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Dissertations / Theses on the topic 'Cell Division - Stochastic Simulation'

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Published: 7 September 2023

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1

Morton-Firth, Carl Jason. "Stochastic simulation of cell signalling pathways." Thesis, University of Cambridge, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.625063.

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2

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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3

Chen, Minghan. "Stochastic Modeling and Simulation of Multiscale Biochemical Systems." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/90898.

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Numerous challenges arise in modeling and simulation as biochemical networks are discovered with increasing complexities and unknown mechanisms. With the improvement in experimental techniques, biologists are able to quantify genes and proteins and their dynamics in a single cell, which calls for quantitative stochastic models for gene and protein networks at cellular levels that match well with the data and account for cellular noise. This dissertation studies a stochastic spatiotemporal model of the Caulobacter crescentus cell cycle. A two-dimensional model based on a Turing mechanism is in

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4

Biehler, Eike [Verfasser], Werner [Akademischer Betreuer] Nagel, and Richard [Akademischer Betreuer] Cowan. "Cell division processes in tessellations : a stochastic geometry approach / Eike Biehler. Gutachter: Werner Nagel ; Richard Cowan." Jena : Thüringer Universitäts- und Landesbibliothek Jena, 2012. http://d-nb.info/1029294216/34.

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5

Ahmadian, Mansooreh. "Hybrid Modeling and Simulation of Stochastic Effects on Biochemical Regulatory Networks." Diss., Virginia Tech, 2020. http://hdl.handle.net/10919/99481.

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A complex network of genes and proteins governs the robust progression through cell cycles in the presence of inevitable noise. Stochastic modeling is viewed as a key paradigm to study the effects of intrinsic and extrinsic noise on the dynamics of biochemical networks. A detailed quantitative description of such complex and multiscale networks via stochastic modeling poses several challenges. First, stochastic models generally require extensive computations, particularly when applied to large networks. Second, the accuracy of stochastic models is highly dependent on the quality of the paramet

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6

Charlebois, Daniel A. "An algorithm for the stochastic simulation of gene expression and cell population dynamics." Thesis, University of Ottawa (Canada), 2010. http://hdl.handle.net/10393/28755.

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Over the past few years, it has been increasingly recognized that stochastic mechanisms play a key role in the dynamics of biological systems. Genetic networks are one example where molecular-level fluctuations are of particular importance. Here stochasticity in the expression of gene products can result in genetically identical cells in the same environment displaying significant variation in biochemical or physical attributes. This variation can influence individual and population-level fitness. In this thesis we first explore the background required to obtain analytical solutions and perfor

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7

Wang, Shuo. "Analysis and Application of Haseltine and Rawlings's Hybrid Stochastic Simulation Algorithm." Diss., Virginia Tech, 2016. http://hdl.handle.net/10919/82717.

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Stochastic effects in cellular systems are usually modeled and simulated with Gillespie's stochastic simulation algorithm (SSA), which follows the same theoretical derivation as the chemical master equation (CME), but the low efficiency of SSA limits its application to large chemical networks. To improve efficiency of stochastic simulations, Haseltine and Rawlings proposed a hybrid of ODE and SSA algorithm, which combines ordinary differential equations (ODEs) for traditional deterministic models and SSA for stochastic models. In this dissertation, accuracy analysis, efficient implementation

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8

Joubaud, Maud. "Processus de Markov déterministes par morceaux branchants et problème d’arrêt optimal, application à la division cellulaire." Thesis, Montpellier, 2019. http://www.theses.fr/2019MONTS031/document.

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Les processus markoviens déterministes par morceaux (PDMP) forment une vaste classe de processus stochastiques caractérisés par une évolution déterministe entre des sauts à mécanisme aléatoire. Ce sont des processus de type hybride, avec une composante discrète de mode et une composante d’état qui évolue dans un espace continu. Entre les sauts du processus, la composante continue évolue de façon déterministe, puis au moment du saut un noyau markovien sélectionne la nouvelle valeur des composantes discrète et continue. Dans cette thèse, nous construisons des PDMP évoluant dans des espaces de me

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9

Dao, Duc Khanh. "Modeling and analysis of neuronal networks, stochastic chemical reactions in cellular micro-domains and telomere dynamics." Paris 6, 2013. http://www.theses.fr/2013PA066513.

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Nous modélisons différents évènements aléatoires intervenant en biologie. Dans une première partie, on étudie certaines propriétés de populations de neurones. En utilisant un modèle de facilitation dépression synaptique, on étudie le phénomène de bursts synchrones observés à différentes échelles de populations. On étudie ensuite la transition entre état haut et bas de neurones induite par le bruit. Afin de comprendre le phénomène d’oscillations du temps de séjour dans l’état haut, onétudie le problème de premier temps de passage pour une classe de processus stochastiquesdans un domaine avec un

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10

Wollrab, Viktoria. "Active gels in vivo : patterns and dynamics in cytokinetic rings and their functions in cell division." Thesis, Strasbourg, 2014. http://www.theses.fr/2014STRAF027/document.

