ABSTRACT

This is one of the first books to provide a systematic study of the many stochastic models used in systems biology. The book shows how the mathematical models are used as technical tools for simulating biological processes and how the models lead to conceptual insights on the functioning of the cellular processing system. Examples cover the phage lambda genetic switch, eukaryotic gene expression, noise propagation in gene networks, and more. Most of the text should be accessible to scientists with basic knowledge in calculus and probability theory.

part I|50 pages

Dynamics of reaction networks: Markov processes

chapter Chapter 1|23 pages

Reaction networks: introduction

chapter Chapter 2|24 pages

Continuous-time Markov chains

part II|85 pages

Illustrations from systems biology

chapter Chapter 3|11 pages

First-order chemical reaction networks

chapter Chapter 4|11 pages

Biochemical pathways

chapter Chapter 5|31 pages

Binding processes and transcription rates

chapter Chapter 6|10 pages

Kinetics of binding processes

chapter Chapter 7|12 pages

Transcription factor binding at nucleosomal DNA

chapter Chapter 8|5 pages

Signalling switches

part III|46 pages

A short course on dynamical systems

chapter Chapter 9|14 pages

Differential equations, flows and vector fields

chapter Chapter 10|16 pages

Equilibria, periodic orbits and limit cycles

chapter Chapter 11|14 pages

Linearisation

part IV|35 pages

Linear noise approximation

chapter Chapter 13|13 pages

Mass action kinetics