{"id":"https://openalex.org/W4361017253","doi":"https://doi.org/10.1371/journal.pcbi.1011013","title":"An associative memory Hamiltonian model for DNA and nucleosomes","display_name":"An associative memory Hamiltonian model for DNA and nucleosomes","publication_year":2023,"publication_date":"2023-03-27","ids":{"openalex":"https://openalex.org/W4361017253","doi":"https://doi.org/10.1371/journal.pcbi.1011013","pmid":"https://pubmed.ncbi.nlm.nih.gov/36972316","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/10079229"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011013","doi":"https://doi.org/10.1371/journal.pcbi.1011013","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011013","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011013&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011013&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038748521","display_name":"Weiqi Lu","orcid":"https://orcid.org/0000-0002-9822-9131","observed_orcids":["https://orcid.org/0000-0002-9822-9131"]},"institutions":[{"id":"https://openalex.org/I4210145836","display_name":"Center for Theoretical Biological Physics","ror":"https://ror.org/04hfg7v94","country_code":"US","type":"facility","lineage":["https://openalex.org/I12912129","https://openalex.org/I181547552","https://openalex.org/I2801539370","https://openalex.org/I4210145836","https://openalex.org/I44461941","https://openalex.org/I74775410"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weiqi Lu","raw_affiliation_strings":["Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, TX, USA","Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, TX, USA","institution_ids":["https://openalex.org/I4210145836","https://openalex.org/I74775410"]},{"raw_affiliation_string":"Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, Texas, United States of America","institution_ids":["https://openalex.org/I4210145836","https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030987631","display_name":"Jos\u00e9 N. Onuchic","orcid":"https://orcid.org/0000-0002-9448-0388","observed_orcids":["https://orcid.org/0000-0002-9448-0388"]},"institutions":[{"id":"https://openalex.org/I4210145836","display_name":"Center for Theoretical Biological Physics","ror":"https://ror.org/04hfg7v94","country_code":"US","type":"facility","lineage":["https://openalex.org/I12912129","https://openalex.org/I181547552","https://openalex.org/I2801539370","https://openalex.org/I4210145836","https://openalex.org/I44461941","https://openalex.org/I74775410"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 N. Onuchic","raw_affiliation_strings":["Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, TX, USA","Department of Chemistry, & Department of Biosciences, Rice University, Houston, TX, USA","Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, Texas, United States of America","Department of Chemistry, & Department of Biosciences, Rice University, Houston, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, TX, USA","institution_ids":["https://openalex.org/I4210145836","https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Chemistry, & Department of Biosciences, Rice University, Houston, TX, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, Texas, United States of America","institution_ids":["https://openalex.org/I4210145836","https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Chemistry, & Department of Biosciences, Rice University, Houston, Texas, United States of America","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015833375","display_name":"Michele Di Pierro","orcid":"https://orcid.org/0000-0002-2889-2632","observed_orcids":["https://orcid.org/0000-0002-2889-2632"]},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michele Di Pierro","raw_affiliation_strings":["Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA","Department of Physics, Northeastern University, Boston, MA, USA","Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, United States of America","Department of Physics, Northeastern University, Boston, Massachusetts, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-2889-2632","affiliations":[{"raw_affiliation_string":"Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Department of Physics, Northeastern University, Boston, MA, USA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Department of Physics, Northeastern University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I12912129"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5015833375"],"corresponding_institution_ids":["https://openalex.org/I12912129"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.2594,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.40652279,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":95},"biblio":{"volume":"19","issue":"3","first_page":"e1011013","last_page":"e1011013"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.5131999850273132,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.5131999850273132,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.40450000762939453,"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":0.027499999850988388,"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/dna-mechanics","display_name":"DNA