{"id":"https://openalex.org/W2150645921","doi":"https://doi.org/10.1145/2382936.2383039","title":"Simulation and study of large-scale bacteria-materials interactions via BioScape enabled by GPUs","display_name":"Simulation and study of large-scale bacteria-materials interactions via BioScape enabled by GPUs","publication_year":2012,"publication_date":"2012-10-07","ids":{"openalex":"https://openalex.org/W2150645921","doi":"https://doi.org/10.1145/2382936.2383039","mag":"2150645921"},"language":"en","primary_location":{"id":"doi:10.1145/2382936.2383039","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2382936.2383039","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","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/A5100428147","display_name":"Jie Li","orcid":"https://orcid.org/0000-0001-5196-2136"},"institutions":[{"id":"https://openalex.org/I108468826","display_name":"Stevens Institute of Technology","ror":"https://ror.org/02z43xh36","country_code":"US","type":"education","lineage":["https://openalex.org/I108468826"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jie Li","raw_affiliation_strings":["Stevens Institute of Technology, Hoboken, NJ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stevens Institute of Technology, Hoboken, NJ","institution_ids":["https://openalex.org/I108468826"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111534073","display_name":"Vishakha Sharma","orcid":null},"institutions":[{"id":"https://openalex.org/I108468826","display_name":"Stevens Institute of Technology","ror":"https://ror.org/02z43xh36","country_code":"US","type":"education","lineage":["https://openalex.org/I108468826"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vishakha Sharma","raw_affiliation_strings":["Stevens Institute of Technology, Hoboken, NJ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stevens Institute of Technology, Hoboken, NJ","institution_ids":["https://openalex.org/I108468826"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081065290","display_name":"Narayan Ganesan","orcid":null},"institutions":[{"id":"https://openalex.org/I108468826","display_name":"Stevens Institute of Technology","ror":"https://ror.org/02z43xh36","country_code":"US","type":"education","lineage":["https://openalex.org/I108468826"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Narayan Ganesan","raw_affiliation_strings":["Stevens Institute of Technology, Hoboken, NJ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stevens Institute of Technology, Hoboken, NJ","institution_ids":["https://openalex.org/I108468826"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014810005","display_name":"Adriana Compagnoni","orcid":null},"institutions":[{"id":"https://openalex.org/I108468826","display_name":"Stevens Institute of Technology","ror":"https://ror.org/02z43xh36","country_code":"US","type":"education","lineage":["https://openalex.org/I108468826"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adriana Compagnoni","raw_affiliation_strings":["Stevens Institute of Technology, Hoboken, NJ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stevens Institute of Technology, Hoboken, NJ","institution_ids":["https://openalex.org/I108468826"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I108468826"],"apc_list":null,"apc_paid":null,"fwci":2.8613,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.9054836,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"13","issue":null,"first_page":"610","last_page":"612"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9941999912261963,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9941999912261963,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9728999733924866,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9682000279426575,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.7903405427932739},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.6565890312194824},{"id":"https://openalex.org/keywords/modeling-and-simulation","display_name":"Modeling and simulation","score":0.4709746837615967},{"id":"https://openalex.org/keywords/complex-system","display_name":"Complex system","score":0.4482003152370453},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.4244816303253174},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4103383421897888},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3605543375015259},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23406484723091125},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.21075931191444397},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.15796136856079102}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7903405427932739},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.6565890312194824},{"id":"https://openalex.org/C167343916","wikidata":"https://www.wikidata.org/wiki/Q6888384","display_name":"Modeling and simulation","level":2,"score":0.4709746837615967},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.4482003152370453},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.4244816303253174},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4103383421897888},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3605543375015259},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23406484723091125},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.21075931191444397},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.15796136856079102},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2382936.2383039","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2382936.2383039","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.6399999856948853}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1604257679","https://openalex.org/W1977168590","https://openalex.org/W2077844926","https://openalex.org/W2124677924","https://openalex.org/W2134224856","https://openalex.org/W2136626795","https://openalex.org/W2155418451","https://openalex.org/W2161575244","https://openalex.org/W2323178299","https://openalex.org/W2989448192","https://openalex.org/W3151409487","https://openalex.org/W6812650097"],"related_works":["https://openalex.org/W2167527468","https://openalex.org/W2586370661","https://openalex.org/W2314053740","https://openalex.org/W2960681633","https://openalex.org/W1970113381","https://openalex.org/W1985494319","https://openalex.org/W2471557603","https://openalex.org/W2526574107","https://openalex.org/W2046625759","https://openalex.org/W2378208906"],"abstract_inverted_index":{"Biological":[0],"systems":[1,18],"encompass":[2],"complexity":[3],"that":[4],"far":[5],"surpasses":[6],"many":[7],"artificial":[8],"systems.":[9],"Modeling":[10],"and":[11,15,87,98,126],"simulation":[12,29,88],"of":[13,69],"large":[14],"complex":[16],"biological":[17,49,96,116],"is":[19,75],"a":[20,26,32,76,111],"computationally":[21],"intensive":[22],"challenge.":[23],"We":[24,51],"present":[25,53],"GPU":[27],"based":[28],"framework":[30,57,89,108],"in":[31,35,44,94],"reactive":[33],"environment":[34],"3D":[36],"space,":[37],"along":[38],"with":[39],"the":[40,60,64,70,130],"modeling":[41,86,121],"language,":[42],"BioScape,":[43],"order":[45],"to":[46,58,100,119],"describe":[47],"various":[48,115],"processes.":[50],"also":[52],"an":[54],"efficient":[55],"computational":[56,107],"study":[59],"interactions":[61],"enabled":[62],"by":[63],"massively":[65],"parallel":[66],"processing":[67],"capability":[68],"GPUs.":[71],"Our":[72],"driving":[73],"example":[74],"bio-triggered":[77],"drug":[78],"delivery":[79],"system":[80],"for":[81],"infection-resistant":[82],"medical":[83],"implants.":[84],"The":[85,106],"presented":[90],"here":[91],"will":[92,109],"help":[93,127],"identifying":[95],"targets":[97],"materials":[99],"treat":[101],"biomaterials":[102],"associated":[103],"bacterial":[104],"infections.":[105],"offer":[110],"deeper":[112],"insight":[113],"into":[114],"processes":[117],"compared":[118],"traditional":[120],"via":[122],"implicit":[123],"differential":[124],"equations,":[125],"us":[128],"observe":[129],"key":[131],"events":[132],"as":[133],"they":[134],"unfold.":[135]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
