{"id":"https://openalex.org/W3004093597","doi":"https://doi.org/10.1186/s12859-019-3338-8","title":"pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems","display_name":"pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems","publication_year":2020,"publication_date":"2020-01-29","ids":{"openalex":"https://openalex.org/W3004093597","doi":"https://doi.org/10.1186/s12859-019-3338-8","mag":"3004093597","pmid":"https://pubmed.ncbi.nlm.nih.gov/31996129"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3338-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3338-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3338-8.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3338-8.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034809455","display_name":"Satya N.V. Arjunan","orcid":"https://orcid.org/0000-0002-2913-3347"},"institutions":[{"id":"https://openalex.org/I4210116810","display_name":"RIKEN Center for Biosystems Dynamics Research","ror":"https://ror.org/023rffy11","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210116810"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Satya N.V. Arjunan","raw_affiliation_strings":["RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan. satya@riken.jp","RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan"],"raw_orcid":"https://orcid.org/0000-0002-2913-3347","affiliations":[{"raw_affiliation_string":"RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan. satya@riken.jp","institution_ids":["https://openalex.org/I4210116810"]},{"raw_affiliation_string":"RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan","institution_ids":["https://openalex.org/I4210116810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003367631","display_name":"Atsushi Miyauchi","orcid":"https://orcid.org/0000-0002-6033-6433"},"institutions":[{"id":"https://openalex.org/I4210089980","display_name":"Research Organization for Information Science and Technology","ror":"https://ror.org/00az65y50","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210089980"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Atsushi Miyauchi","raw_affiliation_strings":["Research Organization for Information Science and Technology, Chuo, Kobe, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Organization for Information Science and Technology, Chuo, Kobe, Japan","institution_ids":["https://openalex.org/I4210089980"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030927963","display_name":"Kazunari Iwamoto","orcid":"https://orcid.org/0000-0001-9794-9420"},"institutions":[{"id":"https://openalex.org/I4210116810","display_name":"RIKEN Center for Biosystems Dynamics Research","ror":"https://ror.org/023rffy11","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210116810"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kazunari Iwamoto","raw_affiliation_strings":["RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan","institution_ids":["https://openalex.org/I4210116810"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102870944","display_name":"Koichi Takahashi","orcid":"https://orcid.org/0000-0002-4235-9914"},"institutions":[{"id":"https://openalex.org/I4210116810","display_name":"RIKEN Center for Biosystems Dynamics Research","ror":"https://ror.org/023rffy11","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210116810"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Koichi Takahashi","raw_affiliation_strings":["RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan","institution_ids":["https://openalex.org/I4210116810"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5034809455"],"corresponding_institution_ids":["https://openalex.org/I4210116810"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.6063,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.59654179,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"21","issue":"1","first_page":"33","last_page":"33"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10492","display_name":"Microtubule and mitosis dynamics","score":0.2264000028371811,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T10492","display_name":"Microtubule and mitosis dynamics","score":0.2264000028371811,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T12859","display_name":"Cell Image Analysis Techniques","score":0.10610000044107437,"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"}},{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.06710000336170197,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.74289470911026},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5857827663421631},{"id":"https://openalex.org/keywords/reaction\u2013diffusion-system","display_name":"Reaction\u2013diffusion system","score":0.5049505829811096},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.5042740106582642},{"id":"https://openalex.org/keywords/correctness","display_name":"Correctness","score":0.5037199854850769},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.47990497946739197},{"id":"https://openalex.org/keywords/lattice","display_name":"Lattice (music)","score":0.4508882462978363},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.42092615365982056},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.41004207730293274},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38599875569343567},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3259708881378174},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.13948789238929749}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.74289470911026},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5857827663421631},{"id":"https://openalex.org/C121231716","wikidata":"https://www.wikidata.org/wiki/Q901210","display_name":"Reaction\u2013diffusion system","level":2,"score":0.5049505829811096},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.5042740106582642},{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.5037199854850769},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.47990497946739197},{"id":"https://openalex.org/C2781204021","wikidata":"https://www.wikidata.org/wiki/Q6497091","display_name":"Lattice (music)","level":2,"score":0.4508882462978363},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.42092615365982056},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.41004207730293274},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38599875569343567},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3259708881378174},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13948789238929749},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020935","descriptor_name":"MAP Kinase Signaling System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020935","descriptor_name":"MAP Kinase Signaling System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020935","descriptor_name":"MAP Kinase Signaling System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-019-3338-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3338-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3338-8.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31996129","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31996129","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:4796a67dd3a74050a343e8735b8a6b47","is_oa":false,"landing_page_url":"https://doaj.org/article/4796a67dd3a74050a343e8735b8a6b47","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss 1, Pp 1-21 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6990473","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6990473","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:unsworks.library.unsw.edu.au:1959.4/unsworks_75111","is_oa":true,"landing_page_url":"http://hdl.handle.net/1959.4/unsworks_75111","pdf_url":null,"source":{"id":"https://openalex.org/S4306401737","display_name":"UNSWorks (University of New South Wales, Sydney, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40053085","host_organization_name":"Australian Defence Force Academy","host_organization_lineage":["https://openalex.org/I40053085"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 21, 1, 33","raw_type":"http://purl.org/coar/resource_type/c_6501"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-3338-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3338-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3338-8.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3467652097","display_name":"Development of cell function editing technology with fast 3D measurement and local-field light perturbation","funder_award_id":"20K20379","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320335125","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3004093597.pdf","grobid_xml":"https://content.openalex.org/works/W3004093597.grobid-xml"},"referenced_works_count":82,"referenced_works":["https://openalex.org/W14569263","https://openalex.org/W1490956705","https://openalex.org/W1528643580","https://openalex.org/W1564227505","https://openalex.org/W1865781989","https://openalex.org/W1974974415","https://openalex.org/W1976488701","https://openalex.org/W1982705472","https://openalex.org/W1994113816","https://openalex.org/W2002505185","https://openalex.org/W2004950702","https://openalex.org/W2030125944","https://openalex.org/W2030765885","https://openalex.org/W2031220210","https://openalex.org/W2036606290","https://openalex.org/W2038823703","https://openalex.org/W2040645185","https://openalex.org/W2041715593","https://openalex.org/W2042321087","https://openalex.org/W2044252584","https://openalex.org/W2047413409","https://openalex.org/W2047723546","https://openalex.org/W2048871574","https://openalex.org/W2052360207","https://openalex.org/W2056599241","https://openalex.org/W2060872711","https://openalex.org/W2063202565","https://openalex.org/W2066100786","https://openalex.org/W2068175266","https://openalex.org/W2068359975","https://openalex.org/W2071590886","https://openalex.org/W2072670807","https://openalex.org/W2076484772","https://openalex.org/W2077346271","https://openalex.org/W2078734278","https://openalex.org/W2081645999","https://openalex.org/W2089785804","https://openalex.org/W2094458649","https://openalex.org/W2095595785","https://openalex.org/W2104680358","https://openalex.org/W2108487867","https://openalex.org/W2113613128","https://openalex.org/W2117897850","https://openalex.org/W2131187223","https://openalex.org/W2132898564","https://openalex.org/W2134542242","https://openalex.org/W2150766477","https://openalex.org/W2151643303","https://openalex.org/W2160658674","https://openalex.org/W2165360511","https://openalex.org/W2170288587","https://openalex.org/W2174499708","https://openalex.org/W2235926820","https://openalex.org/W2271421556","