{"id":"https://openalex.org/W3034073466","doi":"https://doi.org/10.1145/3384441.3395987","title":"Optimizing Discrete Simulations of the Spread of HIV-1 to Handle Billions of Cells on a Workstation","display_name":"Optimizing Discrete Simulations of the Spread of HIV-1 to Handle Billions of Cells on a Workstation","publication_year":2020,"publication_date":"2020-06-07","ids":{"openalex":"https://openalex.org/W3034073466","doi":"https://doi.org/10.1145/3384441.3395987","mag":"3034073466"},"language":"en","primary_location":{"id":"doi:10.1145/3384441.3395987","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3384441.3395987","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2020 ACM SIGSIM Conference on Principles of Advanced Discrete Simulation","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/A5023496425","display_name":"Philippe J. Giabbanelli","orcid":"https://orcid.org/0000-0001-6816-355X"},"institutions":[{"id":"https://openalex.org/I83328450","display_name":"Miami University","ror":"https://ror.org/05nbqxr67","country_code":"US","type":"education","lineage":["https://openalex.org/I83328450"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Philippe J. Giabbanelli","raw_affiliation_strings":["Miami University, Oxford, OH, USA"],"affiliations":[{"raw_affiliation_string":"Miami University, Oxford, OH, USA","institution_ids":["https://openalex.org/I83328450"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023419720","display_name":"Joshua A. Devita","orcid":null},"institutions":[{"id":"https://openalex.org/I102502594","display_name":"Northern Illinois University","ror":"https://ror.org/012wxa772","country_code":"US","type":"education","lineage":["https://openalex.org/I102502594"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua A. Devita","raw_affiliation_strings":["Northern Illinois University, DeKalb, IL, USA"],"affiliations":[{"raw_affiliation_string":"Northern Illinois University, DeKalb, IL, USA","institution_ids":["https://openalex.org/I102502594"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029430276","display_name":"Till K\u00f6ster","orcid":"https://orcid.org/0000-0003-0869-381X"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Till K\u00f6ster","raw_affiliation_strings":["University of Rostock, Rostock, Germany"],"affiliations":[{"raw_affiliation_string":"University of Rostock, Rostock, Germany","institution_ids":["https://openalex.org/I4665924"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027369140","display_name":"Jared A. Kohrt","orcid":null},"institutions":[{"id":"https://openalex.org/I86115722","display_name":"Furman University","ror":"https://ror.org/04ytb9n23","country_code":"US","type":"education","lineage":["https://openalex.org/I86115722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jared A. Kohrt","raw_affiliation_strings":["Furman University, Greenville, SC, USA"],"affiliations":[{"raw_affiliation_string":"Furman University, Greenville, SC, USA","institution_ids":["https://openalex.org/I86115722"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5023496425"],"corresponding_institution_ids":["https://openalex.org/I83328450"],"apc_list":null,"apc_paid":null,"fwci":1.0597,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.75410168,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"67","last_page":"78"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9937999844551086,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9937999844551086,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12162","display_name":"Cellular Automata and Applications","score":0.9785000085830688,"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"}},{"id":"https://openalex.org/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.9520000219345093,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workstation","display_name":"Workstation","score":0.8080010414123535},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7358357310295105},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.6072877049446106},{"id":"https://openalex.org/keywords/cellular-automaton","display_name":"Cellular automaton","score":0.5264818668365479},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.46537017822265625},{"id":"https://openalex.org/keywords/virtual-laboratory","display_name":"Virtual Laboratory","score":0.4214802086353302},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23881012201309204},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.2186494767665863},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14585232734680176},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12942788004875183}],"concepts":[{"id":"https://openalex.org/C67953723","wikidata":"https://www.wikidata.org/wiki/Q192525","display_name":"Workstation","level":2,"score":0.8080010414123535},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7358357310295105},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.6072877049446106},{"id":"https://openalex.org/C35527583","wikidata":"https://www.wikidata.org/wiki/Q189156","display_name":"Cellular automaton","level":2,"score":0.5264818668365479},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.46537017822265625},{"id":"https://openalex.org/C2777609615","wikidata":"https://www.wikidata.org/wiki/Q2527919","display_name":"Virtual