{"id":"https://openalex.org/W2411513433","doi":"https://doi.org/10.1109/tmbmc.2016.2623598","title":"Nonlinear Stochastic Dynamics of Complex Systems, III: Nonequilibrium Thermodynamics of Self-Replication Kinetics","display_name":"Nonlinear Stochastic Dynamics of Complex Systems, III: Nonequilibrium Thermodynamics of Self-Replication Kinetics","publication_year":2016,"publication_date":"2016-06-01","ids":{"openalex":"https://openalex.org/W2411513433","doi":"https://doi.org/10.1109/tmbmc.2016.2623598","mag":"2411513433"},"language":"en","primary_location":{"id":"doi:10.1109/tmbmc.2016.2623598","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmbmc.2016.2623598","pdf_url":null,"source":{"id":"https://openalex.org/S2490853239","display_name":"IEEE Transactions on Molecular Biological and Multi-Scale Communications","issn_l":"2332-7804","issn":["2332-7804","2372-2061"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Molecular, Biological and Multi-Scale Communications","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1606.02391","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"David B. Saakian","orcid":null},"institutions":[{"id":"https://openalex.org/I132091411","display_name":"A. Alikhanyan National Laboratory","ror":"https://ror.org/00ad27c73","country_code":"AM","type":"facility","lineage":["https://openalex.org/I132091411"]},{"id":"https://openalex.org/I4210111779","display_name":"Institute of Physics, Academia Sinica","ror":"https://ror.org/01tpvdq80","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210111779","https://openalex.org/I84653119"]}],"countries":["AM","TW"],"is_corresponding":true,"raw_author_name":"David B. Saakian","raw_affiliation_strings":["A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute) Foundation, Yerevan, Armenia","Institute of Physics, Academia Sinica, Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute) Foundation, Yerevan, Armenia","institution_ids":["https://openalex.org/I132091411"]},{"raw_affiliation_string":"Institute of Physics, Academia Sinica, Taipei, Taiwan","institution_ids":["https://openalex.org/I4210111779"]}]},{"author_position":"last","author":{"id":null,"display_name":"Hong Qian","orcid":"https://orcid.org/0000-0002-5466-8650"},"institutions":[{"id":"https://openalex.org/I4210138199","display_name":"University of Washington Applied Physics Laboratory","ror":"https://ror.org/03d17d270","country_code":"US","type":"facility","lineage":["https://openalex.org/I201448701","https://openalex.org/I4210138199"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hong Qian","raw_affiliation_strings":["Department of Applied Mathematics, University of Washington, Seattle, WA, USA"],"raw_orcid":"https://orcid.org/0000-0002-5466-8650","affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I4210138199"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I132091411","https://openalex.org/I4210111779"],"apc_list":null,"apc_paid":null,"fwci":0.221,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.57240443,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"2","issue":"1","first_page":"40","last_page":"51"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11520","display_name":"Advanced Thermodynamics and Statistical Mechanics","score":0.41290000081062317,"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"}},"topics":[{"id":"https://openalex.org/T11520","display_name":"Advanced Thermodynamics and Statistical Mechanics","score":0.41290000081062317,"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/T11445","display_name":"Origins and Evolution of Life","score":0.32179999351501465,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.048500001430511475,"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/non-equilibrium-thermodynamics","display_name":"Non-equilibrium thermodynamics","score":0.8115000128746033},{"id":"https://openalex.org/keywords/entropy-production","display_name":"Entropy production","score":0.6484000086784363},{"id":"https://openalex.org/keywords/entropy","display_name":"Entropy (arrow of time)","score":0.5730999708175659},{"id":"https://openalex.org/keywords/extended-irreversible-thermodynamics","display_name":"Extended irreversible thermodynamics","score":0.5285999774932861},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.5044000148773193},{"id":"https://openalex.org/keywords/kinetic-energy","display_name":"Kinetic energy","score":0.44359999895095825},{"id":"https://openalex.org/keywords/kinetic-theory","display_name":"Kinetic theory","score":0.42730000615119934},{"id":"https://openalex.org/keywords/autocatalytic-reaction","display_name":"Autocatalytic reaction","score":0.41909998655319214},{"id":"https://openalex.org/keywords/mesoscopic-physics","display_name":"Mesoscopic physics","score":0.41339999437332153},{"id":"https://openalex.org/keywords/isothermal-process","display_name":"Isothermal process","score":0.40549999475479126}],"concepts":[{"id":"https://openalex.org/C74859849","wikidata":"https://www.wikidata.org/wiki/Q2466686","display_name":"Non-equilibrium thermodynamics","level":2,"score":0.8115000128746033},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.6557999849319458},{"id":"https://openalex.org/C207282930","wikidata":"https://www.wikidata.org/wiki/Q5380811","display_name":"Entropy production","level":2,"score":0.6484000086784363},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.5730999708175659},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.5594000220298767},{"id":"https://openalex.org/C140767772","wikidata":"https://www.wikidata.org/wiki/Q5421889","display_name":"Extended irreversible thermodynamics","level":3,"score":0.5285999774932861},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.5044000148773193},{"id":"https://openalex.org/C135889238","wikidata":"https://www.wikidata.org/wiki/Q46276","display_name":"Kinetic energy","level":2,"score":0.44359999895095825},{"id":"https://openalex.org/C19979193","wikidata":"https://www.wikidata.org/wiki/Q25100325","display_name":"Kinetic theory","level":2,"score":0.42730000615119934},{"id":"https://openalex.org/C95514000","wikidata":"https://www.wikidata.org/wiki/Q786897","display_name":"Autocatalytic reaction","level":2,"score":0.41909998655319214},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.4189999997615814},{"id":"https://openalex.org/C177731217","wikidata":"https://www.wikidata.org/wiki/Q2622244","display_name":"Mesoscopic physics","level":2,"score":0.41339999437332153},{"id":"https://openalex.org/C133347239","wikidata":"https://www.wikidata.org/wiki/Q486921","display_name":"Isothermal process","level":2,"score":0.40549999475479126},{"id":"https://openalex.org/C49775889","wikidata":"https://www.wikidata.org/wiki/Q6795896","display_name":"Maximum entropy thermodynamics","level":4,"score":0.38940000534057617},{"id":"https://openalex.org/C37263863","wikidata":"https://www.wikidata.org/wiki/Q786897","display_name":"Autocatalysis","level":3,"score":0.38029998540878296},{"id":"https://openalex.org/C159886148","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov process","level":2,"score":0.36149999499320984},{"id":"https://openalex.org/C177801218","wikidata":"https://www.wikidata.org/wiki/Q36534","display_name":"Chemical reaction","level":2,"score":0.35899999737739563},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.34369999170303345},{"id":"https://openalex.org/C14380042","wikidata":"https://www.wikidata.org/wiki/Q503327","display_name":"Thermodynamic system","level":2,"score":0.3312000036239624},{"id":"https://openalex.org/C5201495","wikidata":"https://www.wikidata.org/wiki/Q739016","display_name":"Chemical thermodynamics","level":3,"score":0.3231000006198883},{"id":"https://openalex.org/C119820323","wikidata":"https://www.wikidata.org/wiki/Q177045","display_name":"Second law of thermodynamics","level":2,"score":0.3160000145435333},{"id":"https://openalex.org/C149441793","wikidata":"https://www.wikidata.org/wiki/Q200726","display_name":"Probability