The construction of an artificial biological logic circuit using systematic strategy is recognised as one of the most important topics for the development of synthetic biology. In this study, a real-structured genetic algorithm (RSGA), which combines general advantages of the traditional real genetic algorithm with those of the structured genetic algorithm, is proposed to deal with the biological logic circuit design problem. A general model with the cis-regulatory input function and appropriate promoter activity functions is proposed to synthesise a wide variety of fundamental logic gates such as NOT, Buffer, AND, OR, NAND, NOR and XOR. The results obtained can be extended to synthesise advanced combinational and sequential logic circuits by topologically distinct connections. The resulting optimal design of these logic gates and circuits are established via the RSGA. The in silico computer-based modelling technology has been verified showing its great advantages in the purpose.

Efforts have been made to establish computer models of genetic oscillation. We have developed a real structured genetic algorithm (RSGA) which combines advantages of the traditional real genetic algorithm (RGA) with those of the structured genetic algorithm (SGA) and applies it as an optimization strategy for genetic oscillator design. For the generalized design, our proposed approach fulfils all types of genes by minimizing the order of oscillator while searching for the optimal network parameters. The design approach is shown to be capable of yielding genetic oscillators with a simpler structure while possessing satisfactory oscillating behavior. In silico experiments show effectiveness of the proposed algorithm to genetic oscillator design. In particular, it is shown that the proposed approach performs better than the traditional GAs in the sense that a cheaper structure of genetic oscillators can be obtained.

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