{"id":"https://openalex.org/W2549616710","doi":"https://doi.org/10.1145/2987373","title":"Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons","display_name":"Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons","publication_year":2016,"publication_date":"2016-11-07","ids":{"openalex":"https://openalex.org/W2549616710","doi":"https://doi.org/10.1145/2987373","mag":"2549616710","pmid":"https://pubmed.ncbi.nlm.nih.gov/28943743"},"language":"en","primary_location":{"id":"doi:10.1145/2987373","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2987373","pdf_url":null,"source":{"id":"https://openalex.org/S38703467","display_name":"ACM Transactions on Modeling and Computer Simulation","issn_l":"1049-3301","issn":["1049-3301","1558-1195"],"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 Modeling and Computer Simulation","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/A5030895241","display_name":"Zhongwei Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhongwei Lin","raw_affiliation_strings":["National University of Defense Technology, Changsha, Hunan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National University of Defense Technology, Changsha, Hunan, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045603103","display_name":"Carl Tropper","orcid":null},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Carl Tropper","raw_affiliation_strings":["McGill University, Montreal, Quebec, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"McGill University, Montreal, Quebec, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025235631","display_name":"Robert A. McDougal","orcid":"https://orcid.org/0000-0001-6394-3127"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert A. McDougal","raw_affiliation_strings":["Yale University, New Haven, Connecticut, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yale University, New Haven, Connecticut, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013842655","display_name":"Mohammand Nazrul Ishlam Patoary","orcid":null},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Mohammand Nazrul Ishlam Patoary","raw_affiliation_strings":["McGill University, Montreal, Quebec, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"McGill University, Montreal, Quebec, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082122443","display_name":"William W. Lytton","orcid":"https://orcid.org/0000-0002-3727-2849"},"institutions":[{"id":"https://openalex.org/I181697535","display_name":"SUNY Downstate Health Sciences University","ror":"https://ror.org/0041qmd21","country_code":"US","type":"education","lineage":["https://openalex.org/I181697535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William W. Lytton","raw_affiliation_strings":["SUNY Downstate Medical Center, Brooklyn, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SUNY Downstate Medical Center, Brooklyn, NY, USA","institution_ids":["https://openalex.org/I181697535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109403093","display_name":"Yiping Yao","orcid":null},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiping Yao","raw_affiliation_strings":["National University of Defense Technology, Changsha, Hunan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National University of Defense Technology, Changsha, Hunan, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027748067","display_name":"Michael L. Hines","orcid":"https://orcid.org/0000-0003-1830-7433"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael L. Hines","raw_affiliation_strings":["Yale University, New Haven, Connecticut, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yale University, New Haven, Connecticut, USA","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.8706,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.77254946,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"27","issue":"2","first_page":"1","last_page":"27"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9961000084877014,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9961000084877014,"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/T10581","display_name":"Neural dynamics and brain function","score":0.9869999885559082,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9657999873161316,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/computer-science","display_name":"Computer science","score":0.5595942139625549},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3903689384460449},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.38893190026283264},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.38213109970092773},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3414701223373413},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3229944109916687}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5595942139625549},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3903689384460449},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.38893190026283264},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.38213109970092773},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3414701223373413},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3229944109916687}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/2987373","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2987373","pdf_url":null,"source":{"id":"https://openalex.org/S38703467","display_name":"ACM Transactions on Modeling and Computer Simulation","issn_l":"1049-3301","issn":["1049-3301","1558-1195"],"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 Modeling and Computer Simulation","raw_type":"journal-article"},{"id":"pmid:28943743","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28943743","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 