Relevant bibliographies by topics / Mathematical modelling/biology / Dissertations / Theses
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Dissertations / Theses on the topic 'Mathematical modelling/biology'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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1

Hunt, Gordon S. "Mathematical modelling of pattern formation in developmental biology." Thesis, Heriot-Watt University, 2013. http://hdl.handle.net/10399/2706.

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The transformation from a single cell to the adult form is one of the remarkable wonders of nature. However, the fundamental mechanisms and interactions involved in this metamorphic change still remain elusive. Due to the complexity of the process, researchers have attempted to exploit simpler systems and, in particular, have focussed on the emergence of varied and spectacular patterns in nature. A number of mathematical models have been proposed to study this problem with one of the most well studied and prominent being the novel concept provided by A.M. Turing in 1952. Turing's simple yet el
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2

Nurtay, Anel. "Mathematical modelling of pathogen specialisation." Doctoral thesis, Universitat Autònoma de Barcelona, 2019. http://hdl.handle.net/10803/667178.

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L’aparició de nous virus causants de malalties està estretament lligada a l’especialització de subpoblacions virals cap a nous tipus d’amfitrions. La modelització matemàtica proporciona un marc quantitatiu que pot ajudar amb la predicció de processos a llarg termini com pot ser l’especialització. A causa de la naturalesa complexa que presenten les interaccions intra i interespecífiques en els processos evolutius, cal aplicar eines matemàtiques complexes, com ara l’anàlisi de bifurcacions, al estudiar dinàmiques de població. Aquesta tesi desenvolupa una jerarquia de models de població per poder
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3

Rata, Scott. "Mathematical modelling of mitotic controls." Thesis, University of Oxford, 2018. https://ora.ox.ac.uk/objects/uuid:7bef862c-2025-4494-a2bb-4fe93584d92a.

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The mitotic cell cycle is fundamental to eukaryotic life. In mitosis, replicated chromosomes are segregated to form two new nuclei. This is essential to ensure the maintenance of chromosome number between parent and daughter cells. In higher eukaryotes, numerous cytological changes occur to facilitate the separation of the genetic material: the nuclear envelope breaks down, the mitotic spindle assembles, and the cell rounds-up. There is a well-conserved control network that regulates these processes to bring about the entry into mitosis, the separation of the genetic material, and the reversal
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4

Catt, Christopher Joseph. "Mathematical modelling of tissue metabolism and growth." Thesis, University of Southampton, 2010. https://eprints.soton.ac.uk/176447/.

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The work presented in this thesis is concerned with modelling the growth of tissue constructs, with particular focus on the effects the local micro environment has on the cell cycle and metabolism. We consider two cases; multicellular tumour spheroids and orthopaedic tissue constructs. This thesis is divided into two parts. In the first part we will present a multispecies model of an avascular tumour that studies how a cell’s metabolism affects the cell cycle, spheroid growth and the mechanical forces that arise during growth. The second part consists of a study of the growth of an engineered
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Modhara, Sunny. "Mathematical modelling of vascular development in zebrafish." Thesis, University of Nottingham, 2015. http://eprints.nottingham.ac.uk/29125/.

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The Notch signalling pathway is pivotal in ensuring that the processes of arterial specification, angiogenic sprouting and haematopoietic stem cell (HSC) specification are correctly carried out in the dorsal aorta (DA), a primary arterial blood vessel in developing vertebrate embryos. Using the zebrafish as a model organism, and additional experimental observations from mouse and cell line models to guide mathematical modelling, this thesis aims to better understand the mechanisms involved in the establishment of a healthy vasculature in the growing embryo. We begin by studying arterial and HS
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6

Durney, Clinton H. "A Two-Component Model For Bacterial Chemotaxis." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1366312981.

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7

Moi, Adriano. "Mathematical modelling of integrin-like receptors systems." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2016. http://amslaurea.unibo.it/11255/.

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Nel presente lavoro, ho studiato e trovato le soluzioni esatte di un modello matematico applicato ai recettori cellulari della famiglia delle integrine. Nel modello le integrine sono considerate come un sistema a due livelli, attivo e non attivo. Quando le integrine si trovano nello stato inattivo possono diffondere nella membrana, mentre quando si trovano nello stato attivo risultano cristallizzate nella membrana, incapaci di diffondere. La variazione di concentrazione nella superficie cellulare di una sostanza chiamata attivatore dà luogo all’attivazione delle integrine. Inoltre, questi ete
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8

Bakshi, Suruchi D. "Mathematical modelling of Centrosomin incorporation in Drosophila centrosomes." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:baefde65-bc38-4a11-bd92-e2e4cccad784.

