Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 25 for “"Biochemical Networks"”.
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Analysis of robustness and stochasticity in biochemical networks
… I present two studies in which I analyze how biochemical circuits that regulate signaling and gene expression can generate robustness or phenotypic variability between otherwise identical yeast cells. Using the osmosensing signaling pathway which consists of a phosphorelay connected to a MAPK …
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Advances in the stochastic and deterministic analysis of multistable biochemical networks
… concentrations in the cell that can arise in biochemical networks. That is, situations where one, or a family of, proteins may sit at one of two or more different steady state concentrations in otherwise identical cells, and in spite of them being in the same environment. Models of multisite …
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Acoustically-levitated drop reactor (ldr) employable for kinetics measurements of biochemical networks
… part of understanding the mechanisms of biochemical reactions. The typical means of studying such systems use stirred cuvettes, stopped-flow apparatus, microfluidic systems, or other small sample containers. These reaction-kinetics measurements reactors are usually made of quartz, glass, …
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An Algebraic Approach to Reverse Engineering with an Application to Biochemical Networks
… to predict and modify the behavior of biological networks by accurately monitoring and modeling their responses to certain types of perturbations. The construction of mathematical models based on observation of these responses, referred to as reverse engineering, is an important step in …
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Computational analysis of biochemical networks for drug target identification and therapeutic intervention design
… to exhaustively evaluate target behaviors in biochemical network, either as single agent or combination therapies. We present our single target therapy work as a problem of identifying good places to intervene in a network. We quantify a relationship between how interventions at different …
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Transcriptional regulation of metabolism and behavior: insights from reconstruction and modeling of complex biochemical networks
… integrate molecular components of the cell into networks and subsequently predict macroscopic phenotypic changes that emerge from these interacting networks. I have developed new tools and algorithms that address this key challenge of multi-scale network integration in order to assemble a …
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Stochastic Modeling and Simulation of Multiscale Biochemical Systems
… 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 …
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Hybrid Modeling and Simulation of Stochastic Effects on Biochemical Regulatory Networks
… 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 …
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Oncogene-induced remodelling of cellular networks
Biochemical networks maintain cellular homeostasis by processing information from the intra- and extra-cellular environments and coordinating appropriate responses to stimuli and stressors. During carcinogenesis, cells accrue genetic alterations that rewire signalling pathways, eventually leading …
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Statistical Analysis of Gene Expression Profile: Transcription Network Inference and Sample Classification
… classifying samples, to discover regulatory gene networks using natural genetic perturbations, to develop statistical methods for model fitting and comparison of biochemical networks, and eventually to advance our capability to understand the principles of biological processes at the system level.
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The Algebra of Systems Biology
In order to understand biochemical networks we need to know not only how their parts work but also how they interact with each other. The goal of systems biology is to look at biological systems as a whole to understand how interactions of the parts can give rise to complex dynamics. In order to do …
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Stochastic processes in T-cell signaling
… at the microscopic level are ubiquitous in biochemical networks, due to stochastic nature of reactions and uncertainties in protein expressions. The prevalence of noise imposes further challenges for T cells to deliver biological functions reliably. The overarching theme of this thesis is to …
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Action potentials as indicators of metabolic perturbations for temporal proteomic analysis
… the time dependent temporal changes in complex biochemical networks, thus limiting our ability to identify possible secondary signaling pathways that could lead to potential toxicity. To overcome this, we have developed an in silico neuronal-metabolic model by coupling the membrane electrical …
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The functionality of spatial and time domain artificial neural models.
… Intelligence systems. Artificial Neural Networks form the foundation of the research and their units, Artificial Neurons, are first compared with alternative models. This initial work is mainly in the spatial-domain and introduces a new neural model, termed a Taylor Series neuron. This is …
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Impact of Stochastic Transcriptional Delay on Gene Networks
… for these reactions in models of gene regulatory networks is to incorporate dynamical delay. The stochastic nature of the reactions necessary to produce protein leads to a waiting time that is randomly distributed, complicating simulation and analysis. We examine this problem using different …
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Sensitivity and Memory in Physics and Biology
… measurable thermodynamic quantities. Applied to biochemical networks, these results extend and unify a patchwork of prior biophysics results on the energetic costs of sharp biochemical switches, accurate sensors, and molecular discrimination—revealing their common origin in the perturbation …
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Contributions to the Analysis of Biochemical Reaction-Diffusion Networks Stability, Analysis, and Numerical Solutions
… systems problems that arise from the study of biochemical networks. Here we prefer a rigorous treatment of the differential equations that govern their spatio-temporal dynamics, at the cost of studying simplified scenarios of the biological systems under study. Although these simplified …
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Stochastic modelling for control and interconnections of biological systems
Biochemical reactions often occur in small volumes within a cell, restricting molecule numbers to the hundreds or even tens. At this scale, reactions are inherently discrete and stochastic. Traditional models based on differential equations and mass-action kinetics fail to capture the behaviour of …
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Analysis and Application of Haseltine and Rawlings's Hybrid Stochastic Simulation Algorithm
… 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. …
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Multiplexed biochemical imaging reveals the extent and complexity of non-genetic heterogeneity in DNA damage-induced caspase dynamics.
… cancer, little is known about how differences in biochemical signalling networks underlie such heterogeneity. State-of-the-art methodologies to study biochemical networks are often invasive and enable to quantify biochemical events only on cell populations or at a single point in time for a single …
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