Lecture 14: Continuous Petri Nets and Differential Equations

Moving from discrete events to continuous flow: semantics of continuous Petri nets; correspondence with chemical reaction equations; deriving ordinary differential equations (ODEs); conservation laws, equilibria, numerical solutions and trajectories through phase space. Relating transition rates for discrete events to reaction rates for continuous flow; dependence on reaction stoichiometry.

Some examples, including derivation of Michaelis-Menten semantics.

Thursday’s lecture will be an introduction to BioPEPA, followed by Stephen Gilmore on Monday.

Link: Slides.


Read §§6–9 of Heiner et al., and §§1–4 of Ciocchetta and Hillston, on BioPEPA.

This earlier paper by Gilbert and Heiner also explains modelling biological processes with continuous Petri nets.

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