{"id":"https://openalex.org/W4382048160","doi":"https://doi.org/10.1145/3592979.3593420","title":"Runtime Steering of Molecular Dynamics Simulations Through In Situ Analysis and Annotation of Collective Variables","display_name":"Runtime Steering of Molecular Dynamics Simulations Through In Situ Analysis and Annotation of Collective Variables","publication_year":2023,"publication_date":"2023-06-26","ids":{"openalex":"https://openalex.org/W4382048160","doi":"https://doi.org/10.1145/3592979.3593420"},"language":"en","primary_location":{"id":"doi:10.1145/3592979.3593420","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3592979.3593420","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3592979.3593420","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Platform for Advanced Scientific Computing Conference","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3592979.3593420","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052995286","display_name":"Silvina Ca\u00edno\u2010Lores","orcid":"https://orcid.org/0000-0002-6922-0138"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Silvina Caino-Lores","raw_affiliation_strings":["University of Tennessee, Knoxville, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-6922-0138","affiliations":[{"raw_affiliation_string":"University of Tennessee, Knoxville, United States of America","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082584620","display_name":"Michel A. Cuendet","orcid":"https://orcid.org/0000-0002-0754-3425"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Michel Cuendet","raw_affiliation_strings":["Cornell University, Lausanne, Switzerland","Swiss Institute of Bioinformatics, Lausanne, Switzerland","Swiss Institute of Bioinformatics, Lausanne, Switzerland Cornell University, Lausanne, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-0754-3425","affiliations":[{"raw_affiliation_string":"Cornell University, Lausanne, Switzerland","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Lausanne, Switzerland Cornell University, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074559167","display_name":"Jack Marquez","orcid":"https://orcid.org/0000-0002-2673-3507"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jack Marquez","raw_affiliation_strings":["University of Tennessee, Knoxville, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-2673-3507","affiliations":[{"raw_affiliation_string":"University of Tennessee, Knoxville, United States of America","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056898407","display_name":"Ekaterina D. Kots","orcid":"https://orcid.org/0000-0002-7139-7098"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ekaterina Kots","raw_affiliation_strings":["Cornell University, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-7139-7098","affiliations":[{"raw_affiliation_string":"Cornell University, New York, United States of America","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073203270","display_name":"Trilce Estrada","orcid":"https://orcid.org/0000-0001-7743-8754"},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Trilce Estrada","raw_affiliation_strings":["University of New Mexico, Albuquerque, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-7743-8754","affiliations":[{"raw_affiliation_string":"University of New Mexico, Albuquerque, United States of America","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031941569","display_name":"Ewa Deelman","orcid":"https://orcid.org/0000-0001-5106-503X"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I2801204180","display_name":"Marina Del Rey Hospital","ror":"https://ror.org/05wqyfz02","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801204180"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ewa Deelman","raw_affiliation_strings":["University of Southern California, Marina del Rey, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-5106-503X","affiliations":[{"raw_affiliation_string":"University of Southern California, Marina del Rey, United States of America","institution_ids":["https://openalex.org/I1174212","https://openalex.org/I2801204180"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014370221","display_name":"Harel Weinstein","orcid":"https://orcid.org/0000-0003-3473-9818"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Harel Weinstein","raw_affiliation_strings":["Cornell University, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-3473-9818","affiliations":[{"raw_affiliation_string":"Cornell University, New York, United States of America","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078387820","display_name":"Michela Taufer","orcid":"https://orcid.org/0000-0002-0031-6377"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michela Taufer","raw_affiliation_strings":["University of Tennessee, Knoxville, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-0031-6377","affiliations":[{"raw_affiliation_string":"University of Tennessee, Knoxville, United States of America","institution_ids":["https://openalex.org/I75027704"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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":0.9986000061035156,"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/T11162","display_name":"Enzyme Structure and Function","score":0.996399998664856,"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/molecular-dynamics","display_name":"Molecular dynamics","score":0.7484591007232666},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7400298118591309},{"id":"https://openalex.org/keywords/petascale-computing","display_name":"Petascale computing","score":0.6864451766014099},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5608789324760437},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.4281136393547058},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3246009945869446},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2775125503540039},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.252098023891449},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.15164780616760254},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.15067362785339355},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.13322052359580994}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7484591007232666},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7400298118591309},{"id":"https://openalex.org/C185410017","wikidata":"https://www.wikidata.org/wiki/Q7171778","display_name":"Petascale