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Numerical Solution Methods in Stochastic Chemical Kinetics
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- Engblom, Stefan, 1976- (author)
- Uppsala universitet,Avdelningen för teknisk databehandling,Numerisk analys
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- Lötstedt, Per, Professor (thesis advisor)
- Uppsala universitet,Avdelningen för teknisk databehandling
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- Huisinga, Wilhelm, Doctor (opponent)
- National University of Ireland Maynooth, Hamilton Institute
- (creator_code:org_t)
- ISBN 9789155473228
- Uppsala : Acta Universitatis Upsaliensis, 2008
- English 68 s.
- Series: Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, 1651-6214 ; 564
- Doctoral thesis (other academic/artistic)
Abstract
Subject headings
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- This study is concerned with the numerical solution of certain stochastic models of chemical reactions. Such descriptions have been shown to be useful tools when studying biochemical processes inside living cells where classical deterministic rate equations fail to reproduce actual behavior. The main contribution of this thesis lies in its theoretical and practical investigation of different methods for obtaining numerical solutions to such descriptions. In a preliminary study, a simple but often quite effective approach to the moment closure problem is examined. A more advanced program is then developed for obtaining a consistent representation of the high dimensional probability density of the solution. The proposed method gains efficiency by utilizing a rapidly converging representation of certain functions defined over the semi-infinite integer lattice. Another contribution of this study, where the focus instead is on the spatially distributed case, is a suggestion for how to obtain a consistent stochastic reaction-diffusion model over an unstructured grid. Here it is also shown how to efficiently collect samples from the resulting model by making use of a hybrid method. In a final study, a time-parallel stochastic simulation algorithm is suggested and analyzed. Efficiency is here achieved by moving parts of the solution phase into the deterministic regime given that a parallel architecture is available. Necessary background material is developed in three chapters in this summary. An introductory chapter on an accessible level motivates the purpose of considering stochastic models in applied physics. In a second chapter the actual stochastic models considered are developed in a multi-faceted way. Finally, the current state-of-the-art in numerical solution methods is summarized and commented upon.
Subject headings
- NATURVETENSKAP -- Matematik -- Beräkningsmatematik (hsv//swe)
- NATURAL SCIENCES -- Mathematics -- Computational Mathematics (hsv//eng)
Keyword
- stochastic models
- chemical master equation
- mesoscopic kinetics
- Markov property
- jump process
- moment closure problem
- spectral-Galerkin method
- high dimensional problem
- hybrid methods
- time-parallel
- homogenization
- Beräkningsvetenskap med inriktning mot numerisk analys
- Scientific Computing with specialization in Numerical Analysis
Publication and Content Type
- vet (subject category)
- dok (subject category)
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