{"id":"https://openalex.org/W7204937108","doi":"https://doi.org/10.64898/2026.08.31.748270","title":"Topological Closure Drives Structural Stabilization and Fast Cooperative Dynamics in Crowded Circular Polysomes","display_name":"Topological Closure Drives Structural Stabilization and Fast Cooperative Dynamics in Crowded Circular Polysomes","publication_year":2026,"publication_date":"2026-09-01","ids":{"openalex":"https://openalex.org/W7204937108","doi":"https://doi.org/10.64898/2026.08.31.748270"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.31.748270","doi":"https://doi.org/10.64898/2026.08.31.748270","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.31.748270","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/01/2026.08.31.748270.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/01/2026.08.31.748270.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5124044329","display_name":"Hideki Kobayashi","orcid":"https://orcid.org/0000-0002-4024-1752","observed_orcids":["https://orcid.org/0000-0002-4024-1752"]},"institutions":[{"id":"https://openalex.org/I100066346","display_name":"University of Stuttgart","ror":"https://ror.org/04vnq7t77","country_code":"DE","type":"education","lineage":["https://openalex.org/I100066346"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Hideki Kobayashi","raw_affiliation_strings":["Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany","institution_ids":["https://openalex.org/I100066346"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087759449","display_name":"Horacio V. Guzman","orcid":"https://orcid.org/0000-0003-2564-3005","observed_orcids":["https://orcid.org/0000-0003-2564-3005"]},"institutions":[{"id":"https://openalex.org/I4210134458","display_name":"Institut de Ci\u00e8ncia de Materials de Barcelona","ror":"https://ror.org/03hasqf61","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210134458"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Horacio V. Guzman","raw_affiliation_strings":["Institut de Ci\u00e8ncia de Materials de Barcelona ICMAB-CSIC, Carrer dels Til.lers, Bellaterra, E-08193 Spain"],"raw_orcid":"https://orcid.org/0000-0003-2564-3005","affiliations":[{"raw_affiliation_string":"Institut de Ci\u00e8ncia de Materials de Barcelona ICMAB-CSIC, Carrer dels Til.lers, Bellaterra, E-08193 Spain","institution_ids":["https://openalex.org/I4210134458"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5087759449"],"corresponding_institution_ids":["https://openalex.org/I4210134458"],"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9990000128746033,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9990000128746033,"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":0.0006000000284984708,"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/T10604","display_name":"RNA Research and Splicing","score":9.999999747378752e-05,"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/topological-closure","display_name":"topological closure","score":0.7609999775886536},{"id":"https://openalex.org/keywords/excluded-volume-interactions","display_name":"excluded volume interactions","score":0.8870000243186951},{"id":"https://openalex.org/keywords/ribosome-density","display_name":"ribosome density","score":0.8489999771118164},{"id":"https://openalex.org/keywords/scaling-exponents","display_name":"scaling exponents","score":0.7369999885559082},{"id":"https://openalex.org/keywords/self-avoiding-walks","display_name":"self-avoiding walks","score":0.765999972820282},{"id":"https://openalex.org/keywords/crossover-model","display_name":"crossover model","score":0.5540000200271606},{"id":"https://openalex.org/keywords/ribosome-mrna-interaction","display_name":"ribosome-mRNA interaction","score":0.33000001311302185}],"concepts":[{"id":"https://openalex.org/C65666806","wikidata":"https://www.wikidata.org/wiki/Q970614","display_name":"Polysome","level":5,"score":0.5853000283241272},{"id":"https://openalex.org/C88478588","wikidata":"https://www.wikidata.org/wiki/Q42244","display_name":"Ribosome","level":4,"score":0.541100025177002},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.5126000046730042},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.45980000495910645},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.4535999894142151},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.4374000132083893},{"id":"https://openalex.org/C146834321","wikidata":"https://www.wikidata.org/wiki/Q2979672","display_name":"Closure (psychology)","level":2,"score":0.43479999899864197},{"id":"https://openalex.org/C2780388253","wikidata":"https://www.wikidata.org/wiki/Q5421508","display_name":"Exponent","level":2,"score":0.4088999927043915},{"id":"https://openalex.org/C177860922","wikidata":"https://www.wikidata.org/wiki/Q788608","display_name":"Decorrelation","level":2,"score":0.39739999175071716},{"id":"https://openalex.org/C201194858","wikidata":"https://www.wikidata.org/wiki/Q898238","display_name":"Steric effects","level":2,"score":0.3847000002861023},{"id":"https://openalex.org/C149333683","wikidata":"https://www.wikidata.org/wiki/Q5189188","display_name":"Crowding","level":2,"score":0.3353999853134155},{"id":"https://openalex.org/C181990884","wikidata":"https://www.wikidata.org/wiki/Q11396092","display_name":"Macromolecular crowding","level":3,"score":0.326200008392334},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.32510000467300415},{"id":"https://openalex.org/C177731217","wikidata":"https://www.wikidata.org/wiki/Q2622244","display_name":"Mesoscopic