Extracting reaction systems from function behavior
Reaction systems, introduced by Ehrenfeucht and Rozenberg, are a theoretical model of computation based on the two main features of biochemical reactions: facilitation and inhibition, which are captured by the individual reactions of the system. All reactions, acting together, determine the global behavior or the result function, res, of the system. In this paper, we study decomposing of a given result function to find a functionally equivalent set of reactions. We propose several approaches, based on identifying reaction systems with Boolean functions, Boolean formulas, and logic circuits. We show how to minimize the number of reactions and their resources for each single output individually, as a group, and when only a subset of the states are considered. These approaches work both when the reactions of the given res function are known and not known. We characterize the minimal number of reactions through the minimal number of logical terms of the Boolean formula representation of the reaction system. Finally, we make applications recommendations for our findings.
Journal of Membrane Computing
Digital Object Identifier (DOI)
Genova, D., Jan Hoogeboom, H., Prodanoff, Z. (2020) Extracting Reaction Systems from Function Behavior. Journal of Membrane Computing, 2(3), 194-206.