mechanics","score":0.6840000152587891},{"id":"https://openalex.org/keywords/nucleosome","display_name":"nucleosome","score":0.9629999995231628},{"id":"https://openalex.org/keywords/chromatin-structure","display_name":"chromatin structure","score":0.6980000138282776},{"id":"https://openalex.org/keywords/hamiltonian-model","display_name":"Hamiltonian model","score":0.8059999942779541},{"id":"https://openalex.org/keywords/b-dna","display_name":"B-DNA","score":0.6019999980926514},{"id":"https://openalex.org/keywords/persistence-length","display_name":"persistence length","score":0.8379999995231628},{"id":"https://openalex.org/keywords/supercoiling","display_name":"supercoiling","score":0.7979999780654907},{"id":"https://openalex.org/keywords/plectonemes","display_name":"plectonemes","score":0.9909999966621399},{"id":"https://openalex.org/keywords/dna-unwrapping","display_name":"DNA unwrapping","score":0.8069999814033508},{"id":"https://openalex.org/keywords/steric-interactions","display_name":"steric interactions","score":0.8180000185966492},{"id":"https://openalex.org/keywords/circular-dna","display_name":"circular DNA","score":0.48100000619888306}],"concepts":[{"id":"https://openalex.org/C158456008","wikidata":"https://www.wikidata.org/wiki/Q412639","display_name":"DNA supercoil","level":4,"score":0.8234165906906128},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.7304314970970154},{"id":"https://openalex.org/C130787639","wikidata":"https://www.wikidata.org/wiki/Q5645293","display_name":"Hamiltonian (control theory)","level":2,"score":0.5051544308662415},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4938676953315735},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.48640942573547363},{"id":"https://openalex.org/C99895341","wikidata":"https://www.wikidata.org/wiki/Q366058","display_name":"Persistence length","level":3,"score":0.463329941034317},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.4617462456226349},{"id":"https://openalex.org/C159423971","wikidata":"https://www.wikidata.org/wiki/Q177251","display_name":"Associative property","level":2,"score":0.4497794508934021},{"id":"https://openalex.org/C2776196297","wikidata":"https://www.wikidata.org/wiki/Q17138781","display_name":"Twist","level":2,"score":0.43997105956077576},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.41578465700149536},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.343317449092865},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.3392876088619232},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3224109709262848},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2550337314605713},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22950604557991028},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.14950978755950928},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14790382981300354},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.1463458240032196},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.10199427604675293},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C73573662","wikidata":"https://www.wikidata.org/wiki/Q130996","display_name":"DNA replication","level":3,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1011013","doi":"https://doi.org/10.1371/journal.pcbi.1011013","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011013","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011013&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"doi:10.1101/2022.10.15.512163","doi":"https://doi.org/10.1101/2022.10.15.512163","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2022.10.15.512163","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2022/10/18/2022.10.15.512163.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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:10079229","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10079229","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10079229/pdf/pcbi.1011013.