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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 | Ching-Kuan Wang | en |
dc.contributor.author | 王靜寬 | zh_TW |
dc.date.accessioned | 2021-06-15T11:22:37Z | - |
dc.date.available | 2016-08-30 | |
dc.date.copyright | 2016-08-30 | |
dc.date.issued | 2016 | |
dc.date.submitted | 2016-08-17 | |
dc.identifier.citation | 1. Randall, G.C. and P.S. Doyle, DNA deformation in electric fields: DNA driven past a cylindrical obstruction. Macromolecules, 2005. 38(6): p. 2410-2418.
2. Watari, N., et al., Simulation of DNA motion in a microchannel using stochastic rotation dynamics. Journal of Chemical Physics, 2007. 126(9). 3. Perkins, T.T., et al., RELAXATION OF A SINGLE DNA MOLECULE OBSERVED BY OPTICAL MICROSCOPY. Science, 1994. 264(5160): p. 822-826. 4. http://www.quia.com/jg/1794185list.html. 5. Israelachvili, J.N., Intermolecular & Surface Forces. 1985. 6. http://avantilipids.com/. 7. Maier, B. and J.O. Radler, DNA on fluid membranes: A model polymer in two dimensions. Macromolecules, 2000. 33(19): p. 7185-7194. 8. Xie, A.F. and S. Granick, Phospholipid membranes as substrates for polymer adsorption. Nature Materials, 2002. 1(2): p. 129-133. 9. Maier, B. and J.O. Radler, Conformation and self-diffusion of single DNA molecules confined to two dimensions. Physical Review Letters, 1999. 82(9): p. 1911-1914. 10. Teraoka, I., Polymer Solutions: An Introduction to Physical Properties. 2002. 11. Flory, P.J., Principles of polymer chemistry. The George Fisher Baker non-resident lectureship in chemistry at Cornell University. 1953, Ithaca: Cornell University Press. 12. 黃秋德, 以布朗動態法模擬DNA在微流道中受流場拉伸之研究. 國立臺灣大學化學工程學系,碩士論文, 民國102年. 13. Teraoka, I., Polymer solutions : an introduction to physical properties. 2002, New York: Wiley. 14. Teraoka, I., Polymer Solutions: An Introduction to Physical Properties. 2002. 15. Liu, Y., et al., Influences of Three Kinds of Springs on the Retraction of a Polymer Ellipsoid in Dissipative Particle Dynamics Simulation. Journal of Polymer Science Part B-Polymer Physics, 2010. 48(23): p. 2484-2489. 16. Hsieh, C.C., S. Jain, and R.G. Larson, Brownian dynamics simulations with stiff finitely extensible nonlinear elastic-Fraenkel springs as approximations to rods in bead-rod models. Journal of Chemical Physics, 2006. 124(4). 17. Hiemenz, P.C.a.T.L., Polymer chemistry. 2007. 18. Tricard, S., et al., Analog modeling of Worm-Like Chain molecules using macroscopic beads-on-a-string. Phys Chem Chem Phys, 2012. 14(25): p. 9041-6. 19. Marko, J.F. and E.D. Siggia, Stretching DNA. Macromolecules, 1995. 28(26): p. 8759-8770. 20. Hsieh, C.C. and P.S. Doyle, Studying confined polymers using single-molecule DNA experiments. Korea-Australia Rheology Journal, 2008. 20(3): p. 127-142. 21. Brochard, F. and P.G. Degennes, DYNAMICS OF CONFINED POLYMER-CHAINS. Journal of Chemical Physics, 1977. 67(1): p. 52-56. 22. Odijk, T., Scaling theory of DNA confined in nanochannels and nanoslits. Physical Review E, 2008. 77(6). 23. Odijk, T., On the Statistics and Dynamics of Confined or Entangled Stiff Polymers. Macromolecules, 1983. 16(8): p. 1340-1344. 24. Wang, Y., D.R. Tree, and K.D. Dorfman, Simulation of DNA Extension in Nanochannels. Macromolecules, 2011. 