臺灣博碩士論文加值系統

我們使用布朗動態法（Brownian dynamics）連結有限元素法（finite element method）來設計能夠更有效率地拉伸DNA的微流道裝置。我們希望能將這種新設計應用於基因圖譜技術。我們的設計以Kim 和 Doyle[1] 的漸縮通道裝置為基礎，以電場梯度來拉伸DNA。為了提高DNA的拉伸效率，我們提出兩種在DNA進入漸縮通道前的預處理策略。第一種為先使用漸擴通道來對DNA做漸縮通道對稱軸垂直方向的預拉伸，然後將已經部分拉伸的DNA往漸縮通道對稱軸旋轉，則此DNA能夠於漸縮通道中經歷第二次拉伸。就結果而言，DNA能在進入漸縮通道前就具有較高的拉伸狀態，因此能夠達到較高的拉伸效率。第二種策略為先將DNA做震盪拉伸的預處理，這種預處理在理想情況下能夠有效率地減低DNA的摺疊率，然而這種預處理模式無法明顯地提升DNA之拉伸效率，我們發現原本的預測會錯誤是由於選擇不正確的流場。
我們接著測試我們的設計是否能夠有效地拉伸更大分子量的DNA。發現新設計的拉伸效率會隨分子量增大而逐漸遞減。藉由分析DNA在裝置中的拉伸分布，我們提出另一種新設計。這種新設計主要是利用裝置邊界對DNA的體積排斥力，以降低DNA摺疊的機率。由我們的模擬結果發現即使在更低電場梯度下，這種新設計也能大幅提高大分子量DNA的拉伸效率與拉伸均勻度。

We use Brownian dynamics-finite element method (BD-FEM) to design microfluidic devices that are capable to efficiently and uniformly stretch DNA for the application of gene mapping. Our design is based on the devices proposed by Kim and Doyle[1] that stretches DNA electrophoretically with the electric field gradient generated in a hyperbolic contraction. To enhance DNA stretching, we propose two strategies that pre-condition DNA before they enter the contraction. For the first approach, we pre-stretch DNA in the direction perpendicular to the funnel axis with a expansion geometry. The partially stretched chains are then turned to align with the axial of the funnel, and experience the second stretching. As a result, DNA chains adapt more extended configurations before going into the funnel, and therefore achieve a higher degree of extension. For the second approach, we pre-condition DNA conformation using an oscillating extensional electric field that has been shown to effectively reducing the population of folded DNA at an ideal condition. However, this approach shows negligible effect in our design, and we find that the original prediction was actually wrong due to the erroneous choice of flow filed.
We further examine the efficiency of our design for stretching longer DNA. It is found the performance of the pre-conditioning strategy deteriorates with increasing DNA molecular weight. By analyzing the probability distribution of DNA extension in the device, we propose a new design that utilizes the excluded volume effect of the device boundary to prevent the formation of folded DNA. Our simulation results indeed show that the design with both tricks can provide very uniform, highly stretched DNA even under relatively low field gradient.

目錄
摘要 ..................................................................................................................... i
ABSTRACT .......................................................................................................... ii
目錄 ..................................................................................................................... iv
圖目錄 ................................................................................................................. vii
表目錄 ................................................................................................................ xiv
符號表 ................................................................................................................. xv
希臘符號表 ....................................................................................................... xvii
第一章 緒論 ............................................................................................................... 1
1.1 前言 ............................................................................................................ 1
1.2 重要名詞釋義 ............................................................................................ 1
1.2.1 去氧核糖核苷酸（DNA） .............................................................. 1
1.2.2 堅韌長度（Persistence length） ...................................................... 2
1.2.3 輪廓長度（Contour length） ........................................................... 3
1.2.4 鬆弛時間（Relaxation time） ......................................................... 3
1.2.5 電動力學（Electrokinetics） ........................................................... 4
1.2.6 應變量與應變率（Strain and Strain rate） ..................................... 7
1.2.7 黛博拉數（Deborah number, De） ................................................. 8
1.2.8 初始形狀（Initial configuration） ................................................... 8
1.3 研究動機與目的 ........................................................................................ 9
第二章 文獻回顧 ..................................................................................................... 12
2.1 線性高分子模型 ...................................................................................... 12
2.1.1 非連續空間模型 ............................................................................. 12
2.1.2 連續空間模型 ................................................................................. 13
2.2 理想鏈（Ideal chain）與真實鏈（Real chain） .................................... 15
2.2.1 理想鏈 ............................................................................................. 15
2.2.1.1 一維隨機漫步 ..................................................................... 15
2.2.1.2 二維與三維隨機漫步 ......................................................... 18
2.2.1.3 理想鏈之尺度 ..................................................................... 18
2.2.1.4 高斯鏈（Gaussian Chain） ................................................ 20
2.2.2 真實鏈 ............................................................................................. 21
2.2.2.1 體積排斥（Excluded volume） ......................................... 21
2.2.2.2 Short-range interaction 與 Long-range interaction ........... 24
2.3 蠕蟲鏈（Worm-like chain） ................................................................... 26
2.4 Bead-spring model .................................................................................... 28
2.5 以流場或電場拉伸DNA .......................................................................... 29
2.6 改進DNA拉伸之策略 .............................................................................. 32
2.7 改善以電場拉伸DNA裝置之設計構想 .................................................. 43
第三章 模擬方法 ..................................................................................................... 46
3.1 布朗動態法（BD） ................................................................................. 46
3.2 有限元素法（FEM） .............................................................................. 49
3.3 FEM連結BD ............................................................................................ 52
3.4 時間步階 .................................................................................................. 53
3.5 參數設定測試 .......................................................................................... 54
第四章 結果討論 ..................................................................................................... 57
4.1 漸擴通道與十字通道 .............................................................................. 58
4.1.1 最大拉伸長度 ................................................................................. 61
4.1.2 DNA拉伸分布之分析 .................................................................... 67
4.1.3 DNA拉伸進程分析 ........................................................................ 70
4.1.4 震盪拉伸模型修正 ......................................................................... 72
4.2 不同分子量DNA之拉伸效率比較 .......................................................... 74
4.2.1 最大拉伸長度 ................................................................................. 75
4.2.2 固定速度梯度之最大拉伸長度比較 ............................................. 79
4.3 可能之優化策略 ...................................................................................... 80
4.3.1 最大拉伸長度比較 ......................................................................... 84
第五章 結論與未來展望 ......................................................................................... 90
5.1 結論 .......................................................................................................... 90
5.2 未來展望 .................................................................................................. 91
第六章 參考文獻 ..................................................................................................... 92

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