Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/91188
標題: 以生物電路合成基因時鐘
Synthesis of Genetic Clocks Using Biological Circuits
作者: 陳柏魁
Po-Kuei Chen
關鍵字: Real structured genetic algorithm (RSGA);toggle switch;linearization;genetic oscillator;biological logic gate;cis-regular input function.;實數型結構基因演算法;切換開關;線性化;基因震盪器;生物邏輯閘;cis-輸入函數
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摘要: 
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.

基因時鐘的作用在於觸發循序邏輯生物電路的邏輯反應。由於生物系統的生化反應是極度緩慢的,而時鐘訊號的觸發反應是一個在最大值和最小值之間的瞬間切換,無法直接在生物系統中實現。因此,本論文嘗試利用已知的生物電路合成基因時鐘。

首先,我們使用傅利葉級數合成近似方波的方法,採用基因振盪器結合實數型結構基因演算法(RSGA)產生正弦訊號,利用多個基因振盪器的輸出訊號合成一個週期性觸發訊號。利用這個觸發訊號驅動大型的循序生物邏輯電路,如 J-K 正反器及計數器等。模擬結果表現了我們的方法的可行性。

更進一步,我們期望能簡化電路的構造,因此本論文提出了一個新穎的方法來合成基因時鐘,利用雙抑制子系統連結基因振盪器與切換開關,使切換開關的狀態隨基因振盪器的週期改變。我們利用線性化分析此合成電路的動態行為,發現與二階系統的特性相似,找到此電路的自然頻率與重要元件參數的關係,並且制定了一套設計流程,方便設計電路的振盪頻率。

最後,本論文嘗試了一個新的結構設計方法,利用回授結構合成基因時鐘。觀看我們發現切換開關非常符合基因時鐘的特性。在切換開關上,利用生物邏輯閘和雙抑制子系統建構回授結構,使切換開關的輸出成為自身的輸入來轉換自身的狀態。這電路簡化了原本需要其它觸發源切換開關的電路,也減少了電路連結所發生的干擾。我們也利用線性化分析這電路的動態,並且能準確估測電路的振盪頻率。

關鍵字:實數型結構基因演算法、切換開關、線性化、基因震盪器、生
物邏輯閘、cis-輸入函數
URI: http://hdl.handle.net/11455/91188
其他識別: U0005-1205201516281700
Rights: 同意授權瀏覽/列印電子全文服務,2018-07-15起公開。
Appears in Collections:電機工程學系所

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