Automatic Synthesis of Process Calculus Using Abstraction

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We developed a method to construct a coarse-grained abstract model of DNA devices in which a graph or a set of graphs that represents DNA structures is approximated by a set of local structures (called abstract nodes). Using the method, we conducted evolutionary search of abstract systems and automatically synthesized DNA devices that implement various circuits and automata. We also applied the abstraction method to simulation of RNAi, and succeeded in simulating complex cases with more than twenty segments, and reproducing distribution of concentrations of siRNA by simulation.