{"id":"https://openalex.org/W4229037342","doi":"https://doi.org/10.1007/s00366-022-01654-1","title":"A 3D multi-agent-based model for lumen morphogenesis: the role of the biophysical properties of the extracellular matrix","display_name":"A 3D multi-agent-based model for lumen morphogenesis: the role of the biophysical properties of the extracellular matrix","publication_year":2022,"publication_date":"2022-05-06","ids":{"openalex":"https://openalex.org/W4229037342","doi":"https://doi.org/10.1007/s00366-022-01654-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/36397878"},"language":"en","primary_location":{"id":"doi:10.1007/s00366-022-01654-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00366-022-01654-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00366-022-01654-1.pdf","source":{"id":"https://openalex.org/S89333158","display_name":"Engineering With Computers","issn_l":"0177-0667","issn":["0177-0667","1435-5663"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Engineering with Computers","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s00366-022-01654-1.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051405429","display_name":"Daniel Camacho-G\u00f3mez","orcid":"https://orcid.org/0000-0002-7153-4101"},"institutions":[{"id":"https://openalex.org/I255234318","display_name":"Universidad de Zaragoza","ror":"https://ror.org/012a91z28","country_code":"ES","type":"education","lineage":["https://openalex.org/I255234318"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Daniel Camacho-G\u00f3mez","raw_affiliation_strings":["Department of Mechanical Engineering, Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Spain","institution_ids":["https://openalex.org/I255234318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029758603","display_name":"Jos\u00e9 Manuel Garc\u00eda\u2010Aznar","orcid":"https://orcid.org/0000-0002-9864-7683"},"institutions":[{"id":"https://openalex.org/I255234318","display_name":"Universidad de Zaragoza","ror":"https://ror.org/012a91z28","country_code":"ES","type":"education","lineage":["https://openalex.org/I255234318"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Manuel Garc\u00eda-Aznar","raw_affiliation_strings":["Department of Mechanical Engineering, Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Spain"],"raw_orcid":"https://orcid.org/0000-0002-9864-7683","affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Spain","institution_ids":["https://openalex.org/I255234318"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009411976","display_name":"Mar\u00eda Jos\u00e9 G\u00f3mez\u2010Benito","orcid":"https://orcid.org/0000-0002-1878-8997"},"institutions":[{"id":"https://openalex.org/I255234318","display_name":"Universidad de Zaragoza","ror":"https://ror.org/012a91z28","country_code":"ES","type":"education","lineage":["https://openalex.org/I255234318"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Mar\u00eda Jos\u00e9 G\u00f3mez-Benito","raw_affiliation_strings":["Department of Mechanical Engineering, Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Spain","institution_ids":["https://openalex.org/I255234318"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5051405429"],"corresponding_institution_ids":["https://openalex.org/I255234318"],"apc_list":{"value":2390,"currency":"EUR","value_usd":2990},"apc_paid":{"value":2390,"currency":"EUR","value_usd":2990},"fwci":1.7476,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.82448165,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"38","issue":"5","first_page":"4135","last_page":"4149"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10379","display_name":"Cellular Mechanics and Interactions","score":0.7296000123023987,"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/T10379","display_name":"Cellular Mechanics and Interactions","score":0.7296000123023987,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.02930000051856041,"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/T10617","display_name":"Cellular transport and secretion","score":0.028699999675154686,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/lumen","display_name":"Lumen (anatomy)","score":0.8530877828598022},{"id":"https://openalex.org/keywords/morphogenesis","display_name":"Morphogenesis","score":0.8215188980102539},{"id":"https://openalex.org/keywords/extracellular-matrix","display_name":"Extracellular matrix","score":0.7712526321411133},{"id":"https://openalex.org/keywords/hydrostatic-pressure","display_name":"Hydrostatic pressure","score":0.553686261177063},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.5375291109085083},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.4277622699737549},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.410768985748291},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.406046599149704},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.39858773350715637},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.33795613050460815},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.32654237747192383},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2908768057823181},{"id":"https://openalex.org/keywords/mechanics","display_name":"Mechanics","score":0.2488599419593811},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.24180346727371216},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.18303564190864563},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07175520062446594},{"id":"https://openalex.org/keywords/composite-material","display_name":"Composite