{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T12:57:01Z","timestamp":1769086621426,"version":"3.49.0"},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2015,10,9]],"date-time":"2015-10-09T00:00:00Z","timestamp":1444348800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004544","type":"journal-article","created":{"date-parts":[[2015,10,9]],"date-time":"2015-10-09T17:58:29Z","timestamp":1444413509000},"page":"e1004544","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":32,"title":["Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components"],"prefix":"10.1371","volume":"11","author":[{"given":"Bruce S.","family":"Gardiner","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kelvin K. L.","family":"Wong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Grand R.","family":"Joldes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Addison J.","family":"Rich","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chin Wee","family":"Tan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antony W.","family":"Burgess","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David W.","family":"Smith","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,10,9]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1115\/1.2746374","article-title":"Estimation of cell Young's modulus of adherent cells probed by optical and magnetic tweezers: influence of cell thickness and bead immersion","volume":"129","author":"A Kamgou\u00e9","year":"2007","journal-title":"J Biomech Eng"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1115\/1.1824129","article-title":"Material properties and residual stress in the stage 12 chick heart during cardiac looping","volume":"126","author":"E Zamir","year":"2004","journal-title":"J Biomech Eng"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/S0021-9290(01)00201-9","article-title":"Contribution of the nucleus to the mechanical properties of endothelial cells","volume":"35","author":"N Caille","year":"2002","journal-title":"Journal of Biomechanics"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1557\/jmr.2006.0262","article-title":"Deformation of the cell nucleus under indentation: Mechanics and mechanisms","volume":"21","author":"A Vaziri","year":"2006","journal-title":"J Mater Res"},{"key":"ref5","first-page":"192618","article-title":"A Finite Element Study of Micropipette Aspiration of Single Cells: Effect of Compressibility","author":"AJ Bidhendi","year":"2012","journal-title":"Computational and Mathematical Methods in Medicine"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1080\/10255842.2014.903933","article-title":"An enhanced version of a bone-remodelling model based on the continuum damage mechanics theory","volume":"18","author":"M Mengoni","year":"2015","journal-title":"Computer Methods in Biomechanics and Biomedical Engineering"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"2456","DOI":"10.1007\/s10439-012-0598-0","article-title":"Multiscale mechanics of articular cartilage: potentials and challenges of coupling musculoskeletal, joint, and microscale computational models","volume":"40","author":"JP Halloran","year":"2012","journal-title":"Annals of Biomedical Engineering"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1122\/1.1917841","article-title":"The link between discrete and continuous modeling of liquid foam at the level of a single bubble","volume":"49","author":"BS Gardiner","year":"2005","journal-title":"Journal of Rheology"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/S0377-0257(00)00102-6","article-title":"The steady shear of three-dimensional wet polydisperse foams","volume":"92","author":"BS Gardiner","year":"2000","journal-title":"Journal of Non-Newtonian Fluid Mechanics"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1002\/nag.343","article-title":"Shear band evolution and accumulated microstructural development in Cosserat media","volume":"28","author":"A Tordesillas","year":"2004","journal-title":"International Journal for Numerical and Analytical Methods in Geomechanics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1093\/bib\/bbq017","article-title":"Computational discrete models of tissue growth and regeneration","volume":"12","author":"F Azuaje","year":"2010","journal-title":"Briefings in Bioinformatics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.biosystems.2004.05.025","article-title":"The epitheliome: agent-based modelling of the social behaviour of cells","volume":"76","author":"DC Walker","year":"2004","journal-title":"BioSystems"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/2191-0855-1-45","article-title":"Modeling formalisms in Systems Biology","volume":"1","author":"D Machado","year":"2011","journal-title":"AMB Express"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"e73204","DOI":"10.1371\/journal.pone.0073204","article-title":"Cell organisation in the colonic crypt: a theoretical comparison of the pedigree and niche concepts","volume":"8","author":"RC Van der Wath","year":"2013","journal-title":"PLoS ONE"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"e1001045","DOI":"10.1371\/journal.pcbi.1001045","article-title":"A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt","volume":"7","author":"P Buske","year":"2011","journal-title":"PLoS Computational