{"id":"https://openalex.org/W2018856948","doi":"https://doi.org/10.1109/eit.2012.6220776","title":"Developing new parallelization techniques for emerging HPC architectures and life science applications","display_name":"Developing new parallelization techniques for emerging HPC architectures and life science applications","publication_year":2012,"publication_date":"2012-05-01","ids":{"openalex":"https://openalex.org/W2018856948","doi":"https://doi.org/10.1109/eit.2012.6220776","mag":"2018856948"},"language":"en","primary_location":{"id":"doi:10.1109/eit.2012.6220776","is_oa":false,"landing_page_url":"https://doi.org/10.1109/eit.2012.6220776","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Electro/Information Technology","raw_type":"proceedings-article"},"type":"article","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/A5088249794","display_name":"Hai Tao Sun","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":"Hai Tao Sun","raw_affiliation_strings":["IBM, Corporation, Rochester, MN, USA","IBM Corporation, Building 30-2, 3605 Highway N, Rochester, MN 55901 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM, Corporation, Rochester, MN, USA","institution_ids":["https://openalex.org/I1341412227"]},{"raw_affiliation_string":"IBM Corporation, Building 30-2, 3605 Highway N, Rochester, MN 55901 USA","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010953826","display_name":"Michael Yu Sun","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 Yu Sun","raw_affiliation_strings":["IBM, Corporation, Rochester, MN, USA","IBM Corporation, Building 30-2, 3605 Highway N, Rochester, MN 55901 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM, Corporation, Rochester, MN, USA","institution_ids":["https://openalex.org/I1341412227"]},{"raw_affiliation_string":"IBM Corporation, Building 30-2, 3605 Highway N, Rochester, MN 55901 USA","institution_ids":["https://openalex.org/I1341412227"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07836599,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"444","issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9779000282287598,"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":0.9779000282287598,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.973800003528595,"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"}},{"id":"https://openalex.org/T10913","display_name":"Molecular Junctions and Nanostructures","score":0.9714000225067139,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8062914609909058},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6599977612495422},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.616856038570404},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5663741230964661},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.4965558648109436},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4194008708000183},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3685608506202698},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3446239233016968},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.320197194814682},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20009845495224},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13238787651062012}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8062914609909058},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6599977612495422},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.616856038570404},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5663741230964661},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.4965558648109436},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4194008708000183},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3685608506202698},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3446239233016968},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.320197194814682},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20009845495224},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13238787651062012},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/eit.2012.6220776","is_oa":false,"landing_page_url":"https://doi.org/10.1109/eit.2012.6220776","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Electro/Information Technology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.44999998807907104,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W565139703","https://openalex.org/W1813030236","https://openalex.org/W1948976984","https://openalex.org/W1984140920","https://openalex.org/W1987130539","https://openalex.org/W1995289651","https://openalex.org/W2020346881","https://openalex.org/W2042870122","https://openalex.org/W2089401955","https://openalex.org/W2090673788","https://openalex.org/W2102481025","https://openalex.org/W2110574506","https://openalex.org/W2111633287","https://openalex.org/W2119043921","https://openalex.org/W2170396259","https://openalex.org/W2260133378","https://openalex.org/W4238826819"],"related_works":["https://openalex.org/W2384867379","https://openalex.org/W4400094300","https://openalex.org/W2329539859","https://openalex.org/W2227905990","https://openalex.org/W2765823764","https://openalex.org/W3214280620","https://openalex.org/W3191490922","https://openalex.org/W1582436825","https://openalex.org/W1996803181","https://openalex.org/W2979588510"],"abstract_inverted_index":{"Parallelization":[0],"of":[1,184,226],"chemistry":[2,49],"and":[3,50,82,121,138],"drug":[4,51],"discovery":[5,52],"codes":[6],"to":[7,28,31,46,57,158,167,182],"leverage":[8],"emerging":[9],"High-Performance":[10],"Computing":[11],"(HPC)":[12],"architectures":[13],"is":[14,20,24,55,94,165],"a":[15,21,86,95,115,168,205,215,223],"difficult":[16],"task.":[17],"However,":[18],"it":[19,54],"task":[22],"that":[23,65,97],"required":[25],"for":[26,73,117,197,240],"one":[27],"be":[29],"able":[30],"simulate":[32],"biologically":[33],"important":[34,56],"molecular":[35,74],"systems":[36],"which":[37,93],"are":[38,130,141,151,172,202,212,228,236],"not":[39],"accessible":[40],"with":[41],"current":[42],"technology.":[43],"In":[44,76,146,177,220],"addition":[45],"parallelizing":[47,85],"existing":[48],"codes,":[53],"explore":[58],"at":[59],"the":[60,111,159,163,170,190,194],"same":[61],"time":[62],"new":[63,87],"methodologies":[64],"address":[66],"limitations":[67,100],"in":[68,101,189],"methods":[69,156],"currently":[70],"being":[71],"used":[72,237],"simulations.":[75],"this":[77,147],"study":[78],"we":[79,180],"combine":[80],"speed":[81],"accuracy":[83],"by":[84,132,143,214],"promising":[88],"explicit":[89,105],"polarization":[90,106],"(X-Pol)":[91,107],"method,":[92,108,137],"method":[96,116,164,192,222],"addresses":[98],"several":[99],"today's":[102],"methodologies.":[103],"The":[104,199],"also":[109],"called":[110],"X-Pol":[112,191],"potential,":[113],"provides":[114],"treating":[118],"both":[119],"bonded":[120],"nonbonded":[122,139],"interactions":[123,129,140],"using":[124,153],"electronic":[125,144,154],"structure":[126,155],"theory.":[127],"Bonded":[128],"treated":[131,142],"an":[133],"iterative":[134],"self-consistent":[135],"field":[136],"embedding.":[145],"approach":[148],"partial":[149],"charges":[150],"obtained":[152],"applied":[157,166],"individual":[160],"fragments.":[161,242],"When":[162],"protein,":[169],"fragments":[171,186,201,227],"defined":[173,188],"as":[174,187,193],"peptide":[175,185,200],"units.":[176],"our":[178,221],"research":[179],"intend":[181],"use":[183],"basic":[195],"units":[196],"parallelization.":[198],"mapped":[203],"onto":[204],"HPC":[206],"hybrid":[207],"architecture":[208],"where":[209],"shared-memory":[210,231],"processors":[211,239],"interconnected":[213],"customized":[216],"or":[217],"standard":[218],"network.":[219],"pre-selected":[224],"number":[225],"parallelized":[229],"via":[230],"algorithms,":[232],"while":[233],"message-passing":[234],"algorithms":[235],"across":[238],"neighboring":[241]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