material","score":0.06422504782676697}],"concepts":[{"id":"https://openalex.org/C131631996","wikidata":"https://www.wikidata.org/wiki/Q1141325","display_name":"Lumen (anatomy)","level":2,"score":0.8530877828598022},{"id":"https://openalex.org/C40692019","wikidata":"https://www.wikidata.org/wiki/Q815547","display_name":"Morphogenesis","level":3,"score":0.8215188980102539},{"id":"https://openalex.org/C189165786","wikidata":"https://www.wikidata.org/wiki/Q193825","display_name":"Extracellular matrix","level":2,"score":0.7712526321411133},{"id":"https://openalex.org/C2910081258","wikidata":"https://www.wikidata.org/wiki/Q177807","display_name":"Hydrostatic pressure","level":2,"score":0.553686261177063},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.5375291109085083},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.4277622699737549},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.410768985748291},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.406046599149704},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.39858773350715637},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.33795613050460815},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.32654237747192383},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2908768057823181},{"id":"https://openalex.org/C57879066","wikidata":"https://www.wikidata.org/wiki/Q41217","display_name":"Mechanics","level":1,"score":0.2488599419593811},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.24180346727371216},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.18303564190864563},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07175520062446594},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.06422504782676697},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":4,"locations":[{"id":"doi:10.1007/s00366-022-01654-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00366-022-01654-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00366-022-01654-1.pdf","source":{"id":"https://openalex.org/S89333158","display_name":"Engineering With Computers","issn_l":"0177-0667","issn":["0177-0667","1435-5663"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Engineering with Computers","raw_type":"journal-article"},{"id":"pmid:36397878","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36397878","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":"Engineering with computers","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9653332","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9653332","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":"Eng Comput","raw_type":"Text"},{"id":"pmh:oai:zaguan.unizar.es:120904","is_oa":true,"landing_page_url":"http://zaguan.unizar.es/record/120904","pdf_url":null,"source":{"id":"https://openalex.org/S4306401812","display_name":"Zaguan (University of Zaragoza Repository)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I255234318","host_organization_name":"Universidad de Zaragoza","host_organization_lineage":["https://openalex.org/I255234318"],"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":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1007/s00366-022-01654-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00366-022-01654-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00366-022-01654-1.pdf","source":{"id":"https://openalex.org/S89333158","display_name":"Engineering With Computers","issn_l":"0177-0667","issn":["0177-0667","1435-5663"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Engineering with Computers","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3487042393","display_name":null,"funder_award_id":"RTI2018-094494-B-C21","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G4175812583","display_name":null,"funder_award_id":"826494","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G510344331","display_name":null,"funder_award_id":"101018587","funder_id":"https://openalex.org/F4320334678","funder_display_name":"European Research Council"},{"id":"https://openalex.org/G6298273575","display_name":null,"funder_award_id":"RTI2018","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G6784498073","display_name":null,"funder_award_id":"826494","funder_id":"https://openalex.org/F4320335254","funder_display_name":"Horizon 2020"},{"id":"https://openalex.org/G727224964","display_name":null,"funder_award_id":"RTI2018-094494-B-C21","funder_id":"https://openalex.org/F4320326262","funder_display_name":"Ministerio de Asuntos Econ\u00f3micos y Transformaci\u00f3n Digital, Gobierno de Espa\u00f1a"},{"id":"https://openalex.org/G7842005466","display_name":null,"funder_award_id":"Horizon 2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320324111","display_name":"Universidad de Zaragoza","ror":"https://ror.org/012a91z28"},{"id":"https://openalex.org/F4320326262","display_name":"Ministerio de Asuntos Econ\u00f3micos y Transformaci\u00f3n Digital, Gobierno de Espa\u00f1a","ror":"https://ror.org/03sv46s19"},{"id":"https://openalex.org/F4320334678","display_name":"European Research Council","ror":"https://ror.org/0472cxd90"},{"id":"https://openalex.org/F4320335254","display_name":"Horizon 2020","ror":null},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4229037342.pdf","grobid_xml":"https://content.openalex.org/works/W4229037342.