{"id":"https://openalex.org/W4313598870","doi":"https://doi.org/10.1109/tpds.2022.3220559","title":"Bio-ESMD: A Data Centric Implementation for Large-Scale Biological System Simulation on Sunway TaihuLight Supercomputer","display_name":"Bio-ESMD: A Data Centric Implementation for Large-Scale Biological System Simulation on Sunway TaihuLight Supercomputer","publication_year":2023,"publication_date":"2023-01-06","ids":{"openalex":"https://openalex.org/W4313598870","doi":"https://doi.org/10.1109/tpds.2022.3220559"},"language":"en","primary_location":{"id":"doi:10.1109/tpds.2022.3220559","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tpds.2022.3220559","pdf_url":null,"source":{"id":"https://openalex.org/S97130795","display_name":"IEEE Transactions on Parallel and Distributed Systems","issn_l":"1045-9219","issn":["1045-9219","1558-2183","2161-9883"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Parallel and Distributed Systems","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/A5003075115","display_name":"Xiaohui Duan","orcid":"https://orcid.org/0000-0002-1913-6683"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210158984","display_name":"National Supercomputing Center in Wuxi","ror":"https://ror.org/04ypjrs34","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210158984"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohui Duan","raw_affiliation_strings":["School of Software, Shandong University, Jinan, Shandong, China","National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China"],"raw_orcid":"https://orcid.org/0000-0002-1913-6683","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China","institution_ids":["https://openalex.org/I4210158984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069811749","display_name":"Qi Shao","orcid":null},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210158984","display_name":"National Supercomputing Center in Wuxi","ror":"https://ror.org/04ypjrs34","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210158984"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qi Shao","raw_affiliation_strings":["School of Software, Shandong University, Jinan, Shandong, China","National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China","institution_ids":["https://openalex.org/I4210158984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084806191","display_name":"Junben Weng","orcid":"https://orcid.org/0000-0002-7642-2045"},"institutions":[{"id":"https://openalex.org/I180585399","display_name":"Dalian Institute of Chemical Physics","ror":"https://ror.org/00prkya54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I180585399","https://openalex.org/I19820366"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junben Weng","raw_affiliation_strings":["Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China","institution_ids":["https://openalex.org/I180585399","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["Institute for Computer Science, Johannes Gutenberg University, Mainz, Germany"],"raw_orcid":"https://orcid.org/0000-0003-2597-8331","affiliations":[{"raw_affiliation_string":"Institute for Computer Science, Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038750675","display_name":"Lin Gan","orcid":"https://orcid.org/0000-0003-1297-4462"},"institutions":[{"id":"https://openalex.org/I4210158984","display_name":"National Supercomputing Center in Wuxi","ror":"https://ror.org/04ypjrs34","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210158984"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Gan","raw_affiliation_strings":["Department of Computer Science and Technology, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China","National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China"],"raw_orcid":"https://orcid.org/0000-0003-1297-4462","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China","institution_ids":["https://openalex.org/I4210158984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100337869","display_name":"Guohui Li","orcid":"https://orcid.org/0000-0001-8223-705X"},"institutions":[{"id":"https://openalex.org/I180585399","display_name":"Dalian Institute of Chemical Physics","ror":"https://ror.org/00prkya54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I180585399","https://openalex.org/I19820366"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guohui Li","raw_affiliation_strings":["Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China","institution_ids":["https://openalex.org/I180585399","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031545295","display_name":"Haohuan Fu","orcid":"https://orcid.org/0000-0002-6982-2235"},"institutions":[{"id":"https://openalex.org/I4210158984","display_name":"National Supercomputing Center in Wuxi","ror":"https://ror.org/04ypjrs34","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210158984"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haohuan Fu","raw_affiliation_strings":["Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing, China","National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China"],"raw_orcid":"https://orcid.org/0000-0002-6982-2235","affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China","institution_ids":["https://openalex.org/I4210158984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091437474","display_name":"Wei Xue","orcid":"https://orcid.org/0000-0001-9740-6581"},"institutions":[{"id":"https://openalex.org/I4210158984","display_name":"National Supercomputing Center in Wuxi","ror":"https://ror.org/04ypjrs34","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210158984"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Xue","raw_affiliation_strings":["Department of Computer Science and Technology, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China","National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China"],"raw_orcid":"https://orcid.org/0000-0001-9740-6581","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China","institution_ids":["https://openalex.org/I4210158984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100620772","display_name":"Weiguo Liu","orcid":"https://orcid.org/0000-0001-8834-0453"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210158984","display_name":"National Supercomputing Center in Wuxi","ror":"https://ror.org/04ypjrs34","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210158984"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiguo Liu","raw_affiliation_strings":["School of Software, Shandong University, Jinan, Shandong, China","National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China"],"raw_orcid":"https://orcid.org/0000-0001-8834-0453","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China","institution_ids":["https://openalex.org/I4210158984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101678397","display_name":"Guangwen Yang","orcid":"https://orcid.org/0000-0002-8673-8254"},"institutions":[{"id":"https://openalex.org/I4210158984","display_name":"National Supercomputing Center in