{"id":"https://openalex.org/W3039317160","doi":"https://doi.org/10.1109/mcse.2020.3020508","title":"Scalable Analysis of Authentic Viral Envelopes on FRONTERA","display_name":"Scalable Analysis of Authentic Viral Envelopes on FRONTERA","publication_year":2020,"publication_date":"2020-08-31","ids":{"openalex":"https://openalex.org/W3039317160","doi":"https://doi.org/10.1109/mcse.2020.3020508","mag":"3039317160","pmid":"https://pubmed.ncbi.nlm.nih.gov/33510584"},"language":"en","primary_location":{"id":"doi:10.1109/mcse.2020.3020508","is_oa":false,"landing_page_url":"https://doi.org/10.1109/mcse.2020.3020508","pdf_url":null,"source":{"id":"https://openalex.org/S107923245","display_name":"Computing in Science & Engineering","issn_l":"1521-9615","issn":["1521-9615","1558-366X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320061","host_organization_name":"AIP Publishing","host_organization_lineage":["https://openalex.org/P4310320061","https://openalex.org/P4310320257"],"host_organization_lineage_names":["AIP Publishing","American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computing in Science &amp; Engineering","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7839976","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024114223","display_name":"Fabio Gonz\u00e1lez-Arias","orcid":null},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fabio Gonzalez-Arias","raw_affiliation_strings":["University of Delaware"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061717074","display_name":"Tyler Reddy","orcid":"https://orcid.org/0000-0003-2364-6157"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tyler Reddy","raw_affiliation_strings":["Los Alamos National Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Los Alamos National Laboratory","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048680880","display_name":"John E. Stone","orcid":"https://orcid.org/0000-0001-7215-762X"},"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":"John E. Stone","raw_affiliation_strings":["University of Illinois at Urbana-Champaign"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056514842","display_name":"Jodi A. Hadden\u2010Perilla","orcid":"https://orcid.org/0000-0003-4685-8291"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jodi A. Hadden-Perilla","raw_affiliation_strings":["University of Delaware"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089406511","display_name":"Juan R. Perilla","orcid":"https://orcid.org/0000-0003-1171-6816"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Juan R. Perilla","raw_affiliation_strings":["University of Delaware"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.9667,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.73365875,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"22","issue":"6","first_page":"11","last_page":"20"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9994000196456909,"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/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9994000196456909,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9941999912261963,"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/scalability","display_name":"Scalability","score":0.6707542538642883},{"id":"https://openalex.org/keywords/envelope","display_name":"Envelope (radar)","score":0.6370164752006531},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5434404611587524},{"id":"https://openalex.org/keywords/viral-envelope","display_name":"Viral envelope","score":0.49451252818107605},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.48290419578552246},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4478432536125183},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3621799349784851},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3621380925178528},{"id":"https://openalex.org/keywords/aerospace-engineering","display_name":"Aerospace engineering","score":0.3431991934776306},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.32665562629699707},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.31708070635795593},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2833038568496704},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.12347382307052612},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.122682124376297},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09906500577926636}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6707542538642883},{"id":"https://openalex.org/C65155139","wikidata":"https://www.wikidata.org/wiki/Q5380912","display_name":"Envelope (radar)","level":3,"score":0.6370164752006531},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5434404611587524},{"id":"https://openalex.org/C97380033","wikidata":"https://www.wikidata.org/wiki/Q994215","display_name":"Viral envelope","level":3,"score":0.49451252818107605},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.48290419578552246},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4478432536125183},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3621799349784851},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3621380925178528},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.3431991934776306},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.32665562629699707},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.31708070635795593},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2833038568496704},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.12347382307052612},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.122682124376297},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09906500577926636},{"id":"https://openalex.org/C554190296","wikidata":"https://www.wikidata.org/wiki/Q47528","display_name":"Radar","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/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1109/mcse.2020.3020508","is_oa":false,"landing_page_url":"https://doi.org/10.1109/mcse.2020.3020508","pdf_url":null,"source":{"id":"https://openalex.org/S107923245","display_name":"Computing