{"id":"https://openalex.org/W2066559049","doi":"https://doi.org/10.1137/070692054","title":"Accelerating Molecular Dynamics Simulations on PlayStation 3 Platform Using Virtual-GRAPE Programming Model","display_name":"Accelerating Molecular Dynamics Simulations on PlayStation 3 Platform Using Virtual-GRAPE Programming Model","publication_year":2008,"publication_date":"2008-01-01","ids":{"openalex":"https://openalex.org/W2066559049","doi":"https://doi.org/10.1137/070692054","mag":"2066559049"},"language":"en","primary_location":{"id":"doi:10.1137/070692054","is_oa":false,"landing_page_url":"https://doi.org/10.1137/070692054","pdf_url":null,"source":{"id":"https://openalex.org/S165512578","display_name":"SIAM Journal on Scientific Computing","issn_l":"1064-8275","issn":["1064-8275","1095-7197"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Scientific Computing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111737458","display_name":"Tetsu Narumi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210141143","display_name":"Nissin Kogyo (Japan)","ror":"https://ror.org/03j9hxf30","country_code":"JP","type":"company","lineage":["https://openalex.org/I4210141143"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Tetsu Narumi","raw_affiliation_strings":["narumi@a7.keio.jp and fsharpminor@a2.keio.jp and yasuoka@mech.keio.ac.jp#TAB#"],"affiliations":[{"raw_affiliation_string":"narumi@a7.keio.jp and fsharpminor@a2.keio.jp and yasuoka@mech.keio.ac.jp#TAB#","institution_ids":["https://openalex.org/I4210141143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013596348","display_name":"Shun Kameoka","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shun Kameoka","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033083222","display_name":"Makoto Taiji","orcid":"https://orcid.org/0000-0002-5317-0500"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Makoto Taiji","raw_affiliation_strings":["[email\u00a0protected]#TAB#"],"affiliations":[{"raw_affiliation_string":"[email\u00a0protected]#TAB#","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004379494","display_name":"Kenji Yasuoka","orcid":"https://orcid.org/0000-0002-4579-0195"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kenji Yasuoka","raw_affiliation_strings":["Department of Mechanical Engineering"],"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5111737458"],"corresponding_institution_ids":["https://openalex.org/I4210141143"],"apc_list":null,"apc_paid":null,"fwci":2.5663,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.90273472,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":95},"biblio":{"volume":"30","issue":"6","first_page":"3108","last_page":"3125"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9891999959945679,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9891999959945679,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13126","display_name":"Scientific Research and Discoveries","score":0.9889000058174133,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9876999855041504,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7795704007148743},{"id":"https://openalex.org/keywords/subroutine","display_name":"Subroutine","score":0.7372769713401794},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5897689461708069},{"id":"https://openalex.org/keywords/xeon","display_name":"Xeon","score":0.5708105564117432},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5557318925857544},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.5536342263221741},{"id":"https://openalex.org/keywords/xeon-phi","display_name":"Xeon Phi","score":0.4985537528991699},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.47945156693458557},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.46908894181251526},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.42972898483276367},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.3457140326499939},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3190028667449951},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10721993446350098}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7795704007148743},{"id":"https://openalex.org/C96147967","wikidata":"https://www.wikidata.org/wiki/Q190686","display_name":"Subroutine","level":2,"score":0.7372769713401794},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5897689461708069},{"id":"https://openalex.org/C145108525","wikidata":"https://www.wikidata.org/wiki/Q656154","display_name":"Xeon","level":2,"score":0.5708105564117432},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5557318925857544},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.5536342263221741},{"id":"https://openalex.org/C96972482","wikidata":"https://www.wikidata.org/wiki/Q1049168","display_name":"Xeon