machinery
Jul2008
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| Materias: | |
| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=hlh&AN=34059129&site=ehost-live header: @attributes: shortDbName: hlh uiTerm: 34059129 longDbName: Humanities International Complete uiTag: AN controlInfo: bkinfo: jinfo: jid: 00010782 ACM jtl: Communications of the ACM issn: 00010782 maglogo: N pubinfo: dt: Jul2008 vid: 51 iid: 7 pid: 68 pub: Association for Computing Machinery artinfo: ui: 34059129 10.1145/1364782.1364802 ppf: 91 ppct: 7 formats: tig: atl: Anton, a Special-Purpose Machine for Molecular Dynamics Simulation. aug: au: Shaw, David E. Deneroff, Martin M. Dror, Ron O. Kuskin, Jeffrey S. Larson, Richard H. Salmon, John K. Young, Cliff Batson, Brannon Bowers, Kevin J. Chao, Jack C. Eastwood, Michael P. Gagliardo, Joseph Grossman, J. P. Ho, C. Richard Ierardi, Douglas J. Kolossváry, István Klepeis, John L. Layman, Timothy McLeavey, Christine Moraes, Mark A. affil: Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032. su: Molecular dynamics Molecular models Computer science Cybernetics Parallel programs (Computer programs) Application-specific integrated circuits Equipment & supplies sug: subj: Molecular dynamics Molecular models Computer science Cybernetics Parallel programs (Computer programs) Application-specific integrated circuits Equipment & supplies ab: The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macro-molecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry, and medicine. A wide range of biologically interesting phenomena, however, occur over timescales on the order of a millisecond—several orders of magnitude beyond the duration of the longest current MD simulations. We describe a massively parallel machine called Anton, which should be capable of executing millisecond-scale classical MD simulations of such biomolecular systems. The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized high-speed communication network. Anton has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation. The remainder of the simulation algorithm is executed by a programmable portion of each chip that achieves a substantial degree of parallelism while preserving the flexibility necessary to accommodate anticipated advances in physical models and simulation methods. pubtype: Periodical doctype: Article src: R language: English refInfo: copyright: @attributes: flag: Y dt: @attributes: year: 2008 holdings: @attributes: islocal: N |
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