Fundamentals of Systems Biology

Chapter 6Variation: Stochastic Simulation

Learning Objectives

• Explain how a system that only involves a small number of molecules can require a different modeling approach
• Understand the physical basis for the Gillespie algorithm
• Implement stochastic simulations for sets of chemical reactions
• Determine the relationship between rate parameters based on ODEs and those based on stochastic simulation

We’re almost finished with our simple circuit, but there is one thing we have not considered in detail yet: the individual cell. For example, all of the ODE-based approaches described in Chapters 3–5 depended on assumptions of mass action kinetics. These assumptions generally hold in a well-mixed system, in which the concentrations of reactants are ...