computing","level":3,"score":0.6864451766014099},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5608789324760437},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.4281136393547058},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3246009945869446},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2775125503540039},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.252098023891449},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.15164780616760254},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.15067362785339355},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.13322052359580994},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3592979.3593420","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3592979.3593420","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3592979.3593420","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Platform for Advanced Scientific Computing Conference","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3592979.3593420","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3592979.3593420","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3592979.3593420","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Platform for Advanced Scientific Computing Conference","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1183150320","display_name":"SHF: Small: Methods, Workflows, and Data Commons for Reducing Training Costs in Neural Architecture Search on High-Performance Computing Platforms","funder_award_id":"2223704","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4167750608","display_name":"OAC: Piloting the National Science Data Fabric: A Platform Agnostic Testbed for Democratizing Data Delivery","funder_award_id":"2138811","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5538080289","display_name":"BIGDATA: IA: Collaborative Research: In Situ Data Analytics for Next Generation Molecular Dynamics Workflows","funder_award_id":"1841758","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6226025055","display_name":"BIGDATA: IA: Collaborative Research: In Situ Data Analytics for Next Generation Molecular Dynamics Workflows","funder_award_id":"1741057","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4382048160.pdf","grobid_xml":"https://content.openalex.org/works/W4382048160.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1971725855","https://openalex.org/W1980782498","https://openalex.org/W1984853348","https://openalex.org/W2007763435","https://openalex.org/W2012029966","https://openalex.org/W2012117816","https://openalex.org/W2020165513","https://openalex.org/W2025296083","https://openalex.org/W2051075107","https://openalex.org/W2051269659","https://openalex.org/W2058971275","https://openalex.org/W2062930790","https://openalex.org/W2065283382","https://openalex.org/W2066795144","https://openalex.org/W2069123478","https://openalex.org/W2091701505","https://openalex.org/W2098055048","https://openalex.org/W2114103981","https://openalex.org/W2118233996","https://openalex.org/W2129213941","https://openalex.org/W2132262459","https://openalex.org/W2132589721","https://openalex.org/W2143592395","https://openalex.org/W2150981663","https://openalex.org/W2163467184","https://openalex.org/W2163915395","https://openalex.org/W2165835468","https://openalex.org/W2296686360","https://openalex.org/W2334531949","https://openalex.org/W2412471540","https://openalex.org/W2578034899","https://openalex.org/W2802988980","https://openalex.org/W2898134157","https://openalex.org/W2950669909","https://openalex.org/W2996385237","https://openalex.org/W3098098342","https://openalex.org/W4221147630","https://openalex.org/W4281643637","https://openalex.org/W4292718909"],"related_works":["https://openalex.org/W2335262827","https://openalex.org/W2515491806","https://openalex.org/W2904305904","https://openalex.org/W2900297768","https://openalex.org/W2138489792","https://openalex.org/W2109720355","https://openalex.org/W280508897","https://openalex.org/W2109656481","https://openalex.org/W2037561415","https://openalex.org/W2088034942"],"abstract_inverted_index":{"This":[0],"paper":[1],"targets":[2],"one":[3],"of":[4,26,40,49,58,66,80,103,115,122,142,163,175,185,196,203],"the":[5,22,37,47,78,88,91,101,113,143,164,169,176,186,197,204],"most":[6],"common":[7],"simulations":[8,20,42],"on":[9,14,55],"petascale":[10],"and,":[11],"very":[12],"likely,":[13],"exascale":[15,44],"machines:":[16],"molecular":[17,28,68,125],"dynamics":[18],"(MD)":[19],"studying":[21],"(classical)":[23],"time":[24],"evolution":[25],"a":[27,50,56,123,182],"system":[29,126,133],"at":[30,43,75],"atomic":[31],"resolution.":[32],"Specifically,":[33,151],"this":[34],"work":[35],"addresses":[36],"data":[38,51],"challenges":[39],"MD":[41,97,110,177,187,206],"through":[45],"(1)":[46],"creation":[48],"analysis":[52],"method":[53,105],"based":[54],"suite":[57],"advanced":[59],"collective":[60],"variables":[61],"(CVs)":[62],"selected":[63],"for":[64,112,127,168,181],"annotation":[65],"structural":[67],"properties":[69],"and":[70,99,106,120],"capturing":[71],"rare":[72,92],"conformational":[73,144,166,198],"events":[74,93],"runtime,":[76],"(2)":[77],"definition":[79],"an":[81,96],"in":[82,153],"situ":[83,154],"framework":[84,107,155],"to":[85,147,193],"automatically":[86],"identify":[87],"frames":[89],"where":[90],"occur":[94],"during":[95],"simulation":[98],"(3)":[100],"integration":[102],"both":[104],"into":[108],"two":[109],"workflows":[111],"study":[114],"early":[116,157],"termination":[117,119,158],"or":[118],"restart":[121,190],"benchmark":[124],"protein":[128],"folding":[129],"---the":[130],"Fs":[131,170],"peptide":[132,171],"(Ace-A_5(AAARA)_3A-NME)---":[134],"using":[135],"Summit.":[136],"The":[137],"approach":[138],"achieves":[139,160],"faster":[140],"exploration":[141],"space":[145,167],"compared":[146],"extensive":[148],"ensemble":[149],"simulations.":[150],"our":[152],"with":[156,172],"alone":[159],"99.6%":[161],"coverage":[162],"reference":[165],"just":[173,200],"60%":[174],"steps":[178],"otherwise":[179],"used":[180],"traditional":[183],"execution":[184],"simulation.":[188],"Annotation-based":[189],"allows":[191],"us":[192],"cover":[194],"94.6%":[195],"space,":[199],"running":[201],"50%":[202],"overall":[205],"steps.":[207]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
