{"id":"https://openalex.org/W1973011350","doi":"https://doi.org/10.1155/2012/423627","title":"The Stochastic Evolution of a Protocell: The Gillespie Algorithm in a Dynamically Varying Volume","display_name":"The Stochastic Evolution of a Protocell: The Gillespie Algorithm in a Dynamically Varying Volume","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W1973011350","doi":"https://doi.org/10.1155/2012/423627","mag":"1973011350","pmid":"https://pubmed.ncbi.nlm.nih.gov/22536297"},"language":"en","primary_location":{"id":"doi:10.1155/2012/423627","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2012/423627","pdf_url":"https://downloads.hindawi.com/journals/cmmm/2012/423627.pdf","source":{"id":"https://openalex.org/S36980176","display_name":"Computational and Mathematical Methods in Medicine","issn_l":"1748-670X","issn":["1748-670X","1748-6718"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational and Mathematical Methods in Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://downloads.hindawi.com/journals/cmmm/2012/423627.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001066958","display_name":"Timot\u00e9o Carletti","orcid":"https://orcid.org/0000-0003-2596-4503"},"institutions":[{"id":"https://openalex.org/I149768937","display_name":"University of Namur","ror":"https://ror.org/03d1maw17","country_code":"BE","type":"education","lineage":["https://openalex.org/I149768937"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"T. Carletti","raw_affiliation_strings":["Namur Center for Complex Systems and University of Namur, 5000 Namur, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Namur Center for Complex Systems and University of Namur, 5000 Namur, Belgium","institution_ids":["https://openalex.org/I149768937"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002135290","display_name":"Alessandro Filisetti","orcid":"https://orcid.org/0000-0002-6389-1109"},"institutions":[{"id":"https://openalex.org/I149461666","display_name":"Ca' Foscari University of Venice","ror":"https://ror.org/04yzxz566","country_code":"IT","type":"education","lineage":["https://openalex.org/I149461666"]},{"id":"https://openalex.org/I4210137980","display_name":"European Centre for Living Technology","ror":"https://ror.org/04kesq777","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210137980"]},{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"A. Filisetti","raw_affiliation_strings":["CIRI, Energy and Environment Interdipartimental Center for Industrial Research, University of Bologna and European Centre for Living Technology, C\u00e1 Foscari University of Venice, 30124 Venice, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CIRI, Energy and Environment Interdipartimental Center for Industrial Research, University of Bologna and European Centre for Living Technology, C\u00e1 Foscari University of Venice, 30124 Venice, Italy","institution_ids":["https://openalex.org/I4210137980","https://openalex.org/I149461666","https://openalex.org/I9360294"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5001066958"],"corresponding_institution_ids":["https://openalex.org/I149768937"],"apc_list":{"value":2100,"currency":"USD","value_usd":2100},"apc_paid":{"value":2100,"currency":"USD","value_usd":2100},"fwci":11.618,"has_fulltext":true,"cited_by_count":208,"citation_normalized_percentile":{"value":0.98751633,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"2012","issue":null,"first_page":"1","last_page":"13"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11445","display_name":"Origins and Evolution of Life","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11445","display_name":"Origins and Evolution of Life","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11520","display_name":"Advanced Thermodynamics and Statistical Mechanics","score":0.9922999739646912,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9904000163078308,"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/protocell","display_name":"Protocell","score":0.9827865362167358},{"id":"https://openalex.org/keywords/container","display_name":"Container (type theory)","score":0.7695774435997009},{"id":"https://openalex.org/keywords/volume","display_name":"Volume (thermodynamics)","score":0.6295897960662842},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6152759194374084},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.561661422252655},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.45605015754699707},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.35241812467575073},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.32361656427383423},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22534453868865967},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.14165416359901428},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1069258451461792},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06622684001922607},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06134098768234253}],"concepts":[{"id":"https://openalex.org/C114032466","wikidata":"https://www.wikidata.org/wiki/Q1389465","display_name":"Protocell","level":3,"score":0.9827865362167358},{"id":"https://openalex.org/C2781018962","wikidata":"https://www.wikidata.org/wiki/Q5164884","display_name":"Container (type theory)","level":2,"score":0.7695774435997009},{"id":"https://openalex.org/C20556612","wikidata":"https://www.wikidata.org/wiki/Q4469374","display_name":"Volume (thermodynamics)","level":2,"score":0.6295897960662842},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6152759194374084},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.561661422252655},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.45605015754699707},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.35241812467575073},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32361656427383423},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22534453868865967},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.14165416359901428},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1069258451461792},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06622684001922607},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06134098768234253},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"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/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058045","descriptor_name":"Artificial Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058045","descriptor_name":"Artificial Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058045","descriptor_name":"Artificial Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1155/2012/423627","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2012/423627","pdf_url":"https://downloads.hindawi.com/journals/cmmm/2012/423627.pdf","source":{"id":"https://openalex.org/S36980176","display_name":"Computational and Mathematical Methods in Medicine","issn_l":"1748-670X","issn":["1748-670X","1748-6718"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational and Mathematical Methods in Medicine","raw_type":"journal-article"},{"id":"pmid:22536297","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22536297","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":"Computational and mathematical methods in medicine","raw_type":null},{"id":"pmh:oai:doaj.org/article:f854099b122b4326bc7be0cb7240c061","is_oa":false,"landing_page_url":"https://doaj.org/article/f854099b122b4326bc7be0cb7240c061","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computational and Mathematical Methods in Medicine, Vol 2012 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2340351","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3318221","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:iris.unive.it:10278/40013","is_oa":true,"landing_page_url":"http://hdl.handle.net/10278/40013","pdf_url":null,"source":{"id":"https://openalex.org/S4306402336","display_name":"ARCA (Universit\u00e0 Ca' Foscari Venezia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149461666","host_organization_name":"Ca' Foscari University of Venice","host_organization_lineage":["https://openalex.org/I149461666"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1155/2012/423627","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2012/423627","pdf_url":"https://downloads.hindawi.com/journals/cmmm/2012/423627.pdf","source":{"id":"https://openalex.org/S36980176","display_name":"Computational and Mathematical Methods in Medicine","issn_l":"1748-670X","issn":["1748-670X","1748-6718"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational and Mathematical Methods in Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321390","display_name":"Fonds De La Recherche Scientifique - FNRS","ror":"https://ror.org/03q83t159"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1973011350.pdf","grobid_xml":"https://content.openalex.org/works/W1973011350.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W75050073","https://openalex.org/W1509581155","https://openalex.org/W2009067194","https://openalex.org/W2011598430","https://openalex.org/W2026829672","https://openalex.org/W2049728397","https://openalex.org/W2080327616","https://openalex.org/W2082731642","https://openalex.org/W2104081802","https://openalex.org/W2112113387","https://openalex.org/W2118443758","https://openalex.org/W2143598250","https://openalex.org/W2155418451","https://openalex.org/W2165948144","https://openalex.org/W2166633151","https://openalex.org/W4235033012"],"related_works":["https://openalex.org/W2488224828","https://openalex.org/W2998115572","https://openalex.org/W2033867172","https://openalex.org/W2499941174","https://openalex.org/W4324018125","https://openalex.org/W3119990432","https://openalex.org/W4390135158","https://openalex.org/W4390267564","https://openalex.org/W2330839048","https://openalex.org/W2981364794"],"abstract_inverted_index":{"We":[0],"propose":[1],"an":[2,16],"improvement":[3],"of":[4,15,18,34,51,58,61],"the":[5,12,32,40,48,59,72],"Gillespie":[6],"algorithm":[7],"allowing":[8],"us":[9,45],"to":[10,31,39,46],"study":[11,47],"time":[13],"evolution":[14,50],"ensemble":[17],"chemical":[19],"reactions":[20,41],"occurring":[21],"in":[22],"a":[23,52],"varying":[24],"volume,":[25],"whose":[26,54],"growth":[27],"is":[28],"directly":[29],"related":[30],"amount":[33],"some":[35],"specific":[36],"molecules,":[37],"belonging":[38],"set.":[42],"This":[43],"allows":[44],"stochastic":[49],"protocell,":[53],"volume":[55],"increases":[56],"because":[57],"production":[60],"container":[62],"molecules.":[63],"Several":[64],"protocell":[65],"models":[66],"are":[67],"considered":[68],"and":[69],"compared":[70],"with":[71],"deterministic":[73],"models.":[74]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":28},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":26},{"year":2018,"cited_by_count":22},{"year":2017,"cited_by_count":25},{"year":2016,"cited_by_count":29},{"year":2015,"cited_by_count":16},{"year":2014,"cited_by_count":23},{"year":2013,"cited_by_count":13},{"year":2012,"cited_by_count":5}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
