乐胖代购免代理版

{"id":"https://openalex.org/W2080474856","doi":"https://doi.org/10.1002/jcc.10196","title":"Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms","display_name":"Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms","publication_year":2002,"publication_date":"2002-12-06","ids":{"openalex":"https://openalex.org/W2080474856","doi":"https://doi.org/10.1002/jcc.10196","mag":"2080474856","pmid":"https://pubmed.ncbi.nlm.nih.gov/12483677"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.10196","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"journal-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/A5033583960","display_name":"Danny Barash","orcid":"https://orcid.org/0000-0003-4389-5302"},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Danny Barash","raw_affiliation_strings":["Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and Howard Hughes Medical Institute, 251 Mercer Street, New York, New York 10012, USA."],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and Howard Hughes Medical Institute, 251 Mercer Street, New York, New York 10012, USA.","institution_ids":["https://openalex.org/I36672615"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030780920","display_name":"Linjing Yang","orcid":"https://orcid.org/0000-0002-1297-4975"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]},{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Linjing Yang","raw_affiliation_strings":["Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and Howard Hughes Medical Institute, 251 Mercer Street, New York, New York 10012"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and Howard Hughes Medical Institute, 251 Mercer Street, New York, New York 10012","institution_ids":["https://openalex.org/I57206974","https://openalex.org/I1344073410","https://openalex.org/I36672615"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000359310","display_name":"Xiaoliang Qian","orcid":"https://orcid.org/0000-0002-4328-6411"},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]},{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1344073410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoliang Qian","raw_affiliation_strings":["Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and Howard Hughes Medical Institute, 251 Mercer Street, New York, New York 10012"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and Howard Hughes Medical Institute, 251 Mercer Street, New York, New York 10012","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974","https://openalex.org/I1344073410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046513501","display_name":"Tamar Schlick","orcid":"https://orcid.org/0000-0002-2392-2062"},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]},{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1344073410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tamar Schlick","raw_affiliation_strings":["Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and Howard Hughes Medical Institute, 251 Mercer Street, New York, New York 10012"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and Howard Hughes Medical Institute, 251 Mercer Street, New York, New York 10012","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974","https://openalex.org/I1344073410"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4840,"currency":"USD","value_usd":4840,"provenance":"doaj"},"apc_paid":null,"fwci":0.565,"has_fulltext":true,"fulltext_origin":"ngrams","cited_by_count":30,"citation_normalized_percentile":{"value":0.738988,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":89},"biblio":{"volume":"24","issue":"1","first_page":"77","last_page":"88"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9931,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9931,"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/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.9892,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.9838,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"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/verlet-integration","display_name":"Verlet integration","score":0.9020499},{"id":"https://openalex.org/keywords/langevin-dynamics","display_name":"Langevin dynamics","score":0.7302476},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6892694},{"id":"https://openalex.org/keywords/ewald-summation","display_name":"Ewald