{"id":"https://openalex.org/W7213357166","doi":"https://doi.org/10.48550/arxiv.2609.13310","title":"Polymerase-mediated quasispecies dynamics: bifurcations, complementation, and robustness of \u03c4-tipping","display_name":"Polymerase-mediated quasispecies dynamics: bifurcations, complementation, and robustness of \u03c4-tipping","publication_year":2026,"publication_date":"2026-09-10","ids":{"openalex":"https://openalex.org/W7213357166","doi":"https://doi.org/10.48550/arxiv.2609.13310"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2609.13310","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2609.13310","pdf_url":"https://arxiv.org/pdf/2609.13310","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2609.13310","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078342141","display_name":"Edward A. Turner","orcid":"https://orcid.org/0000-0002-2959-9227","observed_orcids":["https://orcid.org/0000-0002-2959-9227"]},"institutions":[{"id":"https://openalex.org/I3132875200","display_name":"Vi\u00f1a del Mar University","ror":"https://ror.org/00txsqk22","country_code":"CL","type":"education","lineage":["https://openalex.org/I3132875200"]}],"countries":["CL"],"is_corresponding":false,"raw_author_name":"Turner, Edward A.","raw_affiliation_strings":["Facultad de Ciencias Jur\u00eddicas , Sociales y de la Educaci\u00f3n , Universidad Vi\u00f1a del Mar , Vi\u00f1a del Mar , Chile"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Facultad de Ciencias Jur\u00eddicas , Sociales y de la Educaci\u00f3n , Universidad Vi\u00f1a del Mar , Vi\u00f1a del Mar , Chile","institution_ids":["https://openalex.org/I3132875200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037292181","display_name":"Francisco Crespo","orcid":"https://orcid.org/0000-0002-5930-8523","observed_orcids":["https://orcid.org/0000-0002-5930-8523"]},"institutions":[{"id":"https://openalex.org/I4405252843","display_name":"Embry-Riddle Aeronautical University Daytona Beach Florida Campus","ror":"https://ror.org/001emy730","country_code":"US","type":"education","lineage":["https://openalex.org/I4405252843","https://openalex.org/I84475105"]},{"id":"https://openalex.org/I84475105","display_name":"Embry\u2013Riddle Aeronautical University","ror":"https://ror.org/010jskt71","country_code":"US","type":"education","lineage":["https://openalex.org/I84475105"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Crespo, Francisco","raw_affiliation_strings":["Embry-Riddle Aeronautical University , Aerospace Engineering , Daytona Beach , FL 32114 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Embry-Riddle Aeronautical University , Aerospace Engineering , Daytona Beach , FL 32114 , USA","institution_ids":["https://openalex.org/I4405252843","https://openalex.org/I84475105"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115505080","display_name":"Nolbert Morales","orcid":"https://orcid.org/0009-0009-8114-1537","observed_orcids":["https://orcid.org/0009-0009-8114-1537"]},"institutions":[{"id":"https://openalex.org/I3124150290","display_name":"Universidad San Sebasti\u00e1n","ror":"https://ror.org/04jrwm652","country_code":"CL","type":"education","lineage":["https://openalex.org/I3124150290"]}],"countries":["CL"],"is_corresponding":false,"raw_author_name":"Morales, Nolbert","raw_affiliation_strings":["Facultad de Ingenier\u00eda , Universidad San Sebasti\u00e1n , Lago Panguipulli 1390 , Puerto Montt , Chile"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Facultad de Ingenier\u00eda , Universidad San Sebasti\u00e1n , Lago Panguipulli 1390 , Puerto Montt , Chile","institution_ids":["https://openalex.org/I3124150290"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001395924","display_name":"Santiago F. Elena","orcid":"https://orcid.org/0000-0001-8249-5593","observed_orcids":["https://orcid.org/0000-0001-8249-5593"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Elena, Santiago F.