{"id":"https://openalex.org/W2048593763","doi":"https://doi.org/10.1145/2808719.2808742","title":"Accelerated molecular mechanical and solvation energetics on multicore CPUs and manycore GPUs","display_name":"Accelerated molecular mechanical and solvation energetics on multicore CPUs and manycore GPUs","publication_year":2015,"publication_date":"2015-09-09","ids":{"openalex":"https://openalex.org/W2048593763","doi":"https://doi.org/10.1145/2808719.2808742","mag":"2048593763","pmid":"https://pubmed.ncbi.nlm.nih.gov/32647834"},"language":"en","primary_location":{"id":"doi:10.1145/2808719.2808742","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2808719.2808742","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7347088","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073117458","display_name":"Deukhyun Cha","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Deukhyun Cha","raw_affiliation_strings":["Bluware Inc., Houston, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bluware Inc., Houston, TX","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101744774","display_name":"Qin Zhang","orcid":"https://orcid.org/0000-0003-1627-5423"},"institutions":[{"id":"https://openalex.org/I4693666","display_name":"GGG (France)","ror":"https://ror.org/03end3932","country_code":"FR","type":"company","lineage":["https://openalex.org/I4693666"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Qin Zhang","raw_affiliation_strings":["CGG Houston, TX","CGG Houston, TX#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CGG Houston, TX","institution_ids":[]},{"raw_affiliation_string":"CGG Houston, TX#TAB#","institution_ids":["https://openalex.org/I4693666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026593207","display_name":"Jesmin Jahan Tithi","orcid":"https://orcid.org/0000-0002-2861-8393"},"institutions":[{"id":"https://openalex.org/I1327163397","display_name":"State University of New York","ror":"https://ror.org/01q1z8k08","country_code":"US","type":"education","lineage":["https://openalex.org/I1327163397"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jesmin Jahan Tithi","raw_affiliation_strings":["State University of New York, Stony Brook, NY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State University of New York, Stony Brook, NY","institution_ids":["https://openalex.org/I1327163397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003728153","display_name":"Alexander Rand","orcid":"https://orcid.org/0000-0002-3484-2703"},"institutions":[{"id":"https://openalex.org/I164214545","display_name":"CD-adapco (United Kingdom)","ror":"https://ror.org/05mxb6722","country_code":"GB","type":"company","lineage":["https://openalex.org/I164214545","https://openalex.org/I4210145557"]},{"id":"https://openalex.org/I4210145557","display_name":"CD-adapco (United States)","ror":"https://ror.org/05abbvq76","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145557"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Alexander Rand","raw_affiliation_strings":["CD-adapco, Austin, TX","CD-adapco, Austin, TX#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CD-adapco, Austin, TX","institution_ids":["https://openalex.org/I4210145557"]},{"raw_affiliation_string":"CD-adapco, Austin, TX#TAB#","institution_ids":["https://openalex.org/I164214545"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025290203","display_name":"Rezaul Chowdhury","orcid":"https://orcid.org/0000-0002-7022-5278"},"institutions":[{"id":"https://openalex.org/I1327163397","display_name":"State University of New York","ror":"https://ror.org/01q1z8k08","country_code":"US","type":"education","lineage":["https://openalex.org/I1327163397"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rezaul A. Chowdhury","raw_affiliation_strings":["State University of New York, Stony Brook, NY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State University of New York, Stony Brook, NY","institution_ids":["https://openalex.org/I1327163397"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030896164","display_name":"Chandrajit Bajaj","orcid":"https://orcid.org/0000-0002-9619-3278"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chandrajit Bajaj","raw_affiliation_strings":["University of Texas at Austin, Austin, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Texas at Austin, Austin, TX","institution_ids":["https://openalex.org/I86519309"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.3012,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.61887713,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"2015","issue":null,"first_page":"222","last_page":"231"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.54830002784729,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.54830002784729,"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"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.17110000550746918,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.06319999694824219,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.78363037109375},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.6874617338180542},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6827169060707092},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.6515703201293945},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.6183173656463623},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.5658456087112427},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.5558946132659912},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.5523557662963867},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.5313917398452759},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.5142781138420105},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.47262144088745117},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.45791640877723694},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.349642276763916},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.14094391465187073},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.06786927580833435}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.78363037109375},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.6874617338180542},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6827169060707092},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.6515703201293945},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.6183173656463623},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.5658456087112427},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.5558946132659912},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.5523557662963867},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.5313917398452759},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.5142781138420105},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.47262144088745117},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.45791640877723694},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.349642276763916},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.14094391465187073},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.06786927580833435},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","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/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/2808719.2808742","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2808719.2808742","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},{"id":"pmid:32647834","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32647834","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-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7347088","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7347088","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM BCB","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7347088","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7347088","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM BCB","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7852361890","display_name":null,"funder_award_id":"OCI-1216701, CCF-1162196","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8735678594","display_name":null,"funder_award_id":"R01EB004873","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310620","display_name":"University of Texas at Austin","ror":"https://ror.org/00hj54h04"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320338291","display_name":"Sandia National Laboratories","ror":"https://ror.org/01apwpt12"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1966634937","https://openalex.org/W1970111528","https://openalex.org/W1973858832","https://openalex.org/W1974045947","https://openalex.org/W1974427517","https://openalex.org/W1977949865","https://openalex.org/W1982115588","https://openalex.org/W1984015691","https://openalex.org/W1995660477","https://openalex.org/W1997503006","https://openalex.org/W2000337643","https://openalex.org/W2000636639","https://openalex.org/W2002659345","https://openalex.org/W2003811416","https://openalex.org/W2004822259","https://openalex.org/W2014918217","https://openalex.org/W2019465613","https://openalex.org/W2019504893","https://openalex.org/W2022492426","https://openalex.org/W2027602276","https://openalex.org/W2027978582","https://openalex.org/W2033252344","https://openalex.org/W2033558148","https://openalex.org/W2033767661","https://openalex.org/W2034834303","https://openalex.org/W2047730466","https://openalex.org/W2048740445","https://openalex.org/W2050013934","https://openalex.org/W2051419785","https://openalex.org/W2051844996","https://openalex.org/W2052071439","https://openalex.org/W2053263609","https://openalex.org/W2054622952","https://openalex.org/W2056188446","https://openalex.org/W2057478971","https://openalex.org/W2057761913","https://openalex.org/W2072073580","https://openalex.org/W2075468261","https://openalex.org/W2077852080","https://openalex.org/W2078391824","https://openalex.org/W2083206954","https://openalex.org/W2084423328","https://openalex.org/W2099813373","https://openalex.org/W2100444300","https://openalex.org/W2107317356","https://openalex.org/W2108695135","https://openalex.org/W2131320700","https://openalex.org/W2131754023","https://openalex.org/W2134544924","https://openalex.org/W2146847742","https://openalex.org/W2150981663","https://openalex.org/W2157749636","https://openalex.org/W2159497832","https://openalex.org/W2160544821","https://openalex.org/W2167815357","https://openalex.org/W2172013743","https://openalex.org/W2311078281","https://openalex.org/W2323594350"],"related_works":["https://openalex.org/W1963859303","https://openalex.org/W2364044215","https://openalex.org/W2389600408","https://openalex.org/W240129890","https://openalex.org/W3048701459","https://openalex.org/W2149078538","https://openalex.org/W2080146221","https://openalex.org/W2370314112","https://openalex.org/W1912958759","https://openalex.org/W2792081825"],"abstract_inverted_index":{"MOTIVATION:":[0],"Despite":[1],"several":[2,152],"reported":[3],"acceleration":[4,120],"successes":[5],"of":[6,44,102,110,182,194,202,223],"programmable":[7],"GPUs":[8],"(Graphics":[9],"Processing":[10],"Units)":[11],"for":[12,49,57,74,107,118,200,220],"molecular":[13,75,147,204],"modeling":[14],"and":[15,46,78,80,91,128,138,170,235],"simulation":[16],"tools,":[17],"the":[18,34,39,175,183,203,217,224],"general":[19],"focus":[20],"has":[21,62],"been":[22,65],"on":[23,38,87,156,179],"fast":[24,71],"computation":[25,72,199],"with":[26,149],"small":[27],"molecules.":[28],"This":[29],"was":[30],"primarily":[31],"due":[32],"to":[33,98,143,151,173,212,215],"limited":[35],"memory":[36,129],"size":[37],"GPU.":[40],"Moreover":[41],"simultaneous":[42],"use":[43],"CPU":[45,169],"GPU":[47,119,171],"cores":[48,172],"a":[50,55,135,162],"single":[51],"kernel":[52,117,133],"execution":[53],"-":[54,61],"necessity":[56],"achieving":[58],"high":[59,125],"parallelism":[60],"also":[63],"not":[64],"fully":[66],"considered.":[67],"RESULTS:":[68],"We":[69],"present":[70,161],"methods":[73],"mechanical":[76],"(Lennard-Jones":[77],"Coulombic)":[79],"generalized":[81],"Born":[82],"solvation":[83],"energetics":[84,106,205],"which":[85,123,165],"run":[86],"commodity":[88],"multicore":[89],"CPUs":[90],"manycore":[92],"GPUs.":[93],"The":[94,207],"key":[95],"idea":[96],"is":[97,121,210],"trade":[99],"off":[100],"accuracy":[101],"pairwise,":[103],"long-range":[104],"atomistic":[105],"higher":[108],"speed":[109],"execution.":[111],"A":[112],"simple":[113],"yet":[114],"efficient":[115],"CUDA":[116,132,158,187],"presented":[122],"ensures":[124],"arithmetic":[126],"intensity":[127],"efficiency.":[130],"Our":[131,186],"uses":[134],"cache-friendly,":[136],"recursive":[137],"linear-space":[139],"octree":[140],"data":[141],"structure":[142],"handle":[144],"very":[145],"large":[146],"structures":[148],"up":[150],"million":[153],"atoms.":[154],"Based":[155],"this":[157],"kernel,":[159],"we":[160],"hybrid":[163,208],"method":[164,209],"simultaneously":[166],"exploits":[167],"both":[168],"provide":[174],"best":[176,218],"performance":[177,219],"based":[178],"selected":[180],"parameters":[181],"approximation":[184,225],"scheme.":[185],"kernels":[188],"achieve":[189,216],"more":[190],"than":[191],"two":[192],"orders":[193],"magnitude":[195],"speedup":[196],"over":[197],"serial":[198],"many":[201],"terms.":[206],"shown":[211],"be":[213],"able":[214],"all":[221],"values":[222],"parameter.":[226],"AVAILABILITY:":[227],"(Parallel":[228],"Molecular":[229],"Energetic":[230],"using":[231],"Octree":[232],"Pairwise":[233],"Approximation)":[234],"downloadable":[236],"from":[237],"http://cvcweb.ices.utexas.edu/software.":[238]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