Phi","level":2,"score":0.4985537528991699},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.47945156693458557},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.46908894181251526},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.42972898483276367},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.3457140326499939},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3190028667449951},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10721993446350098},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1137/070692054","is_oa":false,"landing_page_url":"https://doi.org/10.1137/070692054","pdf_url":null,"source":{"id":"https://openalex.org/S165512578","display_name":"SIAM Journal on Scientific Computing","issn_l":"1064-8275","issn":["1064-8275","1095-7197"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Scientific Computing","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1985291569","https://openalex.org/W1988307783","https://openalex.org/W1988537257","https://openalex.org/W1998067986","https://openalex.org/W2003568601","https://openalex.org/W2012407419","https://openalex.org/W2018312454","https://openalex.org/W2023971144","https://openalex.org/W2032516029","https://openalex.org/W2059611221","https://openalex.org/W2067174909","https://openalex.org/W2089686040","https://openalex.org/W2092518977","https://openalex.org/W2137175729","https://openalex.org/W2146459308","https://openalex.org/W2171268876"],"related_works":["https://openalex.org/W1974923383","https://openalex.org/W2475524688","https://openalex.org/W2739740241","https://openalex.org/W2085105049","https://openalex.org/W2526069705","https://openalex.org/W2024016913","https://openalex.org/W2019153376","https://openalex.org/W2981664121","https://openalex.org/W2796552083","https://openalex.org/W2949197156"],"abstract_inverted_index":{"Molecular":[0],"dynamics":[1],"(MD)":[2],"simulation":[3],"requires":[4,93],"huge":[5],"computational":[6],"power":[7],"because":[8,63,102],"each":[9],"atom":[10],"interacts":[11],"with":[12,126,164,248],"another":[13],"by":[14,157],"long-range":[15],"forces,":[16],"such":[17,31],"as":[18,32],"Coulomb":[19],"and":[20,80],"van":[21],"der":[22],"Waals":[23],"forces.":[24],"Therefore,":[25],"parallel":[26,109],"computers":[27],"or":[28,49,143,226],"special":[29,159],"accelerators,":[30],"MDGRAPE-3,":[33],"are":[34,82],"required":[35],"for":[36,59,90,129,255],"accelerating":[37,60],"MD":[38,61,144,187,256],"simulations.":[39,145,257],"A":[40],"video":[41,70,123],"game":[42,71,124],"processor":[43],"in":[44,179,189,242],"a":[45,56,76,106,134,165,180,206,224],"Sony":[46],"PlayStation":[47,181],"3":[48,182],"NVIDIA's":[50],"graphic":[51],"accelerator":[52],"card":[53],"is":[54,133,155,162,218,253],"also":[55,83],"candidate":[57],"hardware":[58,104,120],"simulations,":[62],"the":[64,68,87,103,113,119,147,150,158,173,185,190,231,235,239,243],"peak":[65],"performance":[66,216,233],"of":[67,75,100,108,122,201,223,238],"latest":[69],"processors":[72,92,125],"exceeds":[73],"that":[74,222],"current":[77],"PC's":[78],"CPU,":[79],"they":[81],"very":[84],"cost-effective.":[85],"However,":[86],"software":[88,130,192],"development":[89],"these":[91],"much":[94],"more":[95],"time":[96,128],"compared":[97,204],"to":[98,117,138,169,183,197,205,221],"CPUs":[99],"PCs":[101],"has":[105],"lot":[107],"processing.":[110],"We":[111,175,194],"propose":[112],"virtual-GRAPE":[114],"programming":[115],"model":[116,178],"utilize":[118],"resource":[121],"minimum":[127],"development.":[131],"GRAPE":[132],"special-purpose":[135],"computer":[136],"used":[137,171],"accelerate":[139,184],"particle-based":[140],"simulations:":[141],"astrophysical":[142],"Under":[146],"Virtual-GRAPE":[148],"model,":[149],"subroutine":[151,168],"whose":[152],"calculation":[153],"speed":[154],"accelerated":[156],"hardware,":[160],"GRAPE,":[161],"replaced":[163],"specially":[166],"tuned":[167,244],"be":[170],"without":[172],"accelerator.":[174],"implemented":[176],"this":[177],"\u201csander\u201d":[186],"module":[188],"AMBER":[191],"package.":[193],"were":[195,246],"able":[196],"achieve":[198],"an":[199,210,227],"acceleration":[200],"20":[202],"times,":[203],"serial":[207],"job":[208],"using":[209],"Intel":[211],"Xeon":[212],"5160":[213],"processor.":[214],"Its":[215],"cost":[217],"far":[219],"superior":[220],"PC":[225],"MDGRAPE-3.":[228],"To":[229],"obtain":[230],"highest":[232],"from":[234],"subroutine,":[236],"most":[237],"arithmetic":[240],"operations":[241],"routine":[245],"performed":[247],"single":[249],"precision":[250],"accuracy,":[251],"which":[252],"sufficient":[254]},"counts_by_year":[{"year":2021,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}