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmid:36972316","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36972316","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,"listed_in":[],"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":"PLoS computational biology","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:b07c464eba704d18a2558e12dd7e655f","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/b07c464eba704d18a2558e12dd7e655f","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,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 3, p e1011013 (2023)","raw_type":"article"},{"id":"pmh:oai:repository.rice.edu:1911/114843","doi":null,"is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011013.","pdf_url":null,"source":{"id":"https://openalex.org/S4306401268","display_name":"Rice Research Repository (Rice University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I74775410","host_organization_name":"Rice University","host_organization_lineage":["https://openalex.org/I74775410"],"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":"Journal article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011013","doi":"https://doi.org/10.1371/journal.pcbi.1011013","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011013","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011013&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2062209358","display_name":null,"funder_award_id":"PHY-2019745","funder_id":"https://openalex.org/F4320310133","funder_display_name":"Rice University"},{"id":"https://openalex.org/G2314922425","display_name":null,"funder_award_id":"PHY- 2019745","funder_id":"https://openalex.org/F4320332774","funder_display_name":"Center for Theoretical Biological Physics"},{"id":"https://openalex.org/G294349639","display_name":null,"funder_award_id":"C-1792)","funder_id":"https://openalex.org/F4320306196","funder_display_name":"Welch Foundation"},{"id":"https://openalex.org/G3395635298","display_name":null,"funder_award_id":"2019745","funder_id":"https://openalex.org/F4320310133","funder_display_name":"Rice University"},{"id":"https://openalex.org/G4062440706","display_name":"MRI: Acquisition of Big-Data Private-Cloud Research Cyberinfrastructure (BDPC)","funder_award_id":"1338099","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4152014458","display_name":null,"funder_award_id":"Grant C-1792","funder_id":"https://openalex.org/F4320306196","funder_display_name":"Welch Foundation"},{"id":"https://openalex.org/G4824490719","display_name":null,"funder_award_id":"PHY-2210291","funder_id":"https://openalex.org/F4320310133","funder_display_name":"Rice University"},{"id":"https://openalex.org/G6001776492","display_name":"Center for Theoretical Biological Physics","funder_award_id":"2019745","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6997479561","display_name":"The Energy Landscape for Folding and Function of Biomolecules: From Proteins to Chromatin","funder_award_id":"2210291","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7166483632","display_name":null,"funder_award_id":"R35GM146852","funder_id":"https://openalex.org/F4320306080","funder_display_name":"Foundation for the National Institutes of Health"},{"id":"https://openalex.org/G8556403166","display_name":null,"funder_award_id":"2019745","funder_id":"https://openalex.org/F4320332774","funder_display_name":"Center for Theoretical Biological Physics"},{"id":"https://openalex.org/G9000880429","display_name":"Coevolution and Functional Interactions in the Non-Coding Genome","funder_award_id":"R35GM146852","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306080","display_name":"Foundation for the National Institutes of Health","ror":"https://ror.org/00k86s890"},{"id":"https://openalex.org/F4320306196","display_name":"Welch Foundation","ror":"https://ror.org/00np6vq88"},{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320310133","display_name":"Rice University","ror":"https://ror.org/008zs3103"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332774","display_name":"Center for Theoretical Biological Physics","ror":"https://ror.org/008zs3103"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4361017253.pdf","grobid_xml":"https://content.openalex.org/works/W4361017253.grobid-xml"},"referenced_works_count":93,"referenced_works":["https://openalex.org/W604319760","https://openalex.org/W1535422202","https://openalex.org/W1568631168","https://openalex.org/W1572494942","https://openalex.org/W1969664782","https://openalex.org/W1969865760","https://openalex.org/W1974114013","https://openalex.org/W1976308393","https://openalex.org/W1981050748","https://openalex.org/W1983384818","https://openalex.org/W1983459461","https://openalex.org/W1986302333","https://openalex.org/W1987182457","https://openalex.org/W1992898397","https://openalex.org/W1995133940","https://openalex.org/W2006311225","https://openalex.org/W2014901554","https://openalex.org/W2026829286","https://openalex.org/W2028120697","https://openalex.org/W2031490363","https://openalex.org/W2032951358","https://openalex.org/W2043995349","https://openalex.org/W2045533286","https://openalex.org/W2054739661","https://openalex.org/W2056933486","https://openalex.org/W2061029238","https://openalex.org/W2065728036","https://openalex.org/W2065996552","https://openalex.org/W2073026107","https://openalex.org/W2075048172","https://openalex.org/W2081313354","https://openalex.org/W2083589122","https://openalex.org/W2085217316","https://openalex.org/W2090037139","https://openalex.org/W2090632681","https://openalex.org/W2090708401","https://openalex.org/W2098043275","https://openalex.org/W2103653834","https://openalex.org/W2106863384","