{"id":"https://openalex.org/W2976817289","doi":"https://doi.org/10.1021/acs.jcim.9b00646","title":"Utilizing Machine Learning for Efficient Parameterization of Coarse Grained Molecular Force Fields","display_name":"Utilizing Machine Learning for Efficient Parameterization of Coarse Grained Molecular Force Fields","publication_year":2019,"publication_date":"2019-09-24","ids":{"openalex":"https://openalex.org/W2976817289","doi":"https://doi.org/10.1021/acs.jcim.9b00646","mag":"2976817289","pmid":"https://pubmed.ncbi.nlm.nih.gov/31549507"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00646","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00646","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5014606088","display_name":"James L. McDonagh","orcid":"https://orcid.org/0000-0002-2323-6898"},"institutions":[{"id":"https://openalex.org/I2802015276","display_name":"Daresbury Laboratory","ror":"https://ror.org/0089bg420","country_code":"GB","type":"facility","lineage":["https://openalex.org/I162524378","https://openalex.org/I2802015276","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"James L. McDonagh","raw_affiliation_strings":["IBM Research U.K., Hartree Centre, Daresbury WA4 4AD, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-2323-6898","affiliations":[{"raw_affiliation_string":"IBM Research U.K., Hartree Centre, Daresbury WA4 4AD, United Kingdom","institution_ids":["https://openalex.org/I2802015276"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013964740","display_name":"Ardita Shkurti","orcid":null},"institutions":[{"id":"https://openalex.org/I2802015276","display_name":"Daresbury Laboratory","ror":"https://ror.org/0089bg420","country_code":"GB","type":"facility","lineage":["https://openalex.org/I162524378","https://openalex.org/I2802015276","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ardita Shkurti","raw_affiliation_strings":["STFC Daresbury Laboratories, Daresbury WA4 4AD, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"STFC Daresbury Laboratories, Daresbury WA4 4AD, United Kingdom","institution_ids":["https://openalex.org/I2802015276"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077194514","display_name":"David J. Bray","orcid":"https://orcid.org/0000-0002-6107-0091"},"institutions":[{"id":"https://openalex.org/I2802015276","display_name":"Daresbury Laboratory","ror":"https://ror.org/0089bg420","country_code":"GB","type":"facility","lineage":["https://openalex.org/I162524378","https://openalex.org/I2802015276","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"David J. Bray","raw_affiliation_strings":["STFC Daresbury Laboratories, Daresbury WA4 4AD, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"STFC Daresbury Laboratories, Daresbury WA4 4AD, United Kingdom","institution_ids":["https://openalex.org/I2802015276"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052022139","display_name":"R. L. Anderson","orcid":"https://orcid.org/0000-0002-4320-8472"},"institutions":[{"id":"https://openalex.org/I2802015276","display_name":"Daresbury Laboratory","ror":"https://ror.org/0089bg420","country_code":"GB","type":"facility","lineage":["https://openalex.org/I162524378","https://openalex.org/I2802015276","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard L. Anderson","raw_affiliation_strings":["STFC Daresbury Laboratories, Daresbury WA4 4AD, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-4320-8472","affiliations":[{"raw_affiliation_string":"STFC Daresbury Laboratories, Daresbury WA4 4AD, United Kingdom","institution_ids":["https://openalex.org/I2802015276"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084050064","display_name":"Edward O. Pyzer\u2010Knapp","orcid":"https://orcid.org/0000-0002-8232-8282"},"institutions":[{"id":"https://openalex.org/I2802015276","display_name":"Daresbury Laboratory","ror":"https://ror.org/0089bg420","country_code":"GB","type":"facility","lineage":["https://openalex.org/I162524378","https://openalex.org/I2802015276","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Edward O. Pyzer-Knapp","raw_affiliation_strings":["IBM Research U.K., Hartree Centre, Daresbury WA4 4AD, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-8232-8282","affiliations":[{"raw_affiliation_string":"IBM Research U.K., Hartree Centre, Daresbury WA4 4AD, United Kingdom","institution_ids":["https://openalex.org/I2802015276"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5077194514","https://openalex.org/A5084050064"],"corresponding_institution_ids":["https://openalex.org/I2802015276"],"apc_list":null,"apc_paid":null,"fwci":2.395,"has_fulltext":false,"cited_by_count":57,"citation_normalized_percentile":{"value":0.89479621,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"59","issue":"10","first_page":"4278","last_page":"4288"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9955000281333923,"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/bayesian-optimization","display_name":"Bayesian optimization","score":0.8546499013900757},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.752619743347168},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6091738939285278},{"id":"https://openalex.org/keywords/parametrization","display_name":"Parametrization (atmospheric modeling)","score":0.5721724033355713},{"id":"https://openalex.org/keywords/dissipative-particle-dynamics","display_name":"Dissipative particle dynamics","score":0.5426071882247925},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5300043821334839},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5044041872024536},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4767005145549774},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4213976562023163},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.37911930680274963},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.35736554861068726},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35724666714668274},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2899635434150696},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1256454586982727}],"concepts":[{"id":"https://openalex.org/C2778049539","wikidata":"https://www.wikidata.org/wiki/Q17002908","display_name":"Bayesian optimization","level":2,"score":0.8546499013900757},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.752619743347168},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6091738939285278},{"id":"https://openalex.org/C202887219","wikidata":"https://www.wikidata.org/wiki/Q3895221","display_name":"Parametrization (atmospheric modeling)","level":3,"score":0.5721724033355713},{"id":"https://openalex.org/C45594756","wikidata":"https://www.wikidata.org/wiki/Q5282784","display_name":"Dissipative