IWNET12
IWNET12
Open chemical systems and their biological function
Hong Qian1
1 University of Washington, USA
Abstract
We introduce stochastic Delbruck-Gillespie process, whose Kolmogorov forward equation is known as the Chem-
ical Master Equation and its trajectories can be sampled via the Gillespie algorithm, for nonlinear chemical
reactions dynamics inside a small aqueous volume such as a biological cell. Using this formalism, we (1) illus-
trate the relation between nonlinear bistability with saddle-node bifurcation and rst-order phase transition;
(2) introduce a far-from-equilibrium thermodynamic theory for free energy, entropy and entropy production;
(3) show how an analytical mechanics (i.e., Lagrangian and Hamiltonian systems) arises. We suggest the inter-
attractoral stochastic dynamics as a possible mechanism for isogenetic variations in cellular biology, and present
a Kramers' like formula for the rate of epigenetic phenotype switching.
E-mail: hqian@u.washington.edu

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