{"id":"https://openalex.org/W4390528874","doi":"https://doi.org/10.48550/arxiv.2401.00499","title":"Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms using Molecular Configuration Transformer","display_name":"Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms using Molecular Configuration Transformer","publication_year":2023,"publication_date":"2023-12-31","ids":{"openalex":"https://openalex.org/W4390528874","doi":"https://doi.org/10.48550/arxiv.2401.00499"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2401.00499","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2401.00499","pdf_url":"https://arxiv.org/pdf/2401.00499","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2401.00499","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101287533","display_name":"Sihao Yuan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yuan, Sihao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101556951","display_name":"Xu Han","orcid":"https://orcid.org/0000-0001-6116-3258"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Han, Xu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Zhang, Jun","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Jun","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111198208","display_name":"Zhaoxin Xie","orcid":"https://orcid.org/0009-0003-8724-5173"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xie, Zhaoxin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104042779","display_name":"Cheng Fan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fan, Cheng","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Xiao, Yunlong","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiao, Yunlong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051732177","display_name":"Yi Qin Gao","orcid":"https://orcid.org/0000-0002-4309-9376"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gao, Yi Qin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5101287534","display_name":"Yi Issac Yang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yang, Yi Isaac","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":8,"corresponding_author_ids":[],"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/T10028","display_name":"Topic Modeling","score":0.9865999817848206,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9865999817848206,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9864000082015991,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9642000198364258,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.8201957941055298},{"id":"https://openalex.org/keywords/chemical-reaction","display_name":"Chemical reaction","score":0.5631436109542847},{"id":"https://openalex.org/keywords/quantum-chemical","display_name":"Quantum chemical","score":0.4976349174976349},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48599299788475037},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.46205607056617737},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.43279415369033813},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4234268367290497},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.4195508658885956},{"id":"https://openalex.org/keywords/transition-state","display_name":"Transition state","score":0.4131545424461365},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.40733662247657776},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.34885373711586},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.3344518542289734},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2211119532585144},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15637797117233276},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.1260250210762024}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.8201957941055298},{"id":"https://openalex.org/C177801218","wikidata":"https://www.wikidata.org/wiki/Q36534","display_name":"Chemical reaction","level":2,"score":0.5631436109542847},{"id":"https://openalex.org/C2991951333","wikidata":"https://www.wikidata.org/wiki/Q188403","display_name":"Quantum chemical","level":3,"score":0.4976349174976349},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48599299788475037},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.46205607056617737},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.43279415369033813},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4234268367290497},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.4195508658885956},{"id":"https://openalex.org/C89031862","wikidata":"https://www.wikidata.org/wiki/Q906964","display_name":"Transition state","level":3,"score":0.4131545424461365},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.40733662247657776},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.34885373711586},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3344518542289734},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2211119532585144},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15637797117233276},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.1260250210762024},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","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/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:arXiv.org:2401.00499","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2401.00499","pdf_url":"https://arxiv.org/pdf/2401.00499","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:figshare.com:article/25852744","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/Generating_High-Precision_Force_Fields_for_Molecular_Dynamics_Simulations_to_Study_Chemical_Reaction_Mechanisms_Using_Molecular_Configuration_Transformer/25852744","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"doi:10.48550/arxiv.2401.00499","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2401.00499","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2401.00499","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2401.00499","pdf_url":"https://arxiv.org/pdf/2401.00499","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8500000238418579,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G1041984945","display_name":null,"funder_award_id":"21821004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1943808332","display_name":null,"funder_award_id":"22003042","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2088215124","display_name":null,"funder_award_id":"2022ZD0115003","funder_id":"https://openalex.org/F4320329860","funder_display_name":"National Science and Technology Major Project"},{"id":"https://openalex.org/G4775812314","display_name":null,"funder_award_id":"21927901","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6843369216","display_name":null,"funder_award_id":"22050003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8280670476","display_name":null,"funder_award_id":"22273061","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8654349138","display_name":"\u7ec6\u80de\u53d1\u80b2\u3001\u5206\u5316\u548c\u75be\u75c5\u53d1\u751f\u8fc7\u7a0b\u4e2d\u7684\u67d3\u8272\u8d28\u76f8\u5206\u79bb\u4e0e\u57fa\u56e0\u8c03\u63a7\u673a\u5236\u7814\u7a76","funder_award_id":"92053202","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320329860","display_name":"National Science and Technology Major Project","ror":null},{"id":"https://openalex.org/F4320331248","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390528874.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1968508988","https://openalex.org/W2741336069","https://openalex.org/W3136335663","https://openalex.org/W2010693641","https://openalex.org/W2072798552","https://openalex.org/W1996733108","https://openalex.org/W2000625121","https://openalex.org/W2369845750","https://openalex.org/W2349318783","https://openalex.org/W2091514273"],"abstract_inverted_index":{"Theoretical":[0],"studies":[1],"on":[2,41],"chemical":[3,23,27,45,66,78,143],"reaction":[4,154,159],"mechanisms":[5],"have":[6],"been":[7],"crucial":[8],"in":[9,60],"organic":[10],"chemistry.":[11],"Traditionally,":[12],"calculating":[13],"the":[14,30,73,81,85,140],"manually":[15],"constructed":[16],"molecular":[17,61,108,115,117],"conformations":[18],"of":[19,76,87,139,142],"transition":[20],"states":[21],"for":[22,92,102,107,125],"reactions":[24],"using":[25,110],"quantum":[26],"calculations":[28,138],"is":[29,38],"most":[31],"commonly":[32],"used":[33],"method.":[34],"However,":[35,80],"this":[36,96,147],"way":[37],"heavily":[39],"dependent":[40],"individual":[42],"experience":[43],"and":[44,155],"intuition.":[46],"In":[47],"our":[48],"previous":[49],"study,":[50],"we":[51,98],"proposed":[52],"a":[53,77,100,111,130,151,156],"research":[54],"paradigm":[55],"that":[56],"uses":[57],"enhanced":[58],"sampling":[59],"dynamics":[62],"simulations":[63,128],"to":[64,135,149],"study":[65,150],"reactions.":[67,144],"This":[68,120],"approach":[69,148],"can":[70],"directly":[71],"simulate":[72],"entire":[74],"process":[75],"reaction.":[79],"computational":[82,132],"speed":[83],"limits":[84],"use":[86],"high-precision":[88,104],"potential":[89,121],"energy":[90,122],"functions":[91],"simulations.":[93],"To":[94],"address":[95],"issue,":[97],"present":[99],"scheme":[101],"training":[103],"force":[105],"fields":[106],"modeling":[109],"previously":[112],"developed":[113],"graph-neural-network-based":[114],"model,":[116],"configuration":[118],"transformer.":[119],"function":[123],"allows":[124],"highly":[126],"accurate":[127],"at":[129],"low":[131],"cost,":[133],"leading":[134],"more":[136],"precise":[137],"mechanism":[141],"We":[145],"applied":[146],"Claisen":[152],"rearrangement":[153],"Carbonyl":[157],"insertion":[158],"catalyzed":[160],"by":[161],"Manganese.":[162]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}