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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 江介宏 | |
dc.contributor.author | Tai-Yin Chiu | en |
dc.contributor.author | 邱泰尹 | zh_TW |
dc.date.accessioned | 2021-06-17T01:38:09Z | - |
dc.date.available | 2017-08-20 | |
dc.date.copyright | 2017-08-20 | |
dc.date.issued | 2017 | |
dc.date.submitted | 2017-07-31 | |
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dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/67570 | - |
dc.description.abstract | 隨著合成生物學及DNA奈米科技的發展,許多生物計算機的模型已經被提出或甚至實現。如同經典計算機,生物計算機也可被分類為類比和數位兩種類型,而本篇論文即探討這兩種類型的生物計算器之自動化設計。在類比生物計算中,先前的研究提出了如何利用生化反應來以近似的(approximate)方式拼湊出線性系統,受此啟發,我們改良並提出了一套方法,使得我們能以自動化合成的方式精準的(exact)實現線性系統。我們從數學的分析出發,設計了三個可以直接以DNA鍊取代反應(DNA strand displacement reaction)實現的三個模組,並且證明了這三個模組可用來合成任意線性系統。此外,我們設計了一套自動化合成的流程,透過此流程,我們只需提供待實現系統的轉移函數(transfer function),即可自動化的以這三個模組合成出待實現系統。
而在數位生物計算中,先前的研究提出了如何利用DNA重組酶(recombinase)在大腸桿菌中來實現兩個輸入信號的邏輯閘(two-input logic gate),受此啟發,我們研究了如何將兩個輸入信號推廣至多個輸入訊號,並且探討多輸入訊號邏輯閘(multi-input logic gate)的表現力(expressive power),此外,我們研究如何利用多輸入訊號邏輯閘來合成出性能最佳化(performance-optimized)的大型邏輯電路。為此,我們首先用正規語言來定義DNA序列的語法,藉由此語法來定義出合法的「由重組酶實現的邏輯閘(recombinase-based logic gate)」,此外我們也推導出合法邏輯閘的布林語意(Boolean semantics),並發現由重組酶實現的邏輯閘的語意是一套決策清單(decision list)而且是功能完備的(functionally complete)。有了合法邏輯閘的定義及其語意,我們利用邏輯合成工具將合法邏輯閘合成出任意大型的邏輯電路,且所合成的電路將會是面積或者是延遲最佳化(area and delay optimization)。 | zh_TW |
dc.description.abstract | 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. | en |
dc.description.provenance | Made available in DSpace on 2021-06-17T01:38:09Z (GMT). No. of bitstreams: 1 ntu-106-R03943020-1.pdf: 13014753 bytes, checksum: e3455dc1ce9f9a69dd9a0d479046f10a (MD5) Previous issue date: 2017 | en |
dc.description.tableofcontents | 口試委員會審定書iii
誌謝v 摘要vii Abstract ix 1 Introduction 1 1.1 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Our contributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2 Synthesizing biochemical implementation of linear systems 9 2.1 Configurable primitive components . . . . . . . . . . . . . . . . . . . 10 2.1.1 Integration block . . . . . . . . . . . . . . . . . . . . . . . . . 11 2.1.2 Gain and summation blocks . . . . . . . . . . . . . . . . . . . 12 2.1.3 Case study . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 2.2 DSD realization of configurable primitive components . . . . . . . . . 16 2.3 Implementation of transfer functions in biochemistry . . . . . . . . . 24 2.3.1 Transfer function decomposition . . . . . . . . . . . . . . . . . 24 2.3.2 Naive implementation of elementary modules . . . . . . . . . 25 2.3.3 Exact implementation of elementary modules . . . . . . . . . 29 2.4 DSD realization of transfer functions . . . . . . . . . . . . . . . . . . 31 2.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 2.5.1 Rate matching and configurability . . . . . . . . . . . . . . . 34 2.5.2 Transfer function decomposition . . . . . . . . . . . . . . . . . 36 2.5.3 DSD reaction rates . . . . . . . . . . . . . . . . . . . . . . . . 37 2.5.4 Fuel supply . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 3 Logic synthesis of recombinase-based genetic circuits 39 3.1 Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 3.2 Formalism of recombinase-based logic gates . . . . . . . . . . . . . . 42 3.2.1 Syntax of well-formed sequences . . . . . . . . . . . . . . . . . 42 3.2.2 Semantics of well-formed sequences . . . . . . . . . . . . . . . 44 3.3 Construction of multi-level recombinase-based logic circuits . . . . . . 50 3.4 Experimental evaluation . . . . . . . . . . . . . . . . . . . . . . . . . 55 3.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 4 Conclusions 61 Bibliography 63 | |
dc.language.iso | en | |
dc.title | 類比與數位生物計算機之自動化設計 | zh_TW |
dc.title | Design automation in analog and digital biological computing | en |
dc.type | Thesis | |
dc.date.schoolyear | 105-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 凌嘉鴻,陳倩瑜 | |
dc.subject.keyword | 生物計算,生物系統設計最佳化,系統及合成生物學,DNA奈米科技,基因電路,線性系統,重組?, | zh_TW |
dc.subject.keyword | biological computing,bio-design automation,systems and synthetic biology,DNA nanotechnology,genetic circuits,linear systems,recombinase, | en |
dc.relation.page | 71 | |
dc.identifier.doi | 10.6342/NTU201702239 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2017-07-31 | |
dc.contributor.author-college | 電機資訊學院 | zh_TW |
dc.contributor.author-dept | 電子工程學研究所 | zh_TW |
顯示於系所單位: | 電子工程學研究所 |
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