summation","score":0.41515192},{"id":"https://openalex.org/keywords/position","display_name":"Position (finance)","score":0.41144872}],"concepts":[{"id":"https://openalex.org/C45600393","wikidata":"https://www.wikidata.org/wiki/Q2984997","display_name":"Verlet integration","level":3,"score":0.9020499},{"id":"https://openalex.org/C2780004032","wikidata":"https://www.wikidata.org/wiki/Q6485978","display_name":"Langevin dynamics","level":2,"score":0.7302476},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6892694},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.66729355},{"id":"https://openalex.org/C79518650","wikidata":"https://www.wikidata.org/wiki/Q2081431","display_name":"Integrator","level":3,"score":0.66616875},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5599246},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4558564},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.4194724},{"id":"https://openalex.org/C143551052","wikidata":"https://www.wikidata.org/wiki/Q2426155","display_name":"Ewald summation","level":3,"score":0.41515192},{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.41144872},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.27576506},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.21175662},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.20944932},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.11845952},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.10994515},{"id":"https://openalex.org/C2776257435","wikidata":"https://www.wikidata.org/wiki/Q1576430","display_name":"Bandwidth (computing)","level":2,"score":0.09508738},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019951","descriptor_name":"DNA Polymerase beta","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019951","descriptor_name":"DNA Polymerase beta","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.10196","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12483677","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.82,"id":"https://metadata.un.org/sdg/7"}],"grants":[],"datasets":[],"versions":[],"referenced_works_count":52,"referenced_works":["https://openalex.org/W1566694705","https://openalex.org/W1970747580","https://openalex.org/W1977083651","https://openalex.org/W1991939674","https://openalex.org/W2005386550","https://openalex.org/W2005442221","https://openalex.org/W2006274376","https://openalex.org/W2015623296","https://openalex.org/W2017835622","https://openalex.org/W2019536189","https://openalex.org/W2020036580","https://openalex.org/W2021002797","https://openalex.org/W2025276235","https://openalex.org/W2032785002","https://openalex.org/W2035621643","https://openalex.org/W2035687084","https://openalex.org/W2039425860","https://openalex.org/W2041380982","https://openalex.org/W2051352867","https://openalex.org/W2057494243","https://openalex.org/W2058479011","https://openalex.org/W2062019978","https://openalex.org/W2067174909","https://openalex.org/W2075760680","https://openalex.org/W2081407528","https://openalex.org/W2083206954","https://openalex.org/W2085373032","https://openalex.org/W2091731899","https://openalex.org/W2093381148","https://openalex.org/W2095025461","https://openalex.org/W2103815459","https://openalex.org/W2104090745","https://openalex.org/W2104766043","https://openalex.org/W2109539263","https://openalex.org/W2111609734","https://openalex.org/W2111906305","https://openalex.org/W2117563175","https://openalex.org/W2121432651","https://openalex.org/W2123712613","https://openalex.org/W2127341056","https://openalex.org/W2137007076","https://openalex.org/W2151317657","https://openalex.org/W2166278492","https://openalex.org/W2170120409","https://openalex.org/W2250687410","https://openalex.org/W2323178299","https://openalex.org/W242446277","https://openalex.org/W2488677743","https://openalex.org/W2501078658","https://openalex.org/W2502764147","https://openalex.org/W2905826917","https://openalex.org/W4299790875"],"related_works":["https://openalex.org/W4386963729","https://openalex.org/W3106403548","https://openalex.org/W3102212431","https://openalex.org/W3098407907","https://openalex.org/W2888233795","https://openalex.org/W2190914950","https://openalex.org/W2083164919","https://openalex.org/W2080474856","https://openalex.org/W2035621643","https://openalex.org/W2015623296"],"abstract_inverted_index