{"id":"https://openalex.org/W2117639210","doi":"https://doi.org/10.1109/hpca.2008.4658650","title":"High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation","display_name":"High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation","publication_year":2008,"publication_date":"2008-02-01","ids":{"openalex":"https://openalex.org/W2117639210","doi":"https://doi.org/10.1109/hpca.2008.4658650","mag":"2117639210"},"language":"en","primary_location":{"id":"doi:10.1109/hpca.2008.4658650","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hpca.2008.4658650","pdf_url":null,"source":{"id":"https://openalex.org/S4210184388","display_name":"Proceedings - International Symposium on High-Performance Computer Architecture/Proceedings","issn_l":"1530-0897","issn":["1530-0897","2378-203X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 IEEE 14th International Symposium on High Performance Computer Architecture","raw_type":"proceedings-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/A5026218309","display_name":"Richard H. Larson","orcid":null},"institutions":[{"id":"https://openalex.org/I2799548008","display_name":"D. E. Shaw Research","ror":"https://ror.org/02s04h872","country_code":"US","type":"company","lineage":["https://openalex.org/I2799548008"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard H. Larson","raw_affiliation_strings":["D. E. Shaw Research, NY, USA","D E Shaw Research New York, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D. E. Shaw Research, NY, USA","institution_ids":["https://openalex.org/I2799548008"]},{"raw_affiliation_string":"D E Shaw Research New York, NY#TAB#","institution_ids":["https://openalex.org/I2799548008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030397130","display_name":"John K. Salmon","orcid":null},"institutions":[{"id":"https://openalex.org/I2799548008","display_name":"D. E. Shaw Research","ror":"https://ror.org/02s04h872","country_code":"US","type":"company","lineage":["https://openalex.org/I2799548008"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John K. Salmon","raw_affiliation_strings":["D. E. Shaw Research, NY, USA","D E Shaw Research New York, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D. E. Shaw Research, NY, USA","institution_ids":["https://openalex.org/I2799548008"]},{"raw_affiliation_string":"D E Shaw Research New York, NY#TAB#","institution_ids":["https://openalex.org/I2799548008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061322136","display_name":"Ron O. Dror","orcid":"https://orcid.org/0000-0002-6418-2793"},"institutions":[{"id":"https://openalex.org/I2799548008","display_name":"D. E. Shaw Research","ror":"https://ror.org/02s04h872","country_code":"US","type":"company","lineage":["https://openalex.org/I2799548008"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ron O. Dror","raw_affiliation_strings":["D. E. Shaw Research, NY, USA","D E Shaw Research New York, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D. E. Shaw Research, NY, USA","institution_ids":["https://openalex.org/I2799548008"]},{"raw_affiliation_string":"D E Shaw Research New York, NY#TAB#","institution_ids":["https://openalex.org/I2799548008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065367101","display_name":"Martin M. Deneroff","orcid":null},"institutions":[{"id":"https://openalex.org/I2799548008","display_name":"D. E. Shaw Research","ror":"https://ror.org/02s04h872","country_code":"US","type":"company","lineage":["https://openalex.org/I2799548008"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin M. Deneroff","raw_affiliation_strings":["D. E. Shaw Research, NY, USA","D E Shaw Research New York, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D. E. Shaw Research, NY, USA","institution_ids":["https://openalex.org/I2799548008"]},{"raw_affiliation_string":"D E Shaw Research New York, NY#TAB#","institution_ids":["https://openalex.org/I2799548008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035427716","display_name":"Cliff Young","orcid":"https://orcid.org/0000-0003-2172-1651"},"institutions":[{"id":"https://openalex.org/I2799548008","display_name":"D. E. Shaw Research","ror":"https://ror.org/02s04h872","country_code":"US","type":"company","lineage":["https://openalex.org/I2799548008"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cliff Young","raw_affiliation_strings":["D. E. Shaw Research, NY, USA","D E Shaw Research New York, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D. E. Shaw Research, NY, USA","institution_ids":["https://openalex.org/I2799548008"]},{"raw_affiliation_string":"D E Shaw Research New York, NY#TAB#","institution_ids":["https://openalex.org/I2799548008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112225904","display_name":"J.P. Grossman","orcid":null},"institutions":[{"id":"https://openalex.org/I2799548008","display_name":"D. E. Shaw Research","ror":"https://ror.org/02s04h872","country_code":"US","type":"company","lineage":["https://openalex.org/I2799548008"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J.P. Grossman","raw_affiliation_strings":["D. E. Shaw Research, NY, USA","D E Shaw Research