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 9 of 9 for “"Stochastic simulation algorithm (SSA)"”.
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Handling External Events Efficiently in Gillespie's Stochastic Simulation Algorithm
Gillespie's Stochastic Simulation Algorithm (SSA) provides an elegant simulation approach for simulating models composed of coupled chemical reactions. Although this approach can be used to describe a wide variety biological, chemical, and ecological systems, often systems have external behaviors …
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Investigation of the tau-leap method for stochastic simulation
The use of the relatively new tau-leap algorithm to model the kinematics of regulatory systems and other chemical processes inside the cell, is of great interest; however, the accuracy of the tau-leap algorithm is not known. We introduce a new method that enables us to establish the accuracy of the …
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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
Gillespie's stochastic simulation algorithm (SSA) 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 …
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Computational Techniques for the Analysis of Large Scale Biological Systems
… 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 …
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Analysis and Application of Haseltine and Rawlings's Hybrid Stochastic Simulation Algorithm
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 …
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Unraveling the intricacies of spatial organization of the ErbB receptors and downstream signaling pathways
… signaling. The coupled spatial non-spatial simulation algorithm, CSNSA is a tool that I took part in developing, which implements a spatial kinetic Monte Carlo for capturing receptor interactions on the cell membrane with Gillespies stochastic simulation algorithm, SSA, for temporal …
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Multiscale simulation of heterophase polymerization : application to the synthesis of multicomponent colloidal polymer particles
… has been investigated using suitable numerical simulation techniques at their corresponding time and length scales. These methods, which include Molecular Dynamics (MD) simulation, Brownian Dynamics (BD) simulation and kinetic Monte Carlo (kMC) simulation, have been found to be very powerful and …
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On Efficient Algorithms for Stochastic Simulation of Biochemical Reaction Systems
… is formalized in a precise form by a model. A simulation algorithm will realize the dynamic interactions encoded in the model. The simulation can uncover biological implications and derive further predictive experiments. Several successful approaches with different levels of detail have been …