GA-based Design Algorithms for the Robust Synthetic Genetic Oscillators with Prescribed Amplitude, Period and Phase

• Published in: Gene regulation and systems biology Vol. 2010; no. 4; pp. 35 - 52
• Main Authors: Chen, Bor-Sen, Chen, Po-Wei
• Format: Journal Article
• Language: English
• Published: London, England SAGE Publishing 24.05.2010; SAGE Publications; Sage Publications Ltd. (UK); Sage Publications Ltd; Libertas Academica
• Subjects: Algorithms; Analysis; Anopheles; Evolution; Fitness; Gene regulation; Genes; Genetic research; Kinetics; Natural selection; Original Research; Oscillators; Stochasticity; genetic algorithm (GA); synthetic gene network; robust synthetic gene oscillator; nature selection; evolutionaiy genetic repressilator; evolutionary genetic repressilator
• ISSN: 1177-6250; 1177-6250
• DOI: 10.4137/GRSB.S4818

Bor-Sen Chen1 and Po-Wei Chen11Lab. of Control and Systems Biology, National Tsing-Hua University, 101 Section 2, Kuang Fu Rd., Hsin-chu 300, Taiwan. AbstractIn the past decade, the development of synthetic gene networks has attracted much attention from many researchers. In particular, the genetic oscillator known as the repressilator has become a paradigm for how to design a gene network with a desired dynamic behaviour. Even though the repressilator can show oscillatory properties in its protein concentrations, their amplitudes, frequencies and phases are perturbed by the kinetic parametric fluctuations (intrinsic molecular perturbations) and external disturbances (extrinsic molecular noises) of the environment. Therefore, how to design a robust genetic oscillator with desired amplitude, frequency and phase under stochastic intrinsic and extrinsic molecular noises is an important topic for synthetic biology. In this study, based on periodic reference signals with arbitrary amplitudes, frequencies and phases, a robust synthetic gene oscillator is designed by tuning the kinetic parameters of repressilator via a genetic algorithm (GA) so that the protein concentrations can track the desired periodic reference signals under intrinsic and extrinsic molecular noises. GA is a stochastic optimization algorithm which was inspired by the mechanisms of natural selection and evolution genetics. By the proposed GA-based design algorithm, the repressilator can track the desired amplitude, frequency and phase of oscillation under intrinsic and extrinsic noises through the optimization of fitness function. The proposed GA-based design algorithm can mimic the natural selection in evolutionary process to select adequate kinetic parameters for robust genetic oscillators. The design method can be easily extended to any synthetic gene network design with prescribed behaviours.