{"id":"https://openalex.org/W1981115969","doi":"https://doi.org/10.1145/2535571.2535595","title":"GPU-accelerated molecular visualization on petascale supercomputing platforms","display_name":"GPU-accelerated molecular visualization on petascale supercomputing platforms","publication_year":2013,"publication_date":"2013-11-06","ids":{"openalex":"https://openalex.org/W1981115969","doi":"https://doi.org/10.1145/2535571.2535595","mag":"1981115969"},"language":"en","primary_location":{"id":"doi:10.1145/2535571.2535595","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2535571.2535595","pdf_url":"http://dl.acm.org/ft_gateway.cfm?id=2535595&type=pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th International Workshop on Ultrascale Visualization","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"http://dl.acm.org/ft_gateway.cfm?id=2535595&type=pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","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"]},{"id":"https://openalex.org/I2801919071","display_name":"University of Illinois System","ror":"https://ror.org/05e94g991","country_code":"US","type":"education","lineage":["https://openalex.org/I2801919071"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John E. Stone","raw_affiliation_strings":["University of Illinois, Urbana, IL","[University of Illinois, Urbana, IL]"],"affiliations":[{"raw_affiliation_string":"University of Illinois, Urbana, IL","institution_ids":["https://openalex.org/I2801919071"]},{"raw_affiliation_string":"[University of Illinois, Urbana, IL]","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084705137","display_name":"Kirby L. Vandivort","orcid":null},"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"]},{"id":"https://openalex.org/I2801919071","display_name":"University of Illinois System","ror":"https://ror.org/05e94g991","country_code":"US","type":"education","lineage":["https://openalex.org/I2801919071"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kirby L. Vandivort","raw_affiliation_strings":["University of Illinois, Urbana, IL","[University of Illinois, Urbana, IL]"],"affiliations":[{"raw_affiliation_string":"University of Illinois, Urbana, IL","institution_ids":["https://openalex.org/I2801919071"]},{"raw_affiliation_string":"[University of Illinois, Urbana, IL]","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029996336","display_name":"Klaus Schulten","orcid":"https://orcid.org/0000-0001-7192-9632"},"institutions":[{"id":"https://openalex.org/I2801919071","display_name":"University of Illinois System","ror":"https://ror.org/05e94g991","country_code":"US","type":"education","lineage":["https://openalex.org/I2801919071"]},{"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":["University of Illinois, Urbana, IL","[University of Illinois, Urbana, IL]"],"affiliations":[{"raw_affiliation_string":"University of Illinois, Urbana, IL","institution_ids":["https://openalex.org/I2801919071"]},{"raw_affiliation_string":"[University of Illinois, Urbana, IL]","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5048680880"],"corresponding_institution_ids":["https://openalex.org/I157725225","https://openalex.org/I2801919071"],"apc_list":null,"apc_paid":null,"fwci":16.6331,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.98827203,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.993399977684021,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.993399977684021,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9933000206947327,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.991599977016449,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/petascale-computing","display_name":"Petascale computing","score":0.9963372349739075},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8606207966804504},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.7842377424240112},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.713445246219635},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.5931930541992188},{"id":"https://openalex.org/keywords/terabyte","display_name":"Terabyte","score":0.5717257261276245},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4792916178703308},{"id":"https://openalex.org/keywords/rendering","display_name":"Rendering (computer graphics)","score":0.44471290707588196},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.4368460774421692},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.301941454410553},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10024681687355042},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.0799894630908966}],"concepts":[{"id":"https://openalex.org/C185410017","wikidata":"https://www.wikidata.org/wiki/Q7171778","display_name":"Petascale computing","level":3,"score":0.9963372349739075},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8606207966804504},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.7842377424240112},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.713445246219635},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.5931930541992188},{"id":"https://openalex.org/C199683683","wikidata":"https://www.wikidata.org/wiki/Q8799","display_name":"Terabyte","level":2,"score":0.5717257261276245},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4792916178703308},{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.44471290707588196},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4368460774421692},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.301941454410553},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10024681687355042},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0799894630908966}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2535571.2535595","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2535571.2535595","pdf_url":"http://dl.acm.org/ft_gateway.cfm?id=2535595&type=pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th