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Stochastic Simulations in Systems Biology

Hafner, M. and Koeppl, H. (2011):
Stochastic Simulations in Systems Biology.
In: Handbook of Research on Computational Science and Engineering: Theory and Practice, IGI Global, pp. 267-286, [Online-Edition: http://www.igi-global.com/chapter/handbook-research-computat...],
[Book Section]

Abstract

With the advances in measurement technology for molecular biology, predictive mathematical models of cellular processes come in reach. A large fraction of such models addresses the kinetics of interaction between biomolecules such as proteins, transcription factors, genes and messenger RNA. In contrast to classical chemical kinetics utilizing the reaction-rate equation, the small volume of cellular compartments requires to account for the stochasticity of chemical kinetics. In this chapter we discuss methods to generate sample paths of this underlying stochastic process for situations where the well-stirredness or fast- diffusion assumption holds true. We introduce various approximations to exact simulation algorithms that are more efficient in terms of computational com- plexity. Moreover, we discuss algorithms that account for the multi-scale nature of cellular reaction events.

Item Type: Book Section
Erschienen: 2011
Creators: Hafner, M. and Koeppl, H.
Title: Stochastic Simulations in Systems Biology
Language: English
Abstract:

With the advances in measurement technology for molecular biology, predictive mathematical models of cellular processes come in reach. A large fraction of such models addresses the kinetics of interaction between biomolecules such as proteins, transcription factors, genes and messenger RNA. In contrast to classical chemical kinetics utilizing the reaction-rate equation, the small volume of cellular compartments requires to account for the stochasticity of chemical kinetics. In this chapter we discuss methods to generate sample paths of this underlying stochastic process for situations where the well-stirredness or fast- diffusion assumption holds true. We introduce various approximations to exact simulation algorithms that are more efficient in terms of computational com- plexity. Moreover, we discuss algorithms that account for the multi-scale nature of cellular reaction events.

Title of Book: Handbook of Research on Computational Science and Engineering: Theory and Practice
Volume: 1
Publisher: IGI Global
Divisions: 18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications > Bioinspired Communication Systems
18 Department of Electrical Engineering and Information Technology
18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications
Date Deposited: 04 Apr 2014 13:10
Official URL: http://www.igi-global.com/chapter/handbook-research-computat...
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