Biology"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1111\/j.1365-2184.2009.00627.x","article-title":"An integrative computational model for intestinal tissue renewal","volume":"42","author":"IMM van Leeuwen","year":"2009","journal-title":"Cell Proliferation"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"e8511","DOI":"10.1371\/journal.pone.0008511","article-title":"Development of a three dimensional multiscale computational model of the human epidermis","volume":"5","author":"S Adra","year":"2010","journal-title":"PLoS ONE"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"e1000900","DOI":"10.1371\/journal.pcbi.1000900","article-title":"Linking changes in epithelial morphogenesis to cancer mutations using computational modeling","volume":"6","author":"KA Rejniak","year":"2010","journal-title":"PLoS Computational Biology"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2389","DOI":"10.1093\/bioinformatics\/btp416","article-title":"Cross-scale, cross-pathway evaluation using an agent-based non-small cell lung cancer model","volume":"25","author":"Z Wang","year":"2009","journal-title":"Bioinformatics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.biosystems.2010.07.008","article-title":"An in silico platform for the study of epithelial pre-invasive neoplastic development","volume":"102","author":"M Guillaud","year":"2010","journal-title":"BioSystems"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/1752-0509-3-122","article-title":"A computational approach to resolve cell level contributions to early glandular epithelial cancer progression","volume":"3","author":"SHJ Kim","year":"2009","journal-title":"BMC Systems Biology"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.jtbi.2012.02.002","article-title":"Patient-calibrated agent-based modelling of ductal carcinoma in situ (DCIS): From microscopic measurements to macroscopic predictions of clinicalprogression","volume":"301","author":"P Macklin","year":"2012","journal-title":"Journal of Theoretical Biology"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1093\/bib\/bbm024","article-title":"Combining experiments with multi-cell agent-based modeling to study biological tissue patterning","volume":"8","author":"BC Thorne","year":"2007","journal-title":"Briefings in Bioinformatics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"20374","DOI":"10.1073\/pnas.0808725105","article-title":"Four-dimensional realistic modeling of pancreatic organogenesis","volume":"105","author":"Y Setty","year":"2008","journal-title":"PNAS"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1057\/jos.2010.3","article-title":"Tutorial on agent-based modelling and simulation","volume":"4","author":"CM Macal","year":"2010","journal-title":"J of Sim"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1080\/19648189.2008.9693050","article-title":"Introduction to discrete element methods","volume":"12","author":"S Luding","year":"2008","journal-title":"European Journal of Environmental and Civil Engineering"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-59745-177-2_1","article-title":"Molecular dynamics simulations","volume":"443","author":"ER Lindahl","year":"2008","journal-title":"Methods in Molecular Biology"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1007\/s11831-010-9040-7","article-title":"Smoothed Particle Hydrodynamics (SPH): an Overview and Recent Developments","volume":"17","author":"MB Liu","year":"2010","journal-title":"Archives of Computational Methods in Engineering"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"3305","DOI":"10.1016\/j.cma.2010.06.037","article-title":"Real-Time Nonlinear Finite Element Computations on GPU\u2014Application to Neurosurgical Simulation","volume":"199","author":"GR Joldes","year":"2010","journal-title":"Computer Methods in Applied Mechanics and Engineering"},{"key":"ref30","first-page":"31","article-title":"Advances in discrete element method applied to soil, rock and concrete mechanics","volume":"44","author":"FV Donz\u00e9","year":"2009","journal-title":"State of the art of geotechnical engineering Electronic Journal of Geotechnical Engineering"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1103\/PhysRev.159.98","article-title":"Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard\u2014Jones Molecules","volume":"159","author":"L Verlet","year":"1967","journal-title":"Physical Review"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1002\/cnm.887","article-title":"Total Lagrangian Explicit Dynamics Finite Element Algorithm for Computing Soft Tissue Deformation","volume":"23","author":"K Miller","year":"2007","journal-title":"Communications in Numerical Methods in Engineering"},{"key":"ref33","doi-asserted-by":"crossref","DOI":"10.1007\/978-4-431-73167-2_13","article-title":"A declarative model assembly infrastructure for verification and validation","author":"M North","year":"2007"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"130084","DOI":"10.1098\/rsob.130084","article-title":"Mechanics of spreading cells probed by atomic force microscopy","volume":"3","author":"A Pietuch","year":"2013","journal-title":"Open Biol"},{"key":"ref35","doi-asserted-by":"crossref","unstructured":"Chang H-I, Wang Y (2011) Cell Responses to Surface and Architecture of Tissue Engineering