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Centrosomin (Cnn) is an integral centrosomal protein in Drosophila with orthologues in several species, including humans. The human orthologue of Cnn is required for brain development with Cnn hypothesised to play a similar role in Drosophila. Control of Cnn incorporation into centrosomes is crucial for controlling asymmetric division in certain types of Drosophila stem cells. FRAP experiments on Cnn show that Cnn recovers in a pe- culiar fashion, which suggest that Cnn may be incorporated closest to the centrioles and then spread radially outward, either diffusively or ad- vectively. The aim
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9

Chapman, Lloyd A. C. "Mathematical modelling of cell growth in tissue engineering bioreactors." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:7c9ee131-7d9b-4e5d-8534-04a059fbd039.

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Expanding cell populations extracted from patients or animals is essential to the process of tissue engineering and is commonly performed in laboratory incubation devices known as bioreactors. Bioreactors provide a means of controlling the chemical and mechanical environment experienced by cells to ensure growth of a functional population. However, maximising this growth requires detailed knowledge of how cell proliferation is affected by bioreactor operating conditions, such as the flow rate of culture medium into the bioreactor, and by the initial cell seeding distribution in the bioreactor.
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10

Osman, Mohamad Hussein. "Mathematical modelling and simulation of biofuel cells." Thesis, University of Southampton, 2013. https://eprints.soton.ac.uk/363762/.

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Bio-fuel cells are driven by diverse and abundant bio-fuels and biological catalysts. The production/consumption cycle of bio-fuels is considered to be carbon neutral and, in principle, more sustainable than that of conventional fuel cells. The cost benefits over traditional precious-metal catalysts, and the mild operating conditions represent further advantages. It is important that mathematical models are developed to reduce the burden on laboratory based testing and accelerate the development of practical systems. In this study, recent key developments in bio-fuel cell technology are review
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11

Shabala, Alexander. "Mathematical modelling of oncolytic virotherapy." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:cca2c9bc-cbd4-4651-9b59-8a4dea7245d1.

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This thesis is concerned with mathematical modelling of oncolytic virotherapy: the use of genetically modified viruses to selectively spread, replicate and destroy cancerous cells in solid tumours. Traditional spatially-dependent modelling approaches have previously assumed that virus spread is due to viral diffusion in solid tumours, and also neglect the time delay introduced by the lytic cycle for viral replication within host cells. A deterministic, age-structured reaction-diffusion model is developed for the spatially-dependent interactions of uninfected cells, infected cells and virus par
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12

Wearing, Helen Jane. "Mathematical modelling of cell-cell signalling in developmental biology and wound healing." Thesis, Heriot-Watt University, 2001. http://hdl.handle.net/10399/1184.

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Cobbold, Christina Anne. "Mathematical modelling of problems in human biology : dermal wound healing and atherosclerosis." Thesis, Heriot-Watt University, 2001. http://hdl.handle.net/10399/471.

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14

Schofield, James W. "Aspects of modelling solid tumours." Thesis, University of Oxford, 2010. http://ora.ox.ac.uk/objects/uuid:b7c50880-ed03-451e-9841-209f2de6a982.

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This thesis considers aspects of modelling solid tumours. We begin by considering the common assumption that nutrient or drug concentrations in avascular tumour spheroids are radially symmetric. We derive a simple Poisson equation for biomolecular diffusion into an avascular tumour, but with highly oscillatory boundary conditions due to the surrounding capillary network. We find that the assumption of radial symmetry is legitimate for biomolecules that are taken up in sufficient quantities by proliferating cancer cells; however radially symmetric profiles need not be observed otherwise. We the
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15

Gadelha, Hermes. "Mathematical modelling of human sperm motility." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:34a11669-5d14-470b-b10b-361cf3688a30.