particle dynamics","level":3,"score":0.5426071882247925},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5300043821334839},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5044041872024536},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4767005145549774},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4213976562023163},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.37911930680274963},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35736554861068726},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35724666714668274},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2899635434150696},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1256454586982727},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C74902906","wikidata":"https://www.wikidata.org/wiki/Q1190858","display_name":"Radiative transfer","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002616","descriptor_name":"Chemical Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002616","descriptor_name":"Chemical Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002616","descriptor_name":"Chemical Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","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":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.9b00646","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00646","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:31549507","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31549507","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,"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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:purl.org/net/epubs:work/44857146","is_oa":false,"landing_page_url":"http://purl.org/net/epubs/work/44857146","pdf_url":null,"source":{"id":"https://openalex.org/S4306400334","display_name":"Science and Technology Facilities Council","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320312933","display_name":"Department for Business, Energy and Industrial Strategy, UK Government","ror":"https://ror.org/019ya6433"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":65,"referenced_works":["https://openalex.org/W210395626","https://openalex.org/W1522161842","https://openalex.org/W1523859212","https://openalex.org/W1531674615","https://openalex.org/W1806547840","https://openalex.org/W1911693620","https://openalex.org/W1963731008","https://openalex.org/W1967737979","https://openalex.org/W1971044734","https://openalex.org/W1974974739","https://openalex.org/W1976616324","https://openalex.org/W1981210409","https://openalex.org/W1981998283","https://openalex.org/W1989793475","https://openalex.org/W1997772366","https://openalex.org/W2015625779","https://openalex.org/W2030891958","https://openalex.org/W2032655419","https://openalex.org/W2036973403","https://openalex.org/W2039588355","https://openalex.org/W2039978162","https://openalex.org/W2041189078","https://openalex.org/W2046001409","https://openalex.org/W2047112187","https://openalex.org/W2049801133","https://openalex.org/W2051381895","https://openalex.org/W2060433756","https://openalex.org/W2061308254","https://openalex.org/W2065505215","https://openalex.org/W2077535359","https://openalex.org/W2078811798","https://openalex.org/W2081527338","https://openalex.org/W2083415705","https://openalex.org/W2093381148","https://openalex.org/W2100523398","https://openalex.org/W2101234009","https://openalex.org/W2104489082","https://openalex.org/W2108114251","https://openalex.org/W2108600976","https://openalex.org/W2118076674","https://openalex.org/W2119267663","https://openalex.org/W2159565091","https://openalex.org/W2162166182","https://openalex.org/W2166116468","https://openalex.org/W2192203593","https://openalex.org/W2211308547","https://openalex.org/W2276264794","https://openalex.org/W2483012291","https://openalex.org/W2485658318","https://openalex.org/W2541404351","https://openalex.org/W2547447472","https://openalex.org/W2562301581","https://openalex.org/W2580325886","https://openalex.org/W2595808071","https://openalex.org/W2726359057","https://openalex.org/W2760024123","https://openalex.org/W2762414491","https://openalex.org/W2769775068","https://openalex.org/W2791870314","https://openalex.org/W2793396277","https://openalex.org/W2910948470","https://openalex.org/W2911502027","https://openalex.org/W2951433574","https://openalex.org/W3101439684","https://openalex.org/W3170501715"],"related_works":["https://openalex.org/W2363861645","https://openalex.org/W2717064866","https://openalex.org/W2793851954","https://openalex.org/W2007034665","https://openalex.org/W2050819322","https://openalex.org/W3035069379","https://openalex.org/W1970971962","https://openalex.org/W4391620285","https://openalex.org/W22410277","https://openalex.org/W4401858220"],"abstract_inverted_index":{"We":[0,59],"present":[1],"a":[2,23,36,56,68,110,130,143,166],"machine":[3],"learning":[4],"approach":[5,17,148],"to":[6,21,74,149,154,169],"automated":[7,137],"force":[8,25,57,69,150],"field":[9,26,70,151],"development":[10],"in":[11],"dissipative":[12],"particle":[13],"dynamics":[14],"(DPD).":[15],"The":[16,32,81],"employs":[18],"Bayesian":[19,62,159],"optimization":[20,33,63,86,141,160],"parametrize":[22],"DPD":[24],"against":[27],"experimentally":[28],"determined":[29],"partition":[30],"coefficients.":[31],"process":[34],"covers":[35],"discrete":[37],"space":[38],"of":[39,51,66,71,90,95,103,117,122,135],"over":[40],"40":[41,79],"000":[42,43],"points,":[44],"where":[45],"each":[46],"point":[47],"represents":[48],"the":[49,75,85,100,133],"set":[50,102,112],"potentials":[52],"that":[53,61],"jointly":[54],"forms":[55],"field.":[58],"find":[60],"is":[64,113],"capable":[65],"reaching":[67],"comparable":[72],"performance":[73],"current":[76],"state-of-the-art":[77],"within":[78],"iterations.":[80],"best":[82],"iteration":[83],"during":[84],"achieves":[87],"an":[88,93,120],"R2":[89,116],"0.78":[91],"and":[92,119,138,165],"RMSE":[94,121],"0.63":[96],"log":[97,124],"units":[98],"on":[99],"training":[101],"data,":[104],"these":[105],"metrics":[106],"are":[107],"maintained":[108],"when":[109],"validation":[111],"included,":[114],"giving":[115],"0.8":[118],"0.65":[123],"units.":[125],"This":[126],"work":[127],"hence":[128],"provides":[129],"proof-of-concept,":[131],"expounding":[132],"utility":[134],"coupling":[136],"efficient":[139],"global":[140,162],"with":[142],"top":[144],"down":[145],"data":[146],"driven":[147],"parametrization.":[152],"Compared":[153],"commonly":[155],"employed":[156],"alternative":[157],"methods,":[158],"offers":[161],"parameter":[163],"searching":[164],"low":[167],"time":[168],"solution.":[170]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
