Design automation in analog and digital biological computing

• Main Authors: Tai-Yin Chiu, 邱泰尹
• Other Authors: 江介宏
• Format: Others
• Language: en_US
• Published: 2017
• Online Access: http://ndltd.ncl.edu.tw/handle/d77vd3

碩士 === 國立臺灣大學 === 電子工程學研究所 === 105 === With the advancements of synthetic biology and DNA nanotechnology, more and more biological computing devices were proposed. Like classical computation bio-computing can be categorized into analog and digital computing. In this thesis we study the design automation of both types of bio-computing devices. For the analog regime, motivated by previous work on linear systems implemented approximately with biochemical reactions, we consider a methodology for exact and automatic implementation of biological linear systems. From the mathematical analysis we designed three modules exactly implementable with DNA strand displacement reactions and proved them sufficient to synthesize any linear system. Furthermore, we devised an automated design flow which can synthesize linear systems with these three modules from their transfer function specifications. For the digital regime, inspired by previous work on building two-input genetic logic gates in E. coli cells based on recombinase-mediated DNA inversion, we investigated the expressive power of generalized multi-input recombinase-based logic gates and the performance-optimized design automation for large-scale logic circuits. Here we used formal language to define the syntax of a DNA sequence which forms a legal recombinase-based logic gate. Moreover, We derived the Boolean semantics of legal logic gates, which can be characterized by decision lists and are functionally complete. For design automation we exploited logic synthesis tool to synthesize large-scale recombinase-based circuits with area and delay optimizations.