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http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/73675
標題: | 數位類比混合訊號程式之生化反應編譯 Biochemical Reaction Compilation of Mixed-Signal Programs |
作者: | Wei-Chih Huang 黃韋智 |
指導教授: | 江介宏 |
關鍵字: | 編譯器,數位類比混合信號,生化反應, compiler,mixed-signal,biochemical reaction, |
出版年 : | 2019 |
學位: | 碩士 |
摘要: | 合成生物學是個在生化領域快速發展的項目,有許多的研究致力於利用化學反應網絡來實現實用的模組。其中化學反應網絡已經被證明是個圖靈完備的系統,而這為開發高抽象層程式語言提供了基礎。在這份研究中,我們提出了一套程式語言並利用化學反應作為底層的計算系統。這個語言比起先前的方法提供了更高層的抽象化。除了先前的方法所使用的非負數計算, 我們也支援了負數的計算,因此涵蓋了整個實數的計算並提供更泛用的框架。我們建構了一個編譯器來將該程式語言編譯成化學反應網絡。在這個編譯器中,我們利用非同步的前置與後置條件來實現程式的控制結構,並利用多項初值問題來實現程式中的資料流。在編譯中,sigmoid 函數被用來實作布林運算,如:反向、邏輯與...等,比較運算,如:相等、大於...等,以及程式述句的前置與後置條件。我們也針對不同的 sigmoid 函數進行實驗並探討各自的優缺點。為了讓實作結果更為實際,我們同時探索了不同的機制與技術來減少反應與化合物的數量。實驗的模擬結果顯示我們所提出的編譯方法是可行的。 Synthetic biology is a rapidly developed subject in the biochemical field, and there is much research focusing on developing useful modules with chemical reaction networks. It has been proven that the chemical reaction network is a Turing-complete system, which provides the basis for developing programming languages with a higher level of abstraction. In this research, we propose a programming language and use the chemical reactions as the underlying computation system. The language provides a higher level of abstraction to describe a program compared to prior work. In addition to the non-negative value computation in prior work, the negative value computation is supported, and thus covering the whole real value computation, which provides a more general framework. A compiler is built to compile the language into the chemical reaction network, which exploits asynchronous pre/postcondition to implement the control flow and polynomial initial value problem to implement the data flow of a program. In our compilation, the sigmoid function is used to implement the Boolean operations, such as inversion, conjunction, ..., comparison operations, such as equivalence, greater than, ..., and the pre/postcondition of a program statement. We study the performance of different sigmoid function implementations and discuss their strengths and weaknesses. Different mechanisms and techniques are proposed to reduce the numbers of reactions and species for more practical implementation. Simulation results show the feasibility of our compilation method. |
URI: | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/73675 |
DOI: | 10.6342/NTU201902986 |
全文授權: | 有償授權 |
顯示於系所單位: | 電子工程學研究所 |
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ntu-108-1.pdf 目前未授權公開取用 | 1.38 MB | Adobe PDF |
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