Rule-Based Multiset Programming Paradigm : Applications to Synthetic Biology

This paper describes a rule-based multiset programming paradigm, as a unifying theme for computation. The computations are interpreted as the outcome arising out of deterministic, nondeterministic or stochastic interaction among elements in a multiset object space which includes the environment. These interactions are like chemical reactions and the evolution of the multiset can mimic the biological evolution. Since the reaction rules are inherently parallel, any number of actions can be performed cooperatively or competitively among the subsets of elements, so that the elements evolve toward an equilibrium or an emergent state. Hence, this paradigm is widely applicable to all conventional algorithms, evolutionary algorithms, genetic algorithms, selforganized criticality and active walker models (swarm and ant intelligence), DNA computing and programmable living machines. Practical realization of this paradigm is achieved through the concept of transactions.