44(16): p. 6594-6604. 25. Nakanishi, H., Flory Approach for Polymers in the Stiff Limit. Journal De Physique, 1987. 48(6): p. 979-984. 26. Schaefer, D.W., J.F. Joanny, and P. Pincus, Dynamics of Semiflexible Polymers in Solution. Macromolecules, 1980. 13(5): p. 1280-1289. 27. Jun, S., D. Thirumalai, and B.Y. Ha, Compression and stretching of a self-avoiding chain in cylindrical nanopores. Phys Rev Lett, 2008. 101(13): p. 138101. 28. Odijk, T., Scaling theory of DNA confined in nanochannels and nanoslits. Phys Rev E Stat Nonlin Soft Matter Phys, 2008. 77(6 Pt 1): p. 060901. 29. Kampen, N.G.v., Stochastic processes in physics and chemistry. Rev. and enl. ed. North-Holland personal library. 1992, Amsterdam ; New York: North-Holland. xiv, 465 p. 30. Huang, A., A. Bhattacharya, and K. Binder, Conformations, transverse fluctuations, and crossover dynamics of a semi-flexible chain in two dimensions. J Chem Phys, 2014. 140(21): p. 214902. 31. Huang, A., et al., Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles. J Chem Phys, 2015. 143(24): p. 243102. 32. Huang, A.Q. and A. Bhattacharya, DNA confined in a two-dimensional strip geometry. Epl, 2014. 106(1): p. 18004. 33. Hochrein, M.B., et al., DNA localization and stretching on periodically microstructured lipid membranes. Physical Review Letters, 2006. 96(3). 34. Hochrein, M.B., et al., DNA molecules on periodically microstructured lipid membranes: Localization and coil stretching. Physical Review E, 2007. 75(2). 35. Reisner, W., J.N. Pedersen, and R.H. Austin, DNA confinement in nanochannels: physics and biological applications. Reports on Progress in Physics, 2012. 75(10). 36. van Gunsteren, W.F. and H.J.C. Berendsen, Algorithms for brownian dynamics. Molecular Physics, 2006. 45(3): p. 637-647. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/49297 | - |
dc.description.abstract | DNA於鋪有正電脂雙層的玻璃溝槽與其側壁夾角處拉伸的現象,是因為該處具有一帶狀位能井的結果。但本實驗室所測得之DNA拉伸率與位能井寬度的關係與理論預測有所偏差,我們認為與位能井的形狀有關,故運用模擬方法來進行檢驗。
我們運用布朗動態法(Brownian dynamics, BD)模擬DNA在2D侷限環境下的性質,布朗動態法透過對高分子鏈施予隨機力模擬DNA於脂雙層上運動,而侷限環境則來自於我們所設定的一帶狀位能井。我們使用bead-spring model來模擬DNA,模型中包含Lennard-Jones體積排斥力、彈簧力及撓曲力之作用,在無限深方形位能井的條件下,我們的模擬結果與Odijk及de Gennes的預測情形相同。 首先我們模擬DNA在固定侷限寬度的情況下改變位能井侷限深度的拉伸情形,發現當位能井深度變大,DNA拉伸率也隨之上升,當位能井深度小於系統熱擾動能量時,DNA的運動會開始超出侷限範圍,導致其拉伸率快速下降,到最後完全離開侷限區域,此現象與我們在實驗上的觀察相同。 接著我們模擬位能井深度隨侷限寬度增加而變淺的情形,此趨勢是源自於我們實驗所觀察到的現象。我們的模擬結果顯示位能井的深度與侷限寬度對DNA拉伸率有高度影響,若運用與實驗近似的深度下降趨勢去進行模擬,所得之結果與理論趨勢的對應情形會與實驗所得高度近似。故我們的模擬結果證實了我們對位能井提出的假設,同時也佐證了DNA在帶狀侷限下,實驗結果與理論預期上的偏差。 | zh_TW |
dc.description.abstract | When DNA adsorbed on grooved glass with cationic lipid bilayers, they extend along the roots of the side wall of the grooves where the surface curvature is positive. The phenomenon is spontaneous and is expected to be caused by a deep energy well there. Such energy well can be considered as a strip-like confinement for DNA, and the width of the strip can be inferred from the width of area with positive curvature. However, the experimentally determined relationship between DNA extension and strip width somewhat deviates from the theoretical predictions made by de Gennes and Odijk. We suspect this deviation is related to the shape of the energy well which is assumed to be a deep square but is more likely to be nearly parabolic in reality.
