{"id":"https://openalex.org/W77844427","doi":null,"title":"Free energy reconstruction from irreversible single- molecule pulling experiments","display_name":"Free energy reconstruction from irreversible single- molecule pulling experiments","publication_year":2007,"publication_date":"2007-01-01","ids":{"openalex":"https://openalex.org/W77844427","mag":"77844427"},"language":"en","primary_location":{"id":"pmh:oai:escholarship.org/ark:/13030/qt15x5b2pk","doi":null,"is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/15x5b2pk","pdf_url":"https://escholarship.org/uc/item/15x5b2pk","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"etd"},"volume":null,"type":"dissertation","indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://escholarship.org/uc/item/15x5b2pk","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087396555","display_name":"David D. L. Minh","orcid":"https://orcid.org/0000-0002-4802-2618","observed_orcids":["https://orcid.org/0000-0002-4802-2618"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"David D. L Minh","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5087396555"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11520","display_name":"Advanced Thermodynamics and Statistical Mechanics","score":0.9916999936103821,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11520","display_name":"Advanced Thermodynamics and Statistical Mechanics","score":0.9916999936103821,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.005799999926239252,"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"}},{"id":"https://openalex.org/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/irreversible-processes","display_name":"irreversible processes","score":0.6589999794960022},{"id":"https://openalex.org/keywords/jarzynski-equality","display_name":"Jarzynski equality","score":0.9359999895095825},{"id":"https://openalex.org/keywords/crooks-fluctuation-theorem","display_name":"Crooks fluctuation theorem","score":0.9990000128746033},{"id":"https://openalex.org/keywords/potential-of-mean-force","display_name":"potential of mean force","score":0.8859999775886536},{"id":"https://openalex.org/keywords/free-energy-landscape","display_name":"free energy landscape","score":0.7879999876022339},{"id":"https://openalex.org/keywords/dynamic-force-spectroscopy","display_name":"dynamic force spectroscopy","score":0.8450000286102295},{"id":"https://openalex.org/keywords/spring-stiffness","display_name":"spring stiffness","score":0.6349999904632568},{"id":"https://openalex.org/keywords/nonequilibrium-statistical-mechanics","display_name":"nonequilibrium statistical mechanics","score":0.8339999914169312}],"concepts":[{"id":"https://openalex.org/C119473381","wikidata":"https://www.wikidata.org/wiki/Q49298","display_name":"Force spectroscopy","level":3,"score":0.6767696738243103},{"id":"https://openalex.org/C74859849","wikidata":"https://www.wikidata.org/wiki/Q2466686","display_name":"Non-equilibrium thermodynamics","level":2,"score":0.5965532064437866},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.5812000036239624},{"id":"https://openalex.org/C2778712887","wikidata":"https://www.wikidata.org/wiki/Q102836","display_name":"Spring (device)","level":2,"score":0.5288366079330444},{"id":"https://openalex.org/C108585399","wikidata":"https://www.wikidata.org/wiki/Q900831","display_name":"Fluctuation theorem","level":3,"score":0.5083519816398621},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.5036861300468445},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.43637433648109436},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.37402164936065674},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.36151838302612305},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.34163397550582886},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.33826538920402527},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.21510303020477295},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.1725006103515625},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.10951739549636841},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:escholarship.org/ark:/13030/qt15x5b2pk","doi":null,"is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/15x5b2pk","pdf_url":"https://escholarship.org/uc/item/15x5b2pk","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"etd"},{"id":"mag:77844427","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/content/qt15x5b2pk/qt15x5b2pk.pdf?t=lq6s6v","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:escholarship.org/ark:/13030/qt15x5b2pk","doi":null,"is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/15x5b2pk","pdf_url":"https://escholarship.org/uc/item/15x5b2pk","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"etd"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W77844427.pdf","grobid_xml":"https://content.openalex.org/works/W77844427.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2082546448","https://openalex.org/W1980787308","https://openalex.org/W2033228675","https://openalex.org/W2335409027","https://openalex.org/W2102375526","https://openalex.org/W2033303788","https://openalex.org/W7212365563","https://openalex.org/W2951712345","https://openalex.org/W1976483919","https://openalex.org/W2052153354"],"abstract_inverted_index":{"Recent":[0],"developments":[1],"in":[2,110,186],"nonequilibrium":[3],"statistical":[4],"mechanics,":[5],"including":[6],"Jarzynski's":[7],"equality":[8],"and":[9,56,77,92,106,118,183,197],"the":[10,16,38,52,57,65,99,102,107,124,134,159,172,181],"Crooks":[11],"Fluctuation":[12],"Theorem,":[13],"have":[14,33],"made":[15],"calculation":[17],"of":[18,44,82,101,174],"equilibrium":[19],"free":[20,39],"energy":[21,40],"differences":[22],"from":[23],"irreversible":[24,199],"processes":[25],"possible.":[26],"Building":[27],"off":[28],"these":[29],"theorems,":[30],"two":[31,93],"approaches":[32],"been":[34],"developed":[35],"to":[36,68,78,165,170,192,195],"calculate":[37,79],"surface,":[41],"or":[42],"potential":[43],"mean":[45,83],"force,":[46],"along":[47],"a":[48,167,175],"continuous":[49],"reaction":[50],"coordinate:":[51],"stiff":[53,103,135],"spring":[54,104,116,136],"approximation":[55,105,137],"Hummer-Szabo":[58,66,108,145],"method.":[59],"In":[60],"this":[61,187],"thesis,":[62],"we":[63,97],"extend":[64],"method":[67,109,146],"encompass":[69],"pulling":[70,112,201],"experiments":[71,113,202],"performed":[72],"with":[73],"different":[74,115],"biasing":[75],"protocols":[76],"multidimensional":[80],"potentials":[81],"force.":[84],"These":[85],"extensions":[86],"are":[87,142],"tested":[88],"on":[89,123,133],"toy":[90],"one-dimensional":[91],"-dimensional":[94],"systems.":[95],"Next,":[96],"compare":[98],"efficacy":[100],"interpreting":[111,152],"at":[114],"stiffnesses":[117],"using":[119],"dynamic":[120,153],"force":[121,154],"spectroscopy":[122],"model":[125],"peptide":[126],"deca-alanine.":[127],"We":[128,178],"find":[129],"that":[130,180],"analysis":[131,184],"based":[132],"fails":[138],"when":[139],"weaker":[140],"springs":[141],"used.":[143],"The":[144],"is":[147,163],"generally":[148],"more":[149],"effective":[150],"for":[151],"spectroscopy.":[155],"For":[156],"both":[157],"methods,":[158],"second":[160],"cumulant":[161],"expansion":[162],"found":[164],"be":[166,190],"good":[168],"way":[169],"make":[171],"best":[173],"limited":[176],"sample.":[177],"anticipate":[179],"methods":[182],"presented":[185],"thesis":[188],"will":[189],"useful":[191],"experimentalists":[193],"seeking":[194],"design":[196],"interpret":[198],"single-molecule":[200]},"counts_by_year":[],"updated_date":"2026-08-30T07:30:35.949966","created_date":"2016-06-24T00:00:00"}
