{"id":"https://openalex.org/W1969326610","doi":"https://doi.org/10.1145/2506583.2506649","title":"GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly","display_name":"GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly","publication_year":2013,"publication_date":"2013-09-22","ids":{"openalex":"https://openalex.org/W1969326610","doi":"https://doi.org/10.1145/2506583.2506649","mag":"1969326610"},"language":"en","primary_location":{"id":"doi:10.1145/2506583.2506649","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506649","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","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/A5102247139","display_name":"Andrew J. Proctor","orcid":null},"institutions":[{"id":"https://openalex.org/I47251452","display_name":"Wake Forest University","ror":"https://ror.org/0207ad724","country_code":"US","type":"education","lineage":["https://openalex.org/I47251452"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew J. Proctor","raw_affiliation_strings":["Wake Forest University, Department of Computer Science, 1834 Wake Forest Road, Winston-Salem, NC 27109"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wake Forest University, Department of Computer Science, 1834 Wake Forest Road, Winston-Salem, NC 27109","institution_ids":["https://openalex.org/I47251452"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023419929","display_name":"Cody A. Stevens","orcid":"https://orcid.org/0009-0008-6587-838X"},"institutions":[{"id":"https://openalex.org/I47251452","display_name":"Wake Forest University","ror":"https://ror.org/0207ad724","country_code":"US","type":"education","lineage":["https://openalex.org/I47251452"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cody A. Stevens","raw_affiliation_strings":["Wake Forest University, Department of Computer Science, 1834 Wake Forest Road, Winston-Salem, NC 27109"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wake Forest University, Department of Computer Science, 1834 Wake Forest Road, Winston-Salem, NC 27109","institution_ids":["https://openalex.org/I47251452"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039599790","display_name":"Samuel S. Cho","orcid":"https://orcid.org/0000-0002-6113-135X"},"institutions":[{"id":"https://openalex.org/I47251452","display_name":"Wake Forest University","ror":"https://ror.org/0207ad724","country_code":"US","type":"education","lineage":["https://openalex.org/I47251452"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel S. Cho","raw_affiliation_strings":["Wake Forest University, Departments of Physics and Computer Science, 1834 Wake Forest Road, Winston-Salem, NC 27109","Wake Forest University, Departments of Physics and Computer Science, 1834 Wake Forest Road, Winston-Salem, NC 27109#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wake Forest University, Departments of Physics and Computer Science, 1834 Wake Forest Road, Winston-Salem, NC 27109","institution_ids":["https://openalex.org/I47251452"]},{"raw_affiliation_string":"Wake Forest University, Departments of Physics and Computer Science, 1834 Wake Forest Road, Winston-Salem, NC 27109#TAB#","institution_ids":["https://openalex.org/I47251452"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I47251452"],"apc_list":null,"apc_paid":null,"fwci":0.8978,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.73141597,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"633","last_page":"640"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9983000159263611,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9983000159263611,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976000189781189,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.989300012588501,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.8103823661804199},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7660101652145386},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5827046036720276},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5469165444374084},{"id":"https://openalex.org/keywords/rendering","display_name":"Rendering (computer graphics)","score":0.5213543176651001},{"id":"https://openalex.org/keywords/k-nearest-neighbors-algorithm","display_name":"k-nearest neighbors algorithm","score":0.48645350337028503},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.47832322120666504},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.4635419547557831},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.4320657253265381},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.41179609298706055},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.19486871361732483},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.14340618252754211},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10946634411811829}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.8103823661804199},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7660101652145386},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5827046036720276},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5469165444374084},{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.5213543176651001},{"id":"https://openalex.org/C113238511","wikidata":"https://www.wikidata.org/wiki/Q1071612","display_name":"k-nearest neighbors algorithm","level":2,"score":0.48645350337028503},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.47832322120666504},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4635419547557831},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.4320657253265381},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.41179609298706055},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.19486871361732483},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.14340618252754211},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10946634411811829},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2506583.2506649","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506649","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309558","display_name":"Wake Forest University","ror":"https://ror.org/0207ad724"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1762731526","https://openalex.org/W1979761607","https://openalex.org/W1983728565","https://openalex.org/W1994549640","https://openalex.org/W2002930710","https://openalex.org/W2004822259","https://openalex.org/W2025040605","https://openalex.org/W2035041418","https://openalex.org/W2038164789","https://openalex.org/W2041902442","https://openalex.org/W2065864578","https://openalex.org/W2065963893","https://openalex.org/W2071779674","https://openalex.org/W2078391824","https://openalex.org/W2144836482","https://openalex.org/W2147265244","https://openalex.org/W2147396853","https://openalex.org/W2257916762","https://openalex.org/W2323178299","https://openalex.org/W2963471463"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2013643406","https://openalex.org/W2027972911","https://openalex.org/W2157978810","https://openalex.org/W2597809628","https://openalex.org/W3046370962"],"abstract_inverted_index":{"Molecular":[0],"dynamics":[1],"(MD)":[2],"simulations":[3,29,124],"provide":[4],"a":[5,76,97,139,148,177],"molecular-resolution":[6],"view":[7],"of":[8,18,27,63,105,125,176],"biomolecular":[9],"folding":[10],"and":[11,25,54,87,161],"assembly":[12],"processes,":[13],"but":[14],"the":[15,19,23,28,61,68,103,126,157,162],"computational":[16],"demands":[17],"underlying":[20],"algorithms":[21,65],"limit":[22],"lenth-":[24],"time-scales":[26],"one":[30],"can":[31],"perform.":[32],"Recently,":[33],"graphics":[34],"processing":[35],"units":[36],"(GPUs),":[37],"specialized":[38],"devices":[39],"that":[40,121,153],"were":[41],"originally":[42],"designed":[43],"for":[44,50,82,113,122],"rendering":[45],"images,":[46],"have":[47,56],"been":[48,57],"repurposed":[49],"high":[51],"performance":[52],"computing,":[53],"there":[55],"significant":[58],"increases":[59],"in":[60,70],"performances":[62],"parallel":[64,78,179],"such":[66],"as":[67,136,138,170],"ones":[69],"MD":[71,85,123],"simulations.":[72],"Previously,":[73],"we":[74,88,146],"implemented":[75],"GPU-optimized":[77,131,178],"neighbor":[79,159,180],"list":[80,151,160,181],"algorithm":[81,152],"our":[83,130,143,173],"coarsegrained":[84],"simulations,":[86],"observed":[89],"an":[90],"N-dependent":[91],"speed-up":[92],"(or":[93],"speed-down)":[94],"compared":[95,171],"to":[96,172],"CPU-optimized":[98,140],"algorithm,":[99],"where":[100],"N":[101],"is":[102],"number":[104],"interacting":[106],"beads":[107],"representing":[108],"amino":[109],"acids":[110],"or":[111,115],"nucleotides":[112],"proteins":[114],"RNAs,":[116],"respectively.":[117],"We":[118,165],"had":[119],"demonstrated":[120],"70s":[127],"ribosome":[128],"(N=10,219),":[129],"code":[132],"was":[133],"about":[134,167],"30x":[135],"fast":[137],"version.":[141],"In":[142],"present":[144],"study,":[145],"implement":[147],"hybrid":[149],"neighbor/cell":[150],"borrows":[154],"components":[155],"from":[156],"well-known":[158],"cell-list":[163],"algorithms.":[164],"observe":[166],"10%":[168],"speedup":[169],"previous":[174],"implementation":[175],"algorithm.":[182]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":2}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}
