{"id":"https://openalex.org/W2904990417","doi":"https://doi.org/10.1021/acs.jcim.8b00761","title":"Robustness and Efficiency of Poisson\u2013Boltzmann Modeling on Graphics Processing Units","display_name":"Robustness and Efficiency of Poisson\u2013Boltzmann Modeling on Graphics Processing Units","publication_year":2018,"publication_date":"2018-12-14","ids":{"openalex":"https://openalex.org/W2904990417","doi":"https://doi.org/10.1021/acs.jcim.8b00761","mag":"2904990417","pmid":"https://pubmed.ncbi.nlm.nih.gov/30550277"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.8b00761","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00761","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5012214235","display_name":"Ruxi Qi","orcid":"https://orcid.org/0000-0002-9243-1259"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ruxi Qi","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States"],"raw_orcid":"https://orcid.org/0000-0002-9243-1259","affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032088629","display_name":"Ray Luo","orcid":"https://orcid.org/0000-0002-6346-8271"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ray Luo","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry,\u00a0 Department of Chemical Engineering and Materials Science \u00a0and\u00a0 Department of Biomedical Engineering, University of California, Irvine, California 92697, United States"],"raw_orcid":"https://orcid.org/0000-0002-6346-8271","affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry,\u00a0 Department of Chemical Engineering and Materials Science \u00a0and\u00a0 Department of Biomedical Engineering, University of California, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5012214235","https://openalex.org/A5032088629"],"corresponding_institution_ids":["https://openalex.org/I204250578"],"apc_list":null,"apc_paid":null,"fwci":1.1846,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.8495332,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"59","issue":"1","first_page":"409","last_page":"420"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10320","display_name":"Neural Networks and Applications","score":0.9811000227928162,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10320","display_name":"Neural Networks and Applications","score":0.9811000227928162,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T13650","display_name":"Computational Physics and Python Applications","score":0.9599000215530396,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10591","display_name":"Theoretical and Computational Physics","score":0.935699999332428,"subfield":{"id":"https://openalex.org/subfields/3104","display_name":"Condensed Matter Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.7221543788909912},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.6968086361885071},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6108253002166748},{"id":"https://openalex.org/keywords/poisson\u2013boltzmann-equation","display_name":"Poisson\u2013Boltzmann equation","score":0.5500954985618591},{"id":"https://openalex.org/keywords/poisson-distribution","display_name":"Poisson distribution","score":0.5052910447120667},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.45423904061317444},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4074547588825226},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3943847715854645},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2435951828956604},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.19955390691757202},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.14598748087882996}],"concepts":[{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.7221543788909912},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.6968086361885071},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6108253002166748},{"id":"https://openalex.org/C109757611","wikidata":"https://www.wikidata.org/wiki/Q901009","display_name":"Poisson\u2013Boltzmann equation","level":3,"score":0.5500954985618591},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.5052910447120667},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.45423904061317444},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4074547588825226},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3943847715854645},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2435951828956604},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.19955390691757202},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.14598748087882996},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016012","descriptor_name":"Poisson Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016012","descriptor_name":"Poisson Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016012","descriptor_name":"Poisson Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.8b00761","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00761","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:30550277","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30550277","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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt9bt2m8ps","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/9bt2m8ps","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, vol 