https://openalex.org/W2523214233","https://openalex.org/W2531236954","https://openalex.org/W2573536041","https://openalex.org/W2593960650","https://openalex.org/W2598011934","https://openalex.org/W2625132185","https://openalex.org/W2786551427","https://openalex.org/W2789208112","https://openalex.org/W2793082520","https://openalex.org/W2793745464","https://openalex.org/W2795327628","https://openalex.org/W2801140473","https://openalex.org/W2804403872","https://openalex.org/W2806272738","https://openalex.org/W2808556041","https://openalex.org/W2883596424","https://openalex.org/W2900950055","https://openalex.org/W2901765505","https://openalex.org/W2912012041","https://openalex.org/W2949419072","https://openalex.org/W2950427239","https://openalex.org/W2951031981","https://openalex.org/W2983783141","https://openalex.org/W3034171991","https://openalex.org/W3103927232","https://openalex.org/W3214267983","https://openalex.org/W4232611972","https://openalex.org/W4307697508"],"related_works":["https://openalex.org/W1800827217","https://openalex.org/W27867058","https://openalex.org/W1509211761","https://openalex.org/W4306156203","https://openalex.org/W2391299576","https://openalex.org/W2133693067","https://openalex.org/W1531488649","https://openalex.org/W2070464029","https://openalex.org/W1585350690","https://openalex.org/W2366027386"],"abstract_inverted_index":{"BACKGROUND:":[0],"Studies":[1],"using":[2],"quantitative":[3,28],"experimental":[4],"methods":[5,308],"have":[6],"shown":[7],"that":[8],"intracellular":[9,54,88,313],"spatial":[10],"distribution":[11],"of":[12,38,84,117,163,177,183,195,212,233,265,279,312,319],"molecules":[13,64,70],"plays":[14],"a":[15,92,128,138,142,150,181,210,269,283,300],"central":[16],"role":[17],"in":[18,71,288,309],"many":[19],"cellular":[20],"systems.":[21,40,315],"Spatially":[22],"resolved":[23],"computer":[24],"simulations":[25,311],"can":[26,51],"integrate":[27],"data":[29],"from":[30,62],"these":[31],"experiments":[32],"to":[33,112,134,171,219,239],"construct":[34],"physically":[35],"accurate":[36],"models":[37],"the":[39,75,82,115,161,175,188,193,220,226,244,262,275,280],"Although":[41],"computationally":[42],"expensive,":[43],"microscopic":[44,306],"resolution":[45],"reaction-diffusion":[46,314],"simulators,":[47],"such":[48],"as":[49],"Spatiocyte":[50,94],"directly":[52],"capture":[53],"effects":[55],"comprising":[56],"diffusion-limited":[57],"reactions":[58],"and":[59,120,149,155,166,208,255,261,299],"volume":[60],"exclusion":[61],"crowded":[63,87],"by":[65,169],"explicitly":[66],"representing":[67],"individual":[68],"diffusing":[69],"space.":[72],"To":[73,173],"alleviate":[74],"steep":[76],"computational":[77],"cost":[78],"typically":[79],"associated":[80],"with":[81,199,215,222,237],"simulation":[83],"large":[85,121],"or":[86],"compartments,":[89],"we":[90,179,273],"present":[91],"parallelized":[93,139,143,151,184],"method":[95,102],"called":[96],"pSpatiocyte.":[97],"RESULTS:":[98],"The":[99,316],"new":[100],"high-performance":[101,270],"employs":[103],"unique":[104],"parallelization":[105],"schemes":[106],"on":[107,187,248],"hexagonal":[108],"close-packed":[109],"(HCP)":[110],"lattice":[111,136,197],"efficiently":[113],"exploit":[114],"resources":[116],"common":[118],"workstations":[119],"distributed":[122],"memory":[123],"parallel":[124,206,263],"computers.":[125],"We":[126,159],"introduce":[127],"coordinate":[129],"system":[130],"for":[131,146,153],"fast":[132,297],"accesses":[133],"HCP":[135],"voxels,":[137],"event":[140,152],"scheduler,":[141],"Gillespie's":[144],"direct-method":[145],"unimolecular":[147],"reactions,":[148],"diffusion":[154,167,185],"bimolecular":[156],"reaction":[157,165,285],"processes.":[158],"verified":[160],"correctness":[162],"pSpatiocyte":[164,203,230,252,293,320],"processes":[168],"comparison":[170],"theory.":[172],"evaluate":[174],"performance":[176,302],"pSpatiocyte,":[178],"performed":[180],"series":[182],"runs":[186],"RIKEN":[189],"K":[190],"computer.":[191],"In":[192,225],"case":[194],"fine":[196],"discretization":[198],"low":[200],"voxel":[201],"occupancy,":[202],"exhibited":[204],"74%":[205],"efficiency":[207],"achieved":[209],"speedup":[211],"7686":[213],"times":[214],"663552":[216,240],"cores":[217],"compared":[218],"runtime":[221],"64":[223],"cores.":[224,241],"weak":[227],"scaling":[228],"performance,":[229],"obtained":[231],"efficiencies":[232],"at":[234,323],"least":[235],"60%":[236],"up":[238],"When":[242],"executing":[243],"Michaelis-Menten":[245],"benchmark":[246],"model":[247],"an":[249],"eight-core":[250],"workstation,":[251],"required":[253],"45-":[254],"55-fold":[256],"shorter":[257],"runtimes":[258,298],"than":[259],"Smoldyn":[260],"version":[264],"ReaDDy,":[266],"respectively.":[267],"As":[268],"application":[271],"example,":[272],"study":[274],"dual":[276],"phosphorylation-dephosphorylation":[277],"cycle":[278],"MAPK":[281],"system,":[282],"typical":[284],"network":[286],"motif":[287],"cell":[289],"signaling":[290],"pathways.":[291],"CONCLUSIONS:":[292],"demonstrates":[294],"good":[295],"accuracies,":[296],"significant":[301],"advantage":[303],"over":[304],"well-known":[305],"particle":[307],"large-scale":[310],"source":[317],"code":[318],"is":[321],"available":[322],"https://spatiocyte.org.":[324]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
