{"id":"https://openalex.org/W2086364561","doi":"https://doi.org/10.1145/1862648.1862653","title":"Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems","display_name":"Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems","publication_year":2010,"publication_date":"2010-11-01","ids":{"openalex":"https://openalex.org/W2086364561","doi":"https://doi.org/10.1145/1862648.1862653","mag":"2086364561","pmid":"https://pubmed.ncbi.nlm.nih.gov/21660208"},"language":"en","primary_location":{"id":"doi:10.1145/1862648.1862653","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1862648.1862653","pdf_url":null,"source":{"id":"https://openalex.org/S112809824","display_name":"ACM Transactions on Reconfigurable Technology and Systems","issn_l":"1936-7406","issn":["1936-7406","1936-7414"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Reconfigurable Technology and Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5058876075","display_name":"Matt Chiu","orcid":"https://orcid.org/0000-0002-8186-7241"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Matt Chiu","raw_affiliation_strings":["Boston University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boston University","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021051610","display_name":"Martin Herbordt","orcid":"https://orcid.org/0000-0002-3443-9113"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Martin C. Herbordt","raw_affiliation_strings":["Boston University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boston University","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.2456,"has_fulltext":false,"cited_by_count":86,"citation_normalized_percentile":{"value":0.88994488,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"3","issue":"4","first_page":"1","last_page":"37"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9994999766349792,"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"}},{"id":"https://openalex.org/T10363","display_name":"Low-power high-performance VLSI design","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13182","display_name":"Quantum-Dot Cellular Automata","score":0.9887999892234802,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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":0.8085542917251587},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.6966488361358643},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6507989168167114},{"id":"https://openalex.org/keywords/stratix","display_name":"Stratix","score":0.6392173767089844},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.575075626373291},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.536062479019165},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.5343382358551025},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4694095849990845},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.4472348988056183},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4407999813556671},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.4333404004573822},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2514559328556061},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.203617662191391}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8085542917251587},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.6966488361358643},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6507989168167114},{"id":"https://openalex.org/C2776277307","wikidata":"https://www.wikidata.org/wiki/Q22074755","display_name":"Stratix","level":3,"score":0.6392173767089844},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.575075626373291},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.536062479019165},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5343382358551025},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4694095849990845},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.4472348988056183},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4407999813556671},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.4333404004573822},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2514559328556061},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.203617662191391},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","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/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1145/1862648.1862653","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1862648.1862653","pdf_url":null,"source":{"id":"https://openalex.org/S112809824","display_name":"ACM Transactions on Reconfigurable Technology and Systems","issn_l":"1936-7406","issn":["1936-7406","1936-7414"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Reconfigurable Technology and Systems","raw_type":"journal-article"},{"id":"pmid:21660208","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21660208","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM transactions on reconfigurable technology and systems","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.546.2165","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.546.2165","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.bu.edu/caadlab/trets10.