59, iss 1","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5926775","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6430105","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.6600000262260437}],"awards":[{"id":"https://openalex.org/G1337535711","display_name":null,"funder_award_id":"GM093040","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8759326567","display_name":null,"funder_award_id":"GM079383","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"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":158,"referenced_works":["https://openalex.org/W53817057","https://openalex.org/W95860189","https://openalex.org/W122715520","https://openalex.org/W330835420","https://openalex.org/W769759530","https://openalex.org/W993820914","https://openalex.org/W1862644536","https://openalex.org/W1902949370","https://openalex.org/W1964614899","https://openalex.org/W1967468998","https://openalex.org/W1968984443","https://openalex.org/W1968997586","https://openalex.org/W1969912980","https://openalex.org/W1970036918","https://openalex.org/W1973060079","https://openalex.org/W1973819621","https://openalex.org/W1975289752","https://openalex.org/W1975580333","https://openalex.org/W1978291408","https://openalex.org/W1978330227","https://openalex.org/W1979891593","https://openalex.org/W1984223438","https://openalex.org/W1984738107","https://openalex.org/W1986899369","https://openalex.org/W1987354604","https://openalex.org/W1994662101","https://openalex.org/W1994737524","https://openalex.org/W1995204277","https://openalex.org/W1995842153","https://openalex.org/W1997240546","https://openalex.org/W1997542937","https://openalex.org/W1998208404","https://openalex.org/W1998461805","https://openalex.org/W1999072167","https://openalex.org/W1999245179","https://openalex.org/W2000613080","https://openalex.org/W2004145462","https://openalex.org/W2004822259","https://openalex.org/W2005040897","https://openalex.org/W2007095477","https://openalex.org/W2007258535","https://openalex.org/W2007965478","https://openalex.org/W2008015300","https://openalex.org/W2008246496","https://openalex.org/W2009250131","https://openalex.org/W2014511343","https://openalex.org/W2016168728","https://openalex.org/W2016494318","https://openalex.org/W2020613906","https://openalex.org/W2021534482","https://openalex.org/W2025694445","https://openalex.org/W2026467865","https://openalex.org/W2028031397","https://openalex.org/W2029582401","https://openalex.org/W2029615301","https://openalex.org/W2029788853","https://openalex.org/W2033231433","https://openalex.org/W2034615763","https://openalex.org/W2035629195","https://openalex.org/W2036011280","https://openalex.org/W2036766784","https://openalex.org/W2036856453","https://openalex.org/W2039665613","https://openalex.org/W2039833566","https://openalex.org/W2040530457","https://openalex.org/W2041113042","https://openalex.org/W2041248383","https://openalex.org/W2044701646","https://openalex.org/W2045367749","https://openalex.org/W2048574808","https://openalex.org/W2048744137","https://openalex.org/W2048931055","https://openalex.org/W2050397044","https://openalex.org/W2056070858","https://openalex.org/W2056940848","https://openalex.org/W2057664120","https://openalex.org/W2060098509","https://openalex.org/W2060304556","https://openalex.org/W2060815747","https://openalex.org/W2062056446","https://openalex.org/W2062224822","https://openalex.org/W2063292547","https://openalex.org/W2064388657","https://openalex.org/W2064709968","https://openalex.org/W2066126934","https://openalex.org/W2067525890","https://openalex.org/W2068465600","https://openalex.org/W2070126787","https://openalex.org/W2073146967","https://openalex.org/W2074674539","https://openalex.org/W2075662564","https://openalex.org/W2076057716","https://openalex.org/W2081588627","https://openalex.org/W2082127026","https://openalex.org/W2083665636","https://openalex.org/W2085813531","https://openalex.org/W2087586438","https://openalex.org/W2088652291","https://openalex.org/W2090716237","https://openalex.org/W2091916224","https://openalex.org/W2092422214","https://openalex.org/W2093469889","https://openalex.org/W2095460759","https://openalex.org/W2095474273","https://openalex.org/W2101406819","https://openalex.org/W2102514286","https://openalex.org/W2106560147","https://openalex.org/W2107499603","https://openalex.org/W2110659779","https://openalex.org/