{"id":"https://openalex.org/W2005197846","doi":"https://doi.org/10.1063/1.3609970","title":"Role of loop entropy in the force induced melting of DNA hairpin","display_name":"Role of loop entropy in the force induced melting of DNA hairpin","publication_year":2011,"publication_date":"2011-07-21","ids":{"openalex":"https://openalex.org/W2005197846","doi":"https://doi.org/10.1063/1.3609970","mag":"2005197846","pmid":"https://pubmed.ncbi.nlm.nih.gov/21787024"},"language":"en","primary_location":{"id":"doi:10.1063/1.3609970","doi":"https://doi.org/10.1063/1.3609970","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.3609970","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["arxiv","crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1003.4082","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030161049","display_name":"Garima Mishra","orcid":"https://orcid.org/0000-0002-9914-9053","observed_orcids":["https://orcid.org/0000-0002-9914-9053"]},"institutions":[{"id":"https://openalex.org/I91357014","display_name":"Banaras Hindu University","ror":"https://ror.org/04cdn2797","country_code":"IN","type":"education","lineage":["https://openalex.org/I91357014"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Garima Mishra","raw_affiliation_strings":["Banaras Hindu University 1 Department of Physics, , Varanasi 221 005, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Banaras Hindu University 1 Department of Physics, , Varanasi 221 005, India","institution_ids":["https://openalex.org/I91357014"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112102856","display_name":"Debaprasad Giri","orcid":"https://orcid.org/0000-0002-2035-1671","observed_orcids":["https://orcid.org/0000-0002-2035-1671"]},"institutions":[{"id":"https://openalex.org/I91357014","display_name":"Banaras Hindu University","ror":"https://ror.org/04cdn2797","country_code":"IN","type":"education","lineage":["https://openalex.org/I91357014"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Debaprasad Giri","raw_affiliation_strings":["Banaras Hindu University 2 Department of Applied Physics, IT, , Varanasi 221 005, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Banaras Hindu University 2 Department of Applied Physics, IT, , Varanasi 221 005, India","institution_ids":["https://openalex.org/I91357014"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019636088","display_name":"Mai Suan Li","orcid":"https://orcid.org/0000-0001-7021-7916","observed_orcids":["https://orcid.org/0000-0001-7021-7916"]},"institutions":[{"id":"https://openalex.org/I4210086947","display_name":"Institute of Physics","ror":"https://ror.org/000sfad56","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210086947","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"government","lineage":["https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"M. S. Li","raw_affiliation_strings":["Polish Academy of Sciences 3 Institute of Physics, , Al. Lotnikow 32/46, 02-668 Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Polish Academy of Sciences 3 Institute of Physics, , Al. Lotnikow 32/46, 02-668 Warsaw, Poland","institution_ids":["https://openalex.org/I4210086947","https://openalex.org/I99542240"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048128862","display_name":"Sanjay Kumar","orcid":"https://orcid.org/0000-0002-0257-3051","observed_orcids":["https://orcid.org/0000-0002-0257-3051","https://orcid.org/0000-0002-5439-5015"]},"institutions":[{"id":"https://openalex.org/I91357014","display_name":"Banaras Hindu University","ror":"https://ror.org/04cdn2797","country_code":"IN","type":"education","lineage":["https://openalex.org/I91357014"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sanjay Kumar","raw_affiliation_strings":["Banaras Hindu University 1 Department of Physics, , Varanasi 221 005, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Banaras Hindu University 1 Department of Physics, , Varanasi 221 005, India","institution_ids":["https://openalex.org/I91357014"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":null,"fwci":0.908,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.71364129,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"135","issue":"3","first_page":"035102","last_page":"035102"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.8809000253677368,"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":0.8809000253677368,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.04610000178217888,"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/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.016599999740719795,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-hairpin","display_name":"DNA hairpins","score":0.9549999833106995},{"id":"https://openalex.org/keywords/loop-entropy","display_name":"loop entropy","score":0.8840000033378601},{"id":"https://openalex.org/keywords/lattice-model","display_name":"lattice model","score":0.5929999947547913},{"id":"https://openalex.org/keywords/elastic-energy","display_name":"elastic energy","score":0.8209999799728394}],"concepts":[{"id":"https://openalex.org/C2780004032","wikidata":"https://www.wikidata.org/wiki/Q6485978","display_name":"Langevin dynamics","level":2,"score":0.8296666145324707},{"id":"https://openalex.org/C85906118","wikidata":"https://www.wikidata.org/wiki/Q186693","display_name":"Phase diagram","level":3,"score":0.5925979614257812},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.5275057554244995},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.5080342292785645},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.4871947169303894},{"id":"https://openalex.org/C2985276288","wikidata":"https://www.wikidata.org/wiki/Q16873139","display_name":"Melting temperature","level":2,"score":0.44470253586769104},{"id":"https://openalex.org/C139173117","wikidata":"https://www.wikidata.org/wiki/Q901768","display_name":"Entropic