{"id":"https://openalex.org/W2260331532","doi":"https://doi.org/10.1186/s12859-016-0897-9","title":"The role of structural parameters in DNA cyclization","display_name":"The role of structural parameters in DNA cyclization","publication_year":2016,"publication_date":"2016-02-04","ids":{"openalex":"https://openalex.org/W2260331532","doi":"https://doi.org/10.1186/s12859-016-0897-9","mag":"2260331532","pmid":"https://pubmed.ncbi.nlm.nih.gov/26846597"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-0897-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-0897-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-0897-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-0897-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080997789","display_name":"Ludmil B. Alexandrov","orcid":"https://orcid.org/0000-0003-3596-4515"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I4210131040","display_name":"Los Alamos National Security (United States)","ror":"https://ror.org/037ddaj94","country_code":"US","type":"company","lineage":["https://openalex.org/I4210131040"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ludmil B. Alexandrov","raw_affiliation_strings":["Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA. lba@lanl.gov","Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. lba@lanl.gov","Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA. lba@lanl.gov","institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I4210131040"]},{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. lba@lanl.gov","institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I4210131040"]},{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113506287","display_name":"A. R. Bishop","orcid":"https://orcid.org/0009-0002-4781-387X"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I4210131040","display_name":"Los Alamos National Security (United States)","ror":"https://ror.org/037ddaj94","country_code":"US","type":"company","lineage":["https://openalex.org/I4210131040"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alan R. Bishop","raw_affiliation_strings":["Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. arb@lanl.gov","Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. arb@lanl.gov","institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I4210131040"]},{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078718511","display_name":"K. \u00d8. Rasmussen","orcid":"https://orcid.org/0000-0002-4029-4723"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I4210131040","display_name":"Los Alamos National Security (United States)","ror":"https://ror.org/037ddaj94","country_code":"US","type":"company","lineage":["https://openalex.org/I4210131040"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kim \u00d8. Rasmussen","raw_affiliation_strings":["Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. kor@lanl.gov","Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. kor@lanl.gov","institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I4210131040"]},{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079029372","display_name":"Boian S. Alexandrov","orcid":"https://orcid.org/0000-0001-8636-4603"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I4210131040","display_name":"Los Alamos National Security (United States)","ror":"https://ror.org/037ddaj94","country_code":"US","type":"company","lineage":["https://openalex.org/I4210131040"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Boian S. Alexandrov","raw_affiliation_strings":["Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. boian@lanl.gov","Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. boian@lanl.gov","institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I4210131040"]},{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA","institution_ids":["https://openalex.org/I1343871089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5079029372"],"corresponding_institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I4210131040"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.1741,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.62977811,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"17","issue":"1","first_page":"68","last_page":"68"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.3693999946117401,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.3693999946117401,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.30309998989105225,"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/T13187","display_name":"Diffusion and Search Dynamics","score":0.1817999929189682,"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","display_name":"DNA","score":0.7328848242759705},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5706837177276611},{"id":"https://openalex.org/keywords/nucleosome","display_name":"Nucleosome","score":0.5655396580696106},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5580021739006042},{"id":"https://openalex.org/keywords/a-dna","display_name":"A-DNA","score":0.4883705973625183},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45602816343307495},{"id":"https://openalex.org/keywords/helix","display_name":"Helix (gastropod)","score":0.4411352276802063},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.402988076210022},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.37985995411872864},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.36851823329925537},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3374617099761963},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2649868130683899},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23309019207954407},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.14050880074501038},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10137516260147095}],"concepts":[{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.7328848242759705},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5706837177276611},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.5655396580696106},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5580021739006042},{"id":"https://openalex.org/C191961535","wikidata":"https://www.wikidata.org/wiki/Q2360205","display_name":"A-DNA","level":3,"score":0.4883705973625183},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45602816343307495},{"id":"https://openalex.org/C2778530040","wikidata":"https://www.wikidata.org/wiki/Q1937315","display_name":"Helix (gastropod)","level":3,"score":0.4411352276802063},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.402988076210022},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.37985995411872864},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.36851823329925537},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3374617099761963},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2649868130683899},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23309019207954407},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.14050880074501038},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10137516260147095},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C2779965526","wikidata":"https://www.wikidata.org/wiki/Q308841","display_name":"Snail","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D003500","descriptor_name":"Cyclization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003500","descriptor_name":"Cyclization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003500","descriptor_name":"Cyclization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018583","descriptor_name":"Pliability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018583","descriptor_name":"Pliability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018583","descriptor_name":"Pliability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055592","descriptor_name":"Biophysical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055592","descriptor_name":"Biophysical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055592","descriptor_name":"Biophysical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-016-0897-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-0897-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-0897-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26846597","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26846597","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:osti.gov:1247315","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1247315","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:osti.gov:1618523","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1618523","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4743258","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4743258","pdf_url":null,"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,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-016-0897-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-0897-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-0897-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2613504715","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320332369","funder_display_name":"National Nuclear Security Administration"},{"id":"https://openalex.org/G2980544840","display_name":null,"funder_award_id":"Contract No. DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G359075050","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3700687868","display_name":null,"funder_award_id":"AC52-06NA25396","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G4169061630","display_name":null,"funder_award_id":"Contract No. DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4844714250","display_name":null,"funder_award_id":"No. DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G5657628048","display_name":null,"funder_award_id":"AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G75892134","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332369","display_name":"National Nuclear Security Administration","ror":"https://ror.org/03sk1we31"},{"id":"https://openalex.org/F4320338304","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2260331532.pdf","grobid_xml":"https://content.openalex.org/works/W2260331532.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1480950437","https://openalex.org/W1515974446","https://openalex.org/W1546374223","https://openalex.org/W1596696934","https://openalex.org/W1627398520","https://openalex.org/W1963692635","https://openalex.org/W1964199537","https://openalex.org/W1965496633","https://openalex.org/W1968274931","https://openalex.org/W1970432442","https://openalex.org/W1984048831","https://openalex.org/W1986633057","https://openalex.org/W1988241218","https://openalex.org/W1988740839","https://openalex.org/W1988864647","https://openalex.org/W1990351127","https://openalex.org/W1990708122","https://openalex.org/W1996027497","https://openalex.org/W1996104196","https://openalex.org/W1996245875","https://openalex.org/W1996852546","https://openalex.org/W1997153010","https://openalex.org/W2012627860","https://openalex.org/W2015501292","https://openalex.org/W2024214216","https://openalex.org/W2024300887","https://openalex.org/W2033763942","https://openalex.org/W2034614298","https://openalex.org/W2035824042","https://openalex.org/W2036768112","https://openalex.org/W2038169015","https://openalex.org/W2038874225","https://openalex.org/W2047845822","https://openalex.org/W2059358023","https://openalex.org/W2061111901","https://openalex.org/W2067133629","https://openalex.org/W2067924339","https://openalex.org/W2068126220","https://openalex.org/W2069520341","https://openalex.org/W2081497080","https://openalex.org/W2092916037","https://openalex.org/W2093543052","https://openalex.org/W2093693914","https://openalex.org/W2094829545","https://openalex.org/W2095994064","https://openalex.org/W2098727777","https://openalex.org/W2101536723","https://openalex.org/W2102123683","https://openalex.org/W2115655830","https://openalex.org/W2125235344","https://openalex.org/W2172239224","https://openalex.org/W3021884971","https://openalex.org/W4229769694","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2113512405","https://openalex.org/W3124098632","https://openalex.org/W1525192260","https://openalex.org/W3034809213","https://openalex.org/W2082123987","https://openalex.org/W1994506687","https://openalex.org/W2151373518","https://openalex.org/W2123553257","https://openalex.org/W21018333","https://openalex.org/W1997650976"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,18],"intrinsic":[2],"bendability":[3],"of":[4,14,20,51,57,64,72,85,104,126,136,147,168,177,215,218],"DNA":[5,22,52,77,87,108,144,160,188,223],"plays":[6],"an":[7],"important":[8],"role":[9,71,217],"with":[10,89,110,119,124,155,174],"relevance":[11],"for":[12,33,142,159],"myriad":[13],"essential":[15],"cellular":[16],"mechanisms.":[17],"flexibility":[19],"a":[21,46,211],"fragment":[23],"can":[24],"be":[25],"experimentally":[26,58],"and":[27,53,59,94,98,114],"computationally":[28,60],"examined":[29],"by":[30,36],"its":[31],"propensity":[32],"cyclization,":[34],"quantified":[35],"the":[37,65,70,82,148,181,204,216],"Jacobson-Stockmayer":[38],"J":[39,92],"factor.":[40],"In":[41],"this":[42],"study,":[43],"we":[44],"use":[45],"well-established":[47],"coarse-grained":[48],"three-dimensional":[49],"model":[50],"seven":[54],"distinct":[55],"sets":[56,135,167],"derived":[61],"conformational":[62,193],"parameters":[63,74,137,169,194,220],"double":[66],"helix":[67],"to":[68,203],"evaluate":[69],"structural":[73,219],"in":[75,153,221],"calculating":[76,222],"cyclization.":[78],"RESULTS:":[79],"We":[80],"calculate":[81],"cyclization":[83,189,224],"rates":[84,190],"86":[86],"sequences":[88,109],"previously":[90],"measured":[91],"factors":[93],"lengths":[95,111],"between":[96,112],"57":[97],"325":[99],"bp":[100],"as":[101,103],"well":[102],"20,000":[105],"randomly":[106],"generated":[107],"350":[113],"4000":[115],"bp.":[116],"Our":[117,130,184],"comparison":[118],"experimental":[120,156,182,205],"data":[121,131,185,199],"is":[122],"complemented":[123],"analysis":[125],"simulated":[127],"data.":[128],"CONCLUSIONS:":[129],"demonstrate":[132],"that":[133,187],"all":[134,166],"yield":[138],"very":[139],"similar":[140,202],"results":[141,173],"longer":[143],"fragments,":[145],"regardless":[146],"nucleotide":[149],"sequence,":[150],"which":[151],"are":[152,200],"agreement":[154],"measurements.":[157,183,206],"However,":[158],"fragments":[161],"shorter":[162],"than":[163],"100":[164],"bp,":[165],"performed":[170],"poorly":[171],"yielding":[172],"several":[175],"orders":[176],"magnitude":[178],"difference":[179],"from":[180],"show":[186],"calculated":[191],"using":[192],"based":[195],"on":[196],"nucleosome":[197],"packaging":[198],"most":[201],"Overall,":[207],"our":[208],"study":[209],"provides":[210],"comprehensive":[212],"large-scale":[213],"assessment":[214],"rates.":[225]},"counts_by_year":[{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}