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The propulsion mechanics driving the movement of living cells constitutes one of the most incredible engineering works of nature. Active cell motility via the controlled movement of a flagellum beating is among the phylogentically oldest forms of motility, and has been retained in higher level organisms for spermatozoa transport. Despite this ubiquity and importance, the details of how each structural component within the flagellum is orchestrated to generate bending waves, or even the elastic material response from the sperm flagellum, is far from fully understood. By using microbiomechanical
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16

McGillen, Jessica Buono. "Mathematical modelling of metabolism and acidity in cancer." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:552f9ea8-ac6c-4413-9535-0318e855d85c.

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Human cancers exhibit the common phenotype of elevated glycolytic metabolism, which causes acidification of the tissue microenvironment and may facilitate tumour invasion. In this thesis, we use mathematical models to address a series of open problems underlying the glycolytic tumour phenotype and its attendant acidity. We first explore tissue-scale consequences of metabolically-derived acid. Incorporating more biological detail into a canonical model of acidity at the tumour-host interface, we extend the range of tumour behaviours captured by the modelling framework. We then carry out an asym
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17

Podéus, Henrik. "Neural response of a Neuron population : A mathematical modelling approach." Thesis, Linköpings universitet, Avdelningen för medicinsk teknik, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-177797.

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The brain – the organ that allows us to be aware of our surroundings – consists of a complex network of neurons, which seemingly allows the human brain to be able of abstract thinking, emotions, and cognitive function. To learn how the brain is capable of this, the two main branches of neuroscience study either neurons in detail, or how they communicate within neuronal networks. Both these branches often tackle the complexity using a combination of experiments and mathematical modelling. A third and less studied aspect of neuroscience concerns the neurovascular coupling (NVC), for which my res
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Szekely, Tamas. "Stochastic modelling and simulation in cell biology." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:f9b8dbe6-d96d-414c-ac06-909cff639f8c.

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Modelling and simulation are essential to modern research in cell biology. This thesis follows a journey starting from the construction of new stochastic methods for discrete biochemical systems to using them to simulate a population of interacting haematopoietic stem cell lineages. The first part of this thesis is on discrete stochastic methods. We develop two new methods, the stochastic extrapolation framework and the Stochastic Bulirsch-Stoer methods. These are based on the Richardson extrapolation technique, which is widely used in ordinary differential equation solvers. We believed that i
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19

Pearson, Natalie Clare. "Mathematical modelling of flow and transport phenomena in tissue engineering." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:43688cc7-b523-4676-8c41-72db7fc07814.

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Tissue engineering has great potential as a method for replacing or repairing lost or damaged tissue. However, progress in the field to date has been limited, with only a few clinical successes despite active research covering a wide range of cell types and experimental approaches. Mathematical modelling can complement experiments and help improve understanding of the inherently complex tissue engineering systems, providing an alternative perspective in a more cost- and time-efficient manner. This thesis focusses on one particular experimental setup, a hollow fibre membrane bioreactor (HFMB).
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20

Shipley, Rebecca Julia. "Multiscale modelling of fluid and drug transport in vascular tumours." Thesis, University of Oxford, 2009. http://ora.ox.ac.uk/objects/uuid:8f663f70-8d23-49ad-8348-1763359d8f62.

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Understanding the perfusion of blood and drugs in tumours is fundamental to foreseeing the efficacy of treatment regimes and predicting tumour growth. In particular, the dependence of these processes on the tumour vascular structure is poorly established. The objective of this thesis is to derive effective equations describing blood, and drug perfusion in vascular tumours, and specifically to determine the dependence of these on the tumour vascular structure. This dependence occurs through the interaction between two different length scales - that which characterizes the structure of the vascular n
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21

Duchesne, Ronan. "Erythroid differentiation in vitro under the lens of mathematical modelling." Thesis, Lyon, 2019. http://www.theses.fr/2019LYSEN082.

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Depuis quelques années, de plus en plus d’études démontrent que la différenciation cellulaire est accompagnée d’une augmentation de la variabilité de l’expression des gènes. L’hypothèse de notre équipe est que cette variabilité influence en retour la différenciation. Pour tester cette hypothèse, nous avons identifié trois drogues chimiques (l’artémisinine,l’indométhacine et MB3) qui influencent à la fois cette variabilité, et le nombre de cellules différenciées dans une culture de progéniteurs érythocytaires aviaires. Cette thèse, divisée en deux parties, s’inscrit dans la continuité de ces ob
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22

Norris, Eleanor S. "Modelling the growth of avascular tumours and their response to chemotherapy." Thesis, University of Nottingham, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.246319.