Laboratory","level":2,"score":0.4214802086353302},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23881012201309204},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.2186494767665863},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14585232734680176},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12942788004875183},{"id":"https://openalex.org/C49774154","wikidata":"https://www.wikidata.org/wiki/Q131765","display_name":"Multimedia","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3384441.3395987","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3384441.3395987","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2020 ACM SIGSIM Conference on Principles of Advanced Discrete Simulation","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.7799999713897705,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W645651331","https://openalex.org/W1514059692","https://openalex.org/W1857969216","https://openalex.org/W1999429374","https://openalex.org/W2001917666","https://openalex.org/W2014431146","https://openalex.org/W2028873795","https://openalex.org/W2051525127","https://openalex.org/W2057975334","https://openalex.org/W2086207036","https://openalex.org/W2088092680","https://openalex.org/W2100435084","https://openalex.org/W2105565651","https://openalex.org/W2276662578","https://openalex.org/W2483686803","https://openalex.org/W2528862740","https://openalex.org/W2575278687","https://openalex.org/W2596103771","https://openalex.org/W2596791748","https://openalex.org/W2747753434","https://openalex.org/W2758035875","https://openalex.org/W2767678610","https://openalex.org/W2772527255","https://openalex.org/W2803227027","https://openalex.org/W2836041025","https://openalex.org/W2911528329","https://openalex.org/W2927784395","https://openalex.org/W2947682047","https://openalex.org/W2951716756","https://openalex.org/W2963014186","https://openalex.org/W2979597731","https://openalex.org/W2999289833","https://openalex.org/W3008892598","https://openalex.org/W3136238860","https://openalex.org/W4239537689","https://openalex.org/W4245562072","https://openalex.org/W6732203935"],"related_works":["https://openalex.org/W2164619678","https://openalex.org/W2045348955","https://openalex.org/W2352028719","https://openalex.org/W2584886384","https://openalex.org/W2378667902","https://openalex.org/W2052769075","https://openalex.org/W2791088446","https://openalex.org/W2113544496","https://openalex.org/W2360313292","https://openalex.org/W1669105318"],"abstract_inverted_index":{"Cellular":[0],"Automata":[1],"have":[2,51,77,226],"been":[3,52,67,78],"used":[4,79],"on":[5,113,192,211,243],"many":[6,172],"occasions":[7],"to":[8,27,60,80,130,156,221,229,238],"model":[9,131],"the":[10,13,28,36,89,95,162,174,185,212,255],"spread":[11],"of":[12,31,38,56,88,128,165,173,206,241,257,266,290],"Human":[14],"Immunodeficiency":[15],"Virus":[16],"(HIV)":[17],"within":[18,276],"a":[19,63,102,117,125,244,269,282],"human":[20],"body.":[21],"This":[22],"is":[23,101,154,195],"in":[24,42,48,54,116,203,268,293],"part":[25],"due":[26],"relative":[29],"simplicity":[30],"crafting":[32],"their":[33,58,70],"rules":[34],"and":[35,50,142,215,263],"convenience":[37],"visualizing":[39],"disease":[40],"dynamics":[41],"2D.":[43],"Although":[44,184],"such":[45,149,249],"models":[46,109,169,186,205],"appeared":[47],"2001":[49],"extended":[53],"dozens":[55],"studies,":[57],"potential":[59],"serve":[61],"as":[62,150,181,250],"virtual":[64,182,223],"laboratory":[65],"has":[66],"limited":[68,227],"by":[69,190,246],"computationally":[71,146],"intensive":[72,147],"nature.":[73],"So":[74],"far,":[75],"they":[76],"simulate":[81],"at":[82,254],"most":[83],"0.5":[84],"million":[85],"cells":[86,91,100,129,166,288,292],"instead":[87,289],"billion":[90,287],"that":[92,176],"may":[93,187,225],"harbor":[94],"virus.":[96],"Simulating":[97],"too":[98],"few":[99],"key":[103],"issue":[104],"for":[105,140,217,285],"calibration":[106],"(the":[107],"'small'":[108],"are":[110],"calibrated":[111],"based":[112],"results":[114,273],"observed":[115],"much":[118],"larger":[119],"space),":[120],"prevents":[121,167],"us":[122],"from":[123,170],"using":[124],"sufficient":[126],"proportion":[127],"latent":[132],"HIV":[133,137,207,242],"reservoirs":[134],"(in":[135],"which":[136],"can":[138,280],"hide":[139],"years),":[141],"prohibits":[143],"even":[144],"more":[145],"aspects":[148],"tracking":[151],"mutations":[152],"(which":[153],"essential":[155],"assess":[157],"drug":[158],"resistance).":[159],"In":[160],"short,":[161],"low":[163],"number":[164,261],"these":[168,233],"answering":[171],"questions":[175],"would":[177],"make":[178],"them":[179],"useful":[180],"laboratories.":[183],"be":[188],"scaled":[189],"running":[191],"clusters,":[193],"this":[194],"not":[196],"always":[197],"an":[198,294],"option":[199],"since":[200],"interdisciplinary":[201],"research":[202],"discrete":[204],"often":[208],"takes":[209],"place":[210],"lab's":[213],"computer,":[214],"patients":[216],"whom":[218],"we":[219,235,279],"seek":[220],"provide":[222],"laboratories":[224],"access":[228],"computational":[230],"resources.":[231],"Given":[232],"constraints,":[234],"demonstrate":[236,274],"how":[237],"optimize":[239],"simulations":[240],"workstation":[245],"combining":[247],"features":[248],"just-in-time":[251],"compilation,":[252],"parallelism":[253],"level":[256],"threads,":[258],"pseudo":[259],"random":[260],"generators,":[262],"simplified":[264],"handling":[265],"neighbors":[267],"cellular":[270],"automaton.":[271],"Our":[272],"that,":[275],"10":[277],"minutes,":[278],"finish":[281],"simulation":[283],"run":[284],"6.7":[286],"60,000":[291],"unoptimized":[295],"simulation.":[296]},"counts_by_year":[{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
