{"id":"https://openalex.org/W4409506196","doi":"https://doi.org/10.1021/acs.jcim.4c02287","title":"Quantifying Acyl Chain Interdigitation in Simulated Bilayers via Direct Transbilayer Interactions","display_name":"Quantifying Acyl Chain Interdigitation in Simulated Bilayers via Direct Transbilayer Interactions","publication_year":2025,"publication_date":"2025-04-16","ids":{"openalex":"https://openalex.org/W4409506196","doi":"https://doi.org/10.1021/acs.jcim.4c02287","pmid":"https://pubmed.ncbi.nlm.nih.gov/40237313"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c02287","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02287","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.4c02287","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027308530","display_name":"Emily H. Chaisson","orcid":null},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emily H. Chaisson","raw_affiliation_strings":["Department of Chemistry","University of Tennessee Knoxville"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"University of Tennessee Knoxville","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015058477","display_name":"Frederick A. Heberle","orcid":"https://orcid.org/0000-0002-0424-3240"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["SE","US"],"is_corresponding":true,"raw_author_name":"Frederick A. Heberle","raw_affiliation_strings":["Department of Biochemistry and Biophysics","Department of Chemistry","Stockholm University, Science for Life Laboratory","University of Tennessee Knoxville"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"Stockholm University, Science for Life Laboratory","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I161593684"]},{"raw_affiliation_string":"University of Tennessee Knoxville","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014996012","display_name":"Milka Doktorova","orcid":"https://orcid.org/0000-0003-4366-2242"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Milka Doktorova","raw_affiliation_strings":["Department of Biochemistry and Biophysics","Stockholm University, Science for Life Laboratory"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics","institution_ids":[]},{"raw_affiliation_string":"Stockholm University, Science for Life Laboratory","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I161593684"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014996012","https://openalex.org/A5015058477"],"corresponding_institution_ids":["https://openalex.org/I161593684","https://openalex.org/I2800139495","https://openalex.org/I75027704"],"apc_list":null,"apc_paid":null,"fwci":3.4454,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.92003525,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"65","issue":"8","first_page":"3879","last_page":"3885"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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/T10721","display_name":"Surfactants and Colloidal Systems","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5952786803245544},{"id":"https://openalex.org/keywords/lipid-bilayer","display_name":"Lipid bilayer","score":0.5859584212303162},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.5848242044448853},{"id":"https://openalex.org/keywords/bilayer","display_name":"Bilayer","score":0.5529727935791016},{"id":"https://openalex.org/keywords/chain","display_name":"Chain (unit)","score":0.5047544240951538},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.2947590947151184},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1715468168258667},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13055700063705444},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10768309235572815}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5952786803245544},{"id":"https://openalex.org/C39944091","wikidata":"https://www.wikidata.org/wiki/Q423279","display_name":"Lipid bilayer","level":3,"score":0.5859584212303162},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.5848242044448853},{"id":"https://openalex.org/C192157962","wikidata":"https://www.wikidata.org/wiki/Q4087243","display_name":"Bilayer","level":3,"score":0.5529727935791016},{"id":"https://openalex.org/C199185054","wikidata":"https://www.wikidata.org/wiki/Q552299","display_name":"Chain (unit)","level":2,"score":0.5047544240951538},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.2947590947151184},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1715468168258667},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13055700063705444},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10768309235572815},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.4c02287","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02287","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40237313","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40237313","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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12042268","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12042268","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.4c02287","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02287","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4829970866","display_name":null,"funder_award_id":"R01 