Reflected diffusions and (bio)chemical reaction networks

12 Jul 2018, 15:40
New Law School/--102 (University of Sydney)

New Law School/--102

University of Sydney

Oral Presentation Biochemistry and Cell Biology Reaction networks & stochasticity


Prof. Ruth Williams (University of California, San Diego)


Continuous-time Markov chain models are often used to describe the stochastic dynamics of networks of reacting chemical species, especially in the growing field of systems biology. Discrete-event stochastic simulation of these models rapidly becomes computationally intensive. Consequently, more tractable diffusion approximations are commonly used in numerical computation, even for modest-sized networks. However, existing approximations (e.g., linear noise and Langevin), do not respect the constraint that chemical concentrations are never negative.

In this talk, we propose an approximation for such Markov chains, via reflected diffusion processes, that respects the fact that concentrations of chemical species are non-negative. This fixes a difficulty with Langevin approximations that they are frequently only valid until the boundary of the positive orthant is reached. Our approximation has the added advantage that it can be written down immediately from the chemical reactions. Some numerical examples illustrate the advantages of our approximation over direct simulation of the Markov chain or use of the linear noise approximation.

This talk is based on joint work with Saul Leite, David Anderson and Des Higham.

Primary authors

Prof. Ruth Williams (University of California, San Diego) Dr Saul Leite (Center for Mathematics, Computation and Cognition, Federal University of ABC, Santo Andre, SP, 09210-580, Brazil.)

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