Chemical Organization Theory as a Theoretical Base for Chemical Computing
Naoki Matsumaru, Florian Centler, Pietro Speroni di Fenizio and Peter Dittrich
In chemical computing, the result of a computation appears as an emergent global behavior based on local reaction rules. For programming chemical systems a theoretical method to cope with that emergent behavior is desired. In this paper, we demonstrate how the chemical organization theory can help in designing and understanding chemical computing systems. After providing a recipe for mapping logic circuits to chemical reaction rules, we discuss reaction networks implementing various logic circuits: an xor, a flip-flop, and a controllable oscillator. The theory decomposes reaction networks into a hierarchy of closed and self-maintaining sub-networks (called organizations) using stoichiometric information only. The dynamical behavior of a reaction system is then explained as a movement between organizations. We show how the theoretical analysis provides insight into the potential behavior of chemical reaction systems. The encouraging results suggest that the theory of chemical organizations contributes to a theoretical framework for chemical computing.