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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 謝之真(Chih-Chen Hsieh) | |
dc.contributor.author | Po-Han Huang | en |
dc.contributor.author | 黃伯涵 | zh_TW |
dc.date.accessioned | 2021-06-16T08:38:27Z | - |
dc.date.available | 2016-11-05 | |
dc.date.copyright | 2013-11-05 | |
dc.date.issued | 2013 | |
dc.date.submitted | 2013-10-14 | |
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Lamura, A. and G. Gompper, Numerical study of the flow around a cylinder using multi-particle collision dynamics. European Physical Journal E, 2002. 9(5): p. 477-485. 46. Yeh, J.-W., et al., Supporting Information for Entropy-driven single molecule tug-of-war of DNA at micro-nanofluidic interfaces. Nano Letters, 2012. 47. Swope, W.C. and D.M. Ferguson, Alternative Expressions for Energies and Forces Due to Angle Bending and Torsional Energy. Journal of Computational Chemistry, 1992. 13(5): p. 585-594. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/58914 | - |
dc.description.abstract | 我們使用隨機旋轉動力學法(stochastic rotation dynamics,SRD)混和分子模擬法(molecular dynamics)來模擬DNA侷限在微奈米界面之鬆弛行為,並將結果與近年的實驗相驗證。
SRD模擬法藉由粗化(coarse-grain)流體粒子,以降低模擬所需時間,並仍可在介觀尺度下精確地模擬純流體的行為。DNA則以bead-spring model或Fraenkel spring model描述其在非侷限環境或侷限環境下之行為。結合兩者即可模擬DNA與流體之間的關係。 我們首先模擬在非侷限環境下單一DNA的環動半徑、擴散係數、鬆弛時間與高分子鏈長的關係,再與文獻比較以驗證我們的程式。接著,我們參考最近的實驗文獻,設計一微奈米界面之通道,將DNA置入奈米侷限夾縫中,使其橫跨兩微米區域,觀察當DNA之一端進入奈米通道後經由拉伸回縮(entropic recoil)與縮回(retraction)後至完全離開而恢復其纏繞型態之鬆弛過程。觀察並探討在不同通道高度長度下,拉伸回縮時DNA之長度與時間之關係式。本研究亦探討了在侷限環境下以Fraenkel spring 描述高分子之正確性。 | zh_TW |
dc.description.abstract | We use stochastic rotation dynamics (SRD) and molecular hybrid method to simulate the the recoiling process of DNA at two micro-nanofluidic interfaces bridged by a nanoslit, and make comparison with the recent experiment.
SRD uses coarse-grained fluid particles to describe the behavior of solvent, and therefore it is suitable for simulating solvent behavior at mesoscale. On the other hand, DNA is depicted by the bead-spring model and the Fraenkel spring model in unconfined and confined environment, respectively. The interaction between SRD particles and DNA is modeled by MD simulations. Thus, the system involving both fluid and DNA can be described by the SRD-MD hybrid method. In this thesis, we first simulate the relation between the radius of gyration, the diffusivity and the relaxation time of DNA versus its contour length in unconfined system, and compare the results with literature to verify our code. We then follow the DNA tug-of-war experiments of Yeh et al. to simulate DNA recoiling process at a nano-micro interface. We study the stretch-recoiling behavior of DNA under different slit lengths and heights, and discuss the relation of DNA projected length as a function of time. We also show that the Fraenkel spring model can depict the behavior of polymer well under confinement. | en |
dc.description.provenance | Made available in DSpace on 2021-06-16T08:38:27Z (GMT). No. of bitstreams: 1 ntu-102-R00524013-1.pdf: 4593843 bytes, checksum: c49c103d10876eb3dce0e6decedb1a61 (MD5) Previous issue date: 2013 | en |
dc.description.tableofcontents | 摘要 I
ABSTRACT II 目錄 III 圖目錄 VI 表目錄 XV 符號表 XVI 第1章 緒論 1 1.1 前言 1 1.2 研究目的與動機 1 第2章 文獻回顧 3 2.1 DNA(去氧核糖核酸) 3 2.2 高分子模型 6 2.2.1 理想鏈 6 2.2.2 真實鏈 9 2.2.3 Bead-stick model 10 2.2.4 Bead-spring model 13 2.2.5 Fraenkel spring model 13 2.2.6 蠕蟲鏈(Worm-like Chain) 14 2.3 在侷限環境下之高分子 17 2.3.1 侷限環境之定義 17 2.3.2 流體動力作用 19 2.4 介觀尺度(mesoscale)模擬之簡介 21 2.4.1 耗散粒子動力學 23 2.4.2 隨機旋轉動力學 25 2.5 相關模擬結果 26 2.6 相關實驗結果 32 2.6.1 DNA於次微奈米侷限環境中之受困與逃脫行為 32 2.6.2 DNA於侷限環境中所產生之鬆弛及拉伸回縮 34 2.6.3 DNA於微奈米界面中之亂度拉鋸效應 39 第3章 模擬方法 42 3.1 純流體的設定 42 3.1.1 SRD 粒子 42 3.1.2 格子移動( grid shift) 45 3.2 邊界設定方法 46 3.2.1 週期性邊界條件 46 3.2.2 邊界條件 50 3.2.3 溫度調節(thermostat) 51 3.2.3.1 Padding’s Rule 51 3.2.3.2 Watari’s Rule 52 3.3 DNA模型之使用 53 3.3.1 非侷限環境下之Bead-spring model 53 3.3.2 侷限環境下之Fraenkel spring model 55 3.4 DNA之邊界設定 60 3.4.1 非侷限環境下之DNA 60 3.4.2 侷限環境下之DNA 61 3.5 參數設定 61 3.6 模型之驗證 63 3.7 系統形狀與邊界之設計 67 第4章 結果與討論 70 4.1 驗證SRD系統的正確性 70 4.2 DNA model 之特性 72 4.2.1 鬆弛時間 72 4.2.2 堅韌長度 74 4.2.3 環動半徑 79 4.3 DNA model 之驗證 80 4.3.1 環動半徑 80 4.3.2 小球間之平衡長度 80 4.3.3 修正之蠕蟲鏈 82 4.4 DNA於奈米通道兩側之拉鋸行為 83 4.5 DNA於微奈米界面之鬆弛行為 84 第5章 結論 95 第6章 參考文獻 97 | |
dc.language.iso | zh-TW | |
dc.title | 以隨機旋轉動力學法模擬於微奈米界面DNA之鬆弛行為 | zh_TW |
dc.title | Simulating the Recoil of DNA at Micro-Nanofluidic Interfaces Using Stochastic Rotation Dynamics | en |
dc.type | Thesis | |
dc.date.schoolyear | 102-1 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 諶玉真(Yu-Jane Sheng),趙玲(Ling Chao) | |
dc.subject.keyword | 隨機旋轉動力學法,SRD-MD 混合模擬法,介觀尺度,侷限環境,拉伸回縮, | zh_TW |
dc.subject.keyword | Stochastic Rotation Dynamics,SRD-MD hybrid method,Mesoscale,slit-like confinement,stretch-recoiling, | en |
dc.relation.page | 100 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2013-10-14 | |
dc.contributor.author-college | 工學院 | zh_TW |
dc.contributor.author-dept | 化學工程學研究所 | zh_TW |
顯示於系所單位: | 化學工程學系 |
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