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5022876719","display_name":"Josep Sardany\u00e9s A","orcid":"https://orcid.org/0000-0001-7225-5158","observed_orcids":["https://orcid.org/0000-0001-7225-5158"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sardanyes, Josep","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.7445999979972839,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.7445999979972839,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.25220000743865967,"subfield":{"id":"https://openalex.org/subfields/2604","display_name":"Applied Mathematics"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11152","display_name":"Stochastic processes and statistical mechanics","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/2610","display_name":"Mathematical Physics"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/quasispecies-theory","display_name":"quasispecies theory","score":0.8529999852180481},{"id":"https://openalex.org/keywords/rna-dependent-rna-polymerase","display_name":"RNA-dependent RNA polymerase","score":0.8059999942779541},{"id":"https://openalex.org/keywords/delay-differential-equations","display_name":"delay differential equations","score":0.8560000061988831},{"id":"https://openalex.org/keywords/error-catastrophe","display_name":"error catastrophe","score":0.5989999771118164},{"id":"https://openalex.org/keywords/complementation","display_name":"complementation","score":0.6010000109672546},{"id":"https://openalex.org/keywords/basins-of-attraction","display_name":"basins of attraction","score":0.7210000157356262},{"id":"https://openalex.org/keywords/transcritical-bifurcation","display_name":"transcritical bifurcation","score":0.8180000185966492},{"id":"https://openalex.org/keywords/saddle-node-bifurcation","display_name":"saddle-node bifurcation","score":0.9990000128746033},{"id":"https://openalex.org/keywords/population-extinction","display_name":"population extinction","score":0.5860000252723694},{"id":"https://openalex.org/keywords/rna-virus-evolution","display_name":"RNA virus evolution","score":0.5260000228881836},{"id":"https://openalex.org/keywords/viral-persistence","display_name":"viral persistence","score":0.6000000238418579}],"concepts":[{"id":"https://openalex.org/C14500911","wikidata":"https://www.wikidata.org/wiki/Q3413375","display_name":"Viral quasispecies","level":4,"score":0.8299999833106995},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5630000233650208},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.499099999666214},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4986000061035156},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.4426000118255615},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4108000099658966},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40130001306533813},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.39160001277923584},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.37880000472068787},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.3684000074863434},{"id":"https://openalex.org/C188082640","wikidata":"https://www.wikidata.org/wiki/Q1780899","display_name":"Complementation","level":4,"score":0.3675000071525574},{"id":"https://openalex.org/C2776449523","wikidata":"https://www.wikidata.org/wiki/Q272631","display_name":"RNA polymerase","level":4,"score":0.33570000529289246},{"id":"https://openalex.org/C2779174946","wikidata":"https://www.wikidata.org/wiki/Q751911","display_name":"RNA virus","level":4,"score":0.32359999418258667},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.3167000114917755},{"id":"https://openalex.org/C98638677","wikidata":"https://www.wikidata.org/wiki/Q2067051","display_name":"Mutation rate","level":3,"score":0.29260000586509705},{"id":"https://openalex.org/C82381507","wikidata":"https://www.wikidata.org/wiki/Q416878","display_name":"Polymerase","level":3,"score":0.2865000069141388},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2849999964237213},{"id":"https://openalex.org/C8769409","wikidata":"https://www.wikidata.org/wiki/Q2066554","display_name":"Viral evolution","level":4,"score":0.28450000286102295},{"id":"https://openalex.org/C140704245","wikidata":"https://www.wikidata.org/wiki/Q3933202","display_name":"Viral replication","level":3,"score":0.27549999952316284},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2558000087738037},{"id":"https://openalex.org/C8272713","wikidata":"https://www.wikidata.org/wiki/Q176737","display_name":"Stochastic process","level":2,"score":0.251800000667572},{"id":"https://openalex.org/C87590526","wikidata":"https://www.wikidata.org/wiki/Q3592884","display_name":"Experimental evolution","level":3,"score":0.250900000333786}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2609.13310","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2609.13310","pdf_url":"https://arxiv.org/pdf/2609.13310","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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"},{"id":"doi:10.48550/arxiv.2609.13310","doi":"https://doi.org/10.48550/arxiv.2609.13310","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2609.13310","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2609.13310","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2609.13310","pdf_url":"https://arxiv.org/pdf/2609.13310","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320315062","display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades","ror":null},{"id":"https://openalex.org/F4320315803","display_name":"Centres