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Les structures d'acto-myosine sont impliquées dans de nombreuses fonctions cellulaires. Comprendre leur organisation et leur comportement collectif est toujours difficile. Nous avons étudié l'anneau cytokinétique dans les cellules de mammifères et dans les levures de fission, en orientant les cellules dans les microcavités, ce qui permet de voir l'anneau dans un seul plan focal. Avec cette configuration, nous révélons de nouvelles structures et des dynamiques distinctes pour les deux systèmes cellulaires. Dans les cellules de mammifères, nous trouvons des motifs réguliers de la myosine et la f

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11

Abdennur, Nezar A. "A Framework for Individual-based Simulation of Heterogeneous Cell Populations." Thèse, Université d'Ottawa / University of Ottawa, 2011. http://hdl.handle.net/10393/20478.

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An object-oriented framework is presented for developing and simulating individual-based models of cell populations. The framework supplies classes to define objects called simulation channels that encapsulate the algorithms that make up a simulation model. These may govern state-updating events at the individual level, perform global state changes, or trigger cell division. Simulation engines control the scheduling and execution of collections of simulation channels, while a simulation manager coordinates the engines according to one of two scheduling protocols. When the ensemble of cells bei

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12

Ahn, Tae-Hyuk. "Computational Techniques for the Analysis of Large Scale Biological Systems." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/77162.

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An accelerated pace of discovery in biological sciences is made possible by a new generation of computational biology and bioinformatics tools. In this dissertation we develop novel computational, analytical, and high performance simulation techniques for biological problems, with applications to the yeast cell division cycle, and to the RNA-Sequencing of the yellow fever mosquito. Cell cycle system evolves stochastic effects when there are a small number of molecules react each other. Consequently, the stochastic effects of the cell cycle are important, and the evolution of cells is best desc

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13

Charlebois, Daniel. "Computational Investigations of Noise-mediated Cell Population Dynamics." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/30339.

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Fluctuations, or "noise", can play a key role in determining the behaviour of living systems. The molecular-level fluctuations that occur in genetic networks are of particular importance. Here, noisy gene expression can result in genetically identical cells displaying significant variation in phenotype, even in identical environments. This variation can act as a basis for natural selection and provide a fitness benefit to cell populations under stress. This thesis focuses on the development of new conceptual knowledge about how gene expression noise and gene network topology influence drug re

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14

Lichtenstein, Joseph. "Low computational complexity bit error rate simulation for personal communications systems in multipath and fading environments." Thesis, This resource online, 1994. http://scholar.lib.vt.edu/theses/available/etd-06102009-063138/.

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15

Li, Yingjie. "Bit error rate simulation of a CDMA system for personal communications." Thesis, This resource online, 1993. http://scholar.lib.vt.edu/theses/available/etd-07282008-135717/.

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16

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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17

Meige, Albert, and albert@meige net. "Numerical modeling of low-pressure plasmas: applications to electric double layers." The Australian National University. Research School of Physical Sciences and Engineering, 2006. http://thesis.anu.edu.au./public/adt-ANU20070111.002333.

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Inductive plasmas are simulated by using a one-dimensional particle-in-cell simulation including Monte Carlo collision techniques (pic/mcc). To model inductive heating, a non-uniform radio-frequency (rf) electric field, perpendicular to the electron motion is included into the classical particle-in-cell scheme. The inductive plasma pic simulation is used to confirm recent experimental results that electric double layers can form in current-free plasmas. These results differ from previous experimental or simulation systems where the double layers are driven by a current or by imposed potential

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18

Magno, Alessandra Cristina Gomes. "Relação entre o volume da célula e dinâmica do ciclo celular em mamíferos." Universidade Federal de Juiz de Fora (UFJF), 2016. https://repositorio.ufjf.br/jspui/handle/ufjf/4784.

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19

Lautenschlager, Willian Wagner. "Um modelo estocástico de simulação da dinâmica dos queratinócitos, melanócitos e melanomas no desenvolvimento dos tumores." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/100/100132/tde-21082017-174520/.

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Durante as últimas décadas, pesquisas em biologia do tumor com a utilização de novas técnicas de biologia molecular produziram informações em profusão, motivando e dando condições para que fossem criados novos modelos matemáticos dedicados à análise de vários aspectos de crescimento e proliferação da população celular. Alguns desses modelos têm sido dedicados à descrição e análise do regime estacionário do processo de desenvolvimento de uma população celular sob condições químicas que se consideram favorecer a aceleração ou desaceleração do crescimento da população de células tumorais. Todavia

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20

Erenay, Bulent. "Concurrent Supply Chain Network & Manufacturing Systems Design Under Uncertain Parameters." Ohio University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1459206318.

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21

Meacci, Giovanni. "Physical Aspects of Min Oscillations in Escherichia Coli." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2007. http://nbn-resolving.de/urn:nbn:de:swb:14-1169728830839-77682.

