Discrete element framework for modelling extracellular matrix, deformable cells and subcellular components

B.S. Gardiner; K.K.L. Wong; G.R. Joldes; A.J. Rich; C.W. Tan; A.W. Burgess; D.W. Smith

doi:10.1371/journal.pcbi.1004544

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Discrete element framework for modelling extracellular matrix, deformable cells and subcellular components

Journal article

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Peer reviewed

Discrete element framework for modelling extracellular matrix, deformable cells and subcellular components

B.S. Gardiner, K.K.L. Wong, G.R. Joldes, A.J. Rich, C.W. Tan, A.W. Burgess and D.W. Smith

PLOS Computational Biology, Vol.11(10), e1004544

2015

DOI: https://doi.org/10.1371/journal.pcbi.1004544

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Abstract

This paper presents a framework for modelling biological tissues based on discrete particles. Cell components (e.g. cell membranes, cell cytoskeleton, cell nucleus) and extracellular matrix (e.g. collagen) are represented using collections of particles. Simple particle to particle interaction laws are used to simulate and control complex physical interaction types (e.g. cell-cell adhesion via cadherins, integrin basement membrane attachment, cytoskeletal mechanical properties). Particles may be given the capacity to change their properties and behaviours in response to changes in the cellular microenvironment (e.g., in response to cell-cell signalling or mechanical loadings). Each particle is in effect an 'agent', meaning that the agent can sense local environmental information and respond according to pre-determined or stochastic events. The behaviour of the proposed framework is exemplified through several biological problems of ongoing interest. These examples illustrate how the modelling framework allows enormous flexibility for representing the mechanical behaviour of different tissues, and we argue this is a more intuitive approach than perhaps offered by traditional continuum methods. Because of this flexibility, we believe the discrete modelling framework provides an avenue for biologists and bioengineers to explore the behaviour of tissue systems in a computational laboratory.

Details

Title: Discrete element framework for modelling extracellular matrix, deformable cells and subcellular components
Authors/Creators: B.S. Gardiner (Author/Creator) - Murdoch University
K.K.L. Wong (Author/Creator) - The University of Western Australia
G.R. Joldes (Author/Creator) - The University of Western Australia
A.J. Rich (Author/Creator) - The University of Western Australia
C.W. Tan (Author/Creator) - Walter and Eliza Hall Institute of Medical Research
A.W. Burgess (Author/Creator) - Walter and Eliza Hall Institute of Medical Research
D.W. Smith (Author/Creator) - The University of Western Australia
Publication Details: PLOS Computational Biology, Vol.11(10), e1004544
Publisher: Public Library of Science
Identifiers: 991005545060107891
Copyright: © 2015 Gardiner et al.
Murdoch Affiliation: School of Engineering and Information Technology
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration
Citation topics: 9 Mathematics; 9.162 Numerical Methods; 9.162.1864 Cancer Modeling
Web Of Science research areas: Biochemical Research Methods; Mathematical & Computational Biology
ESI research areas: Biology & Biochemistry