{"id":"https://openalex.org/W2252287572","doi":"https://doi.org/10.1145/2827696","title":"PAM","display_name":"PAM","publication_year":2016,"publication_date":"2016-01-29","ids":{"openalex":"https://openalex.org/W2252287572","doi":"https://doi.org/10.1145/2827696","mag":"2252287572"},"language":"en","primary_location":{"id":"doi:10.1145/2827696","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2827696","pdf_url":null,"source":{"id":"https://openalex.org/S38703467","display_name":"ACM Transactions on Modeling and Computer Simulation","issn_l":"1049-3301","issn":["1049-3301","1558-1195"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Modeling and Computer Simulation","raw_type":"journal-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/A5057790429","display_name":"Witold Dzwinel","orcid":"https://orcid.org/0000-0001-8321-5928"},"institutions":[{"id":"https://openalex.org/I686019","display_name":"AGH University of Krakow","ror":"https://ror.org/00bas1c41","country_code":"PL","type":"education","lineage":["https://openalex.org/I686019"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Witold Dzwinel","raw_affiliation_strings":["AGH University of Science and Technology, Poland"],"affiliations":[{"raw_affiliation_string":"AGH University of Science and Technology, Poland","institution_ids":["https://openalex.org/I686019"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065549698","display_name":"Rafa\u0142 Wcis\u0142o","orcid":"https://orcid.org/0000-0002-8610-6070"},"institutions":[{"id":"https://openalex.org/I686019","display_name":"AGH University of Krakow","ror":"https://ror.org/00bas1c41","country_code":"PL","type":"education","lineage":["https://openalex.org/I686019"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Rafal Wcis\u0142o","raw_affiliation_strings":["AGH University of Science and Technology, Poland"],"affiliations":[{"raw_affiliation_string":"AGH University of Science and Technology, Poland","institution_ids":["https://openalex.org/I686019"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110077901","display_name":"David A. Yuen","orcid":null},"institutions":[{"id":"https://openalex.org/I4400573273","display_name":"Minnesota Supercomputing Institute","ror":"https://ror.org/038kp1442","country_code":null,"type":"facility","lineage":["https://openalex.org/I4400573273"]},{"id":"https://openalex.org/I3124059619","display_name":"China University of Geosciences","ror":"https://ror.org/04gcegc37","country_code":"CN","type":"education","lineage":["https://openalex.org/I3124059619"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"David A. Yuen","raw_affiliation_strings":["China University of Geosciences, Wuhan, China; Minnesota Supercomputing Institute, Minneapolis, MN","China University of Geosciences, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"China University of Geosciences, Wuhan, China; Minnesota Supercomputing Institute, Minneapolis, MN","institution_ids":["https://openalex.org/I3124059619","https://openalex.org/I4400573273"]},{"raw_affiliation_string":"China University of Geosciences, Wuhan, China","institution_ids":["https://openalex.org/I3124059619"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112027943","display_name":"Shea Miller","orcid":null},"institutions":[{"id":"https://openalex.org/I4390039273","display_name":"Ottawa Research and Development Centre","ror":"https://ror.org/03fx3ra47","country_code":null,"type":"facility","lineage":["https://openalex.org/I1331897569","https://openalex.org/I2802286613","https://openalex.org/I4390039273"]},{"id":"https://openalex.org/I1331897569","display_name":"Agriculture and Agri-Food Canada","ror":"https://ror.org/051dzs374","country_code":"CA","type":"government","lineage":["https://openalex.org/I1331897569","https://openalex.org/I2802286613"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Shea Miller","raw_affiliation_strings":["Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Canada"],"affiliations":[{"raw_affiliation_string":"Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Canada","institution_ids":["https://openalex.org/I1331897569","https://openalex.org/I4390039273"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5057790429"],"corresponding_institution_ids":["https://openalex.org/I686019"],"apc_list":null,"apc_paid":null,"fwci":2.0008,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.86069933,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"26","issue":"3","first_page":"1","last_page":"21"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9972000122070312,"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":0.9972000122070312,"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":0.9958000183105469,"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"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9811000227928162,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7084813117980957},{"id":"https://openalex.org/keywords/cellular-automaton","display_name":"Cellular automaton","score":0.6732747554779053},{"id":"https://openalex.org/keywords/bridging","display_name":"Bridging (networking)","score":0.5203761458396912},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4939325451850891},{"id":"https://openalex.org/keywords/scope","display_name":"Scope (computer science)","score":0.46789395809173584},{"id":"https://openalex.org/keywords/automaton","display_name":"Automaton","score":0.4602225720882416},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.45930349826812744},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.44873082637786865},{"id":"https://openalex.org/keywords/particle-system","display_name":"Particle system","score":0.4154480993747711},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.30010682344436646},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09502241015434265}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7084813117980957},{"id":"https://openalex.org/C35527583","wikidata":"https://www.wikidata.org/wiki/Q189156","display_name":"Cellular automaton","level":2,"score":0.6732747554779053},{"id":"https://openalex.org/C174348530","wikidata":"https://www.wikidata.org/wiki/Q188635","display_name":"Bridging (networking)","level":2,"score":0.5203761458396912},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4939325451850891},{"id":"https://openalex.org/C2778012447","wikidata":"https://www.wikidata.org/wiki/Q1034415","display_name":"Scope (computer science)","level":2,"score":0.46789395809173584},{"id":"https://openalex.org/C112505250","wikidata":"https://www.wikidata.org/wiki/Q787116","display_name":"Automaton","level":2,"score":0.4602225720882416},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.45930349826812744},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.44873082637786865},{"id":"https://openalex.org/C179003449","wikidata":"https://www.wikidata.org/wiki/Q1757458","display_name":"Particle system","level":2,"score":0.4154480993747711},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.30010682344436646},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09502241015434265},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2827696","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2827696","pdf_url":null,"source":{"id":"https://openalex.org/S38703467","display_name":"ACM Transactions on Modeling and Computer Simulation","issn_l":"1049-3301","issn":["1049-3301","1558-1195"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Modeling and Computer Simulation","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":71,"referenced_works":["https://openalex.org/W102033946","https://openalex.org/W108555510","https://openalex.org/W140674759","https://openalex.org/W239018198","https://openalex.org/W250252983","https://openalex.org/W251810509","https://openalex.org/W275890692","https://openalex.org/W346057038","https://openalex.org/W361750976","https://openalex.org/W377201621","https://openalex.org/W571710515","https://openalex.org/W586537888","https://openalex.org/W1040263557","https://openalex.org/W1532334717","https://openalex.org/W1559632398","https://openalex.org/W1598099041","https://openalex.org/W1599268017","https://openalex.org/W1600015713","https://openalex.org/W1603988686","https://openalex.org/W1633687939","https://openalex.org/W1672666614","https://openalex.org/W1965499304","https://openalex.org/W1973202568","https://openalex.org/W1973231699","https://openalex.org/W1983915714","https://openalex.org/W2007700616","https://openalex.org/W2015102116","https://openalex.org/W2016895770","https://openalex.org/W2022297469","https://openalex.org/W2024809291","https://openalex.org/W2025432833","https://openalex.org/W2029030701","https://openalex.org/W2032655419","https://openalex.org/W2038729819","https://openalex.org/W2039023576","https://openalex.org/W2041585319","https://openalex.org/W2043244472","https://openalex.org/W2044944052","https://openalex.org/W2046848016","https://openalex.org/W2056167609","https://openalex.org/W2065703403","https://openalex.org/W2076976053","https://openalex.org/W2077012341","https://openalex.org/W2080207198","https://openalex.org/W2088452582","https://openalex.org/W2090241789","https://openalex.org/W2091834741","https://openalex.org/W2093310284","https://openalex.org/W2094976376","https://openalex.org/W2095978797","https://openalex.org/W2110032173","https://openalex.org/W2112090702","https://openalex.org/W2142171814","https://openalex.org/W2142703690","https://openalex.org/W2147532327","https://openalex.org/W2148693904","https://openalex.org/W2158317262","https://openalex.org/W2159957996","https://openalex.org/W2162774006","https://openalex.org/W2164727176","https://openalex.org/W2165215367","https://openalex.org/W2165591850","https://openalex.org/W2184881690","https://openalex.org/W2407185716","https://openalex.org/W2482599886","https://openalex.org/W2913756371","https://openalex.org/W3022388728","https://openalex.org/W3102395314","https://openalex.org/W4205490020","https://openalex.org/W4254942564","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W4388870064","https://openalex.org/W2164619678","https://openalex.org/W4235186151","https://openalex.org/W1669105318","https://openalex.org/W2056057048","https://openalex.org/W2054685365","https://openalex.org/W2272354214","https://openalex.org/W2113544496","https://openalex.org/W2388153048","https://openalex.org/W2089583955"],"abstract_inverted_index":{"Serious":[0],"problems":[1],"with":[2,36],"bridging":[3],"multiple":[4],"scales":[5],"in":[6],"the":[7,33,41,49,65,89,111,138],"scope":[8,113],"of":[9,28,52,68,71,77,91,99,106,114,116,122,155,158],"a":[10,25,53,69],"single":[11],"numerical":[12],"model":[13,44],"make":[14],"computer":[15],"simulations":[16],"too":[17],"demanding":[18],"computationally":[19],"and":[20,131,140,152],"highly":[21],"unreliable.":[22],"We":[23,46,135],"present":[24,119],"new":[26],"concept":[27],"modeling":[29,142],"framework":[30,143],"that":[31,48,137],"integrates":[32],"particle":[34,42,101],"method":[35],"graph":[37,70],"dynamical":[38],"systems,":[39],"called":[40],"automata":[43],"(PAM).":[45],"assume":[47],"mechanical":[50],"response":[51],"macroscopic":[54],"system":[55],"on":[56],"internal":[57,100],"or":[58,85],"external":[59],"stimuli":[60],"can":[61,94],"be":[62,95],"simulated":[63],"by":[64,97,104,145],"spatiotemporal":[66],"dynamics":[67,90],"interacting":[72],"particles":[73],"representing":[74],"fine-grained":[75],"components":[76],"biological":[78,125,161],"tissue,":[79],"such":[80],"as":[81],"cells,":[82],"cell":[83],"clusters,":[84],"microtissue":[86],"fragments.":[87],"Meanwhile,":[88],"microscopic":[92],"processes":[93],"represented":[96,103],"evolution":[98],"states":[102],"vectors":[105],"finite-state":[107],"automata.":[108],"To":[109],"demonstrate":[110],"broad":[112],"application":[115],"PAM,":[117],"we":[118],"three":[120],"models":[121,157],"very":[123],"different":[124],"phenomena:":[126],"blood":[127],"clotting,":[128],"tumor":[129],"proliferation,":[130],"fungal":[132],"wheat":[133],"infection.":[134],"conclude":[136],"generic":[139],"flexible":[141],"provided":[144],"PAM":[146],"may":[147],"contribute":[148],"to":[149],"more":[150],"intuitive":[151],"faster":[153],"development":[154],"computational":[156],"complex":[159],"multiscale":[160],"processes.":[162]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