in Science & Engineering","issn_l":"1521-9615","issn":["1521-9615","1558-366X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320061","host_organization_name":"AIP Publishing","host_organization_lineage":["https://openalex.org/P4310320061","https://openalex.org/P4310320257"],"host_organization_lineage_names":["AIP Publishing","American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computing in Science &amp; Engineering","raw_type":"journal-article"},{"id":"pmid:33510584","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33510584","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":"Computing in science & engineering","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7839976","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7839976","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Comput Sci Eng","raw_type":"Text"},{"id":"pmh:oai:osti.gov:1815507","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1815507","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:1836306","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1836306","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:1861113","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1861113","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7839976","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7839976","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Comput Sci Eng","raw_type":"Text"},"sustainable_development_goals":[{"score":0.8100000023841858,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G1017065088","display_name":null,"funder_award_id":"#89233218CNA000001","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1104241873","display_name":null,"funder_award_id":"P41 GM104601","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2216673573","display_name":"RAPID: Biophysical characterization of the native SARS-CoV-2 virion by atomistic simulations","funder_award_id":"2027096","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3644531907","display_name":"Center for Macromolecular Modeling and Bioinformatics","funder_award_id":"5p41gm104601-32","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1939198418","https://openalex.org/W2020579993","https://openalex.org/W2029667189","https://openalex.org/W2066414494","https://openalex.org/W2119267663","https://openalex.org/W2150981663","https://openalex.org/W2160544821","https://openalex.org/W2270926164","https://openalex.org/W2889460279","https://openalex.org/W2974527921","https://openalex.org/W3003012057","https://openalex.org/W3043992826"],"related_works":["https://openalex.org/W2384867379","https://openalex.org/W2329539859","https://openalex.org/W3191490922","https://openalex.org/W2227905990","https://openalex.org/W2765823764","https://openalex.org/W3214280620","https://openalex.org/W2794038527","https://openalex.org/W2151092287","https://openalex.org/W2523801036","https://openalex.org/W2505959877"],"abstract_inverted_index":{"Enveloped":[0],"viruses,":[1],"such":[2],"as":[3],"SARS-CoV-2,":[4],"infect":[5],"cells":[6],"via":[7],"fusion":[8],"of":[9,31,44,91,107,133,143],"their":[10],"envelope":[11,87],"with":[12,59],"the":[13,34,105,141,144],"host":[14],"membrane.":[15],"By":[16],"employing":[17,114],"molecular":[18],"simulations":[19],"to":[20,83,104,117],"characterize":[21,120],"viral":[22,46],"envelopes,":[23,47],"researchers":[24],"can":[25],"gain":[26],"insights":[27],"into":[28,72],"key":[29],"determinants":[30],"infection.":[32],"Here,":[33],"Frontera":[35,137],"supercomputer":[36],"is":[37,63,138],"leveraged":[38],"for":[39,61,128],"large-scale":[40],"modeling":[41],"and":[42,53,69,97,119],"analysis":[43,132],"authentic":[45,85,122],"whose":[48],"lipid":[49],"compositions":[50],"are":[51,101,112],"complex":[52],"realistic.":[54],"Visual":[55],"Molecular":[56],"Dynamics":[57],"(VMD)":[58],"support":[60],"MPI":[62],"employed,":[64],"overcoming":[65],"previous":[66],"computational":[67],"limitations":[68],"enabling":[70],"investigation":[71],"virus":[73],"biology":[74],"at":[75,88],"an":[76,84,121],"unprecedented":[77],"scale.":[78],"The":[79,110],"techniques":[80,116],"applied":[81],"here":[82],"HIV-1":[86],"two":[89],"levels":[90],"spatial":[92],"resolution":[93],"(29":[94],"million":[95,99],"particles":[96],"280":[98],"atoms)":[100],"broadly":[102],"applicable":[103],"study":[106],"other":[108],"viruses.":[109],"authors":[111],"actively":[113],"these":[115],"develop":[118],"SARS-CoV-2":[123],"envelope.":[124],"A":[125],"general":[126],"framework":[127],"carrying":[129],"out":[130],"scalable":[131],"simulation":[134],"trajectories":[135],"on":[136],"presented,":[139],"expanding":[140],"utility":[142],"machine":[145],"in":[146],"humanity's":[147],"ongoing":[148],"fight":[149],"against":[150],"infectious":[151],"diseases.":[152]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3}],"updated_date":"2026-08-13T07:04:57.449891","created_date":"2020-07-10T00:00:00"}