Scaffolds.","DOI":"10.5772\/21983"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1073\/pnas.94.3.849","article-title":"Demonstration of mechanical connections between integrins,cytoskelet al filaments, and nucleoplasm that stabilize nuclear structure","volume":"94","author":"AJ Maniotis","year":"1997","journal-title":"Proceeding of the National Academy of Sciences of the United States of America"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"557","DOI":"10.3233\/BIR-1991-28607","article-title":"Cytoplasmic rheology of passive neutrophils","volume":"28","author":"C Dong","year":"1991","journal-title":"Biorheology"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1006\/bbrc.2000.2360","article-title":"Viscoelastic properties of the cell nucleus","volume":"269","author":"F Guilak","year":"2000","journal-title":"Biochemical and Biophysical Research Communications"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1016\/j.jbiomech.2005.06.003","article-title":"Flow-induced hardening of endothelial nucleus as an intracellular stress-bearing organelle","volume":"38","author":"S Deguchi","year":"2005","journal-title":"J Biomech"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1073\/pnas.1312076111","article-title":"Theory of epithelial sheet morphology in three dimensions","volume":"111","author":"E Hannezo","year":"2014","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref41","article-title":"Molecular Biology of the Cell","author":"B Alberts","year":"2002"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1242\/dev.118.1.33","article-title":"Epithelial cell proliferation and islet neogenesis in IFN-g transgenic mice","volume":"118","author":"D Gu","year":"1993","journal-title":"Development"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"e1001045","DOI":"10.1371\/journal.pcbi.1001045","article-title":"A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt","volume":"7","author":"P Buske","year":"2011","journal-title":"PLoS Computational Biology"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1165\/ajrcmb.23.5.4046","article-title":"Loss of Epithelial Integrity Resulting from E-Cadherin Dysfunction Predisposes Airway Epithelial Cells to Adenoviral Infection","volume":"23","author":"Y Man","year":"2000","journal-title":"American Journal of Respiratory Cell and Molecular Biology"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"065011","DOI":"10.1088\/1367-2630\/15\/6\/065011","article-title":"Morphological instabilities of stratified epithelia: a mechanical instability in tumour formation","volume":"15","author":"T Risler","year":"2013","journal-title":"New J Phys"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1007\/s10237-010-0280-0","article-title":"Growth-induced buckling of an epithelial layer","volume":"10","author":"MR Nelson","year":"2011","journal-title":"Biomechanics and Modeling in Mechanobiology"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"078104","DOI":"10.1103\/PhysRevLett.107.078104","article-title":"Instabilities of Monolayered Epithelia: Shape and Structure of Villi and Crypts","volume":"107","author":"E Hannezo","year":"2011","journal-title":"Phys Rev Lett"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1073\/pnas.1312076111","article-title":"Theory of epithelial sheet morphology in three dimensions","volume":"111","author":"E Hannezo","year":"2014","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1927","DOI":"10.1007\/s11538-007-9199-8","article-title":"Biomechanical modelling of colorectal crypt budding and fission","volume":"69","author":"CM Edwards","year":"2007","journal-title":"Bulletin of Mathematical Biology"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.jtbi.2011.12.013","article-title":"Modelling the role of the basement membrane beneath a growing epithelial monolayer","volume":"298","author":"S-J Dunn","year":"2012","journal-title":"Journal of Theoretical Biology"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1164\/rccm.201409-1663OE","article-title":"On the Tricks Alveolar Epithelial Cells Play to Make a Good Lung","volume":"191","author":"ER Weibel","year":"2015","journal-title":"Am J Respir Crit Care Med"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1097\/01.MP.0000062996.66432.12","article-title":"Barrett's Esophagus and Barrett's-Related Dysplasia","volume":"16","author":"JR Goldblum","year":"2003","journal-title":"Modern Pathology"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"021024","DOI":"10.1115\/1.4026179","article-title":"Agent-based modeling traction force mediated compaction of cell-populated collagen gels using physically realistic fibril mechanics","volume":"136","author":"JW Reinhardt","year":"2014","journal-title":"Journal of Biomechanical Engineering"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004544","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,22]],"date-time":"2022-05-22T23:19:02Z","timestamp":1653261542000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004544"}},"subtitle":[],"editor":[{"given":"Jeffrey J.","family":"Saucerman","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,10,9]]},"references-count":53,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2015,10,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004544","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,10,9]]}}}