W2112855704","https://openalex.org/W2114634948","https://openalex.org/W2122199548","https://openalex.org/W2123382909","https://openalex.org/W2125323855","https://openalex.org/W2125531202","https://openalex.org/W2127116852","https://openalex.org/W2133520776","https://openalex.org/W2133543883","https://openalex.org/W2134413226","https://openalex.org/W2134544924","https://openalex.org/W2140387994","https://openalex.org/W2144272974","https://openalex.org/W2145803858","https://openalex.org/W2145899756","https://openalex.org/W2146177233","https://openalex.org/W2148147555","https://openalex.org/W2149537211","https://openalex.org/W2150785142","https://openalex.org/W2152160921","https://openalex.org/W2155417823","https://openalex.org/W2156777159","https://openalex.org/W2157281740","https://openalex.org/W2160983486","https://openalex.org/W2161288709","https://openalex.org/W2163906551","https://openalex.org/W2165759309","https://openalex.org/W2313116527","https://openalex.org/W2314622687","https://openalex.org/W2329374371","https://openalex.org/W2407746632","https://openalex.org/W2443006538","https://openalex.org/W2498157954","https://openalex.org/W2515356632","https://openalex.org/W2555103584","https://openalex.org/W2559754635","https://openalex.org/W2577894816","https://openalex.org/W2606184670","https://openalex.org/W2609229915","https://openalex.org/W2768823327","https://openalex.org/W2783351753","https://openalex.org/W2792856911","https://openalex.org/W2795498385","https://openalex.org/W2891791233","https://openalex.org/W2951985956","https://openalex.org/W2963106000","https://openalex.org/W2997945685","https://openalex.org/W3021550876","https://openalex.org/W4247600657"],"related_works":["https://openalex.org/W1488915263","https://openalex.org/W2770593030","https://openalex.org/W1995993799","https://openalex.org/W3154990682","https://openalex.org/W2560201613","https://openalex.org/W2077799587","https://openalex.org/W2913945979","https://openalex.org/W2171975302","https://openalex.org/W2022352247","https://openalex.org/W4301806107"],"abstract_inverted_index":{"Poisson-Boltzmann":[0],"equation":[1],"(PBE)":[2],"based":[3],"continuum":[4],"electrostatics":[5],"models":[6],"have":[7,43,107],"been":[8,44,95,108],"widely":[9],"used":[10,191],"in":[11,15,19,31,138],"modeling":[12,57],"electrostatic":[13],"interactions":[14],"biochemical":[16],"processes,":[17],"particularly":[18],"estimating":[20],"protein-ligand":[21],"binding":[22,32],"affinities.":[23],"Fast":[24],"convergence":[25,74],"of":[26,58,78,147,163,222,239],"PBE":[27,48,228],"solvers":[28,49,185],"is":[29,116,122,172,190],"crucial":[30],"affinity":[33],"computations":[34],"as":[35,120,136],"numerous":[36],"snapshots":[37],"need":[38],"to":[39,46,97,199,213],"be":[40,98],"processed.":[41],"Efforts":[42],"reported":[45,109],"develop":[47],"on":[50,102,113,129,149,165,242],"graphics":[51],"processing":[52],"units":[53],"(GPUs)":[54],"for":[55,84,110,179,192,236],"efficient":[56],"biomolecules,":[59],"though":[60,104],"only":[61],"relatively":[62],"simple":[63],"successive":[64],"over-relaxation":[65],"and":[66,127,145,159,182,202,208,224],"conjugate":[67,209],"gradient":[68],"methods":[69,81,134],"were":[70],"implemented.":[71],"However,":[72],"neither":[73],"nor":[75],"scaling":[76],"properties":[77],"the":[79,88,187,233,243],"two":[80],"are":[82,151],"optimal":[83,100],"large":[85],"biomolecules.":[86,194],"On":[87],"other":[89,183],"hand,":[90],"geometric":[91],"multigrid":[92],"(MG)":[93],"has":[94],"shown":[96],"an":[99,157],"solver":[101,217,229],"CPUs,":[103],"no":[105],"MG":[106,148,164,181],"biomolecular":[111,240],"applications":[112,241],"GPUs.":[114,166],"This":[115],"not":[117],"a":[118,123,160,173,214,219,237],"surprise":[119],"it":[121],"more":[124,174],"complex":[125,193],"method":[126],"depends":[128],"simpler":[130],"but":[131],"limited":[132],"iterative":[133],"such":[135],"Gauss-Seidel":[137],"its":[139],"core":[140],"relaxation":[141],"procedure.":[142],"The":[143,226],"robustness":[144,171,201],"efficiency":[146,178,203,207,223],"GPUs":[150],"also":[152],"unclear.":[153],"Here":[154],"we":[155],"present":[156],"implementation":[158],"thorough":[161],"analysis":[162,168],"Our":[167],"shows":[169],"that":[170],"pronounced":[175],"issue":[176],"than":[177],"both":[180],"tested":[184],"when":[186],"single":[188],"precision":[189],"We":[195],"further":[196],"show":[197],"how":[198],"balance":[200,221],"utilizing":[204],"MG's":[205],"overall":[206],"gradient's":[210],"robustness,":[211],"pointing":[212],"hybrid":[215],"GPU":[216,244],"with":[218],"good":[220],"accuracy.":[225],"new":[227],"will":[230],"significantly":[231],"improve":[232],"computational":[234],"throughput":[235],"range":[238],"platforms.":[245]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2018-12-22T00:00:00"}