New York, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D. E. Shaw Research, NY, USA","institution_ids":["https://openalex.org/I2799548008"]},{"raw_affiliation_string":"D E Shaw Research New York, NY#TAB#","institution_ids":["https://openalex.org/I2799548008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062359517","display_name":"Yibing Shan","orcid":"https://orcid.org/0000-0002-3865-8110"},"institutions":[{"id":"https://openalex.org/I2799548008","display_name":"D. E. Shaw Research","ror":"https://ror.org/02s04h872","country_code":"US","type":"company","lineage":["https://openalex.org/I2799548008"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yibing Shan","raw_affiliation_strings":["D. E. Shaw Research, NY, USA","D E Shaw Research New York, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D. E. Shaw Research, NY, USA","institution_ids":["https://openalex.org/I2799548008"]},{"raw_affiliation_string":"D E Shaw Research New York, NY#TAB#","institution_ids":["https://openalex.org/I2799548008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000327032","display_name":"John L. Klepeis","orcid":"https://orcid.org/0000-0001-5180-3696"},"institutions":[{"id":"https://openalex.org/I2799548008","display_name":"D. E. Shaw Research","ror":"https://ror.org/02s04h872","country_code":"US","type":"company","lineage":["https://openalex.org/I2799548008"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John L. Klepeis","raw_affiliation_strings":["D. E. Shaw Research, NY, USA","D E Shaw Research New York, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D. E. Shaw Research, NY, USA","institution_ids":["https://openalex.org/I2799548008"]},{"raw_affiliation_string":"D E Shaw Research New York, NY#TAB#","institution_ids":["https://openalex.org/I2799548008"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5105412737","display_name":"David E. Shaw","orcid":null},"institutions":[{"id":"https://openalex.org/I2799548008","display_name":"D. E. Shaw Research","ror":"https://ror.org/02s04h872","country_code":"US","type":"company","lineage":["https://openalex.org/I2799548008"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David E. Shaw","raw_affiliation_strings":["D. E. Shaw Research, NY, USA","D E Shaw Research New York, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D. E. Shaw Research, NY, USA","institution_ids":["https://openalex.org/I2799548008"]},{"raw_affiliation_string":"D E Shaw Research New York, NY#TAB#","institution_ids":["https://openalex.org/I2799548008"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I2799548008"],"apc_list":null,"apc_paid":null,"fwci":3.6583,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.93265832,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"331","last_page":"342"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13126","display_name":"Scientific Research and Discoveries","score":0.9872999787330627,"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"}},"topics":[{"id":"https://openalex.org/T13126","display_name":"Scientific Research and Discoveries","score":0.9872999787330627,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.9843999743461609,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.978600025177002,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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":0.7343422174453735},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.7086864709854126},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6323227286338806},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.587497353553772},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5358667969703674},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5267966389656067},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4959436357021332},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.4715728163719177},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.42999914288520813},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33836829662323},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10103955864906311}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7343422174453735},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.7086864709854126},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6323227286338806},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.587497353553772},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5358667969703674},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5267966389656067},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4959436357021332},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.4715728163719177},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.42999914288520813},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33836829662323},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10103955864906311},{"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/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"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/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/hpca.2008.4658650","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hpca.2008.4658650","pdf_url":null,"source":{"id":"https://openalex.org/S4210184388","display_name":"Proceedings - International Symposium on High-Performance Computer Architecture/Proceedings","issn_l":"1530-0897","issn":["1530-0897","2378-203X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 IEEE 14th International Symposium on High Performance Computer Architecture","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.192.2910","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.192.2910","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.utah.edu/hpca08/papers/6A_1_Larson.