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23

Goodes, L. R. "Observation and prediction of biocide release with fluorescence techniques and mathematical modelling." Thesis, University of Southampton, 2013. https://eprints.soton.ac.uk/360332/.

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Antifouling coatings are crucial for protection of vessels’ hulls against marine biofouling. A range of technologies is available, although biocidal coatings - containing toxic or deterrent compounds – still represent a majority of the market. A long-term goal is the development of less environmentally harmful and persistent compounds; one of many potential avenues is that of synthetic analogues of natural products from marine organisms. The development of coatings using natural products has been hampered by poor performance in the field without sufficient work on their leach rates and behavio
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24

Martins, Bruno Miguel Cardoso. "Mathematical modelling of signal sensing and transduction : revisiting classical mechanisms." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/17969.

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The ability of cells to react to changes in their environment is critical to their survival. Effective decision making strategies leading to the activation of specific intracellular pathways hinge on cells sensing and processing extracellular variation. We will only be able to understand and manipulate how cells make decisions if we understand the “design” of the mechanisms that enable them to make such decisions, in terms of how they function, and in terms of their limitations and architecture. In this thesis, using mathematical modelling, I revisited classical signal sensing and transduction
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25

Bowden, Lucie Grace. "Mathematical approaches to modelling healing of full thickness circular skin wounds." Thesis, University of Oxford, 2015. http://ora.ox.ac.uk/objects/uuid:f28f39d3-923d-45ac-8faf-2750d8e8f96e.

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Wound healing is a complex process, in which a sequence of interrelated events at both the cell and tissue levels interact and contribute to the reduction in wound size. For diabetic patients, many of these processes are compromised, so that wound healing slows down and in some cases halts. In this thesis we develop a series of increasingly detailed mathematical models to describe and investigate healing of full thickness skin wounds. We begin by developing a time-dependent ordinary differential equation model. This phenomenological model focusses on the main processes contributing to closure
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Gilbert, Mark. "Modelling species invasions in heterogeneous landscapes." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:944d15d3-257a-47e5-acb9-9bdfba26985b.

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Biological invasions are devastating ecosystems and economies world-wide, while many native species' survival depends on their ability to track climate change. Characterising the spread of biological populations is therefore of utmost importance, and can be studied with spatially explicit, discrete-time integro-difference equations (IDEs), which reflect numerous species' processes of demography and dispersal. While spatial variation has often been ignored when implementing IDE models, real landscapes are rarely spatially uniform and environmental variation is crucial in determining biological
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Rosser, Gabriel A. "Mathematical modelling and analysis of aspects of bacterial motility." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:1af98367-aa2f-4af3-9344-8c361311b553.

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The motile behaviour of bacteria underlies many important aspects of their actions, including pathogenicity, foraging efficiency, and ability to form biofilms. In this thesis, we apply mathematical modelling and analysis to various aspects of the planktonic motility of flagellated bacteria, guided by experimental observations. We use data obtained by tracking free-swimming Rhodobacter sphaeroides under a microscope, taking advantage of the availability of a large dataset acquired using a recently developed, high-throughput protocol. A novel analysis method using a hidden Markov model for the i
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Bentil, Daniel Ekow. "Aspects of dynamic pattern generation in embryology and epidemiology." Thesis, University of Oxford, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.276528.

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Connor, Anthony J. "In silico modelling of tumour-induced angiogenesis." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:f6b6c496-3adb-43c4-a3b3-aaf4d1b866b4.

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Angiogenesis, the process by which new vessels form from existing ones, is a key event in the development of a large and malignant vascularised tumour. A rapid expansion in in vivo and in vitro angiogenesis research in recent years has led to increased knowledge about the processes underlying angiogenesis and to promising steps forward in the development of anti-angiogenic therapies for the treatment of various cancers. However, substantial gaps in knowledge persist and the development of effective treatments remains a major challenge. In this thesis we study tumour-induced angiogenesis within
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Li, Liren. "Modelling of calcium handling in genetically modified mice." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:fa351516-9b3c-43c0-8bdc-5b0317cd5967.