distribution","level":2,"score":0.31150001287460327},{"id":"https://openalex.org/C8272713","wikidata":"https://www.wikidata.org/wiki/Q176737","display_name":"Stochastic process","level":2,"score":0.2985999882221222},{"id":"https://openalex.org/C111663737","wikidata":"https://www.wikidata.org/wiki/Q10860570","display_name":"Equilibrium thermodynamics","level":3,"score":0.29840001463890076},{"id":"https://openalex.org/C2993277463","wikidata":"https://www.wikidata.org/wiki/Q209082","display_name":"Chemical reaction kinetics","level":4,"score":0.2896000146865845},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2892000079154968},{"id":"https://openalex.org/C131157278","wikidata":"https://www.wikidata.org/wiki/Q51363","display_name":"Thermodynamic equilibrium","level":2,"score":0.2888999879360199},{"id":"https://openalex.org/C99874945","wikidata":"https://www.wikidata.org/wiki/Q188715","display_name":"Statistical mechanics","level":2,"score":0.28110000491142273},{"id":"https://openalex.org/C118419359","wikidata":"https://www.wikidata.org/wiki/Q682585","display_name":"Supercritical fluid","level":2,"score":0.2782000005245209},{"id":"https://openalex.org/C18815010","wikidata":"https://www.wikidata.org/wiki/Q849392","display_name":"Laws of thermodynamics","level":3,"score":0.2750000059604645},{"id":"https://openalex.org/C151342819","wikidata":"https://www.wikidata.org/wiki/Q62542","display_name":"Phase space","level":2,"score":0.27160000801086426},{"id":"https://openalex.org/C57476982","wikidata":"https://www.wikidata.org/wiki/Q582857","display_name":"Transition state theory","level":4,"score":0.2671000063419342},{"id":"https://openalex.org/C12668873","wikidata":"https://www.wikidata.org/wiki/Q230875","display_name":"Thermodynamic state","level":3,"score":0.26570001244544983},{"id":"https://openalex.org/C35304006","wikidata":"https://www.wikidata.org/wiki/Q5962","display_name":"Boltzmann constant","level":2,"score":0.2632000148296356},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.26249998807907104},{"id":"https://openalex.org/C122203268","wikidata":"https://www.wikidata.org/wiki/Q5862903","display_name":"Probability theory","level":2,"score":0.2524000108242035}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tmbmc.2016.2623598","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmbmc.2016.2623598","pdf_url":null,"source":{"id":"https://openalex.org/S2490853239","display_name":"IEEE Transactions on Molecular Biological and Multi-Scale Communications","issn_l":"2332-7804","issn":["2332-7804","2372-2061"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Molecular, Biological and Multi-Scale Communications","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:1606.02391","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1606.02391","pdf_url":"https://arxiv.org/pdf/1606.02391","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":{"id":"pmh:oai:arXiv.org:1606.02391","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1606.02391","pdf_url":"https://arxiv.org/pdf/1606.02391","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6821045444","display_name":null,"funder_award_id":"R01-GM109964","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"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":56,"referenced_works":["https://openalex.org/W571141297","https://openalex.org/W1521661628","https://openalex.org/W1525068335","https://openalex.org/W1644749979","https://openalex.org/W1935394376","https://openalex.org/W1972633005","https://openalex.org/W1973923921","https://openalex.org/W1978586665","https://openalex.org/W1999333609","https://openalex.org/W2003292748","https://openalex.org/W2005097301","https://openalex.org/W2006077744","https://openalex.org/W2006248254","https://openalex.org/W2016320357","https://openalex.org/W2025232786","https://openalex.org/W2029680915","https://openalex.org/W2034747152","https://openalex.org/W2056896652","https://openalex.org/W2062936056","https://openalex.org/W2071214852","https://openalex.org/W2073560602","https://openalex.org/W2085027190","https://openalex.org/W2085056826","https://openalex.org/W2091880147","https://openalex.org/W2093014477","https://openalex.org/W2093456062","https://openalex.org/W2102277728","https://openalex.org/W2104525378","https://openalex.org/W2105984138","https://openalex.org/W2107626567","https://openalex.org/W2108184883","https://openalex.org/W2110083561","https://openalex.org/W2125605221","https://openalex.org/W2128706048","https://openalex.org/W2138192576","https://openalex.org/W2167154952","https://openalex.org/W2235572757","https://openalex.org/W2236970913","https://openalex.org/W2238770515","https://openalex.org/W2246026444","https://openalex.org/W2278014507","https://openalex.org/W2316589146","https://openalex.org/W2346207789","https://openalex.org/W2357503186","https://openalex.org/W2409181828","https://openalex.org/W2484873947","https://openalex.org/W2512745720","https://openalex.org/W3021395152","https://openalex.org/W4233798822","https://openalex.org/W4244360209","https://openalex.org/W4251170832","https://openalex.org/W6637782272","https://openalex.org/W6666035025","https://openalex.org/W6712475285","https://openalex.org/W6786268933","https://openalex.org/W6948054561"],"related_works":[],"abstract_inverted_index":{"We":[0,118],"briefly":[1],"review":[2],"the":[3,18,184,189,200],"recently":[4],"developed":[5],"Markov":[6],"process-based":[7],"isothermal":[8],"chemical":[9,82,96,142],"thermodynamics":[10],"for":[11,148],"nonlinear":[12],"driven":[13,141],"mesoscopic":[14],"kinetic":[15,167,173],"systems.":[16],"Both":[17],"instantaneous":[19],"Shannon":[20],"entropy":[21,31,113],"<inline-formula":[22,32,45,60,98,105,206],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[23,33,46,61,99,106,164,207],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">":[24,34,47,62,100,107,208],"<tex-math":[25,35,48,63,101,108,209],"notation=\"LaTeX\">$S[\\,p_{\\alpha":[26],"}(t)]$":[27,37],"</tex-math></inline-formula>":[28,38,55,66,103,110,211],"and":[29,75,104,114,151],"relative":[30],"notation=\"LaTeX\">$F[\\,p_{\\alpha":[36],",":[39,67,212],"defined":[40],"based":[41],"on":[42],"probability":[43],"distribution":[44],"notation=\"LaTeX\">$\\{\\,p_{\\alpha":[49],"}(t);\\alpha":[50],"\\in":[51],"\\boldsymbol":[52],"{\\mathscr":[53],"{S}}\\}$":[54],"over":[56],"a":[57,77,81,123,131,135,155,172,178],"state":[58],"space":[59],"notation=\"LaTeX\">$\\mathscr":[64],"{S}$":[65],"play":[68],"prominent":[69],"roles.":[70],"The":[71,139,160],"theory":[72,121,157],"is":[73,85,169,181,196],"general;":[74],"as":[76,145,183],"special":[78],"case":[79],"when":[80],"reaction":[83,127],"system":[84,143,174],"situated":[86],"in":[87,134,203],"an":[88,146],"equilibrium":[89],"environment,":[90],"it":[91],"agrees":[92],"perfectly":[93],"with":[94],"Gibbsian":[95],"thermodynamics:":[97],"notation=\"LaTeX\">$k_{B}S$":[102],"notation=\"LaTeX\">$k_{B}TF$":[109],"become":[111],"thermodynamic":[112],"free":[115],"energy,":[116],"respectively.":[117],"apply":[119],"this":[120],"to":[122,199,214],"fully":[124],"reversible":[125],"autocatalytic":[126],"kinetics,":[128],"represented":[129],"by":[130],"Delbr\u00fcck\u2013Gillespie":[132],"process,":[133],"chemostatic":[136],"nonequilibrium":[137],"environment.":[138],"open":[140],"serves":[144],"archetype":[147],"biochemical":[149],"self-replication":[150],"provides":[152],"insight":[153],"into":[154],"recent":[156],"of":[158,162,177,186,191,205],"England.":[159],"significance":[161],"<italic":[163],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">thermodynamically":[165],"consistent</i>":[166],"coarse-graining":[168],"emphasized.":[170],"In":[171],"where":[175],"death":[176],"biological":[179],"organism":[180],"treated":[182],"reversal":[185],"its":[187],"birth,":[188],"meaning":[190],"mathematically":[192],"emergent":[193],"\u201cdissipation,\u201d":[194],"which":[195],"not":[197],"related":[198],"heat":[201],"measured":[202],"terms":[204],"notation=\"LaTeX\">$k_{B}T$":[210],"remains":[213],"be":[215],"further":[216],"investigated.":[217]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}