{"id":"https://openalex.org/W2053783019","doi":"https://doi.org/10.1137/060651100","title":"Thermodynamic Analysis of Interacting Nucleic Acid Strands","display_name":"Thermodynamic Analysis of Interacting Nucleic Acid Strands","publication_year":2007,"publication_date":"2007-01-01","ids":{"openalex":"https://openalex.org/W2053783019","doi":"https://doi.org/10.1137/060651100","mag":"2053783019"},"language":"en","primary_location":{"id":"doi:10.1137/060651100","is_oa":false,"landing_page_url":"https://doi.org/10.1137/060651100","pdf_url":null,"source":{"id":"https://openalex.org/S160107561","display_name":"SIAM Review","issn_l":"0036-1445","issn":["0036-1445","1095-7200"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Review","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089151288","display_name":"Robert M. Dirks","orcid":null},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert M. Dirks","raw_affiliation_strings":["Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051551345","display_name":"Justin S. Bois","orcid":"https://orcid.org/0000-0001-7137-8746"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Justin S. Bois","raw_affiliation_strings":["Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026597533","display_name":"Joseph Schaeffer","orcid":null},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph M. Schaeffer","raw_affiliation_strings":["Department of Computer Science, California Institute of Technology, Pasadena, CA 91125"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, California Institute of Technology, Pasadena, CA 91125","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000956443","display_name":"Erik Winfree","orcid":"https://orcid.org/0000-0002-5899-7523"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erik Winfree","raw_affiliation_strings":["Departments of Computer Science and Computation & Neural Systems, California Institute of Technology, Pasadena, CA 91125"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Computer Science and Computation & Neural Systems, California Institute of Technology, Pasadena, CA 91125","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049814739","display_name":"Niles A. Pierce","orcid":"https://orcid.org/0000-0003-2367-4406"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Niles A. Pierce","raw_affiliation_strings":["Departments of Applied & Computational Mathematics and Bioengineering, California Institute of Technology, Pasadena, CA 91125"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Applied & Computational Mathematics and Bioengineering, California Institute of Technology, Pasadena, CA 91125","institution_ids":["https://openalex.org/I122411786"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":7.6718,"has_fulltext":false,"cited_by_count":370,"citation_normalized_percentile":{"value":0.98180662,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"49","issue":"1","first_page":"65","last_page":"88"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":1.0,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":1.0,"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":0.9998999834060669,"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":0.9995999932289124,"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/partition-function","display_name":"Partition function (quantum field theory)","score":0.6047625541687012},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5399105548858643},{"id":"https://openalex.org/keywords/nucleic-acid","display_name":"Nucleic acid","score":0.4911656081676483},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4642646312713623},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.41506534814834595},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.3439849019050598},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.33962249755859375},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3260360360145569},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.2536773681640625},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.23446762561798096},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20782512426376343},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.1049470603466034}],"concepts":[{"id":"https://openalex.org/C2778401447","wikidata":"https://www.wikidata.org/wiki/Q7140637","display_name":"Partition function (quantum field theory)","level":2,"score":0.6047625541687012},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5399105548858643},{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.4911656081676483},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4642646312713623},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.41506534814834595},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.3439849019050598},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.33962249755859375},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3260360360145569},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.2536773681640625},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23446762561798096},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20782512426376343},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.1049470603466034},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1137/060651100","is_oa":false,"landing_page_url":"https://doi.org/10.1137/060651100","pdf_url":null,"source":{"id":"https://openalex.org/S160107561","display_name":"SIAM Review","issn_l":"0036-1445","issn":["0036-1445","1095-7200"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Review","raw_type":"journal-article"},{"id":"pmh:oai:authors.library.caltech.edu:7706","is_oa":false,"landing_page_url":"https://authors.library.caltech.edu/7706/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402161","display_name":"CaltechAUTHORS (California Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I122411786","host_organization_name":"California Institute of Technology","host_organization_lineage":["https://openalex.org/I122411786"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.144.461","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.144.461","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.dna.caltech.edu/Papers/multistrand_thermo2007.