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This thesis develops biophysically-based data-driven mathematical models of intracellular calciumdynamics in ventricularmyocytes for both normal and genetically modified mouse hearts, based on species- and temperature-consistent experimental data. The models were subsequently applied to quantitatively examine the changes in calcium dynamics in mice with cardiomyocyte-specific knockout (KO) of the cardiac sarco/endoplasmic reticulum ATPase (SERCA2) gene, to determine the contributing mechanisms which underlie the ultimate development of heart failure in these animals. In Chapter 1, with emphasi
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Johnston, Matthew David. "Mathematical modelling of cell population dynamics in the colonic crypt with application to colorectal cancer." Thesis, University of Oxford, 2008. http://ora.ox.ac.uk/objects/uuid:eb1daf53-203c-4ed5-a8af-ab261a61a88c.

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Colorectal cancer has the third highest mortality and incidence rates of all cancers worldwide, but the prognosis for long-term survival is good if diagnosed early. It is a well-characterised disease, and is initiated in colonic crypts which line the colon wall. The aim of this thesis is to use mathematical modelling to describe the heavily regulated cell renewal cycle in the crypt to determine the key features of the system kinetics, and help to explain the initiation of tumourigenesis. The dynamics of a single colorectal crypt is considered using a compartmental approach, which accounts for
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Koivumäki, J. (Jussi). "Regulation of excitation-contraction coupling in cardiac myocytes:insights from mathematical modelling." Doctoral thesis, University of Oulu, 2009. http://urn.fi/urn:isbn:9789514293047.

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Abstract Background – The heart cell is a prime example of a system, in which numerous interconnected regulatory mechanisms affect the dynamic balance of cellular function. The function of the system emerges from the interactions of its components rather than from their individual properties. Thus, it is a challenging task to understand the causal relations within such a system, based on the analysis of experimental results. Facing this complexity, the systems biological approach has gained interest during recent years, since with using it we can make an effort to observe, quantitatively and s
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Moxon, Thomas Edward. "Mathematical modelling of gastric emptying and nutrient absorption in the human digestive system." Thesis, University of Birmingham, 2017. http://etheses.bham.ac.uk//id/eprint/7857/.

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Mathematical modelling of the digestive system can be achieved by assuming the digestive system is described as a series of ideal reactors. A well formulated model could give an understanding of how food products behave within the body, and offer some predictive possibility allowing the design of functional foods to have tailored nutritional responses. The models developed showed good estimates of the gastric emptying rates and glucose absorption rates for solutions with different viscosities and glucose concentrations, when a feedback mechanism is included. Implementing a population balance f
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Smith, Robert William. "Mathematical modelling of photoperiodic external coincidence mechanisms in the model plant, Arabidopsis thaliana." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/11734.

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As plants are sessile organisms, processes controlling plant growth and development must react to fluctuations in the external environment to aid plant survival. However, as the climate of the Earth changes and becomes more extreme, plants become less able to develop to their optimal capacity and this can have an adverse effect on crop yield and biofuel feedstock production. Thus, it is becoming increasingly important to understand the molecular mechanisms used by plants to respond to external stimuli. One important system that plants utilise in their response to environmental fluctuations is
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Batenchuk, Cory. "Development of a Mathematical Model to Understand, Design & Improve Oncolytic Virus Therapies." Thesis, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31182.

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Oncolytic viruses (OVs) are emerging as a potent therapeutic platform for the treatment of malignant disease. The tumor cells inability to induce antiviral defences in response to a small cytokine known as interferon (IFN) is a common defect exploited by OVs. Heterogeneity in IFN signalling across tumors is therefore a pillar element of resistance to these therapies. I have generated a mathematical model and simulation platform to study the impact of IFN on OV dynamics in normal and cancerous tissues. In the first part of my thesis, I used this model to identify novel OV engineering strategies
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Leonard, Katherine H. L. "Mathematical and computational modelling of tissue engineered bone in a hydrostatic bioreactor." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:05845740-1a74-4e19-95ea-6b5229d1af27.

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In vitro tissue engineering is a method for developing living and functional tissues external to the body, often within a device called a bioreactor to control the chemical and mechanical environment. However, the quality of bone tissue engineered products is currently inadequate for clinical use as the implant cannot bear weight. In an effort to improve the quality of the construct, hydrostatic pressure, the pressure in a fluid at equilibrium that is required to balance the force exerted by the weight of the fluid above, has been investigated as a mechanical stimulus for promoting extracellul
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Dyson, Louise. "Mathematical models of cranial neural crest cell migration." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:66955fb9-691f-4d27-ad26-39bb2b089c64.

