{"id":"https://openalex.org/W2077931315","doi":"https://doi.org/10.1109/cscs.2013.101","title":"A Modified Stochastic Simulation Algorithm for Time-Dependent Intensity Rates","display_name":"A Modified Stochastic Simulation Algorithm for Time-Dependent Intensity Rates","publication_year":2013,"publication_date":"2013-05-01","ids":{"openalex":"https://openalex.org/W2077931315","doi":"https://doi.org/10.1109/cscs.2013.101","mag":"2077931315"},"language":"en","primary_location":{"id":"doi:10.1109/cscs.2013.101","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cscs.2013.101","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 19th International Conference on Control Systems and Computer Science","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/A5089381929","display_name":"Raluca Roxana Purnichescu Purtan","orcid":null},"institutions":[{"id":"https://openalex.org/I61641377","display_name":"Universitatea Na\u021bional\u0103 de \u0218tiin\u021b\u0103 \u0219i Tehnologie Politehnica Bucure\u0219ti","ror":"https://ror.org/0558j5q12","country_code":"RO","type":"education","lineage":["https://openalex.org/I61641377"]}],"countries":["RO"],"is_corresponding":true,"raw_author_name":"Raluca Roxana Purnichescu Purtan","raw_affiliation_strings":["Faculty of Applied Science, Department of Mathematical Methods and Models, University Politehnica of Bucharest, Bucharest, Romania","Dept. of Math. Methods & Models, Univ. \u201cPoliteh.\u201d of Bucharest, Bucharest, Romania"],"affiliations":[{"raw_affiliation_string":"Faculty of Applied Science, Department of Mathematical Methods and Models, University Politehnica of Bucharest, Bucharest, Romania","institution_ids":["https://openalex.org/I61641377"]},{"raw_affiliation_string":"Dept. of Math. Methods & Models, Univ. \u201cPoliteh.\u201d of Bucharest, Bucharest, Romania","institution_ids":["https://openalex.org/I61641377"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067148127","display_name":"Andreea Udrea","orcid":"https://orcid.org/0000-0002-3450-2047"},"institutions":[{"id":"https://openalex.org/I61641377","display_name":"Universitatea Na\u021bional\u0103 de \u0218tiin\u021b\u0103 \u0219i Tehnologie Politehnica Bucure\u0219ti","ror":"https://ror.org/0558j5q12","country_code":"RO","type":"education","lineage":["https://openalex.org/I61641377"]}],"countries":["RO"],"is_corresponding":false,"raw_author_name":"Andreea Udrea","raw_affiliation_strings":["Faculty of Automatic Control and Computers, Department of Automatic Control and Systems Engineering, University Politehnica of Bucharest, Bucharest, Romania","Dept. of Autom. Control & Syst. Eng., Univ. \u201cPoliteh.\u201d of Bucharest, Bucharest, Romania"],"affiliations":[{"raw_affiliation_string":"Faculty of Automatic Control and Computers, Department of Automatic Control and Systems Engineering, University Politehnica of Bucharest, Bucharest, Romania","institution_ids":["https://openalex.org/I61641377"]},{"raw_affiliation_string":"Dept. of Autom. Control & Syst. Eng., Univ. \u201cPoliteh.\u201d of Bucharest, Bucharest, Romania","institution_ids":["https://openalex.org/I61641377"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5089381929"],"corresponding_institution_ids":["https://openalex.org/I61641377"],"apc_list":null,"apc_paid":null,"fwci":0.1462,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.56374414,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"149","issue":null,"first_page":"365","last_page":"369"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9761000275611877,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9592000246047974,"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/markov-process","display_name":"Markov process","score":0.5857596397399902},{"id":"https://openalex.org/keywords/stochastic-process","display_name":"Stochastic process","score":0.584256112575531},{"id":"https://openalex.org/keywords/master-equation","display_name":"Master equation","score":0.5630565285682678},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.5286127924919128},{"id":"https://openalex.org/keywords/discrete-time-stochastic-process","display_name":"Discrete-time stochastic process","score":0.519425630569458},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.502507209777832},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4942004978656769},{"id":"https://openalex.org/keywords/stochastic-differential-equation","display_name":"Stochastic differential equation","score":0.46259206533432007},{"id":"https://openalex.org/keywords/position","display_name":"Position (finance)","score":0.4513392448425293},{"id":"https://openalex.org/keywords/moment","display_name":"Moment (physics)","score":0.4321141839027405},{"id":"https://openalex.org/keywords/discrete-time-and-continuous-time","display_name":"Discrete time and continuous time","score":0.4188779592514038},{"id":"https://openalex.org/keywords/dynamical-systems-theory","display_name":"Dynamical systems theory","score":0.4167410135269165},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.4075765609741211},{"id":"https://openalex.org/keywords/continuous-time-stochastic-process","display_name":"Continuous-time stochastic process","score":0.3991532027721405},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.35267147421836853},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.08418932557106018},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08389106392860413}],"concepts":[{"id":"https://openalex.org/C159886148","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov process","level":2,"score":0.5857596397399902},{"id":"https://openalex.org/C8272713","wikidata":"https://www.wikidata.org/wiki/Q176737","display_name":"Stochastic