GM138887","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8030113496","display_name":null,"funder_award_id":"KAW 2024.0159","funder_id":"https://openalex.org/F4320325677","funder_display_name":"Science for Life Laboratory"}],"funders":[{"id":"https://openalex.org/F4320325677","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1106171373","https://openalex.org/W1983319593","https://openalex.org/W2005570063","https://openalex.org/W2007320109","https://openalex.org/W2021520922","https://openalex.org/W2024181684","https://openalex.org/W2029667189","https://openalex.org/W2035112673","https://openalex.org/W2042070444","https://openalex.org/W2046025180","https://openalex.org/W2052177681","https://openalex.org/W2059169173","https://openalex.org/W2062807652","https://openalex.org/W2066414494","https://openalex.org/W2084797639","https://openalex.org/W2095754217","https://openalex.org/W2119109208","https://openalex.org/W2123833699","https://openalex.org/W2132262459","https://openalex.org/W2152085988","https://openalex.org/W2171458923","https://openalex.org/W2186547554","https://openalex.org/W2229680495","https://openalex.org/W2607133944","https://openalex.org/W2607433115","https://openalex.org/W2622346504","https://openalex.org/W2745775385","https://openalex.org/W2802326368","https://openalex.org/W2949796571","https://openalex.org/W2950669909","https://openalex.org/W2999430643","https://openalex.org/W3023677370","https://openalex.org/W3033676007","https://openalex.org/W3046751266","https://openalex.org/W3047592084","https://openalex.org/W3093416033","https://openalex.org/W3173830284","https://openalex.org/W4224627762","https://openalex.org/W4232772234","https://openalex.org/W4237178631","https://openalex.org/W4310714332","https://openalex.org/W4310953844","https://openalex.org/W4313894604","https://openalex.org/W4388648245"],"related_works":["https://openalex.org/W2389992822","https://openalex.org/W2061481432","https://openalex.org/W2100090167","https://openalex.org/W2718515487","https://openalex.org/W4367601614","https://openalex.org/W2072230736","https://openalex.org/W1963901611","https://openalex.org/W2059795428","https://openalex.org/W4206087209","https://openalex.org/W2289704112"],"abstract_inverted_index":{"In":[0,66],"a":[1,144,217,231],"lipid":[2,8],"bilayer,":[3],"the":[4,7,21,35,40,117,125,131,153,172,208,235],"interactions":[5,19,79,129],"between":[6,171],"hydrocarbon":[9],"chains":[10],"from":[11,52],"opposing":[12,41],"leaflets":[13],"can":[14,73,81],"influence":[15],"membrane":[16,236],"properties.":[17],"These":[18],"include":[20,124],"phenomenon":[22],"of":[23,30,92,115,119,127,133,148,158,165,204,234],"interdigitation,":[24],"in":[25,49,63],"which":[26,183],"an":[27,161],"acyl":[28],"chain":[29,120,176],"one":[31],"leaflet":[32],"extends":[33],"past":[34],"bilayer":[36,209,225],"midplane":[37],"and":[38,107,140,174,191,227,229],"into":[39],"leaflet.":[42],"While":[43],"static":[44],"interdigitation":[45,62],"is":[46,58],"well":[47],"understood":[48],"gel-phase":[50],"bilayers":[51,156],"X-ray":[53],"diffraction":[54],"measurements,":[55],"much":[56],"less":[57],"known":[59],"about":[60],"dynamic":[61,149],"fluid":[64],"phases.":[65],"this":[67],"regard,":[68],"atomistic":[69],"molecular":[70,222],"dynamics":[71,228],"simulations":[72],"provide":[74,97,196],"mechanistic":[75],"information":[76],"on":[77,155,186],"interleaflet":[78],"that":[80,96,99,180,199],"be":[82],"used":[83],"to":[84,194],"generate":[85],"experimentally":[86],"testable":[87],"hypotheses.":[88],"To":[89],"address":[90],"limitations":[91],"existing":[93],"computational":[94],"methodologies":[95],"results":[98],"are":[100,184,192],"either":[101],"indirect":[102],"or":[103],"averaged":[104],"over":[105],"time":[106],"space,":[108],"here":[109],"we":[110],"introduce":[111],"three":[112],"novel":[113],"ways":[114],"quantifying":[116],"extent":[118],"interdigitation.":[121,150],"Our":[122],"protocols":[123],"analysis":[126],"instantaneous":[128],"at":[130,207,220],"level":[132],"individual":[134],"carbon":[135,166],"atoms,":[136,167],"thus":[137,214],"providing":[138],"temporal":[139],"spatial":[141],"resolution":[142],"for":[143,216],"more":[145],"nuanced":[146],"picture":[147],"We":[151,178],"compare":[152],"methods":[154],"composed":[157],"lipids":[159],"with":[160],"equal":[162],"total":[163],"number":[164],"but":[168],"different":[169],"mismatches":[170],"<i>sn</i>-1":[173],"<i>sn</i>-2":[175],"lengths.":[177],"find":[179],"these":[181],"metrics,":[182],"based":[185],"freely":[187],"available":[188],"software":[189],"packages":[190],"easy":[193],"implement,":[195],"complementary":[197],"details":[198],"help":[200],"characterize":[201],"various":[202],"features":[203],"lipid-lipid":[205],"contacts":[206],"midplane.":[210],"The":[211],"new":[212],"frameworks":[213],"allow":[215],"deeper":[218],"look":[219],"fundamental":[221],"mechanisms":[223],"underlying":[224],"structure":[226],"present":[230],"valuable":[232],"expansion":[233],"biophysics":[237],"toolkit.":[238]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
