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System Modeling in Cellular BiologyFrom Concepts to Nuts and Bolts$
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Zoltan Szallasi, Jorg Stelling, and Vipul Periwal

Print publication date: 2006

Print ISBN-13: 9780262195485

Published to MIT Press Scholarship Online: August 2013

DOI: 10.7551/mitpress/9780262195485.001.0001

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Stochastic Modeling of Intracellular Kinetics

Stochastic Modeling of Intracellular Kinetics

(p.149) 8 Stochastic Modeling of Intracellular Kinetics
System Modeling in Cellular Biology

Johan Paulsson

Johan Elf

The MIT Press

This chapter discusses some theoretical aspects of randomness in simple genetic and metabolic networks, including both general mathematical techniques and specific biological phenomena. The chapter is organized as follows. Section 8.2 discusses the assumptions behind stochastic modeling of chemical reactions. Section 8.3 presents a multivariate model for stochastic gene expression that can be solved exactly. Section 8.4 gives an interpretation of the fluctuation-dissipation theorem (FDT), tailored to biochemical processes. Section 8.5 uses simulations and FDT approximations for systems that operate near critical points, and Section 8.6 shows how such fluctuations can be tamed by negative feedback. Section 8.7 gives some examples of noise-induced transitions and constructive roles of noise.

Keywords:   genetic networks, metabolic networks, stochastic modeling, chemical reactions, gene expression, fluctuation-dissipation theorem, noise-induced transitions

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