{"id":"https://openalex.org/W2282959781","doi":"https://doi.org/10.1137/140972676","title":"Optimization-based Shrinking Dimer Method for Finding Transition States","display_name":"Optimization-based Shrinking Dimer Method for Finding Transition States","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2282959781","doi":"https://doi.org/10.1137/140972676","mag":"2282959781"},"language":"en","primary_location":{"id":"doi:10.1137/140972676","is_oa":false,"landing_page_url":"https://doi.org/10.1137/140972676","pdf_url":null,"source":{"id":"https://openalex.org/S165512578","display_name":"SIAM Journal on Scientific Computing","issn_l":"1064-8275","issn":["1064-8275","1095-7197"],"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 Journal on Scientific Computing","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/A5101876066","display_name":"Lei Zhang","orcid":"https://orcid.org/0009-0003-2733-4756"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Lei Zhang","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056115552","display_name":"Qiang Du","orcid":"https://orcid.org/0000-0002-1067-8937"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Qiang Du","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5070971434","display_name":"Zhenzhen Zheng","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhenzhen Zheng","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101876066"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.1135,"has_fulltext":false,"cited_by_count":53,"citation_normalized_percentile":{"value":0.75807252,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"38","issue":"1","first_page":"A528","last_page":"A544"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9994000196456909,"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"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9994000196456909,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983999729156494,"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/T11471","display_name":"Block Copolymer Self-Assembly","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/mathematics","display_name":"Mathematics","score":0.6139788627624512},{"id":"https://openalex.org/keywords/dimer","display_name":"Dimer","score":0.5206112861633301},{"id":"https://openalex.org/keywords/saddle-point","display_name":"Saddle point","score":0.5105813145637512},{"id":"https://openalex.org/keywords/phase-transition","display_name":"Phase transition","score":0.43384069204330444},{"id":"https://openalex.org/keywords/convergence","display_name":"Convergence (economics)","score":0.4273817837238312},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.4186950623989105},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3378961682319641},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.16160687804222107},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.15531766414642334},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.14570757746696472},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.09674504399299622}],"concepts":[{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.6139788627624512},{"id":"https://openalex.org/C2779546866","wikidata":"https://www.wikidata.org/wiki/Q531306","display_name":"Dimer","level":2,"score":0.5206112861633301},{"id":"https://openalex.org/C2681867","wikidata":"https://www.wikidata.org/wiki/Q690935","display_name":"Saddle point","level":2,"score":0.5105813145637512},{"id":"https://openalex.org/C149288129","wikidata":"https://www.wikidata.org/wiki/Q185357","display_name":"Phase transition","level":2,"score":0.43384069204330444},{"id":"https://openalex.org/C2777303404","wikidata":"https://www.wikidata.org/wiki/Q759757","display_name":"Convergence (economics)","level":2,"score":0.4273817837238312},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.4186950623989105},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3378961682319641},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.16160687804222107},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.15531766414642334},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.14570757746696472},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.09674504399299622},{"id":"https://openalex.org/C50522688","wikidata":"https://www.wikidata.org/wiki/Q189833","display_name":"Economic