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.523.4764","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.523.4764","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.piercelab.caltech.edu/assets/papers/sirev07.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W15601582","https://openalex.org/W162457275","https://openalex.org/W1483357708","https://openalex.org/W1510478584","https://openalex.org/W1553702074","https://openalex.org/W1567090568","https://openalex.org/W1569752386","https://openalex.org/W1574643310","https://openalex.org/W1725615870","https://openalex.org/W1968245790","https://openalex.org/W1971951387","https://openalex.org/W1981777358","https://openalex.org/W1984675364","https://openalex.org/W1991159148","https://openalex.org/W1996723024","https://openalex.org/W1998215345","https://openalex.org/W2009215595","https://openalex.org/W2009818318","https://openalex.org/W2017302704","https://openalex.org/W2022916085","https://openalex.org/W2025763720","https://openalex.org/W2043653977","https://openalex.org/W2047982902","https://openalex.org/W2051713039","https://openalex.org/W2054931730","https://openalex.org/W2061158331","https://openalex.org/W2070999095","https://openalex.org/W2076756368","https://openalex.org/W2085523918","https://openalex.org/W2096883982","https://openalex.org/W2104141342","https://openalex.org/W2109297587","https://openalex.org/W2117431427","https://openalex.org/W2123241418","https://openalex.org/W2123281294","https://openalex.org/W2135995702","https://openalex.org/W2148304424","https://openalex.org/W2148339059","https://openalex.org/W2148602202","https://openalex.org/W2153140501","https://openalex.org/W2155544170","https://openalex.org/W2158476854","https://openalex.org/W2163638609","https://openalex.org/W2166007193","https://openalex.org/W2169436912","https://openalex.org/W2170472690","https://openalex.org/W2171582839","https://openalex.org/W2296319761","https://openalex.org/W2318995768","https://openalex.org/W3029645440","https://openalex.org/W4211070391","https://openalex.org/W4234667141"],"related_works":["https://openalex.org/W1971444612","https://openalex.org/W1543504406","https://openalex.org/W633173308","https://openalex.org/W2383750441","https://openalex.org/W1572021523","https://openalex.org/W2802691951","https://openalex.org/W2061946247","https://openalex.org/W2135990064","https://openalex.org/W2085406081","https://openalex.org/W2011393572"],"abstract_inverted_index":{"Abstract.":[0],"Motivated":[1],"by":[2,129],"the":[3,15,20,47,65,68,95,98,118],"analysis":[4],"of":[5,23,27,42,67,79,92,97,105,155,163],"natural":[6],"and":[7,10,52,137,152,177],"engineered":[8],"DNA":[9],"RNA":[11],"systems,":[12],"we":[13,115],"present":[14],"first":[16],"algorithm":[17],"for":[18,59,71,89,102,108],"calculating":[19],"partition":[21,69],"function":[22,70,136],"an":[24,160],"unpseudoknotted":[25],"complex":[26,120],"multiple":[28],"interacting":[29],"nucleic":[30,80],"acid":[31,81],"strands.":[32],"This":[33,83],"dynamic":[34,172],"program":[35],"is":[36],"based":[37],"on":[38],"a":[39,72,76,112,131],"rigorous":[40],"extension":[41],"secondary":[43],"structure":[44],"models":[45],"to":[46,123,144,159],"multistranded":[48],"case,":[49],"addressing":[50],"representa-tion":[51],"distinguishability":[53],"issues":[54],"that":[55,117],"do":[56],"not":[57],"arise":[58],"single-stranded":[60],"structures.":[61],"We":[62],"then":[63,141],"derive":[64],"form":[66],"fixed":[73],"volume":[74],"containing":[75],"dilute":[77],"solution":[78],"complexes.":[82],"expression":[84],"can":[85,126,140],"be":[86,127,142],"evaluated":[87],"explicitly":[88],"small":[90],"numbers":[91],"strands,":[93],"allowing":[94],"calculation":[96],"equilibrium":[99,125,146],"population":[100],"distribution":[101],"each":[103],"species":[104],"complex.":[106],"Alternatively,":[107],"large":[109],"systems":[110],"(e.g.,":[111],"test":[113],"tube),":[114],"show":[116],"unique":[119],"concentrations":[121],"corresponding":[122],"thermodynamic":[124],"obtained":[128],"solving":[130],"convex":[132,175],"programming":[133],"problem.":[134],"Partition":[135],"concentration":[138],"information":[139],"used":[143],"calculate":[145],"base-pairing":[147],"observables.":[148],"The":[149],"underlying":[150],"physics":[151],"mathematical":[153],"formulation":[154],"these":[156],"problems":[157],"lead":[158],"interesting":[161],"blend":[162],"approaches,":[164],"including":[165],"ideas":[166],"from":[167],"graph":[168],"theory,":[169,171],"group":[170],"programming,":[173],"combinatorics,":[174],"optimization,":[176],"Lagrange":[178],"duality.":[179]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":23},{"year":2022,"cited_by_count":27},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":21},{"year":2019,"cited_by_count":29},{"year":2018,"cited_by_count":26},{"year":2017,"cited_by_count":17},{"year":2016,"cited_by_count":22},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":33},{"year":2013,"cited_by_count":12},{"year":2012,"cited_by_count":20}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}