process","level":2,"score":0.584256112575531},{"id":"https://openalex.org/C128805008","wikidata":"https://www.wikidata.org/wiki/Q722878","display_name":"Master equation","level":3,"score":0.5630565285682678},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.5286127924919128},{"id":"https://openalex.org/C92703954","wikidata":"https://www.wikidata.org/wiki/Q176737","display_name":"Discrete-time stochastic process","level":4,"score":0.519425630569458},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.502507209777832},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4942004978656769},{"id":"https://openalex.org/C51955184","wikidata":"https://www.wikidata.org/wiki/Q1545585","display_name":"Stochastic differential equation","level":2,"score":0.46259206533432007},{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.4513392448425293},{"id":"https://openalex.org/C179254644","wikidata":"https://www.wikidata.org/wiki/Q13222844","display_name":"Moment (physics)","level":2,"score":0.4321141839027405},{"id":"https://openalex.org/C55689738","wikidata":"https://www.wikidata.org/wiki/Q15963867","display_name":"Discrete time and continuous time","level":2,"score":0.4188779592514038},{"id":"https://openalex.org/C79379906","wikidata":"https://www.wikidata.org/wiki/Q3174497","display_name":"Dynamical systems theory","level":2,"score":0.4167410135269165},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.4075765609741211},{"id":"https://openalex.org/C158535547","wikidata":"https://www.wikidata.org/wiki/Q5165437","display_name":"Continuous-time stochastic process","level":3,"score":0.3991532027721405},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.35267147421836853},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.08418932557106018},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08389106392860413},{"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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.0},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cscs.2013.101","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cscs.2013.101","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 19th International Conference on Control Systems and Computer Science","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.47999998927116394,"display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1516725535","https://openalex.org/W1946177469","https://openalex.org/W2024206769","https://openalex.org/W2042321087","https://openalex.org/W2044859335","https://openalex.org/W2059719532","https://openalex.org/W2078734278","https://openalex.org/W2084924279","https://openalex.org/W2125744693","https://openalex.org/W2155418451"],"related_works":["https://openalex.org/W4238487991","https://openalex.org/W2022292713","https://openalex.org/W2171105877","https://openalex.org/W2912324827","https://openalex.org/W4302305711","https://openalex.org/W171914860","https://openalex.org/W1560814075","https://openalex.org/W2138230037","https://openalex.org/W4249195393","https://openalex.org/W2949098703"],"abstract_inverted_index":{"There":[0,72],"are":[1,22,32,61,73,88,93,117,186,215,229],"two":[2],"main":[3],"approaches":[4],"in":[5],"the":[6,97,103,110,118,133,151,155,178,188,223,235],"mathematical":[7],"modeling":[8],"of":[9,12,34,51,53,59,81,102,113,142,154,160,164,173,234],"coupled":[10],"systems":[11,44,60,84],"(bio)chemical":[13],"reactions:":[14],"continuous,":[15],"represented":[16,26],"by":[17,27,149],"differential":[18],"equations":[19],"whose":[20,30],"variables":[21,31],"concentrations":[23],"or":[24],"discrete,":[25,82],"stochastic":[28,75,83,111,120],"processes":[29],"numbers":[33],"molecules.":[35],"The":[36,162,183],"latter":[37],"approach":[38],"is":[39,167,190,225],"used":[40,106],"mostly":[41],"for":[42,108],"biochemical":[43],"with":[45,201,218],"a":[46,114,139],"low":[47],"to":[48,77,96,157],"moderate":[49],"number":[50],"molecules":[52],"certain":[54],"species":[55],"and":[56,85,129,221],"this":[57,165],"kind":[58],"typically":[62],"modeled":[63],"as":[64,126],"continuous":[65],"time":[66,232],"-":[67,144,148],"discrete":[68],"state":[69,79],"Markov":[70],"Process.":[71],"exact":[74,119],"algorithms":[76,87],"simulate":[78],"trajectories":[80],"these":[86],"based":[89],"on":[90],"methods":[91,107],"that":[92,187,194,207,222],"rigorously":[94],"equivalent":[95],"Master":[98],"Equation":[99],"approach.":[100],"Two":[101],"most":[104],"widely":[105],"simulating":[109],"dynamics":[112],"chemical":[115],"system":[116,189,224],"simulation":[121],"algorithm":[122],"(SSA,":[123],"known":[124],"also":[125],"Gillespie":[127],"algorithm)":[128],"its":[130],"approximate":[131],"variant,":[132],"tau-leaping":[134],"algorithm.":[135],"This":[136],"paper":[137],"describes":[138],"modified":[140],"version":[141],"SSA":[143],"First":[145],"reaction":[146],"method":[147],"letting":[150],"intensity":[152],"rates":[153],"reactions":[156,199,217,236],"be":[158],"functions":[159],"time.":[161],"importance":[163],"adaptation":[166],"obvious":[168],"when":[169],"considering":[170],"some":[171],"classes":[172],"biological":[174],"models":[175],"(for":[176],"example,":[177],"one":[179],"involving":[180],"circadian":[181],"rhythm).":[182],"underlying":[184],"assumptions":[185],"well":[191],"stirred":[192],"such":[193],"at":[195,204],"any":[196,205],"moment,":[197],"each":[198,208],"occur":[200],"equal":[202],"probability":[203],"position,":[206],"reaction,":[209],"once":[210],"occurred,":[211],"completes":[212],"instantaneously":[213],"(there":[214,228],"no":[216,230],"delay":[219],"involved)":[220],"non":[226],"stiff":[227],"different":[231],"scales":[233],"involved).":[237]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