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From the developing embryo to the evacuation of football stadiums, the migration and movement of populations of individuals is a vital part of human life. Such movement often occurs in crowded conditions, where the space occupied by each individual impacts on the freedom of others. This thesis aims to analyse and understand the effects of occupied volume (volume exclusion) on the movement of the individual and the population. We consider, as a motivating system, the rearrangement of individuals required to turn a clump of cells into a functioning embryo. Specifically, we consider the migration
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Maddison, Louise. "Experimental and theoretical modelling of the MAPK pathway." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/experimental-and-theoretical-modelling-of-the-mapk-pathway(46773da5-85dd-4a3f-8e6c-e3559ba04f46).html.

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The MAPK pathway plays a crucial role in regulating cellular response to external stimuli. Binding of growth factors and other mitogenic signals to cell surface receptors initiates a phosphorylation-dependent relay of protein activation, resulting in altered transcription, ultimately regulating cell proliferation and differentiation. Signalling through this pathway is regulated by the coordinated function of specific protein kinases and protein phosphatases. As perturbation of this signalling system is often associated with diseases such as cancer, modelling is a useful means to help understan
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González, Flo Eva 1993. "Engineering living biomedical devices : Mathematical and experimental tools for the rational design of cellular devices." Doctoral thesis, TDX (Tesis Doctorals en Xarxa), 2020. http://hdl.handle.net/10803/670358.

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The engineering of biology strives on the creation of biological devices concerning society-impact applications. In this PhD thesis, we developed mathematical and experimental tools for the standard and rational design of living devices for biomedical purposes, offering robust and reliable responses. By breaking-up cellular device complexity into functional modules, we have analysed how extracellular information is detected, processed and transformed thanks to re-engineering intrinsic cellular components. We show how the desired range of action of a biosensor could be tuned by modifying the re
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Mohd, Jaffar Mai. "Mathematical models of hyphal tip growth." Thesis, University of Dundee, 2012. https://discovery.dundee.ac.uk/en/studentTheses/140f9a81-12ca-4337-a311-2f82441f1ea6.

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Filamentous fungi are important in an enormous variety of ways to our life, with examples ranging from bioremediation, through the food and drinks industry to human health. These organisms can form huge networks stretching metres and even kilometres. However, their mode of growth is by the extension of individual hyphal tips only a few microns in diameter. Tip growth is mediated by the incorporation of new wall building materials at the soft apex. Just how this process is controlled (in fungi and in cell elongation in other organisms) has been the subject of intense study over many years and h
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Gill, Mandeep Singh. "Application of software engineering methodologies to the development of mathematical biological models." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:35178f3a-7951-4f1c-aeab-390cdd622b05.

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Mathematical models have been used to capture the behaviour of biological systems, from low-level biochemical reactions to multi-scale whole-organ models. Models are typically based on experimentally-derived data, attempting to reproduce the observed behaviour through mathematical constructs, e.g. using Ordinary Differential Equations (ODEs) for spatially-homogeneous systems. These models are developed and published as mathematical equations, yet are of such complexity that they necessitate computational simulation. This computational model development is often performed in an ad hoc fashion b
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Blount, Kathryn. "Cancer systems biology : is the devil in the glycolytic detail?" Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/cancer-systems-biology-is-the-devil-in-the-glycolytic-detail(e0ad0c6b-76ec-4bba-8dd3-b583910f46f4).html.

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An approach to investigating cancer that has recently seen resurgence of interest is the “Warburg effect”. Otto Warburg originally described the altered metabolism of cancer cells and identified that they exhibit an increase in glucose uptake and lactate production. This up-regulation of glycolytic flux and glucose transport is now associated with 90% of cancers. In order to improve the overall understanding of the “Warburg effect” two forms of systems biology have been implemented - comparative in vitro analysis of kinetic activities and dynamic modelling. In this analysis, human breast cance
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43

Nguyen, Lan K. "Dynamical modelling of feedback gene regulatory networks." Diss., Lincoln University, 2009. http://hdl.handle.net/10182/1340.

