Artificial Biochemistry

Chemical and biochemical systems are presented as collectives of interacting stochastic automata: each automaton represents a molecule that undergoes state transitions. This framework constitutes an artificial biochemistry, where automata interact by the equivalent of the law of mass action. We analyze several example systems and networks, both by stochastic simulation and by ordinary differential equations. This is the preliminary version of a paper that was later published in Algorithmic Bioprocesses, A. Condon, D. Harel, J.N. Kok, A. Salomaa, and E. Winfree (Eds.), Springer, 2009, ISBN: 978-3-540-88868-0, available at http://www.springer.com/computer/foundations/book/978-3-540-88868-0