https://openalex.org/W2113253885","https://openalex.org/W2117208578","https://openalex.org/W2126147931","https://openalex.org/W2126466006","https://openalex.org/W2131340135","https://openalex.org/W2144965078","https://openalex.org/W2151553287","https://openalex.org/W2154456026","https://openalex.org/W2157366872","https://openalex.org/W2172170093","https://openalex.org/W2202710059","https://openalex.org/W2259423114","https://openalex.org/W2267962174","https://openalex.org/W2319900881","https://openalex.org/W2321759319","https://openalex.org/W2330073554","https://openalex.org/W2404671429","https://openalex.org/W2466311327","https://openalex.org/W2485301169","https://openalex.org/W2523898334","https://openalex.org/W2581551676","https://openalex.org/W2595443678","https://openalex.org/W2616798345","https://openalex.org/W2735202559","https://openalex.org/W2738317363","https://openalex.org/W2767327558","https://openalex.org/W2806123558","https://openalex.org/W2889483899","https://openalex.org/W2890385335","https://openalex.org/W2897474346","https://openalex.org/W2898311068","https://openalex.org/W2903091331","https://openalex.org/W2903457010","https://openalex.org/W2912364028","https://openalex.org/W2914490422","https://openalex.org/W2920845725","https://openalex.org/W2921773684","https://openalex.org/W2946219248","https://openalex.org/W2946459547","https://openalex.org/W2948526042","https://openalex.org/W2949223833","https://openalex.org/W2992752060","https://openalex.org/W3095424969","https://openalex.org/W3100189422","https://openalex.org/W3103586898","https://openalex.org/W3124332276","https://openalex.org/W3129867584","https://openalex.org/W3130709842","https://openalex.org/W3139211464","https://openalex.org/W3160655886","https://openalex.org/W3164981937","https://openalex.org/W3178897453","https://openalex.org/W4304203516","https://openalex.org/W4307860677"],"related_works":["https://openalex.org/W7203519452","https://openalex.org/W2151317664","https://openalex.org/W2089588871","https://openalex.org/W434453064","https://openalex.org/W2580061216","https://openalex.org/W1509133511","https://openalex.org/W6907593873","https://openalex.org/W7099719646","https://openalex.org/W4307181419","https://openalex.org/W1964541633"],"abstract_inverted_index":{"A":[0],"model":[1,92,135],"for":[2,228],"DNA":[3,108,174],"and":[4,48,52,69,82,114,126,224],"nucleosomes":[5],"is":[6,62,100,164,179,198,217,225],"introduced":[7],"with":[8,141],"the":[9,20,29,36,40,53,57,79,86,104,110,122,160,169,183,189,211,220],"goal":[10],"of":[11,39,56,64,85,90,106,112,124,127,167,172,188,195,214],"studying":[12],"chromosomes":[13],"from":[14,176],"a":[15],"single":[16],"base":[17],"level":[18],"all":[19,74],"way":[21],"to":[22,78,95,102,143,149,181,200,204,209],"higher-order":[23],"chromatin":[24],"structures.":[25],"This":[26],"model,":[27],"dubbed":[28],"Widely":[30],"Editable":[31],"Chromatin":[32],"Model":[33],"(WEChroM),":[34],"reproduces":[35],"complex":[37],"mechanics":[38],"double":[41],"helix":[42],"including":[43],"its":[44,97,196],"bending":[45],"persistence":[46,50],"length":[47],"twisting":[49],"length,":[51],"temperature":[54],"dependence":[55],"former.":[58],"The":[59,134],"WEChroM":[60,99,178,216],"Hamiltonian":[61,163],"composed":[63],"chain":[65],"connectivity,":[66],"steric":[67],"interactions,":[68],"associative":[70,161],"memory":[71,162],"terms":[72],"representing":[73],"remaining":[75],"interactions":[76],"leading":[77],"structure,":[80],"dynamics,":[81],"mechanical":[83,132,186],"characteristics":[84],"B-DNA.":[87],"Several":[88],"applications":[89],"this":[91],"are":[93],"discussed":[94],"demonstrate":[96],"applicability.":[98],"used":[101],"investigate":[103,210],"behavior":[105,140],"circular":[107],"in":[109,154,219],"presence":[111],"positive":[113,144],"negative":[115,146],"supercoiling.":[116],"We":[117],"show":[118,158],"that":[119,130,159],"it":[120],"recapitulates":[121],"formation":[123],"plectonemes":[125],"structural":[128,212],"defects":[129],"relax":[131],"stress.":[133],"spontaneously":[136],"manifests":[137],"an":[138],"asymmetric":[139],"respect":[142],"or":[145],"supercoiling,":[147],"similar":[148],"what":[150],"was":[151],"previously":[152],"observed":[153],"experiments.":[155],"Additionally,":[156],"we":[157],"also":[165],"capable":[166],"reproducing":[168],"free":[170],"energy":[171],"partial":[173],"unwrapping":[175],"nucleosomes.":[177],"designed":[180],"emulate":[182],"continuously":[184],"variable":[185],"properties":[187],"10nm":[190],"fiber":[191],"and,":[192],"by":[193],"virtue":[194],"simplicity,":[197],"ready":[199],"be":[201],"scaled":[202],"up":[203],"molecular":[205],"systems":[206],"large":[207],"enough":[208],"ensembles":[213],"genes.":[215],"implemented":[218],"OpenMM":[221],"simulation":[222],"toolkits":[223],"freely":[226],"available":[227],"public":[229],"use.":[230]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2023-03-30T00:00:00"}