{"id":"https://openalex.org/W1994547446","doi":"https://doi.org/10.1016/j.bpj.2013.11.2316","title":"Generalized Scalable Multiple Copy Algorithms for Biological Molecular Dynamics Simulations in NAMD","display_name":"Generalized Scalable Multiple Copy Algorithms for Biological Molecular Dynamics Simulations in NAMD","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W1994547446","doi":"https://doi.org/10.1016/j.bpj.2013.11.2316","mag":"1994547446"},"language":"en","primary_location":{"id":"doi:10.1016/j.bpj.2013.11.2316","doi":"https://doi.org/10.1016/j.bpj.2013.11.2316","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.bpj.2013.11.2316","pdf_url":"http://www.cell.com/article/S0006349513035741/pdf","source":{"id":"https://openalex.org/S98085912","display_name":"Biophysical Journal","issn_l":"0006-3495","issn":["0006-3495","1542-0086"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","jufo-2","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biophysical Journal","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"http://www.cell.com/article/S0006349513035741/pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100776149","display_name":"Wei Jiang","orcid":"https://orcid.org/0000-0001-7707-6247","observed_orcids":["https://orcid.org/0000-0001-7707-6247"]},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I4390039261","display_name":"Argonne Leadership Computing Facility","ror":"https://ror.org/01svjdw65","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166","https://openalex.org/I4390039261"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Jiang","raw_affiliation_strings":["leadership computing facility, argonne national lab, lemont, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"leadership computing facility, argonne national lab, lemont, IL, USA","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I4390039261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046242311","display_name":"J. Richard Phillips","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Phillips","raw_affiliation_strings":["Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006400951","display_name":"Lei Huang","orcid":"https://orcid.org/0000-0001-9355-2709","observed_orcids":["https://orcid.org/0000-0001-9355-2709"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lei Huang","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Chicago, chicago, IL, USA","Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Chicago, chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025402203","display_name":"Mikolai Fajer","orcid":"https://orcid.org/0000-0003-2116-3514","observed_orcids":["https://orcid.org/0000-0003-2116-3514"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mikolai Fajer","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Chicago, chicago, IL, USA","Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Chicago, chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108439443","display_name":"Yilin Meng","orcid":"https://orcid.org/0009-0003-9468-3956","observed_orcids":["https://orcid.org/0009-0003-9468-3956"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yilin Meng","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Chicago, chicago, IL, USA","Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Chicago, chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080510232","display_name":"James C. Gumbart","orcid":"https://orcid.org/0000-0002-1510-7842","observed_orcids":["https://orcid.org/0000-0002-1510-7842"]},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James C. Gumbart","raw_affiliation_strings":["School of Physics, Georgia Institute of Technology, Atlanta, GA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physics, Georgia Institute of Technology, Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101602550","display_name":"Yun Luo","orcid":"https://orcid.org/0000-0003-3581-754X","observed_orcids":["https://orcid.org/0000-0003-3581-754X","https://orcid.org/0000-0002-1948-5832"]},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I4390039261","display_name":"Argonne Leadership Computing Facility","ror":"https://ror.org/01svjdw65","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166","https://openalex.org/I4390039261"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"yun luo","raw_affiliation_strings":["[Leadership Computing Facility, Argonne National Laboratory, Lemont, IL, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"[Leadership Computing Facility, Argonne National Laboratory, Lemont, IL, USA]","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I4390039261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029996336","display_name":"Klaus J. Schulten","orcid":"https://orcid.org/0000-0001-7192-9632","observed_orcids":["https://orcid.org/0000-0001-7192-9632"]},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Klaus Schulten","raw_affiliation_strings":["Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102778212","display_name":"Beno\u0131\u0302t Roux","orcid":"https://orcid.org/0000-0002-5254-2712","observed_orcids":["https://orcid.org/0000-0002-5254-2712"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"benoit roux","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Chicago, chicago, IL, USA","Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Chicago, chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3000,"currency":"USD","value_usd":3000},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.07759993,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"106","issue":"2","first_page":"412a","last_page":"412a"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8065999746322632,"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":0.8065999746322632,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.10339999943971634,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.019700000062584877,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/replica-exchange-molecular-dynamics","display_name":"replica exchange molecular dynamics","score":0.8379999995231628},{"id":"https://openalex.org/keywords/neovascular-age-related-macular-degeneration","display_name":"neovascular age-related macular degeneration","score":0.7649999856948853},{"id":"https://openalex.org/keywords/charm","display_name":"charm","score":0.7329999804496765},{"id":"https://openalex.org/keywords/parallel-molecular-dynamics","display_name":"parallel molecular dynamics","score":0.6110000014305115},{"id":"https://openalex.org/keywords/free-energy-calculations","display_name":"free energy calculation","score":0.6269999742507935},{"id":"https://openalex.org/keywords/alchemical-free-energy-perturbation","display_name":"alchemical free energy perturbation","score":0.9120000004768372},{"id":"https://openalex.org/keywords/umbrella-sampling","display_name":"umbrella sampling","score":0.9179999828338623},{"id":"https://openalex.org/keywords/string-method","display_name":"string method","score":0.7599999904632568},{"id":"https://openalex.org/keywords/conformational-transition-pathways","display_name":"conformational transition pathways","score":0.8809999823570251},{"id":"https://openalex.org/keywords/ibm-blue-gene-q","display_name":"IBM Blue Gene/Q","score":0.6539999842643738},{"id":"https://openalex.org/keywords/scalability","display_name":"scalability","score":0.43799999356269836}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7692229747772217},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6856039762496948},{"id":"https://openalex.org/C2775937380","wikidata":"https://www.wikidata.org/wiki/Q1232589","display_name":"Replica","level":2,"score":0.6092376708984375},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4389249384403229},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.42064282298088074},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3861624002456665},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.10719823837280273},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1016/j.bpj.2013.11.2316","doi":"https://doi.org/10.1016/j.bpj.2013.11.2316","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.bpj.2013.11.2316","pdf_url":"http://www.cell.com/article/S0006349513035741/pdf","source":{"id":"https://openalex.org/S98085912","display_name":"Biophysical Journal","issn_l":"0006-3495","issn":["0006-3495","1542-0086"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","jufo-2","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biophysical Journal","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1016/j.bpj.2013.11.2316","doi":"https://doi.org/10.1016/j.bpj.2013.11.2316","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.bpj.2013.11.2316","pdf_url":"http://www.cell.com/article/S0006349513035741/pdf","source":{"id":"https://openalex.org/S98085912","display_name":"Biophysical Journal","issn_l":"0006-3495","issn":["0006-3495","1542-0086"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","jufo-2","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biophysical Journal","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1994547446.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1984853348","https://openalex.org/W2150981663","https://openalex.org/W2161532098","https://openalex.org/W3046751266","https://openalex.org/W7099609312","https://openalex.org/W1992999387","https://openalex.org/W2326979787","https://openalex.org/W1677676180","https://openalex.org/W2103815459","https://openalex.org/W2901939489"],"abstract_inverted_index":null,"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2026-10-30T12:39:25.321706","created_date":"2016-06-24T00:00:00"}