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:2131230","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3109751","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.49000000953674316,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G2883975500","display_name":null,"funder_award_id":"R01 RR023168","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G651622515","display_name":null,"funder_award_id":"R01-RR023168-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334350","display_name":"High Performance Research Computing, Texas A and M University","ror":null},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W60782494","https://openalex.org/W1514336338","https://openalex.org/W1757537413","https://openalex.org/W1965067299","https://openalex.org/W1978281521","https://openalex.org/W1979573134","https://openalex.org/W1981452224","https://openalex.org/W1991939674","https://openalex.org/W1996174326","https://openalex.org/W2012632603","https://openalex.org/W2013173369","https://openalex.org/W2058874255","https://openalex.org/W2062446822","https://openalex.org/W2067174909","https://openalex.org/W2073289615","https://openalex.org/W2078391824","https://openalex.org/W2086889049","https://openalex.org/W2088187609","https://openalex.org/W2097525317","https://openalex.org/W2106942255","https://openalex.org/W2109266807","https://openalex.org/W2110338379","https://openalex.org/W2114702066","https://openalex.org/W2117639210","https://openalex.org/W2124745044","https://openalex.org/W2125441126","https://openalex.org/W2138376372","https://openalex.org/W2146717187","https://openalex.org/W2148983145","https://openalex.org/W2151204271","https://openalex.org/W2153228625","https://openalex.org/W2159497832","https://openalex.org/W2163112106","https://openalex.org/W2169594918","https://openalex.org/W2170396259","https://openalex.org/W2171268876","https://openalex.org/W2336528065","https://openalex.org/W3140968848","https://openalex.org/W3149078497","https://openalex.org/W3150878027","https://openalex.org/W4245503759"],"related_works":["https://openalex.org/W2187189666","https://openalex.org/W2949084706","https://openalex.org/W631639522","https://openalex.org/W2818116514","https://openalex.org/W2540664775","https://openalex.org/W1509155667","https://openalex.org/W2518118925","https://openalex.org/W3208151864","https://openalex.org/W1564576805","https://openalex.org/W4254372399"],"abstract_inverted_index":{"The":[0],"acceleration":[1],"of":[2,54,63,102,105,127,156],"molecular":[3],"dynamics":[4],"(MD)":[5],"simulations":[6],"using":[7],"high-performance":[8],"reconfigurable":[9],"computing":[10],"(HPRC)":[11],"has":[12],"been":[13],"much":[14],"studied.":[15],"Given":[16],"the":[17,40,45,55,60,64,93,98,103,128,140,157,180,199],"intense":[18],"competition":[19],"from":[20],"multicore":[21],"and":[22,75,82,131,136,182],"GPUs,":[23],"there":[24],"is":[25,203],"now":[26],"a":[27,113,124,143,153],"question":[28],"whether":[29],"MD":[30,41,117],"on":[31,39,89,179],"HPRC":[32],"can":[33,148,177,185],"be":[34,149],"competitive.":[35],"We":[36,79],"concentrate":[37],"here":[38],"kernel":[42],"computation:":[43],"determining":[44],"short-range":[46,200],"force":[47,65,170],"between":[48],"particle":[49,106,129],"pairs.":[50],"In":[51,92],"one":[52],"part":[53],"study,":[56],"we":[57,96,161],"systematically":[58],"explore":[59],"design":[61],"space":[62],"pipeline":[66],"with":[67,108,151],"respect":[68],"to":[69,205],"arithmetic":[70,72],"algorithm,":[71],"mode,":[73],"precision,":[74],"various":[76],"other":[77,94],"optimizations.":[78],"examine":[80],"simplifications":[81],"find":[83,162],"that":[84,183],"some":[85],"have":[86],"little":[87],"effect":[88],"simulation":[90],"quality.":[91],"part,":[95],"present":[97],"first":[99],"FPGA":[100],"study":[101],"filtering":[104,135,147],"pairs":[107],"nearly":[109,174],"zero":[110],"mutual":[111],"force,":[112,201],"standard":[114],"optimization":[115],"in":[116,192],"codes.":[118],"There":[119],"are":[120],"several":[121],"innovations,":[122],"including":[123],"novel":[125],"partitioning":[126],"space,":[130],"new":[132],"methods":[133],"for":[134,164,198,210],"mapping":[137],"work":[138],"onto":[139],"pipelines.":[141],"As":[142],"consequence,":[144],"highly":[145,208],"efficient":[146],"implemented":[150],"only":[152],"small":[154],"fraction":[155],"FPGA's":[158],"resources.":[159],"Overall,":[160],"that,":[163],"an":[165,193],"Altera":[166],"Stratix-III":[167],"EP3ES260,":[168],"8":[169],"pipelines":[171],"running":[172],"at":[173,187],"200":[175],"MHz":[176],"fit":[178],"FPGA,":[181],"they":[184],"perform":[186],"95%":[188],"efficiency.":[189],"This":[190],"results":[191],"80-fold":[194],"per":[195],"core":[196],"speed-up":[197],"which":[202],"likely":[204],"make":[206],"FPGAs":[207],"competitive":[209],"MD.":[211]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