force","level":2,"score":0.43255841732025146},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.42169952392578125},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4168965816497803},{"id":"https://openalex.org/C149288129","wikidata":"https://www.wikidata.org/wiki/Q185357","display_name":"Phase transition","level":2,"score":0.41340339183807373},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.23803073167800903},{"id":"https://openalex.org/C44280652","wikidata":"https://www.wikidata.org/wiki/Q104837","display_name":"Phase (matter)","level":2,"score":0.1611471176147461},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.13354191184043884},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","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":false}],"locations_count":4,"locations":[{"id":"doi:10.1063/1.3609970","doi":"https://doi.org/10.1063/1.3609970","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.3609970","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},{"id":"pmid:21787024","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21787024","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":"The Journal of chemical physics","raw_type":"Journal Article"},{"id":"pmh:oai:arXiv.org:1003.4082","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1003.4082","pdf_url":"https://arxiv.org/pdf/1003.4082","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.1003.4082","doi":"https://doi.org/10.48550/arxiv.1003.4082","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1003.4082","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1003.4082","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1003.4082","pdf_url":"https://arxiv.org/pdf/1003.4082","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":76,"referenced_works":["https://openalex.org/W785620092","https://openalex.org/W984882857","https://openalex.org/W1499020433","https://openalex.org/W1660177314","https://openalex.org/W1682036307","https://openalex.org/W1964934737","https://openalex.org/W1966611416","https://openalex.org/W1970690847","https://openalex.org/W1972920570","https://openalex.org/W1974618862","https://openalex.org/W1981742364","https://openalex.org/W1983655186","https://openalex.org/W1985340571","https://openalex.org/W1985950164","https://openalex.org/W1990409982","https://openalex.org/W1993655177","https://openalex.org/W1995152728","https://openalex.org/W1996265376","https://openalex.org/W1999119486","https://openalex.org/W2002311755","https://openalex.org/W2005858142","https://openalex.org/W2006085671","https://openalex.org/W2007147905","https://openalex.org/W2008965400","https://openalex.org/W2011600104","https://openalex.org/W2012195021","https://openalex.org/W2013696161","https://openalex.org/W2016307290","https://openalex.org/W2016533552","https://openalex.org/W2024358967","https://openalex.org/W2025374847","https://openalex.org/W2028869879","https://openalex.org/W2030773205","https://openalex.org/W2035720425","https://openalex.org/W2036251513","https://openalex.org/W2038358093","https://openalex.org/W2040830330","https://openalex.org/W2041583866","https://openalex.org/W2047736240","https://openalex.org/W2048273174","https://openalex.org/W2052905339","https://openalex.org/W2062097701","https://openalex.org/W2065013877","https://openalex.org/W2067008143","https://openalex.org/W2069087043","https://openalex.org/W2071212394","https://openalex.org/W2071538891","https://openalex.org/W2074437338","https://openalex.org/W2075111320","https://openalex.org/W2076863390","https://openalex.org/W2077968459","https://openalex.org/W2078261679","https://openalex.org/W2081315067","https://openalex.org/W2081407528","https://openalex.org/W2081617833","https://openalex.org/W2086254111","https://openalex.org/W2087616070","https://openalex.org/W2087672399","https://openalex.org/W2097246107","https://openalex.org/W2110975678","https://openalex.org/W2123904529","https://openalex.org/W2124158235","https://openalex.org/W2130632191","https://openalex.org/W2141634848","https://openalex.org/W2151273455","https://openalex.org/W2152585559","https://openalex.org/W2154475799","https://openalex.org/W2157205030","https://openalex.org/W2159578267","https://openalex.org/W2166372815","https://openalex.org/W2169109192","https://openalex.org/W2169371925","https://openalex.org/W2313953460","https://openalex.org/W3103649439","https://openalex.org/W4232054842","https://openalex.org/W4234422402"],"related_works":["https://openalex.org/W188598989","https://openalex.org/W4377820396","https://openalex.org/W2073974625","https://openalex.org/W7067459728","https://openalex.org/W3135130701","https://openalex.org/W3174750554","https://openalex.org/W3205455816","https://openalex.org/W2056544321","https://openalex.org/W3103649439","https://openalex.org/W2958921433"],"abstract_inverted_index":{"Dynamics":[0],"of":[1,41,45],"a":[2,9,94,101],"single":[3],"stranded":[4],"DNA,":[5],"which":[6,28],"can":[7],"form":[8],"hairpin":[10,54,80],"have":[11],"been":[12],"studied":[13],"in":[14,66],"the":[15,25,31,36,42,46,53,62,73,79,83,90,103,109],"constant":[16],"force":[17,76],"ensemble.":[18],"Using":[19],"Langevin":[20],"dynamics":[21],"simulations,":[22],"we":[23],"obtained":[24],"force-temperature":[26,104],"diagram,":[27],"differs":[29,106],"from":[30,82],"theoretical":[32,110],"prediction":[33],"based":[34],"on":[35],"lattice":[37],"model.":[38],"Probability":[39],"analysis":[40],"extreme":[43],"bases":[44],"stem":[47,84],"revealed":[48],"that":[49,89],"at":[50,70,97],"high":[51,98],"temperature,":[52,72],"to":[55],"coil":[56],"transition":[57,74],"is":[58,75,87],"entropy":[59],"dominated":[60],"and":[61,78],"loop":[63],"contributes":[64],"significantly":[65,107],"its":[67],"opening.":[68],"However,":[69],"low":[71],"driven":[77],"opens":[81],"side.":[85],"It":[86],"shown":[88],"elastic":[91],"energy":[92],"plays":[93],"crucial":[95],"role":[96],"force.":[99],"As":[100],"result,":[102],"diagram":[105],"with":[108],"prediction.":[111]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":4}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}