Wuxi","ror":"https://ror.org/04ypjrs34","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210158984"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guangwen Yang","raw_affiliation_strings":["Department of Computer Science and Technology, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China","National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"National Supercomputing Center in Wuxi, Wuxi, Jiangsu, China","institution_ids":["https://openalex.org/I4210158984"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5662,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.60094929,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"34","issue":"3","first_page":"881","last_page":"893"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.98580002784729,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.98580002784729,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9855999946594238,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9829000234603882,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.8644124269485474},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7476549744606018},{"id":"https://openalex.org/keywords/locality","display_name":"Locality","score":0.6408094763755798},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5604309439659119},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.46115732192993164},{"id":"https://openalex.org/keywords/code-refactoring","display_name":"Code refactoring","score":0.447361022233963},{"id":"https://openalex.org/keywords/atom","display_name":"Atom (system on chip)","score":0.44646525382995605},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.44226008653640747},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32022085785865784},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14664235711097717},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.12340375781059265}],"concepts":[{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.8644124269485474},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7476549744606018},{"id":"https://openalex.org/C2779808786","wikidata":"https://www.wikidata.org/wiki/Q6664603","display_name":"Locality","level":2,"score":0.6408094763755798},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5604309439659119},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.46115732192993164},{"id":"https://openalex.org/C152752567","wikidata":"https://www.wikidata.org/wiki/Q116877","display_name":"Code refactoring","level":3,"score":0.447361022233963},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.44646525382995605},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.44226008653640747},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32022085785865784},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14664235711097717},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.12340375781059265},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tpds.2022.3220559","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tpds.2022.3220559","pdf_url":null,"source":{"id":"https://openalex.org/S97130795","display_name":"IEEE Transactions on Parallel and Distributed Systems","issn_l":"1045-9219","issn":["1045-9219","1558-2183","2161-9883"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Parallel and Distributed Systems","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1513273297","display_name":null,"funder_award_id":"62102114","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4140447210","display_name":"\u9762\u5411\u8d85\u5927\u89c4\u6a21\u77ed\u8bfb\u751f\u7269\u5e8f\u5217\u6570\u636e\u7684\u9ad8\u6027\u80fd\u5339\u914d\u7b97\u6cd5\u7814\u7a76","funder_award_id":"61972231","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6690759662","display_name":null,"funder_award_id":"T2125006","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8368203158","display_name":null,"funder_award_id":"U1839206","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1981021420","https://openalex.org/W2013173369","https://openalex.org/W2029667189","https://openalex.org/W2065963893","https://openalex.org/W2103325328","https://openalex.org/W2162166182","https://openalex.org/W2313116527","https://openalex.org/W2475126267","https://openalex.org/W2582572759","https://openalex.org/W2744007529","https://openalex.org/W2902659137","https://openalex.org/W2923126305","https://openalex.org/W2975164014","https://openalex.org/W2987526375","https://openalex.org/W3015060795","https://openalex.org/W3020586295","https://openalex.org/W3046751266","https://openalex.org/W3131779325","https://openalex.org/W3135244911","https://openalex.org/W3142513090","https://openalex.org/W3208186749","https://openalex.org/W4235810972","https://openalex.org/W6802709207"],"related_works":["https://openalex.org/W4313549863","https://openalex.org/W4231266416","https://openalex.org/W2395465245","https://openalex.org/W2072205733","https://openalex.org/W3176957927","https://openalex.org/W4296534969","https://openalex.org/W3194667890","https://openalex.org/W1582436825","https://openalex.org/W1996803181","https://openalex.org/W2979588510"],"abstract_inverted_index":{"Molecular":[0],"dynamics":[1],"(MD)":[2],"simulations":[3,25],"of":[4,16,36,52,134,149],"biological":[5,24],"systems":[6],"are":[7],"playing":[8],"an":[9],"increasingly":[10],"important":[11],"role":[12],"in":[13],"the":[14,28,46,117],"research":[15],"pathogens":[17],"and":[18,91],"drugs.":[19],"Most":[20],"MD":[21,83,113],"methods":[22],"for":[23,72,100,111],"rely":[26],"on":[27,60,94,140],"listed":[29,86],"bonds":[30],"which":[31],"interact":[32],"among":[33],"specific":[34],"groups":[35],"atoms":[37,152,159],"identified":[38],"by":[39,115],"atom":[40,43,55],"tags":[41,44,53],"(unique":[42],"regardless":[45],"storage":[47],"location).":[48],"However,":[49],"efficient":[50],"mapping":[51],"to":[54,122,138],"locations":[56],"is":[57,89],"often":[58],"challenging":[59],"modern":[61],"many-core":[62,101],"processors":[63],"because":[64],"data":[65,120,128],"locality":[66],"can":[67,145],"not":[68],"always":[69],"be":[70],"guaranteed":[71,127],"large-scale":[73],"systems.":[74],"In":[75,103],"this":[76],"paper,":[77],"we":[78,105],"present":[79],"Bio-ESMD,":[80,104],"a":[81,108,147],"new":[82],"implementation":[84,131],"supporting":[85],"bonds.":[87],"Bio-ESMD":[88,144],"designed":[90,97],"developed":[92],"based":[93],"our":[95],"previously":[96],"ESMD":[98],"framework":[99],"processors.":[102],"have":[106],"introduced":[107],"data-centric":[109],"approach":[110],"refactoring":[112],"algorithms":[114],"reorganizing":[116],"cell":[118],"list":[119],"structure":[121],"adopt":[123],"bond":[124],"lists":[125],"with":[126,163],"locality.":[129],"Our":[130],"achieves":[132],"speedups":[133],"over":[135],"two":[136],"compared":[137],"SW_GROMACS":[139],"Sunway":[141],"TaihuLight.":[142],"Furthermore,":[143],"simulate":[146],"system":[148],"308.8":[150],"million":[151,158],"at":[153,160],"1.33":[154],"ns/day":[155,162],"or":[156],"14.44":[157],"17.28":[161],"linear":[164],"weak":[165],"scaling":[166],"efficiency.":[167]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