modeling and computer simulation : a publication of the Association for Computing Machinery","raw_type":null},{"id":"pmh:oai:europepmc.org:4975754","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5604336","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":[],"awards":[{"id":"https://openalex.org/G3239253146","display_name":"\u5e76\u884c\u4eff\u771f\u53ef\u89c6\u5316\u7ec4\u4ef6\u5efa\u6a21\u7406\u8bba\u4e0e\u6280\u672f\u7814\u7a76","funder_award_id":"61170048","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6913835149","display_name":null,"funder_award_id":"R01MH086638 and T15LM007056","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W120905807","https://openalex.org/W153106689","https://openalex.org/W1481371813","https://openalex.org/W1599698343","https://openalex.org/W1963659409","https://openalex.org/W1964663180","https://openalex.org/W1966903828","https://openalex.org/W1973016141","https://openalex.org/W1974974415","https://openalex.org/W1979748495","https://openalex.org/W1982056554","https://openalex.org/W1982903250","https://openalex.org/W2006338283","https://openalex.org/W2007019343","https://openalex.org/W2024048296","https://openalex.org/W2041265238","https://openalex.org/W2043617261","https://openalex.org/W2053132205","https://openalex.org/W2054225000","https://openalex.org/W2055867673","https://openalex.org/W2057970414","https://openalex.org/W2059223531","https://openalex.org/W2061186544","https://openalex.org/W2077346271","https://openalex.org/W2086060503","https://openalex.org/W2086134353","https://openalex.org/W2088019372","https://openalex.org/W2088093088","https://openalex.org/W2088219312","https://openalex.org/W2094727853","https://openalex.org/W2096199252","https://openalex.org/W2102261910","https://openalex.org/W2122061174","https://openalex.org/W2123027306","https://openalex.org/W2123693663","https://openalex.org/W2125531944","https://openalex.org/W2132118008","https://openalex.org/W2132545874","https://openalex.org/W2132898564","https://openalex.org/W2134882900","https://openalex.org/W2143144653","https://openalex.org/W2148023570","https://openalex.org/W2149502453","https://openalex.org/W2155418451","https://openalex.org/W2157513018","https://openalex.org/W2163059351","https://openalex.org/W2171437709","https://openalex.org/W2296636214","https://openalex.org/W2385109307","https://openalex.org/W2599271158","https://openalex.org/W4206466197","https://openalex.org/W4214775604","https://openalex.org/W4254942564"],"related_works":["https://openalex.org/W1979597421","https://openalex.org/W2007980826","https://openalex.org/W4245490552","https://openalex.org/W4225152035","https://openalex.org/W2061531152","https://openalex.org/W3002753104","https://openalex.org/W2077600819","https://openalex.org/W1587224694","https://openalex.org/W2911598644","https://openalex.org/W2042127053"],"abstract_inverted_index":{"Cells":[0],"exhibit":[1],"stochastic":[2,13,72],"behavior":[3],"when":[4,170],"the":[5,31,48,57,64,87,115,134,154,201,237],"number":[6],"of":[7,17,27,50,54,59,74,86,110,126,136,153,203,239],"molecules":[8],"is":[9,63,91,142,161,225],"small.":[10],"Hence":[11],"a":[12,23,36,78,111,120,185,194,204,210,215,243,248],"reaction-diffusion":[14],"simulator":[15,69,81,183,208,212,224,241],"capable":[16],"working":[18],"at":[19],"scale":[20],"can":[21],"provide":[22],"more":[24,249],"accurate":[25],"view":[26],"molecular":[28],"dynamics":[29],"within":[30,146],"cell.":[32],"This":[33],"paper":[34],"describes":[35],"parallel":[37,66],"discrete":[38,67],"event":[39,68,117],"simulator,":[40],"Neuron":[41],"Time":[42,141],"Warp-Multi":[43],"Thread":[44],"(NTW-MT),":[45],"developed":[46,83],"for":[47,114,156,219],"simulation":[49,73],"reaction":[51],"diffusion":[52],"models":[53],"neurons.":[55],"To":[56],"best":[58],"our":[60,182,240],"knowledge,":[61],"this":[62],"first":[65],"oriented":[70],"towards":[71],"chemical":[75],"reactions":[76],"in":[77,103,124,163],"neuron.":[79],"The":[80],"was":[82],"as":[84],"part":[85],"NEURON":[88],"project.":[89],"NTW-MT":[90],"optimistic":[92,207],"and":[93,119,132,147,168,172,175,209,247],"thread-based,":[94],"which":[95,213],"attempts":[96],"to":[97,129,150,165,176,200,227,231],"capitalize":[98],"on":[99,184,193,242],"multi-core":[100],"architectures":[101],"used":[102],"high":[104],"performance":[105,192,202,230],"machines.":[106],"It":[107],"makes":[108],"use":[109],"multi-level":[112],"queue":[113,218],"pending":[116],"set":[118],"single":[121,216],"roll-back":[122],"message":[123],"place":[125],"individual":[127],"anti-messages":[128],"disperse":[130],"contention":[131],"decrease":[133],"overhead":[135,155],"processing":[137],"rollbacks.":[138],"Global":[139],"Virtual":[140],"computed":[143],"asynchronously":[144],"both":[145],"among":[148],"processes":[149],"get":[151],"rid":[152],"synchronizing":[157],"threads.":[158],"Memory":[159],"usage":[160],"managed":[162],"order":[164],"avoid":[166],"locking":[167],"unlocking":[169],"allocating":[171],"de-allocating":[173],"memory":[174],"maximize":[177],"cache":[178],"locality.":[179],"We":[180,189],"verified":[181],"calcium":[186,195],"buffer":[187],"model.":[188,252],"examined":[190],"its":[191],"wave":[196],"model,":[197],"comparing":[198],"it":[199],"process":[205],"based":[206],"threaded":[211],"uses":[214],"priority":[217],"each":[220],"thread.":[221],"Our":[222],"multi-threaded":[223],"shown":[226],"achieve":[228],"superior":[229],"these":[232],"simulators.":[233],"Finally,":[234],"we":[235],"demonstrated":[236],"scalability":[238],"larger":[244],"CICR":[245,251],"model":[246],"detailed":[250]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}