growth","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","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},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1137/140972676","is_oa":false,"landing_page_url":"https://doi.org/10.1137/140972676","pdf_url":null,"source":{"id":"https://openalex.org/S165512578","display_name":"SIAM Journal on Scientific Computing","issn_l":"1064-8275","issn":["1064-8275","1095-7197"],"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 Journal on Scientific Computing","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8999999761581421,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W115385722","https://openalex.org/W1241391259","https://openalex.org/W1497566274","https://openalex.org/W1543736827","https://openalex.org/W1601132577","https://openalex.org/W1953396270","https://openalex.org/W1963983827","https://openalex.org/W1977069262","https://openalex.org/W1982067912","https://openalex.org/W1986614779","https://openalex.org/W1988675445","https://openalex.org/W1993018469","https://openalex.org/W1995102330","https://openalex.org/W1996655763","https://openalex.org/W1999513324","https://openalex.org/W2004751437","https://openalex.org/W2005461875","https://openalex.org/W2012663156","https://openalex.org/W2026258334","https://openalex.org/W2031430816","https://openalex.org/W2034061131","https://openalex.org/W2038828876","https://openalex.org/W2049043767","https://openalex.org/W2050096287","https://openalex.org/W2076605490","https://openalex.org/W2078123111","https://openalex.org/W2081159460","https://openalex.org/W2081567253","https://openalex.org/W2084781518","https://openalex.org/W2112378505","https://openalex.org/W2127437840","https://openalex.org/W2139916893","https://openalex.org/W2152710595","https://openalex.org/W2167035284","https://openalex.org/W2169281157","https://openalex.org/W2205647194","https://openalex.org/W2315468834","https://openalex.org/W2898889412","https://openalex.org/W2913109846","https://openalex.org/W2949094027"],"related_works":["https://openalex.org/W2066844763","https://openalex.org/W2033071165","https://openalex.org/W2016688944","https://openalex.org/W2376447813","https://openalex.org/W2051848413","https://openalex.org/W1986190647","https://openalex.org/W3147406161","https://openalex.org/W3213146639","https://openalex.org/W3215007808","https://openalex.org/W2027492144"],"abstract_inverted_index":{"We":[0,83,104],"present":[1],"a":[2,17,116,153],"new":[3,167],"and":[4,38,100,131,151,161],"efficient":[5,155],"optimization-based":[6],"shrinking":[7,96],"dimer":[8,44,97],"(OSD)":[9],"algorithm":[10,160],"for":[11,179],"finding":[12],"transition":[13,22,68,180],"states":[14,23],"associated":[15],"with":[16,143],"given":[18,25],"energy":[19,32],"landscape.":[20],"The":[21,136],"are":[24,51],"by":[26],"index-one":[27],"saddle":[28],"points":[29],"of":[30,56,67,81,93,118,127],"the":[31,36,42,65,71,86,90,94,124,140,144,158,174],"surface.":[33],"By":[34],"constructing":[35],"rotation":[37],"translation":[39],"steps":[40],"in":[41,133,176],"classical":[43],"method":[45,74,88,142],"under":[46],"an":[47,78,128],"optimization":[48,59],"framework,":[49],"we":[50],"able":[52],"to":[53,61,171],"take":[54],"advantage":[55],"more":[57,154],"powerful":[58],"methods":[60,178],"substantially":[62],"speed":[63],"up":[64],"computation":[66],"states.":[69],"Specifically,":[70],"Barzilai--Borwein":[72,146],"gradient":[73],"is":[75,89,148],"proposed":[76,145],"as":[77],"effective":[79,150],"implementation":[80,156],"OSD.":[82],"show":[84],"that":[85,139],"OSD":[87,141],"generalized":[91],"formulation":[92],"original":[95],"dynamics":[98],"(SDD)":[99],"enjoys":[101],"superlinear":[102],"convergence.":[103],"test":[105,114],"various":[106],"numerical":[107],"examples,":[108,115],"including":[109],"some":[110,162],"standard":[111],"lower":[112],"dimensional":[113],"cluster":[117],"seven":[119],"particles,":[120],"seven-atom":[121],"island":[122],"on":[123],"(111)":[125],"surface":[126],"FCC":[129],"crystal,":[130],"nucleation":[132],"phase":[134],"transformations.":[135],"results":[137],"demonstrate":[138],"stepsize":[147],"very":[149],"provides":[152],"than":[157],"SDD":[159],"other":[163],"dimer-type":[164,177],"methods.":[165],"Our":[166],"algorithms":[168],"offer":[169],"potential":[170],"significantly":[172],"advance":[173],"state-of-the-art":[175],"state":[181],"search.":[182]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-10-10T00:00:00"}
