Synthesis of Genetic Clocks Using Biological Circuits

• Main Authors: Po-Kuei Chen, 陳柏魁
• Other Authors: 林俊良
• Format: Others
• Language: en_US
• Published: 2014
• Online Access: http://ndltd.ncl.edu.tw/handle/09868728945932377884

碩士 === 國立中興大學 === 電機工程學系所 === 102 === The potential of the clock lies in its role of triggering logic reaction for sequential biological circuits. This research introduces an idea of designing a genetic clock generator by Fourier series based on genetic oscillators synthesized. We adopt and generalize the design approach using real structured genetic algorithm (RSGA) to generate fundamental sinusoidal signals. Because biochemical reaction of the biological system is extremely slow, however, transition between minimal and maximal levels is instantaneous for an ideal clock signal; it is thus not directly realizable in biological systems. That means that it would be hard to directly synthesize a square wave generator as a genetic clock. We apply Fourier series to represent a square wave as a finite summation of sinusoidal waves generated by some genetic oscillators with different harmonic oscillating frequencies, in which the amplitude alternates at a steady frequency between the fixed minimal and maximal levels with the same duration. This research also develops a new genetic clock generator based on a genetic oscillator. In which, a common sine wave generator is used as an oscillator. It is shown that combination of a genetic oscillator with a toggle switch is able to generate clock signals forming a direct and efficient way to generate a near square wave. Furthermore, this research presents another new method of synthesizing a genetic clock generator based on the combination of a toggle switch with biological logic gates. A dual repressor is used to connect the two fundamental biologic circuits. Analysis of the characteristic responses of this genetic clock with its relation to the key parameters is provided. Keywords: Real structured genetic algorithm (RSGA), toggle switch, linearization,genetic oscillator, biological logic gate, cis-regular input function.