臺灣博碩士論文加值系統

耗散粒子動力學是一種粗化的模擬方法，在此法中我們是用一顆粒子代表一團原子，保留重要的化學特性，來達到以較少的粒子代替多數原子作運算的目的。系統中主要是以保守力、隨機力、耗散力作用在粒子上，由於此模擬法可以節省運算時間，故在模擬上時間與空間可以達到介觀尺度。本研究主要以耗散粒子動力學模擬單鏈、雙鏈兩親分子，在不同的分子疏水端長度之下，探討面密度對薄膜形貌的影響。為了能夠了解在不同情況下兩親分子結構與薄膜結構的改變，本文使用了秩序參數、粗糙度、覆蓋率來解釋薄膜結構轉換和鏈長效應。而從研究中發現，單鏈兩親分子的行為與其構成的薄膜和實驗上大致吻合，反而在雙鏈兩親分子的行為上看不出與實驗有相同的趨勢。我們再用表面粗糙度將薄膜表面起伏量化，且得到不錯的效果。

Dissipative Particle Dynamics is a methodology of the coarse grained simulation. We use one particle to represent a group of atoms and retain the important nature of chemistry in this methodology. In order to achieve the purpose of computation we use fewer particles to represent many atoms. In the system, mainly Conservative Force, Random Force and Dissipative Force acts on the particle. Due to this methodology can save computing time, so the scale of time and space can reach mesoscopic scale.This work mainly uses Dissipative Particle Dynamics to simulate that how the surface density of amphiphiles with single and double tails affect the morphology of membranes in different hydrophobic beads length. In order to understand the changes of architecture of amphiphiles and membranes, this work uses Orientation Order Parameters, Roughness and Degree of overlap to interpret the transformation of membranes architecture and effects of chain length. The behaviors of membranes assembled by single tail amphiphiles and single tail amphiphiles are almost in agreement with the results of experiments. But in the case of double tails amphiphiles, we cannot find the qualitative trend observed in experiments. Then we use roughness to quantify the fluctuation of membrane surface and obtain good result.

目錄
摘要 I
Abstract II
致謝 IV
目錄 V
表目錄 VII
圖目錄 VIII
符號說明 XI
第一章 緒論 1
1-1前言 1
1-2文獻回顧 5
1-3研究動機與目的 9
1-4本文架構 12
第二章 模擬理論基礎 13
2-1耗散粒子動力學簡介 13
2-2耗散粒子動力學原理 15
2-3尺度無因次化 20
2-4 噪音參數的選取 21
2-5運動軌跡的積分方法 22
2-6相同粒子間斥力參數的選取 23
2-7相異粒子間斥力參數的選取 25
2-8週期性邊界 29
2-9最小映像法法則 30
2-10截斷半徑與鄰近表列法 32
第三章 分析薄膜型態理論 36
3-1單一分子佔的面積(Area per molecule) 36
3-2分子尾鏈的覆蓋(Overlap)程度 38
3-3秩序參數(Orientation Order Parameters) 40
3-4表面粗糙度(Roughness) 42
第四章 結果與討論 43
4-1模擬物理模型 43
4-2 分子密度對薄膜形態的影響 48
4-3 疏水鏈段長度對形態的影響 52
4-4 溫度對薄膜形態影響 70
第五章 結論與未來展望 73
5-1結論 73
5-2 未來展望 75
參考文獻 76

