{"id":"https://openalex.org/W2016841815","doi":"https://doi.org/10.1145/1878537.1878629","title":"Stiffness detection and reduction in discrete stochastic simulation of biochemical systems","display_name":"Stiffness detection and reduction in discrete stochastic simulation of biochemical systems","publication_year":2010,"publication_date":"2010-04-11","ids":{"openalex":"https://openalex.org/W2016841815","doi":"https://doi.org/10.1145/1878537.1878629","mag":"2016841815"},"language":"en","primary_location":{"id":"doi:10.1145/1878537.1878629","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1878537.1878629","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2010 Spring Simulation Multiconference","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/A5102004582","display_name":"Pu Yang","orcid":"https://orcid.org/0000-0003-1399-9207"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yang Pu","raw_affiliation_strings":["Virginia Polytechnic Institute and State University, Blacksburg, VA"],"affiliations":[{"raw_affiliation_string":"Virginia Polytechnic Institute and State University, Blacksburg, VA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108116806","display_name":"Layne T. Watson","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Layne T. Watson","raw_affiliation_strings":["Virginia Polytechnic Institute and State University, Blacksburg, VA"],"affiliations":[{"raw_affiliation_string":"Virginia Polytechnic Institute and State University, Blacksburg, VA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022834433","display_name":"Yang Cao","orcid":"https://orcid.org/0000-0001-9336-3748"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Cao","raw_affiliation_strings":["Virginia Polytechnic Institute and State University, Blacksburg, VA"],"affiliations":[{"raw_affiliation_string":"Virginia Polytechnic Institute and State University, Blacksburg, VA","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5102004582"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08126616,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9998999834060669,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9973999857902527,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9969000220298767,"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/stiffness","display_name":"Stiffness","score":0.837209165096283},{"id":"https://openalex.org/keywords/reduction","display_name":"Reduction (mathematics)","score":0.7338716983795166},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6269533634185791},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5365915298461914},{"id":"https://openalex.org/keywords/shock","display_name":"Shock (circulatory)","score":0.480571985244751},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4158467650413513},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3504452705383301},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1678067445755005},{"id":"https://openalex.org/keywords/structural-engineering","display_name":"Structural engineering","score":0.1650940477848053},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.14080524444580078},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08068835735321045}],"concepts":[{"id":"https://openalex.org/C2779372316","wikidata":"https://www.wikidata.org/wiki/Q569057","display_name":"Stiffness","level":2,"score":0.837209165096283},{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.7338716983795166},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6269533634185791},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5365915298461914},{"id":"https://openalex.org/C2781300812","wikidata":"https://www.wikidata.org/wiki/Q178061","display_name":"Shock (circulatory)","level":2,"score":0.480571985244751},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4158467650413513},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3504452705383301},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1678067445755005},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.1650940477848053},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.14080524444580078},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08068835735321045},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"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/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1878537.1878629","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1878537.1878629","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2010 Spring Simulation Multiconference","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","score":0.46000000834465027,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G2729655968","display_name":null,"funder_award_id":"CCF-0726763","funder_id":"https://openalex.org/F4320337387","funder_display_name":"Division of Computing and Communication Foundations"},{"id":"https://openalex.org/G7099455443","display_name":null,"funder_award_id":"GM073744","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/F4320309646","display_name":"Virginia Polytechnic Institute and State University","ror":"https://ror.org/02smfhw86"},{"id":"https://openalex.org/F4320322999","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332500","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463"},{"id":"https://openalex.org/F4320337387","display_name":"Division of Computing and Communication Foundations","ror":"https://ror.org/01mng8331"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1597944220","https://openalex.org/W1969670130","https://openalex.org/W1973890190","https://openalex.org/W1974272479","https://openalex.org/W1978017495","https://openalex.org/W2011432832","https://openalex.org/W2018670096","https://openalex.org/W2036862428","https://openalex.org/W2042321087","https://openalex.org/W2072822008","https://openalex.org/W2074681199","https://openalex.org/W2084924279","https://openalex.org/W2087760732","https://openalex.org/W2093179886","https://openalex.org/W2119272407","https://openalex.org/W2151207209","https://openalex.org/W2153901189","https://openalex.org/W2155418451","https://openalex.org/W2170697535","https://openalex.org/W2401135644","https://openalex.org/W6677838577"],"related_works":["https://openalex.org/W585100505","https://openalex.org/W1993699589","https://openalex.org/W4386004832","https://openalex.org/W2317038355","https://openalex.org/W2508382938","https://openalex.org/W1978561773","https://openalex.org/W2325836299","https://openalex.org/W2088429012","https://openalex.org/W1979349227","https://openalex.org/W2368974034"],"abstract_inverted_index":{"Typical":[0],"multiscale":[1,81],"biochemical":[2,82],"models":[3],"contain":[4],"fast-scale":[5],"and":[6,33,50,74],"slow-scale":[7],"reactions,":[8],"where":[9],"fast":[10],"reactions":[11],"fire":[12],"much":[13],"more":[14],"frequently":[15],"than":[16],"slow":[17],"ones.":[18],"This":[19,40],"feature":[20],"often":[21],"causes":[22],"stiffness":[23,49],"in":[24],"discrete":[25],"stochastic":[26],"simulation":[27],"methods":[28,35,58],"such":[29],"as":[30],"Gillespie's":[31],"algorithm":[32],"tau-leaping":[34],"leading":[36],"to":[37,46],"inefficient":[38],"simulation.":[39],"paper":[41],"proposes":[42],"a":[43,65],"new":[44],"strategy":[45],"automatically":[47],"detect":[48],"identify":[51],"species":[52],"that":[53],"cause":[54],"stiffness.":[55],"Stiffness":[56],"reduction":[57],"are":[59],"also":[60],"discussed.":[61],"Numerical":[62],"results":[63],"on":[64],"heat":[66],"shock":[67],"protein":[68],"regulation":[69],"model":[70],"demonstrate":[71],"the":[72,77],"efficiency":[73],"accuracy":[75],"of":[76],"proposed":[78],"method":[79],"for":[80],"systems.":[83]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
