{"id":"https://openalex.org/W4401753269","doi":"https://doi.org/10.1109/asap61560.2024.00047","title":"Raising Compute Density of Molecular Dynamics Simulation Through Approximate Memoization","display_name":"Raising Compute Density of Molecular Dynamics Simulation Through Approximate Memoization","publication_year":2024,"publication_date":"2024-07-24","ids":{"openalex":"https://openalex.org/W4401753269","doi":"https://doi.org/10.1109/asap61560.2024.00047"},"language":"en","primary_location":{"id":"doi:10.1109/asap61560.2024.00047","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/asap61560.2024.00047","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE 35th International Conference on Application-specific Systems, Architectures and Processors (ASAP)","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/A5106662581","display_name":"Salim Khemira","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Salim Khemira","raw_affiliation_strings":["University of Toronto,Dept. of Electrical and Computer Engineering,Toronto,Canada"],"affiliations":[{"raw_affiliation_string":"University of Toronto,Dept. of Electrical and Computer Engineering,Toronto,Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100634221","display_name":"Xinyuan Wang","orcid":"https://orcid.org/0009-0006-8330-342X"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Xinyuan Wang","raw_affiliation_strings":["University of Toronto,Dept. of Electrical and Computer Engineering,Toronto,Canada"],"affiliations":[{"raw_affiliation_string":"University of Toronto,Dept. of Electrical and Computer Engineering,Toronto,Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Anh Nguyen","orcid":null},"institutions":[{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Anh Nguyen","raw_affiliation_strings":["Fujitsu Laboratories,Kawasaki,Japan"],"affiliations":[{"raw_affiliation_string":"Fujitsu Laboratories,Kawasaki,Japan","institution_ids":["https://openalex.org/I2252096349"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013791098","display_name":"Yutaka Tamiya","orcid":null},"institutions":[{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yutaka Tamiya","raw_affiliation_strings":["Fujitsu Laboratories,Kawasaki,Japan"],"affiliations":[{"raw_affiliation_string":"Fujitsu Laboratories,Kawasaki,Japan","institution_ids":["https://openalex.org/I2252096349"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033083222","display_name":"Makoto Taiji","orcid":"https://orcid.org/0000-0002-5317-0500"},"institutions":[{"id":"https://openalex.org/I4210116810","display_name":"RIKEN Center for Biosystems Dynamics Research","ror":"https://ror.org/023rffy11","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210116810"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Makoto Taiji","raw_affiliation_strings":["RIKEN Center for Biosystems Dynamics Research,Kobe,Japan"],"affiliations":[{"raw_affiliation_string":"RIKEN Center for Biosystems Dynamics Research,Kobe,Japan","institution_ids":["https://openalex.org/I4210116810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108775300","display_name":"Takahide Yoshikawa","orcid":null},"institutions":[{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takahide Yoshikawa","raw_affiliation_strings":["Fujitsu Laboratories,Kawasaki,Japan"],"affiliations":[{"raw_affiliation_string":"Fujitsu Laboratories,Kawasaki,Japan","institution_ids":["https://openalex.org/I2252096349"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102812429","display_name":"Jason H. Anderson","orcid":"https://orcid.org/0000-0001-9083-6853"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jason H. Anderson","raw_affiliation_strings":["University of Toronto,Dept. of Electrical and Computer Engineering,Toronto,Canada"],"affiliations":[{"raw_affiliation_string":"University of Toronto,Dept. of Electrical and Computer Engineering,Toronto,Canada","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5106662581"],"corresponding_institution_ids":["https://openalex.org/I185261750"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08085773,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"195","last_page":"203"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9922999739646912,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9922999739646912,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9872999787330627,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9794999957084656,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/raising","display_name":"Raising (metalworking)","score":0.8179947137832642},{"id":"https://openalex.org/keywords/memoization","display_name":"Memoization","score":0.8082449436187744},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7116411328315735},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5206115245819092},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.43540796637535095},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3541514277458191},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.340645432472229},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15433889627456665},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12741303443908691},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07563668489456177},{"id":"https://openalex.org/keywords/mechanical-engineering","display_name":"Mechanical engineering","score":0.0682128369808197},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.060970306396484375}],"concepts":[{"id":"https://openalex.org/C2780589192","wikidata":"https://www.wikidata.org/wiki/Q7285140","display_name":"Raising (metalworking)","level":2,"score":0.8179947137832642},{"id":"https://openalex.org/C79516417","wikidata":"https://www.wikidata.org/wiki/Q1376168","display_name":"Memoization","level":4,"score":0.8082449436187744},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7116411328315735},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5206115245819092},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.43540796637535095},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3541514277458191},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.340645432472229},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15433889627456665},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12741303443908691},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07563668489456177},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0682128369808197},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.060970306396484375},{"id":"https://openalex.org/C42560504","wikidata":"https://www.wikidata.org/wiki/Q15419395","display_name":"Top-down parsing","level":3,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/asap61560.2024.00047","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/asap61560.2024.00047","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE 35th International Conference on Application-specific Systems, Architectures and Processors (ASAP)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W222213312","https://openalex.org/W1850221914","https://openalex.org/W1965784613","https://openalex.org/W2019823285","https://openalex.org/W2027053193","https://openalex.org/W2027295570","https://openalex.org/W2030898836","https://openalex.org/W2030980866","https://openalex.org/W2055564206","https://openalex.org/W2062143991","https://openalex.org/W2070753604","https://openalex.org/W2079199763","https://openalex.org/W2114489396","https://openalex.org/W2127466997","https://openalex.org/W2171268876","https://openalex.org/W2537959404","https://openalex.org/W2737817368","https://openalex.org/W2913371199","https://openalex.org/W2980612421","https://openalex.org/W3156455449","https://openalex.org/W3167345128","https://openalex.org/W3169244019","https://openalex.org/W3209739359","https://openalex.org/W4235722944","https://openalex.org/W4283024935","https://openalex.org/W4293238286","https://openalex.org/W4313259721","https://openalex.org/W4317104064"],"related_works":["https://openalex.org/W2966056201","https://openalex.org/W2182406401","https://openalex.org/W2349031816","https://openalex.org/W2772415251","https://openalex.org/W1985929414","https://openalex.org/W2278916097","https://openalex.org/W2971785569","https://openalex.org/W2354572397","https://openalex.org/W4387885752","https://openalex.org/W1773535258"],"abstract_inverted_index":{"Molecular":[0],"dynamics":[1],"(MD)":[2],"simulation":[3,132],"involves":[4],"simulating":[5],"the":[6,44,51,63,101,104,108,113,135,181,188,193],"interactions":[7],"of":[8,30,47,56,65,148,199],"particles.":[9,57],"MD":[10,48,69,156],"has":[11],"many":[12],"applications":[13],"in":[14,68,90,96],"basic":[15],"biological":[16],"sciences,":[17],"drug":[18],"discovery,":[19],"materials":[20],"science,":[21],"and":[22,93,177,196],"other":[23],"fields.":[24],"Simulating":[25],"<tex":[26,167],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[27,39,41,168],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$1\\mu":[28],"\\mathrm{s}$</tex>":[29],"a":[31,71,91,145],"100K-atom":[32],"system":[33,190],"can":[34,117],"take":[35],"hours":[36],"or":[37,110],"days<sup":[38],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">1</sup><sup":[40],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">1</sup>https://www.bdr.riken.jp/en/research/labs/taiji-mlmdgrape4.html,":[42],"where":[43,82],"compute-heavy":[45],"aspect":[46],"is":[49,123,140,171,185],"calculating":[50],"long-range":[52],"forces":[53,85],"between":[54,174],"pairs":[55],"In":[58,125],"this":[59],"paper,":[60],"we":[61,78,129],"explore":[62],"application":[64],"approximate":[66,80],"computing":[67],"as":[70,166],"means":[72],"to":[73,103,133,137,150],"improve":[74],"compute":[75,163],"density.":[76],"Specifically,":[77],"employ":[79],"memoization,":[81],"previously":[83],"computed":[84],"(and":[86],"more)":[87],"are":[88,94,107],"stored":[89],"table,":[92],"retrieved":[95],"subsequent":[97],"force":[98,105],"calculations,":[99],"provided":[100],"inputs":[102],"calculation":[106],"same":[109],"similar.":[111],"If":[112],"prior-computed":[114],"table":[115,194],"values":[116],"be":[118,151],"used,":[119],"significant":[120],"computational":[121],"work":[122],"avoided.":[124],"an":[126,154],"experimental":[127],"study,":[128],"apply":[130],"software":[131],"understand":[134],"degree":[136],"which":[138],"approximation":[139],"feasible.":[141],"We":[142,160],"then":[143],"propose":[144],"hardware":[146],"implementation":[147],"memoization":[149],"used":[152],"within":[153],"ASIC":[155],"simulator,":[157],"MDGRAPE-4A":[158],"[18].":[159],"show":[161],"that":[162],"density,":[164],"measured":[165],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$\\text{pair-interactions}/(s\\cdot\\mu":[169],"m^{2})$</tex>":[170],"improved":[172],"substantially,":[173],"40":[175],"%":[176,179],"70":[178],"for":[180],"studied":[182],"cases.":[183],"This":[184],"contingent":[186],"on":[187],"particular":[189],"being":[191],"simulated,":[192],"size,":[195],"permitted":[197],"level":[198],"approximation.":[200]},"counts_by_year":[],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
