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 6 of 6 for “"Rule Based Modeling"”.
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Mathematical modeling approaches for dynamical analysis of protein regulatory networks with applications to the budding yeast cell cycle and the circadian rhythm in cyanobacteria
Mathematical modeling has become increasingly popular as a tool to study regulatory interactions within gene-protein networks. From the modeler's perspective, two challenges arise in the process of building a mathematical model. First, the same regulatory network can be translated into different …
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Spatiotemporal modeling and model restructuration approaches in studies of intracellular signalling pathways
… and cell biology in a single cell. Mathematical modeling and experimental evaluation are widely used approaches for this kind of research. Firstly, A multiscale framework for protein-protein interaction has been established using Brownian dynamics algorithm. Sit specific feature, steric …
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Modeling steric effects in antibody aggregation using rule-based methods
… antibody-receptor complexes. Computational modeling of antibody- antigen aggregate formation as well as the size and structure of these aggregates is an important tool for greater understanding of the allergic response. In addition, the incorporation of molecular geometry into aggregation …
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Stochastic Simulation Methods for Biochemical Systems with Multi-state and Multi-scale Features
In this thesis we study stochastic modeling and simulation methods for biochemical systems. The thesis is focused on systems with multi-state and multi-scale features and divided into two parts. In the first part, we propose new algorithms that improve existing multi-state simulation methods. We …
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Stochastic Simulation Methods for Solving Systems with Multi-State Species
… has been a conventional method for stochastic modeling and simulation of biochemical systems. However, its population-based scheme faces the challenge from multi-state situations in many biochemical models. To tackle this problem, Morton-Firth and Bray's stochastic simulator (StochSim) was …
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Extending Regulatory Network Modeling with Multistate Species
… to comply with multistate species and reactions modeling and presented a proposal for enhancing SBML (the Systems Biology Markup Language) standards to support multistate models.