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Living cells are made up of networks of interacting genes, proteins and other bio-molecules. Simple interactions between network components in forms of feedback regulations can lead to complex collective dynamics. A key task in cell biology is to gain a thorough understanding of the dynamics of intracellular systems and processes. In this thesis, a combined approach of mathematical modelling, computational simulation and analytical techniques, has been used to obtain a deeper insight into the dynamical aspects of a variety of feedback systems commonly encountered in cells. These systems range
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Shum, Henry. "Simulations and modelling of bacterial flagellar propulsion." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:c9f002d8-2939-4744-987e-9a4e659d93ef.

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Motility of flagellated bacteria has been a topic of increasing scientific interest over the past decades, attracting the attention of mathematicians, physicists, biologists and engineers alike. Bacteria and other micro-organisms cause substantial damage through biofilm growth on submerged interfaces in water cooling systems, ship hulls and medical implants. This gives social and economic motivations for learning about how micro-organisms swim and behave in different environments. Fluid flows on such small scales are dominated by viscosity and therefore behave differently from the inertia-domi
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Franz, Benjamin. "Recent modelling frameworks for systems of interacting particles." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:ac76d159-4cdd-40c9-b378-6ea1faf48aed.

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In this thesis we study three different modelling frameworks for biological systems of dispersal and combinations thereof. The three frameworks involved are individual-based models, group-level models in the form of partial differential equations (PDEs) and robot swarms. In the first two chapters of the thesis, we present ways of coupling individual based models with PDEs in so-called hybrid models, with the aim of achieving improved performance of simulations. Two classes of such hybrid models are discussed that allow an efficient simulation of multi-species systems of dispersal with reaction
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46

Robison, Pamula J. "Mathematical Modelling of Biofilm Growth and Decay Through Various Deliveries of Antimicrobial." University of Akron / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=akron1258769688.

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Smith, Amy. "Multi-scale modelling of blood flow in the coronary microcirculation." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:e6f576a2-75d9-4778-a640-a1e8551141a6.

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The importance of coronary microcirculatory perfusion is highlighted by the severe impact of microvascular diseases such as diabetes and hypertension on heart function. Recently, highly-detailed three-dimensional (3D) data on ex vivo coronary microvascular structure have become available. However, hemodynamic information in individual myocardial capillaries cannot yet be obtained using current in vivo imaging techniques. In this thesis, a novel data-driven modelling framework is developed to predict tissue-scale flow properties from discrete anatomical data, which can in future be used to aid
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Alshammari, Abdullah A. A. M. F. "Mathematical modelling of oxygen transport in skeletal and cardiac muscles." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:65a34cb0-ef00-44c9-a04d-4147844c76ac.

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Understanding and characterising the diffusive transport of capillary oxygen and nutrients in striated muscles is key to assessing angiogenesis and investigating the efficacy of experimental and therapeutic interventions for numerous pathological conditions, such as chronic ischaemia. In articular, the influence of both muscle tissue and microvascular heterogeneities on capillary oxygen supply is poorly understood. The objective of this thesis is to develop mathematical and computational modelling frameworks for the purpose of extending and generalising the current use of histology in estimati
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Al-Nuaimi, Yusur Mamoon. "A systems biology approach to the human hair cycle." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/a-systems-biology-approach-to-the-human-hair-cycle(a576aff0-5fbe-4db6-9e13-8211f07e2883).html.

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The hair cycle represents a dynamic process during which a complex mini- organ, the hair follicle, rhythmically regresses and regenerates. The control mechanism that governs the hair cycle ('hair cycle clock') is thought to be an autonomous oscillator system, however, its exact nature is not known. This thesis aims to understand the human hair cycle as a systems biology problem using theoretical and experimental techniques in three distinct study approaches. Using mathematical modelling, a simple two-compartment model of the human hair cycle was developed. The model concentrates on the growth
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Dunn, Sara-Jane Nicole. "Towards a computational model of the colonic crypt with a realistic, deformable geometry." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:c3c9440a-52ac-4a3d-8e1c-5dc276b8eb6c.

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Colorectal cancer (CRC) is one of the most prevalent and deadly forms of cancer. Its high mortality rate is associated with difficulties in early detection, which is crucial to survival. The onset of CRC is marked by macroscopic changes in intestinal tissue, originating from a deviation in the healthy cell dynamics of glands known as the crypts of Lieberkuhn. It is believed that accumulated genetic alterations confer on mutated cells the ability to persist in the crypts, which can lead to the formation of a benign tumour through localised proliferation. Stress on the crypt walls can lead to bu
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