de Recerca de Catalunya","ror":"https://ror.org/01bkbaq61"},{"id":"https://openalex.org/F4320321505","display_name":"Generalitat de Catalunya","ror":"https://ror.org/01bg62x04"},{"id":"https://openalex.org/F4320321864","display_name":"Generalitat Valenciana","ror":"https://ror.org/0097mvx21"},{"id":"https://openalex.org/F4320331146","display_name":"Agencia Nacional de Investigaci\u00f3n y Desarrollo","ror":"https://ror.org/05btm5233"},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":"https://ror.org/003x0zc53"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7213357166.pdf","grobid_xml":"https://content.openalex.org/works/W7213357166.grobid-xml"},"referenced_works_count":1,"referenced_works":["https://openalex.org/W3190560493"],"related_works":["https://openalex.org/W7166850799","https://openalex.org/W2082676515","https://openalex.org/W4299359829","https://openalex.org/W4405468108","https://openalex.org/W2625682396","https://openalex.org/W7100736906","https://openalex.org/W3143226247","https://openalex.org/W2060809008","https://openalex.org/W7096778889","https://openalex.org/W2791015709"],"abstract_inverted_index":{"Quasispecies":[0],"theory":[1],"describes":[2],"how":[3],"mutation":[4,119],"and":[5,29,67,78,88,94,109,120,205,211,223,236],"selection":[6],"shape":[7],"highly":[8],"variable":[9],"RNA":[10,20,234],"virus":[11],"populations,":[12],"but":[13],"most":[14],"models":[15,165],"explicitly":[16],"consider":[17],"neither":[18],"RNA-dependent":[19],"polymerases":[21,176],"nor":[22],"the":[23,100,137,159,163,168,181,201,229],"delays":[24,98],"associated":[25],"with":[26,130],"their":[27,105],"synthesis":[28],"functional":[30,72,175,237],"activation.":[31],"A":[32],"recent":[33],"minimal":[34],"model":[35,63,141],"showed":[36],"that":[37,113,167],"delayed":[38],"polymerase":[39],"availability":[40],"can":[41,110],"induce":[42],"extinction":[43,90,196],"by":[44,92],"reorganizing":[45],"basins":[46,106],"of":[47,107,158,170,180,194,203,231],"attraction,":[48],"a":[49,59,143,155],"mechanism":[50,218],"termed":[51],"\u03c4-tipping.":[52],"Here,":[53],"we":[54,215],"extend":[55],"this":[56,217],"framework":[57],"to":[58,128,173,227],"delay":[60],"differential":[61],"equation":[62],"in":[64,146,185,197],"which":[65,147],"master":[66,182],"mutant":[68,132,171,186],"genomes":[69,149,172],"encode":[70,174],"distinct":[71],"polymerases.":[73],"We":[74,134],"characterize":[75],"its":[76],"equilibrium":[77],"bifurcation":[79,160],"structure,":[80],"identifying":[81],"master-mutant":[82],"coexistence,":[83],"mutant-only":[84],"persistence":[85],"(error":[86],"catastrophe),":[87],"complete":[89,189],"governed":[91],"transcritical":[93],"saddle-node":[95],"bifurcations.":[96],"Although":[97],"leave":[99],"equilibria":[101],"unchanged,":[102],"they":[103],"reorganize":[104],"attraction":[108],"redirect":[111],"populations":[112],"would":[114],"otherwise":[115],"persist":[116],"at":[117],"fixed":[118],"replication":[121,208],"parameters":[122],"toward":[123],"extinction,":[124],"thereby":[125],"extending":[126],"\u03c4-tipping":[127,204],"systems":[129],"autonomous":[131],"replication.":[133],"also":[135],"recover":[136],"previously":[138],"studied":[139],"complementation":[140,238],"as":[142],"limiting":[144],"case":[145],"defective":[148],"depend":[150],"on":[151,239],"master-derived":[152],"polymerase,":[153],"providing":[154],"comprehensive":[156],"analysis":[157],"structure.":[161],"Comparing":[162],"two":[164],"shows":[166],"ability":[169],"determines":[177],"whether":[178],"loss":[179],"sequence":[183],"results":[184],"replacement":[187],"or":[188],"population":[190],"extinction.":[191,213],"The":[192],"occurrence":[193],"delay-induced":[195],"both":[198],"settings":[199],"demonstrates":[200],"robustness":[202],"connects":[206],"intracellular":[207],"kinetics,":[209],"complementation,":[210],"quasispecies":[212],"Finally,":[214],"translate":[216],"into":[219],"concrete":[220],"virological":[221],"predictions":[222],"propose":[224],"experimental":[225],"strategies":[226],"test":[228],"effects":[230],"replicase":[232],"timing,":[233],"degradation,":[235],"viral":[240],"persistence.":[241]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2026-09-16T00:00:00"}