physics","level":2,"score":0.31060001254081726},{"id":"https://openalex.org/C130603088","wikidata":"https://www.wikidata.org/wiki/Q4976526","display_name":"Brownian dynamics","level":3,"score":0.2985000014305115},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.27000001072883606},{"id":"https://openalex.org/C114847915","wikidata":"https://www.wikidata.org/wiki/Q16948788","display_name":"Ribosomal binding site","level":5,"score":0.2676999866962433},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.26510000228881836}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.08.31.748270","doi":"https://doi.org/10.64898/2026.08.31.748270","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.31.748270","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/01/2026.08.31.748270.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.08.31.748270","doi":"https://doi.org/10.64898/2026.08.31.748270","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.31.748270","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/01/2026.08.31.748270.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1995364615","display_name":null,"funder_award_id":"PID2023-150536NA-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G3743529912","display_name":null,"funder_award_id":"CEX2023001263\u2010S","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G5235593086","display_name":"St\u00e4rken der Qualit\u00e4t und der Nutzer*innenschaft der Forschungssoftware ESPResSo f\u00fcr partikelbasierte Simulationen","funder_award_id":"528726435","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G745419941","display_name":null,"funder_award_id":"PID2023","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7204937108.pdf","grobid_xml":"https://content.openalex.org/works/W7204937108.grobid-xml"},"referenced_works_count":1,"referenced_works":["https://openalex.org/W7130575500"],"related_works":["https://openalex.org/W7155523403","https://openalex.org/W7125776128","https://openalex.org/W2030045395","https://openalex.org/W207631500","https://openalex.org/W1976173025","https://openalex.org/W2059253136","https://openalex.org/W4313312922","https://openalex.org/W2069055899","https://openalex.org/W2026612003","https://openalex.org/W2069122773"],"abstract_inverted_index":{"In":[0],"linear":[1,14,43,92,182],"polysomes,":[2],"excluded-volume":[3],"interactions":[4],"among":[5],"ribosomes":[6],"can":[7,28],"induce":[8],"dimensional":[9],"reduction":[10],"of":[11,48,73,174,188,218,233],"mRNA.":[12],"Yet":[13],"architectures":[15],"allow":[16],"steric":[17,239],"stress":[18],"to":[19,84,107,117,180,204,223],"relax":[20],"at":[21,206],"open":[22],"ends\u2013":[23],"limiting":[24],"how":[25],"strongly":[26,141],"crowding":[27,81,93,196],"remodel":[29],"the":[30,132,144,159,170,185,199,207,215,219,230,237],"mRNA\u2019s":[31],"structure":[32],"and":[33,42,79,143],"dynamics.":[34],"Using":[35],"coarse-grained":[36],"molecular-dynamics":[37],"simulations,":[38],"we":[39],"compare":[40],"circular":[41,77,175,234,253],"polysomes":[44,176],"over":[45,70,158],"a":[46,54,63,71,128,245],"range":[47,72],"ribosome":[49,74,80,125,195],"densities.":[50,75],"Circular":[51],"closure":[52,89,235],"selects":[53],"predominantly":[55],"quasi-planar":[56],"global":[57,96,137,220],"conformational":[58,250],"ensemble,":[59,194],"as":[60],"indicated":[61],"by":[62,177,202],"shape":[64,67],"dimensionality":[65],"d":[66],"\u2248":[68,108,118],"2":[69],"Crucially,":[76],"topology":[78],"act":[82],"cooperatively":[83],"suppress":[85],"structural":[86],"fluctuations.":[87],"While":[88],"alone":[90],"or":[91],"reduces":[94,198],"relative":[95,179],"size":[97,138],"fluctuations":[98,139],"(\u0394":[99],"R":[100,103],"g":[101,104],"/":[102],")":[105],"only":[106],"0.16,":[109],"their":[110],"combined":[111],"effect":[112],"drives":[113,127],"this":[114,121,192],"fluctuation":[115],"down":[116],"0.07.":[119],"Within":[120,191],"stabilized":[122],"architecture,":[123],"increasing":[124],"density":[126,216],"distinct":[129],"in-plane":[130],"reorganization:":[131],"ring":[133],"becomes":[134],"more":[135],"isotropic,":[136],"are":[140],"suppressed,":[142],"scaling":[145,221],"exponent":[146,222],"increases":[147],"toward":[148],"\u03bd":[149],"\u2243":[150],"0.74\u20130.77,":[151],"consistent":[152],"with":[153],"two-dimensional":[154],"self-avoiding":[155],"walk-like":[156],"value":[157],"accessible":[160],"finite-size":[161],"window,":[162],"1000":[163],"\u2264":[164,166],"N":[165],"4969.":[167],"Closure":[168],"shortens":[169],"radius-of-gyration":[171],"decorrelation":[172,200],"time":[173,201],"40-fold":[178],"matched":[181],"systems,":[183],"reflecting":[184],"topological":[186],"elimination":[187],"free":[189],"ends.":[190],"closure-selected":[193],"further":[197],"up":[203],"20%":[205],"highest":[208],"density.":[209],"A":[210],"fluctuation-informed":[211],"crossover":[212],"model":[213],"links":[214],"dependence":[217],"inter-ribosomal":[224],"subchain":[225],"statistics.":[226],"These":[227],"results":[228],"distinguish":[229],"geometric":[231],"role":[232],"from":[236],"density-dependent":[238],"response":[240],"that":[241],"it":[242],"enables,":[243],"revealing":[244],"confined":[246],"yet":[247],"dynamically":[248],"responsive":[249],"regime":[251],"for":[252],"polysomes.":[254]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-09-02T00:00:00"}