[1]王鳳英, 界面活性劑的原理與應用, 1986
[2]R. Goetz, R. Lipowsky, “Computer simulations of bilayer membranes:Self-assembly and interfacial tension, J.Chem. Phys. 108, 7397-7409, 1998.
[3]L. Rekvig, M. Kranenburg, J. Vreede, B. Hafskjold, B. smit, Langmuir , “Investigation of surfactant efficiency using dissipative particle dynamics, American Chemical Society, 19, 8195-8205, 2003.
[4]E. Goter, F.Grendel, “On bimolecular layers of lipoids on the chromocytes of the blood, J.Exper.Med , 41, 439-443, 1925.
[5]M. Venturoli, M. Sperotto, M. Kranenburg, B. Smit, “Mesoscopic models of biological membranes, Physics Reports, 437, 1-54, 2006..
[6]S. Singer, G. Nicolson, “Fluid mosaic Model of structure of Cell Membranes, J. Cell. Comput. Physiol Science, 175, 720–731,1972.
[7]S. K?nig, E. Sackmann, “Molecular and collective dynamics of lipid bilayers, Curr. Opin. Colloid Interface Sci, 1, 78-82, 1996.
[8]E. Sackmann, R. Lipowsky, “Structure and Dynamics of Membranes, Elsevier, 1-65, 1995.
[9]K. Merz , B. Roux, “Biological Membranes: A Molecular Perspective from Computation and Experiment, 1996.
[10]M. Sperotto, S. May, A. Baumg?rtner, “Modelling of proteins in membranes, J.Chem.Phys., 141, 2–29, 2006.
[11]P. Cullis, B. Kruijff, Lipid polymorphism and the functional roles of lipids in biological membranes, Biochim. Biophys.Acta, 559, 399–420, 1979.
[12]M. Venturoli, M. Sperotto, M. Kranenburg, B. Smit, “Mesoscopic models of biological membranes, Physics Reports, 437 ,1-54, 2006.
[13]O. Mouritsen, M. Sperotto, J. Risbo, Z. Zhang, M. Zuckermann, “Computational approach to lipid-protein interactions in membranes. Adv. Comput. Biol., 2, 15–64, 1996.
[14]D. Tieleman, S. Marrink, H. Berendsen, “A computer perspective of membranes:molecular dynamics studies of lipid bilayer systems, Biochim. Biophys.Acta, 1331, 235–270, 1997.
[15]G. Brannigan, L. Lin, F. Brown, “Implicit solvent simulation models for biomembranes, Eur. Biophys. J. Biophys., 35, 104-124, 2006.
[16]G. Ayton, A. Smondyrev, S. Bardenhagen, P. McMurtry, G. Voth, “Caculating the bulk modulus for a lipid bilayer with noneequilibrium molecular dynamics simulation, Biophys. J., 82 ,1226–1238, 2002.
[17]R. Groot, K. Rabone, “Mesoscopic simulation of cell membrane damage ,morphology change and rupture by nonionic surfactants, Biophys.J., 81, 725-736, 2001.
[18]M. Kranenburg, M. Venturoli, B. Smit, “Molecular simulation of mesoscopic bilayer phases, Phys. Rev. E , 67 ,Art.No.060901, 2003.
[19]M. Kranenburg, M. Venturoli, B. Smit, “Phase behavior and induced interdigitation in bilayers studied with dissipative particle dynamics, J. Phys. Chem., B 107 (41) , 11491–11501, 2003.
[20]T. McIntosh, R. McDaniel, S. Simon, “Induction of an interdigitated gel phase in fully hydrated phosphatidylcholine bilayers, Biochim. Biophys.Acta1, 731,109–114, 1983.
[21]T. Hata, S. Kaneshina, “Effect of local anesthetics on bilayer membrane of dipalmitoylphosphatidylcholine: interdigitation of lipid bilayer and vesicle-micelle transition, Biophys. Chem., 87, 25-36, 2000.
[22]M. Venturoli, B. Smit, M. Sperotto, “Simulation studies of protein-induced bilayer deformation, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins, Biophys. J., 88 ,1778–1798, 2005.
[23]F. Frezard, A. Garniersuillerot, “Permeability of lipid bilayer to anthracycline derivatives.Role of the bilayer composition and of the temperature, Biochimica etBiophysicaActa-Lipids and Lipid Metabolism, 1389, 13-22, 1998.
[24]R. Chang, S.Nir, F. Poulain, “Analysis of binding and membrane destabilization of phospholipid membranes by surfactant apoprotein B, Biochimica etBiophysicaActa–Biomembranes, 1371, 254-264, 1998.
[25]S. Semple, A. Chonn, P. Cullis, “Interactions of liposomes and lipid-based carrier systems with blood proteins:Relation to clearance behavior in vivo, Advanced Drug Delivery Reviews , 32, 3-17, 1998.
[26]G. Gregoriadis, “Liposome Technology—v1, 1-36, 1993.
[27]A. Grafmuller, J.Shillcock, R.Lipowsky, “Dissipative particle dynamics of tension-induced membrane fusion, Molecular Simulation, 35, 554 -560, 2008.
[28]R. Rudd, J. Broughton, “Coarse-grained Molecular Dynamics and Atomic Limit of Finite Elements, Physical Review B, 58, 5893-5896, 1998.
[29]P. Hoogerbrugge, J .Koelman, “Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics, Europhys.Lett. 19, 155-160, 1992.
[30]R. Groot, P. Warren, “Dissipative particle dynamics:Bridging the gap between atomistic and mesoscopic simulation, J. Chem. Phys. 107, 4423-4435, 1997.
[31]S. Yamamoto, Y. Maruyama, S. Hyodo, “Dissipative particle dynamics study of spontaneous vesicle formation of amphiphilic molecules, J. Chem. Phys. 116, 5842-5849, 2002.
[32]M. Laradji, P. Sunil, Kumar, “Dynamics of domain growth in self–assembled fluid vesicles , Phys. Rev. Lett. 93, 198105 , 2004.
[33]J. Shillcock, R. Lipowsky, “Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulation, J. Chem. Phys. 117, 5048-5061 , 2002.
[34]J. Israelachvili, H. Wennerstrom, “Entropic forces between amphiphilic surfaces in liquids, J.Phys.Chem. 96, 520-531, 1992.
[35]T. C. Lim , “Mathematical relationships between bond-bending force field, Journal of Mathematical Chemistry , 32, 3, 2003.
[36]M. Allen, D. Tidesley , Computer Simulation of Liquids, Clarendon,Oxford,1987.
[37]L. Gao, J. Shillcock, R. Lipowsky, “Improve dissipative particle dynamics simulations of bilayers, J. Chem. Phys., 126, 015101, 2007.
[38]李俊賢, “以耗散粒子動力學法研究嵌段高分子刷於選擇性溶劑中之表面結構, 碩士論文, 國立台灣大學, 2007.
[39]Petrache, H. Dodd, S. Brown, “Area per lipid and acyl length distributions in fluid phosphatidylcholines determined by H-2 NMR spectroscopy, Biophys. J, 79, 3172-3192, 2000.
[40]J. Shillcock, R. Lipowsky, “Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations, J. Chem. Phys., 117, 5048-5061, 2002.
[41]Tristram-Nagle, S. Zhang, R. Suter, R. Worthington, C. Sun, W. Nagle, Biophys.J, 64, 1097-1109, 64, 1993.
[42]W. Rawicz, K. Olbrich, T. Mclntosh, D. Needham, E. Evans, “Effect of chain length and unsaturation on elasticity of lipid bilayers, Biophys. J, 79, 328-339, 2000.
[43]R. Goetz, G. Gompper, R. Lipowsky, “Mobility and elasticity of self –assembled membranes, Phys. Rev. Lett. , 221-224, 1999.
[44]M. Kranenburg, B. Smit, “Phase behavior of model lipid bilayers, J.Phys.Chem, 109, 6553-6563, 2005.