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The subject of this thesis is the generation of spatial temporal structures in living cells. Specifically, we studied the Min-system in the bacterium Escherichia coli. It consists of the MinC, the MinD, and the MinE proteins, which play an important role in the correct selection of the cell division site. The Min-proteins oscillate between the two cell poles and thereby prevent division at these locations. In this way, E. coli divides at the center, producing two daughter cells of equal size, providing them with the complete genetic patrimony. Our goal is to perform a quantitative study, both

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22

Friedrich, Benjamin M. "Nonlinear dynamics and fluctuations in biological systems." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-234307.

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The present habilitation thesis in theoretical biological physics addresses two central dynamical processes in cells and organisms: (i) active motility and motility control and (ii) self-organized pattern formation. The unifying theme is the nonlinear dynamics of biological function and its robustness in the presence of strong fluctuations, structural variations, and external perturbations. We theoretically investigate motility control at the cellular scale, using cilia and flagella as ideal model system. Cilia and flagella are highly conserved slender cell appendages that exhibit spontaneous

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23

Meacci, Giovanni. "Physical Aspects of Min Oscillations in Escherichia Coli." Doctoral thesis, Technische Universität Dresden, 2006. https://tud.qucosa.de/id/qucosa%3A23940.

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The subject of this thesis is the generation of spatial temporal structures in living cells. Specifically, we studied the Min-system in the bacterium Escherichia coli. It consists of the MinC, the MinD, and the MinE proteins, which play an important role in the correct selection of the cell division site. The Min-proteins oscillate between the two cell poles and thereby prevent division at these locations. In this way, E. coli divides at the center, producing two daughter cells of equal size, providing them with the complete genetic patrimony. Our goal is to perform a quantitative study, both

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24

Mauro, Ava J. "Numerical methods and stochastic simulation algorithms for reaction-drift-diffusion systems." Thesis, 2014. https://hdl.handle.net/2144/15259.

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In recent years, there has been increased awareness that stochasticity in chemical reactions and diffusion of molecules can have significant effects on the outcomes of intracellular processes, particularly given the low copy numbers of many proteins and mRNAs present in a cell. For such molecular species, the number and locations of molecules can provide a more accurate and detailed description than local concentration. In addition to diffusion, drift in the movements of molecules can play a key role in the dynamics of intracellular processes, and can often be modeled as arising from potential

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25

Eren, Ezgi. "Stochastic Modeling and Analysis of Plant Microtubule System Characteristics." Thesis, 2012. http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-11085.

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In this dissertation, we consider a complex biological system known as cortical microtubule (CMT) system, where stochastic dynamics of the components (i.e., the CMTs) are defined in both space and time. CMTs have an inherent spatial dimension of their own, as their length changes over time in addition to their location. As a result of their dynamics in a confined space, they run into and interact with each other according to simple stochastic rules. Over time, CMTs acquire an ordered structure that is achieved without any centralized control beginning with a completely disorganized system. It

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26

Shen, Pai-Hsiang, and 沈柏翔. "Simulation and Implementation of Handset Synchronization and Cell Search Methods for Next Generation Massive Antenna Multipath Division Multiple Access Cellular System." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/46nd2x.

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27

John, Mathias. "Reaction Constraints for the Pi-Calculus - A Language for the Stochastic and Spatial Modeling of Cell-Biological Processes." Phd thesis, 2010. http://tel.archives-ouvertes.fr/tel-00825257.

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For cell-biological processes, it is the complex interaction of their biochemical components, affected by both stochastic and spatial considerations, that create the overall picture. Formal modeling provides a method to overcome the limits of experimental observation in the wet-lab by moving to the abstract world of the computer. The limits of the abstract world again depend on the expressiveness of the modeling language used to formally describe the system under study. In this thesis, reaction constraints for the pi-calculus are proposed as a language for the stochastic and spatial modeling o

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28

Meige, Albert. "Numerical modeling of low-pressure plasmas: applications to electric double layers." Phd thesis, 2006. http://hdl.handle.net/1885/45749.

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Inductive plasmas are simulated by using a one-dimensional particle-in-cell simulation including Monte Carlo collision techniques (pic/mcc). To model inductive heating, a non-uniform radio-frequency (rf) electric field, perpendicular to the electron motion is included into the classical particle-in-cell scheme. The inductive plasma pic simulation is used to confirm recent experimental results that electric double layers can form in current-free plasmas. These results differ from previous experimental or simulation systems where the double layers are driven by a current or by imposed potential

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29

Friedrich, Benjamin M. "Nonlinear dynamics and fluctuations in biological systems." Doctoral thesis, 2016. https://tud.qucosa.de/id/qucosa%3A30879.

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Abstract:

The present habilitation thesis in theoretical biological physics addresses two central dynamical processes in cells and organisms: (i) active motility and motility control and (ii) self-organized pattern formation. The unifying theme is the nonlinear dynamics of biological function and its robustness in the presence of strong fluctuations, structural variations, and external perturbations. We theoretically investigate motility control at the cellular scale, using cilia and flagella as ideal model system. Cilia and flagella are highly conserved slender cell appendages that exhibit spontaneou

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