":{"Abstract":[0],"Multiple":[1],"time":[2,26,112,152,222,234,303],"step":[3,153],"(MTS)":[4],"algorithms":[5],"present":[6],"an":[7,50,278],"effective":[8,51],"integration":[9],"approach":[10],"to":[11,23,48,86,108,149,176,181,226,238,283,308,350],"reduce":[12],"the":[13,29,56,63,89,93,117,128,138,143,150,189,192,244,249,255,265,269,289,295,309,327,352],"computational":[14,35],"cost":[15],"of":[16,55,65,92,114,142,191,224,236,251,334],"dynamics":[17,311],"simulations.":[18],"By":[19],"using":[20,133,166],"force":[21,33],"splitting":[22],"allow":[24,348],"larger":[25],"steps":[27,113,223,235],"for":[28,72,169,217,344],"more":[30],"slowly":[31],"varying":[32],"components,":[34],"savings":[36],"can":[37,214],"be":[38,215,261,322],"realized.":[39],"The":[40,120],"Particle\u2010Mesh\u2010Ewald":[41],"(PME)":[42],"method":[43],"has":[44],"been":[45],"independently":[46],"devised":[47],"provide":[49],"and":[52,140,172,211,229,274,304],"efficient":[53],"treatment":[54],"long\u2010range":[57],"electrostatics":[58,346],"interactions.":[59],"Here":[60],"we":[61,242,314],"examine":[62,188],"performance":[64,148,190],"a":[66,75,195],"combined":[67],"MTS/PME":[68,122],"algorithm":[69,193],"previously":[70],"developed":[71,121],"AMBER":[73,160],"on":[74,194,268],"large":[76],"polymerase":[77],"\u03b2/DNA":[78],"complex":[79],"containing":[80],"40,673":[81],"atoms.":[82],"Our":[83],"goal":[84],"is":[85,277],"carefully":[87],"combine":[88],"robust":[90],"features":[91],"Langevin/MTS":[94],"(LN)":[95],"methodology":[96],"implemented":[97],"in":[98,159,294,302],"CHARMM\u2014which":[99],"uses":[100],"position":[101],"rather":[102],"than":[103,342],"velocity":[104],"Verlet":[105,155],"with":[106,203,220,232],"stochasticity":[107],"make":[109],"possible":[110],"outer":[111,221,233,271],"150":[115],"fs\u2014with":[116],"PME":[118,256,319,328,343],"formulation.":[119],"integrator":[123,156],"removes":[124],"fast":[125,345],"terms":[126],"from":[127,288,355],"reciprocal\u2010space":[129,296],"Ewald":[130],"component":[131],"by":[132,146,161,248,325],"switch":[134],"functions.":[135],"We":[136,186,337],"analyze":[137],"advantages":[139,354],"limitations":[141,246],"resulting":[144],"scheme":[145],"comparing":[147],"single":[151],"leapfrog":[154],"currently":[157],"used":[158],"evaluating":[162],"different":[163],"time\u2010step":[164,272],"protocols":[165,219,231],"three":[167],"assessors":[168],"accuracy,":[170],"speedup,":[171,276],"stability,":[173],"all":[174],"applied":[175],"long":[177],"(i.e.,":[178],"nanosecond)":[179],"simulations":[180],"ensure":[182],"proper":[183],"energy":[184,209],"conservation.":[185],"also":[187],"parallel,":[196],"distributed":[197],"shared\u2010memory":[198],"computer":[199],"(SGI":[200],"Origin":[201],"2000":[202],"8":[204,227],"300\u2010MHz":[205],"R12000":[206],"processors).":[207],"Good":[208],"conservation":[210],"stability":[212],"behavior":[213],"demonstrated,":[216],"Newtonian":[218],"up":[225,237],"fs":[228],"Langevin":[230],"16":[239],"fs.":[240],"Still,":[241],"emphasize":[243],"inherent":[245,282],"imposed":[247],"incorporation":[250],"MTS":[252,356],"methods":[253,340],"into":[254],"formulation":[257],"that":[258,316,339],"may":[259,347],"not":[260],"widely":[262],"appreciated.":[263],"Namely,":[264],"limiting":[266],"factor":[267],"largest":[270],"size,":[273],"hence":[275],"intramolecular":[279],"cancellation":[280,299],"error":[281,286,300,320],"PME.":[284],"This":[285,298],"stems":[287],"excluded\u2010nonbonded":[290],"correction":[291],"term":[292],"contained":[293],"component.":[297],"varies":[301],"introduces":[305],"artificial":[306],"frequencies":[307],"governing":[310],"motion.":[312],"Unfortunately,":[313],"find":[315],"this":[317],"numerical":[318],"cannot":[321],"easily":[323],"eliminated":[324],"refining":[326],"parameters":[329],"(grid":[330],"resolution":[331],"and/or":[332],"order":[333],"interpolating":[335],"polynomial).":[336],"suggest":[338],"other":[341],"users":[349],"reap":[351],"full":[353],"algorithms.":[357],"\u00a9":[358],"2003":[359,368],"Wiley":[360],"Periodicals,":[361],"Inc.":[362],"J":[363],"Comput":[364],"Chem":[365],"24:":[366],"77\u201388,":[367]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2080474856","counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2024-12-11T01:35:50.868820","created_date":"2016-06-24"}