International Workshop on Ultrascale Visualization","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/2535571.2535595","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2535571.2535595","pdf_url":"http://dl.acm.org/ft_gateway.cfm?id=2535595&type=pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th International Workshop on Ultrascale Visualization","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2741124455","display_name":null,"funder_award_id":"9P41GM10460","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2902128777","display_name":null,"funder_award_id":"9P41GM104601 and 5R01GM098243-02","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6461054833","display_name":null,"funder_award_id":"GM104601","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6476835034","display_name":null,"funder_award_id":"OCI 07-25070","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G696918205","display_name":null,"funder_award_id":"9P41GM104601","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7581742385","display_name":null,"funder_award_id":"9P41GM104601, 5R01GM098243-02","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8137055185","display_name":null,"funder_award_id":"P41GM104601","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8159600759","display_name":null,"funder_award_id":"5R01GM098243-02","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/F4320312143","display_name":"National Centre for Supercomputing Applications","ror":"https://ror.org/03r10zj06"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332222","display_name":"University of Illinois at Urbana-Champaign","ror":"https://ror.org/047426m28"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1981115969.pdf","grobid_xml":"https://content.openalex.org/works/W1981115969.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W118889687","https://openalex.org/W336063547","https://openalex.org/W1519330792","https://openalex.org/W1535111405","https://openalex.org/W1573103858","https://openalex.org/W1971619264","https://openalex.org/W1977115694","https://openalex.org/W1977974544","https://openalex.org/W1993828173","https://openalex.org/W2004383436","https://openalex.org/W2021064626","https://openalex.org/W2022597857","https://openalex.org/W2028753963","https://openalex.org/W2029667189","https://openalex.org/W2050513283","https://openalex.org/W2063831812","https://openalex.org/W2065963893","https://openalex.org/W2071004993","https://openalex.org/W2072973641","https://openalex.org/W2086841337","https://openalex.org/W2102927018","https://openalex.org/W2125404364","https://openalex.org/W2128918568","https://openalex.org/W2131662064","https://openalex.org/W2139635799","https://openalex.org/W2143848552","https://openalex.org/W2151643303","https://openalex.org/W2159497832","https://openalex.org/W2177731497","https://openalex.org/W2244686166","https://openalex.org/W2295862081","https://openalex.org/W4251841159"],"related_works":["https://openalex.org/W2021702679","https://openalex.org/W3038449658","https://openalex.org/W1525924016","https://openalex.org/W1582746211","https://openalex.org/W3129378740","https://openalex.org/W2607572736","https://openalex.org/W2266027327","https://openalex.org/W2278366184","https://openalex.org/W1486544172","https://openalex.org/W2018090346"],"abstract_inverted_index":{"Petascale":[0,49],"supercomputers":[1],"create":[2],"new":[3],"opportunities":[4,143],"for":[5,106,118,124,144],"the":[6,9,81,84,90],"study":[7],"of":[8,13,28,32,34,57,59,92,96],"structure":[10],"and":[11,20,39,76,103,120,135,148],"function":[12],"large":[14],"biomolecular":[15],"complexes":[16],"such":[17],"as":[18],"viruses":[19],"photosynthetic":[21],"organelles,":[22],"permitting":[23],"all-atom":[24],"molecular":[25,50,101,127],"dynamics":[26,51],"simulations":[27,52],"tens":[29,54],"to":[30,55,65,67,73],"hundreds":[31,56],"millions":[33],"atoms.":[35],"Together":[36],"with":[37,44],"simulation":[38,128],"analysis,":[40],"visualization":[41,75,94,102],"provides":[42],"researchers":[43],"a":[45,98],"powerful":[46],"\"computational":[47],"microscope\".":[48],"produce":[53],"terabytes":[58],"data":[60,85],"that":[61],"can":[62],"be":[63],"impractical":[64],"transfer":[66],"remote":[68],"facilities,":[69],"making":[70],"it":[71],"necessary":[72],"perform":[74],"analysis":[77,104],"tasks":[78],"in-place":[79],"on":[80,131],"supercomputer":[82],"where":[83],"are":[86],"generated.":[87],"We":[88,110],"describe":[89],"adaptation":[91],"key":[93],"features":[95],"VMD,":[97],"widely":[99],"used":[100],"tool,":[105],"GPU-accelerated":[107],"petascale":[108,126],"computers.":[109],"discuss":[111],"early":[112],"experiences":[113],"adapting":[114],"ray":[115],"tracing":[116],"algorithms":[117],"GPUs,":[119],"compare":[121],"rendering":[122],"performance":[123],"recent":[125],"test":[129],"cases":[130],"Cray":[132],"XE6":[133],"(CPU-only)":[134],"XK7":[136],"(GPU-accelerated)":[137],"compute":[138],"nodes.":[139],"Finally,":[140],"we":[141],"highlight":[142],"further":[145],"algorithmic":[146],"improvements":[147],"optimizations.":[149]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
