Sayyid, Faiz (2016) Computational models of morphology's effects on cellular dynamics. PhD thesis, University of Warwick.

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Abstract

Spatial effects such as cell shape, internal cellular organisation and cellular plasticity have very often been considered negligible in models of cellular pathways, and many existing simulation infrastructures do not take such effects into consideration. However, recent experimental results and systems level theories suggest that even small variations in shape can make a large difference to the fate of the cell. This is particularly the case when considering eukaryotic cells, which have a complex physical structure and many subtle control mechanisms. Bacteria are also interesting for their variation in shape, both between species and in different states of adaptation.

In this thesis we perform simulations that quantify the effect of three aspects of morphology - external cellular shape, internal cellular organisation and processes that change the shape of the cell - on the behaviour of model cellular pathways. To perform these simulations we develop Reaction-Diffusion Cell (ReDi-Cell), a highly scalable General Purpose Graphics Processing Unit Computing (GPGPU) cell simulation infrastructure for the modelling of cellular pathways in spatially detailed environments. ReDi-Cell is validated against known-good simulations, prior to its use in new work.

By measuring reaction trajectories and concentration gradients we quantify the responses of simulated cellular pathways to these three spatial aspects. Our results show that model cell behaviour is the composite of cellular morphology and reaction system. Different reaction systems display different dynamics even when placed in identical environments.

Traditionally, computational approaches to cell biology have been focussed upon investigating how changes to reaction dynamics alter cellular behaviour. This thesis, on the other hand, demonstrates another way in which reaction dynamics can be altered, by changing the morphology of the cell.

Item Type:	Thesis or Dissertation (PhD)
Subjects:	Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software
Library of Congress Subject Headings (LCSH):	Cells -- Morphology -- Computer simulation, Cytology -- Computer simulation, Molecular dynamics -- Computer simulation, Cellular control mechanisms -- Computer simulation, Reaction-diffusion equations, Differential equations
Official Date:	September 2016
Dates:	Date Event September 2016 Submitted
Institution:	University of Warwick
Theses Department:	Department of Computer Science
Thesis Type:	PhD
Publication Status:	Unpublished
Supervisor(s)/Advisor:	Kalvala, Sara
Sponsors:	Engineering and Physical Sciences Research Council
Format of File:	pdf
Extent:	263 leaves : illustrations, charts
Language:	eng

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