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 17 of 17 for “"Chemical Reaction Networks"”.
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Bayesian inference of chemical reaction networks
The development of chemical reaction models aids system design and optimization, along with fundamental understanding, in areas including combustion, catalysis, electrochemistry, and biology. A systematic approach to building reaction network models uses available data not only to estimate unknown …
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Algorithms for Reconstructing and Reasoning about Chemical Reaction Networks
… pathways. These mechanisms are modeled by chemical reaction networks (CRNs) which are typically simulated by converting to ordinary differential equations (ODEs), so that the goal is to closely reproduce the observed quantitative and qualitative behaviors of the modeled process. This thesis …
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In Silico Evolution of Oscillating Mass-Action Chemical Reaction Networks
… systems, including the evolution of mass-action chemical reaction networks. This dissertation explores the application of evolutionary algorithms in this domain, presenting a novel approach inspired by neural network evolution methodologies. A key feature of the algorithm is speciation, …
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Multi-scale stochastic analysis of cellular chemical reaction networks and their response to environmental change
Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-05-01
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Approximation and System Identification Techniques for Stochastic Biomolecular Systems
Many biomolecular systems can be modeled as chemical reaction networks with a set of relevant species interacting via chemical reactions. When the molecular counts of the species are small, the inherent stochasticity in the occurrence of the reactions plays an important role in the behavior of the …
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Statistical Study of Chemical Reaction Network Models for Prebiotic Evolution
… evolution. The models abstractly describe chemical reaction networks and their dynamic evolution. The goal is to findquantitative measures of their generic features that can be used to identify lifelike systems in the solar system and on exoplanets, as well as to identify the origin of …
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Automatic Bayesian Inference of Reaction Networks via Guiding
Jump process models based on chemical reaction networks are ubiquitous, especially in systems biology modeling. However, performing inference on the latent variables and parameters of such models is challenging, particularly when the observations of the system state are noisy and incomplete. This …
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High Throughput, Multiplex Quantification via Nucleic Acid Chemical Reaction Network Perturbation
… perturbative quantification, a nucleic acid chemical reaction network-based approach as a potential solution, and builds the foundation for this approach. The fundamental idea of perturbative quantification is to translate the molecular composition of a sample into a nucleic acid signature …
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Nano/Bio-Receiver Architectures and Detection Methods for Molecular Communications
… and biological environments with collaborative networks of artificial nanomachines and biological entities integrated into the Internet. To enable the IoNT and its groundbreaking applications, such as real-time intrabody health monitoring, it is imperative to devise nanoscale communication …
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Autocatalytic closure and the evolution of cellular information processing networks
Cellular Information Processing Networks (CIPNs) are chemical networks of interacting molecules occurring in living cells. Through complex molecular interactions, CIPNs are able to coordinate critical cellular activities in response to internal and external stimuli. We hypothesise that CIPNs may be …
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How bacteria tune mixed positive/negative feedback loops to generate diverse gene expression dynamics
… we present the Catalyst.jl tool for modelling chemical reaction networks. It is a useful systems biology tool that we will use to implement models of one general, and two specific (σV and σB , both in Bacillus subtilis), sigma factor circuits. Our σV model demonstrates how this circuit’s …
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Advanced technologies in molecular and wireless communication networks: analysis, design, and optimisation
Communication networks have vital roles in our daily lives, both in small-scale and large-scale perspective. First, in small-scale networks, nanonetworks consisting of nano-scale devices have been proposed to solve problems in environmental monitoring, healthcare (in the form of nanomedicine), …
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Polynomial systems : graphical structure, geometry, and applications
… systems, computer vision, cryptography, and chemical reaction networks, can be modeled by systems of polynomial equations, and in many cases the resulting systems have a simple sparsity structure. In the first part of this thesis we represent this sparsity structure with a graph, and study …
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Circular chemistry through network science and optimisation on big data
… the transition towards sustainable practices. In chemical engineering, the choice of feedstock, i.e. fossil or renewable, greatly influences the sustainability of chemical processing routes. At present, 90% of feedstocks in the chemical industry are non-renewable, thus, large-scale supply chain …
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Tools for dynamic model development
… bodies to projectile motion to biological and chemical reaction networks. This thesis focuses on applications in chemical kinetic systems. Ordinary differential equations (ODEs) are sufficient to model many dynamic systems, such as those listed above. Differential-algebraic equations (DAEs) can …
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Is metabolism goal-directed? Investigating the validity of modeling biological systems with cybernetic control via omic data
… the time-dependent regulation of cellular reactions in terms of dynamic "metabolic goals." This approach contrasts starkly with purely mechanistic descriptions of metabolic regulation which seek to explain metabolic processes in high resolution — a clearly daunting undertaking. Over a span …