{"id":"https://openalex.org/W2110338379","doi":"https://doi.org/10.1145/1188455.1188547","title":"Molecular dynamics---Blue matter","display_name":"Molecular dynamics---Blue matter","publication_year":2006,"publication_date":"2006-01-01","ids":{"openalex":"https://openalex.org/W2110338379","doi":"https://doi.org/10.1145/1188455.1188547","mag":"2110338379"},"language":"en","primary_location":{"id":"doi:10.1145/1188455.1188547","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1188455.1188547","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2006 ACM/IEEE conference on Supercomputing  - SC '06","raw_type":"proceedings-article"},"type":"conference-paper","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/A5078270488","display_name":"Blake G. Fitch","orcid":null},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Blake G. Fitch","raw_affiliation_strings":["IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038125184","display_name":"Aleksandr Rayshubskiy","orcid":"https://orcid.org/0009-0009-3139-7606"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aleksandr Rayshubskiy","raw_affiliation_strings":["IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101830455","display_name":"Maria Eleftheriou","orcid":"https://orcid.org/0000-0002-1842-5838"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maria Eleftheriou","raw_affiliation_strings":["IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103349848","display_name":"T. J. Christopher Ward","orcid":null},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. J. Christopher Ward","raw_affiliation_strings":["IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031192121","display_name":"Mark Giampapa","orcid":null},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Giampapa","raw_affiliation_strings":["IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082216809","display_name":"Michael C. Pitman","orcid":null},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael C. Pitman","raw_affiliation_strings":["IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058526411","display_name":"Robert S. Germain","orcid":null},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert S. Germain","raw_affiliation_strings":["IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Thomas J. Watson Research Center Yorktown Heights, NY#TAB#","institution_ids":["https://openalex.org/I1341412227"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I1341412227"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":52,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"87","last_page":"87"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.996999979019165,"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":0.996999979019165,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9940000176429749,"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/T12029","display_name":"DNA and Biological Computing","score":0.9936000108718872,"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/computer-science","display_name":"Computer science","score":0.44823169708251953},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.42981356382369995},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2421727180480957}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44823169708251953},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.42981356382369995},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2421727180480957},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1188455.1188547","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1188455.1188547","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2006 ACM/IEEE conference on Supercomputing  - SC '06","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W837249533","https://openalex.org/W1555540498","https://openalex.org/W1833612708","https://openalex.org/W1968458135","https://openalex.org/W1994549640","https://openalex.org/W2020346881","https://openalex.org/W2027223749","https://openalex.org/W2029564559","https://openalex.org/W2030119651","https://openalex.org/W2035720425","https://openalex.org/W2035854618","https://openalex.org/W2040809566","https://openalex.org/W2061388644","https://openalex.org/W2062446822","https://openalex.org/W2068944150","https://openalex.org/W2073059665","https://openalex.org/W2076455102","https://openalex.org/W2080131977","https://openalex.org/W2099933160","https://openalex.org/W2108354375","https://openalex.org/W2110435342","https://openalex.org/W2124035137","https://openalex.org/W2126667465","https://openalex.org/W2131025577","https://openalex.org/W2144803600","https://openalex.org/W2170321583","https://openalex.org/W2170396259","https://openalex.org/W2176300081","https://openalex.org/W3098444613","https://openalex.org/W3144368627"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2130043461","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"This":[0,17],"paper":[1],"describes":[2],"a":[3,73],"novel":[4],"spatial-force":[5],"decomposition":[6],"for":[7,10,29,36,124],"N-body":[8],"simulations":[9,97],"which":[11],"we":[12],"observe":[13],"O(sqrt(p))":[14],"communication":[15,82],"scaling.":[16],"has":[18,49,92],"enabled":[19,93],"Blue":[20,43,47,70],"Matter":[21,44,71],"to":[22,65,86],"approach":[23],"the":[24,126],"effective":[25],"limits":[26],"of":[27,55,121],"concurrency":[28],"molecular":[30],"dynamics":[31],"using":[32],"particle-mesh":[33],"(FFT-based)":[34],"methods":[35],"handling":[37],"electrostatic":[38],"interactions.":[39],"Using":[40],"this":[41],"decomposition,":[42],"running":[45],"on":[46,98,112],"Gene/L":[48],"achieved":[50,91],"simulation":[51],"rates":[52],"in":[53],"excess":[54],"1000":[56],"time":[57,107],"steps":[58],"per":[59,68],"second":[60],"and":[61],"demonstrated":[62],"significant":[63],"speed-ups":[64],"O(1)":[66],"atom":[67],"node.":[69],"employs":[72],"Communicating":[74],"Sequential":[75],"Process":[76],"(CSP)":[77],"style":[78],"model":[79],"with":[80],"application":[81],"state":[83],"machines":[84],"compiled":[85],"hardware":[87],"interfaces.":[88],"The":[89],"scalability":[90],"methodologically":[94],"rigorous":[95],"biomolecular":[96],"biologically":[99],"interesting":[100],"systems,":[101,114],"such":[102],"as":[103],"membrane-bound":[104],"proteins,":[105],"whose":[106],"scales":[108],"dwarf":[109],"previous":[110],"work":[111],"those":[113],"Major":[115],"scaling":[116],"improvements":[117],"will":[118],"require":[119],"exploration":[120],"alternative":[122],"algorithms":[123],"treating":[125],"long":[127],"range":[128],"electrostatics.":[129]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
