ABSTRACT
Designing new drugs or chemicals, understanding the kinetics of combustion and petroleum refining, studying the dynamics of metabolic networks, and using metabolism to synthesize compounds in microorganisms are applications that require us to generate reaction networks.As the networksmay be quite large, there is a need to automate the procedure. The purpose of this chapter is to present algorithms that have been developed to handle that task. Section 11.2 introduces the problem and the challenges associated with network generation. Section 11.3 gives various methods used to represent chemical reactions and reaction networks. Section 11.4 introduces techniques to simulate the dynamics of reaction networks and, in particular, approaches to estimate rate constants of the reactions. Section 11.5 presents deterministic techniques to generate networks. It is not always possible to deterministically produce reaction networks due to the combinatorial explosion of the number of species involved; stochastic network generation methods are presented in Section 11.6.