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1500490922","https://openalex.org/W1969588976","https://openalex.org/W1972204116","https://openalex.org/W1979904464","https://openalex.org/W1981962653","https://openalex.org/W1988326784","https://openalex.org/W1996269383","https://openalex.org/W1998865371","https://openalex.org/W2002315827","https://openalex.org/W2003636559","https://openalex.org/W2021649658","https://openalex.org/W2032461554","https://openalex.org/W2055536282","https://openalex.org/W2055940657","https://openalex.org/W2058324879","https://openalex.org/W2065191902","https://openalex.org/W2069354876","https://openalex.org/W2072888577","https://openalex.org/W2077029264","https://openalex.org/W2078290150","https://openalex.org/W2087252982","https://openalex.org/W2090667207","https://openalex.org/W2096180495","https://openalex.org/W2099023480","https://openalex.org/W2099052265","https://openalex.org/W2099378655","https://openalex.org/W2100122781","https://openalex.org/W2104124840","https://openalex.org/W2113452409","https://openalex.org/W2114952275","https://openalex.org/W2116379215","https://openalex.org/W2126070753","https://openalex.org/W2127938800","https://openalex.org/W2128231056","https://openalex.org/W2128884401","https://openalex.org/W2131775349","https://openalex.org/W2146428402","https://openalex.org/W2147819429","https://openalex.org/W2162791825","https://openalex.org/W2166223265","https://openalex.org/W2169333761","https://openalex.org/W2187933120","https://openalex.org/W2613147216","https://openalex.org/W2773740187","https://openalex.org/W2801929954","https://openalex.org/W2884791788","https://openalex.org/W2891662364","https://openalex.org/W2899148412","https://openalex.org/W2936719190","https://openalex.org/W2944902923","https://openalex.org/W2949391359","https://openalex.org/W2949797623","https://openalex.org/W3003264827","https://openalex.org/W3175538825","https://openalex.org/W4213083993"],"related_works":["https://openalex.org/W2001312180","https://openalex.org/W2468936369","https://openalex.org/W4246868616","https://openalex.org/W2418452667","https://openalex.org/W3008888037","https://openalex.org/W2026277664","https://openalex.org/W2791272313","https://openalex.org/W4388412113","https://openalex.org/W1788072961","https://openalex.org/W2126964995"],"abstract_inverted_index":{"The":[0,177],"correct":[1],"function":[2],"of":[3,15,37,66,72,94,109,125],"many":[4],"organs":[5],"depends":[6],"on":[7,34],"proper":[8],"lumen":[9,44,84,127,142,146,157],"morphogenesis,":[10],"which":[11],"requires":[12],"the":[13,35,50,55,60,64,67,73,92,95,103,106,114,123,126,137,141,152,160,170],"orchestration":[14],"both":[16],"biological":[17,107],"and":[18,63,91,131,144,165],"mechanical":[19,115],"aspects.":[20],"However,":[21],"how":[22],"these":[23],"factors":[24],"coordinate":[25],"is":[26,163,173],"not":[27],"yet":[28],"fully":[29],"understood.":[30],"Here,":[31],"we":[32,48,78,121,149],"focus":[33],"development":[36],"a":[38,80],"mechanistic":[39],"model":[40,101,153],"for":[41,83],"computationally":[42],"simulating":[43],"morphogenesis.":[45,147],"In":[46],"particular,":[47],"consider":[49],"hydrostatic":[51],"pressure":[52],"generated":[53],"by":[54],"cells'":[56,88],"fluid":[57,89],"secretion":[58,90],"as":[59,70],"driving":[61],"force":[62],"density":[65,93,139,162,172],"extracellular":[68,96],"matrix":[69,138,161,171],"regulators":[71],"process.":[74],"For":[75],"this":[76,99],"purpose,":[77],"develop":[79],"3D":[81],"agent-based-model":[82],"morphogenesis":[85,158],"that":[86,117,133,151],"includes":[87],"matrix.":[97],"Moreover,":[98],"computer-based":[100],"considers":[102],"variation":[104],"in":[105,111,136],"behavior":[108],"cells":[110],"response":[112],"to":[113],"forces":[116],"they":[118],"sense.":[119],"Then,":[120],"study":[122],"formation":[124,168],"under":[128],"different-mechanical":[129],"scenarios":[130],"conclude":[132],"an":[134],"increase":[135],"reduces":[140],"volume":[143],"hinders":[145],"Finally,":[148],"show":[150],"successfully":[154],"predicts":[155],"normal":[156],"when":[159,169],"physiological":[164],"aberrant":[166],"multilumen":[167],"excessive.":[174],"Supplementary":[175],"Information:":[176],"online":[178],"version":[179],"contains":[180],"supplementary":[181],"material":[182],"available":[183],"at":[184],"10.1007/s00366-022-01654-1.":[185]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2}],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2025-10-10T00:00:00"}
