Johnson, Connah G. M. (2022) Developing hybrid continuum-discrete models for the study of environment-metabolism feedback in cellular systems. PhD thesis, University of Warwick.

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Abstract

Cellular systems are ubiquitous in nature. They form tissues and multicellular organisms where the cell interactions form complex biological structures. Understanding cell system dynamics is of vital importance to a range of fields, such as in medical infection studies and natural product production in industrial bioreactors. Cells change their environment to form ecological niches through the excretion and uptake of chemicals which form complex chemical gradients that influence organisation and signalling between cells. However, how cell growth rate changes and the organisation of different species emerge from these gradients is unclear. Here, we are concerned with developing methods to understand the impact that these feedback cycles may have on the development of cell systems. Mathematical modelling can help us improve our understanding of such systems with the aim to facilitate the design of informative experiments. However, no general simulation framework is widely available to study these problems. Therefore we introduce ChemChaste, a software framework that couples an extensive agent based model to reaction-diffusion partial differential equation solvers. ChemChaste builds and expands the capabilities of the Chaste software and we introduce a powerful method to solve the complex cell-environment problems necessary to elucidate the complex chemical interactions occurring within cell systems. Using ChemChaste we explore and demonstrate some illustrative cases to show how cell systems can change their environment and how environment feedback can change the species proliferation through simple chemical excretions and uptake. Therein we motivate the importance of considering the cell-environment feedback in modelling cell systems.

Item Type:	Thesis (PhD)
Subjects:	Q Science > QA Mathematics Q Science > QH Natural history Q Science > QR Microbiology
Library of Congress Subject Headings (LCSH):	Biofilms -- Mathematical models, Cellular control mechanisms -- Mathematical models, Microbial ecology -- Computer programs, Feedback control systems, Biological control systems -- Mathematical models, Cells -- Evolution
Official Date:	April 2022
Dates:	Date Event April 2022 UNSPECIFIED
Institution:	University of Warwick
Theses Department:	Centre for Complexity Science
Thesis Type:	PhD
Publication Status:	Unpublished
Supervisor(s)/Advisor:	Soyer, Orkun S.
Format of File:	pdf
Extent:	xii, 211 pages : illustrations, charts
Language:	eng

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