To support our argument, we use Brownian dynamics to simulate DNA behavior in a strip confinement. DNA is represented by a bead-spring model that includes Lennard-Jones excluded-volume force, spring force and bending force. The force applied by lipid molecules is simulated by a random force. The model was tested in a strip confinement with infinitely deep well and the results were founded to match predictions by de Gennes and Odijk. At first we simulate DNA extension in a fixed depth of energy well with varying confinement width. DNA extension was found decreases with increasing width of energy well. As we expected, the simulation results are not in agreement with theoretical prediction. As the second step, we simulate DNA extension under a fixed width of confinement with varying depth of energy well. We found that DNA extension gradually increases as the energy well gets deeper. If the depth of energy well is below the thermal energy of the system, DNA starts to cross the boundary of confinement and the degree of DNA extension drops rapidly. With further reducing the depth of the energy well, DNA can no longer be confined by the well. We also simulate the cases that the depth of energy well decrease while the width of confinement increase because such scenario is closer to the real situation in experiments. We find that the relative rate of change between the depth of energy well and the width of confinement has critical influence to DNA extension. Employing a relationship between the depth of energy well and the width of confinement similar to experimental condition, we found the simulation results show very similar deviation from theoretical prediction as the experiments do. In conclusion, the simulation results support our argument that the energy well is not a deep square in reality. This finding also bridges the gap between the theoretical predictions and experimental observation for DNA behavior in strip confinement. | en |
dc.description.provenance | Made available in DSpace on 2021-06-15T11:22:37Z (GMT). No. of bitstreams: 1 ntu-105-R03524091-1.pdf: 3919682 bytes, checksum: 7d50fa93cc49a9019a2937b3d6fa0c7c (MD5) Previous issue date: 2016 | en |
dc.description.tableofcontents | 摘要 i
Abstract ii 目錄 iv 圖目錄 vii 表目錄 xiii 符號表 xiv 第1章 緒論 1 1.1 前言 1 1.2 研究動機與目的 2 第2章 文獻回顧 3 2.1 DNA的物理性質 3 2.1.1 去氧核糖核苷酸( DNA ) 3 2.1.2 堅韌長度( Persistence length ) 3 2.1.3 輪廓長度( contour length ) 4 2.1.4 擴散係數( Diffusivity) 4 2.1.5 鬆弛時間( Relaxation time ) 4 2.2 脂質 5 2.2.1 脂質結構 5 2.2.2 脂質自組裝 6 2.2.3 DNA在脂雙層上行為 8 2.3 高分子模型 10 2.3.1 理想鏈 10 2.3.1.1 首尾長度( end-to-end distance ) 11 2.3.1.2 環動半徑( Radius of gyration ) 12 2.3.2 真實鏈 14 2.3.3 Short-range interaction 與 Long-range interaction 16 2.3.4 Bead-stick model (Bead-rod model) 18 2.3.5 Bead-spring model 19 2.3.5.1 FENE spring 20 2.3.6 蠕蟲鏈( Worm-like Chain ) 21 2.4 DNA於侷限環境內的行為 23 2.4.1 侷限環境定義 23 2.4.2 DNA之伸長量與侷限寬度之關係 26 2.5 介觀尺度(mesoscale)模擬之簡介 29 2.6 DNA於2-D環境之模擬結果 30 2.6.1 2D環境MD與MC模擬結果的比較 30 2.6.2 2D侷限環境下過渡區域的探討 32 2.7 於圖案脂雙層上拉伸DNA之相關實驗結果 35 2.8 本實驗室改良之圖案脂雙層實驗 38 2.8.1 DNA於本實驗室基板上的拉伸情形 38 2.8.2 實驗基板的凹槽性質 40 2.9 本研究模擬策略之設計 44 第3章 模擬方法 47 3.1 布朗動態法(BD) 47 3.2 DNA模型 50 3.2.1 DNA本身的交互作用力 50 3.2.1.1 Lennard-Jones體積排斥力 50 3.2.1.2 FENE彈簧力 51 3.2.1.3 彎曲力 51 3.2.2 模擬參數 52 3.2.3 與文獻模擬結果之比較 52 3.3 位能井 54 第4章 結果討論 57 4.1 DNA於極深方形位能井中的拉伸情形 57 4.2 DNA於固定侷限寬度情形下,不同位能井深度對其拉伸率的影響 59 4.3 DNA於固定位能井深度情形下,不同侷限寬度對其拉伸率的影響 65 4.4 位能井深度隨侷限寬度改變的模擬結果 70 4.4.1 Odijk regime中位能井深度隨侷限寬度改變的模擬結果 70 4.4.2 De Gennes regime中位能井深度隨侷限寬度改變的模擬結果 74 4.4.3 與實驗結果之比較討論 77 第5章 結論與未來展望 79 第6章 參考文獻 81 | |
dc.language.iso | zh-TW | |
dc.title | 模擬DNA於脂雙層上自發展開之行為 | zh_TW |
dc.title | Simulating the Spontaneous Unraveling of DNA on Lipid Bilayers | en |
dc.type | Thesis | |
dc.date.schoolyear | 104-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 戴子安(Chi-An Dai),王勝仕(Sheng-Shih Wang),康敦彥(Dun-Yen Kang) | |
dc.subject.keyword | DNA,帶狀侷限,脂雙層,布朗動態法, | zh_TW |
dc.subject.keyword | DNA,strip confinement,lipid bilayers,Brownian dynamics, | en |
dc.relation.page | 83 | |
dc.identifier.doi | 10.6342/NTU201603147 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2016-08-19 | |
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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