Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components.
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 a...
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2015-10-01
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Series: | PLoS Computational Biology |
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doaj-905d4ff472c849bd81088898c31288a42020-11-25T01:38:40ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582015-10-011110e100454410.1371/journal.pcbi.1004544Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components.Bruce S GardinerKelvin K L WongGrand R JoldesAddison J RichChin Wee TanAntony W BurgessDavid W SmithThis 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.http://europepmc.org/articles/PMC4599884?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Bruce S Gardiner Kelvin K L Wong Grand R Joldes Addison J Rich Chin Wee Tan Antony W Burgess David W Smith |
spellingShingle |
Bruce S Gardiner Kelvin K L Wong Grand R Joldes Addison J Rich Chin Wee Tan Antony W Burgess David W Smith Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components. PLoS Computational Biology |
author_facet |
Bruce S Gardiner Kelvin K L Wong Grand R Joldes Addison J Rich Chin Wee Tan Antony W Burgess David W Smith |
author_sort |
Bruce S Gardiner |
title |
Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components. |
title_short |
Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components. |
title_full |
Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components. |
title_fullStr |
Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components. |
title_full_unstemmed |
Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components. |
title_sort |
discrete element framework for modelling extracellular matrix, deformable cells and subcellular components. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Computational Biology |
issn |
1553-734X 1553-7358 |
publishDate |
2015-10-01 |
description |
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. |
url |
http://europepmc.org/articles/PMC4599884?pdf=render |
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