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4300000071525574,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1555540498","https://openalex.org/W1565282391","https://openalex.org/W1966743338","https://openalex.org/W1975353473","https://openalex.org/W1978159078","https://openalex.org/W1978281521","https://openalex.org/W1987284299","https://openalex.org/W1991966795","https://openalex.org/W2002257715","https://openalex.org/W2013979082","https://openalex.org/W2019465613","https://openalex.org/W2028263411","https://openalex.org/W2031504050","https://openalex.org/W2035720425","https://openalex.org/W2058874255","https://openalex.org/W2062446822","https://openalex.org/W2065052886","https://openalex.org/W2084800760","https://openalex.org/W2093221728","https://openalex.org/W2104766043","https://openalex.org/W2109395397","https://openalex.org/W2110338379","https://openalex.org/W2115451770","https://openalex.org/W2144803600","https://openalex.org/W2150981663","https://openalex.org/W2153228625","https://openalex.org/W2153597830","https://openalex.org/W2171268876","https://openalex.org/W3142945824","https://openalex.org/W3149078497"],"related_works":["https://openalex.org/W2073684863","https://openalex.org/W1582436825","https://openalex.org/W2167527468","https://openalex.org/W2586370661","https://openalex.org/W1996803181","https://openalex.org/W2979588510","https://openalex.org/W2314053740","https://openalex.org/W2960681633","https://openalex.org/W1970113381","https://openalex.org/W1985494319"],"abstract_inverted_index":{"Anton":[0,140,222],"is":[1,153,181],"a":[2,78,101,116,130,154],"massively":[3],"parallel":[4,247],"special-purpose":[5,246],"supercomputer":[6],"designed":[7],"to":[8,38,113,121,133,145,198,215,223,242],"accelerate":[9],"molecular":[10],"dynamics":[11],"(MD)":[12],"simulations":[13,50,237],"by":[14,62,77,174],"several":[15],"orders":[16],"of":[17,28,44,54,87,136,188,201,204],"magnitude,":[18],"making":[19],"possible":[20],"for":[21,48,159],"the":[22,25,45,52,160,199,202],"first":[23,152],"time":[24,40,196,239],"atomic-level":[26],"simulation":[27],"many":[29],"biologically":[30],"important":[31],"phenomena":[32],"that":[33,106,164,185],"take":[34,134],"place":[35],"over":[36],"microsecond":[37],"millisecond":[39],"scales.":[41],"The":[42,83,151,179],"majority":[43],"computation":[46],"required":[47],"MD":[49,236],"involves":[51],"calculation":[53],"pairwise":[55,225],"interactions":[56,74,226],"between":[57],"particles":[58],"and/or":[59],"gridpoints":[60],"separated":[61],"no":[63],"more":[64],"than":[65],"some":[66],"specified":[67],"cutoff":[68],"radius.":[69],"In":[70,119],"Anton,":[71],"such":[72],"range-limited":[73,161],"are":[75],"handled":[76],"high-throughput":[79],"interaction":[80],"subsystem":[81],"(HTIS).":[82],"HTIS":[84],"on":[85,103,115,238],"each":[86,99],"Antonpsilas":[88],"512":[89],"ASICs":[90],"includes":[91],"32":[92],"computational":[93,138],"pipelines":[94,124],"running":[95],"at":[96,129],"800":[97],"MHz,":[98],"producing":[100],"result":[102],"every":[104],"cycle":[105],"would":[107],"require":[108],"approximately":[109],"50":[110],"arithmetic":[111],"operations":[112],"compute":[114],"general-purpose":[117],"processor.":[118],"order":[120],"feed":[122],"these":[123,219],"and":[125,148,171,210,231,245],"collect":[126],"their":[127,216],"results":[128],"speed":[131],"sufficient":[132],"advantage":[135],"this":[137],"power,":[139],"uses":[141],"two":[142,192],"novel":[143],"techniques":[144],"limit":[146],"inter-":[147],"intra-chip":[149],"communication.":[150],"recently":[155],"developed":[156],"parallelization":[157],"algorithm":[158],"N-body":[162],"problem":[163],"offers":[165],"major":[166],"advantages":[167],"in":[168,195],"both":[169],"asymptotic":[170],"absolute":[172],"terms":[173],"comparison":[175],"with":[176,208,227],"traditional":[177],"methods.":[178],"second":[180],"an":[182],"architectural":[183],"feature":[184],"processes":[186],"pairs":[187],"points":[189],"chosen":[190],"from":[191],"point":[193],"sets":[194],"proportional":[197,213],"product":[200],"sizes":[203],"those":[205],"sets,":[206],"but":[207],"input":[209],"output":[211],"volume":[212],"only":[214],"sum.":[217],"Together,":[218],"features":[220],"allow":[221],"perform":[224],"very":[228],"high":[229],"throughput":[230],"unusually":[232],"low":[233],"latency,":[234],"enabling":[235],"scales":[240],"inaccessible":[241],"other":[243],"general-":[244],"systems.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}
