近年來在奈米尺度下觀察奈米通道內流體的傳輸特性日趨熱門，其中包含了應用於生物醫學和奈米機械元件的可能性，又以奈米金管具有優異的生物相容性，因此常被應用在生技相關的分析化學或檢測上和模仿生物分子在通道內的傳輸功能，而此類生醫分子之輸送及流體物理，將能作為未來生物醫學技術之重要發展方向之一。
本文以分子動力學理論來模擬在奈米金管中通入水分子，並使用Spohr、F3C、Tight-binding等勢能進行模擬，且為了得知不同的系統密度、溫度下金原子對水分子所產生的吸附情形和傳輸行為，和了解在不同管徑大小下，奈米金管的管徑對於流體分子之影響。因此，本研究探討了不同的系統密度和溫度下的奈米金管管內之水分子的密度分佈、氫鍵數目和秩序參數及水分子之速度自相關函數，以便了解水分子於動態和靜態下之行為。

In recent years, the characteristic of Nano fluid channel has important contribute in bio-technology and nano-machine. Gold atoms in all materials have significant effects on human bodies, which have attracted considerable academic interests when applied to biotechnology. Especially the Au nanotubes has combine an excellent bio-compatible not only using in chemical analyzed and chemical inspect, but also has function on transport fluid molecule in micro channel.
This study utilizes molecular dynamics to the behavior of water molecules inside Au nanotubes. We used the potential of Spohr, F3C and Tight-binding in different water density and temperature to investigate the adsorption mechanism and dynamic behavior of water molecules inside Au nanotubes. We discuss the numbers of absorbed water molecule near the inner tube wall all achieve to saturation at three different densities, temperature and size of Au nanotubes. This work we compared water density, the percentage profiles of hydrogen bond, orientational order and flux for water molecules inside the Au nanotubes.

誌謝 I
目錄 II
圖目錄 V
表目錄 VIII
符號說明 IX
中文摘要 X
英文摘要 XI
第一章 緒論 1
1.1研究背景介紹 1
1.2 本文架構 9
第二章 分子動力學理論方法 10
2.1 運動方程式 10
2.2 勢能函數 11
2.2.1水分子與水分子間的作用勢能 12
2.2.2水分子與金奈米管間之作用勢能 14
2.2.3 金原子間作用勢能 15
2.3 溫度修正法 17
2.4 週期性邊界條件 18
第三章 分子動力學數值方法及其他相關物理量之求法 20
3.1鄰近原子表列法 21
3.1.1 Verlet List 表列法 21
3.1.2 Cell Link 表列法 22
3.1.3 Verlet List表列法結合Cell Link表列法 23
3.2 無因次化 25
3.3 分子動力學之流程圖 27
3.4 密度分佈 29
3.5氫鍵 29
3.6 秩序參數 29
3.7 流通量 30
3.8 速度-速度自相關函數 (Velocity-Velocity Autocorrlation Function,VACF) 30
第四章 結果分析與討論 33
4.1不同系統密度下之比較 33
4.1.1模擬模型 33
4.1.2系統密度之影響 33
4.2 不同系統溫度和奈米金管管徑之影響 44
4.2.1 模擬模型 44
4.2.2 奈米金管管徑大小及溫度之影響 44
4.3水分子之動態行為 53
4.3.1水分子之氫鍵動態特性 53
4.3.2 氫鍵動態特性之定義 53
4.3.3 不同區域及密度下之氫鍵動態特性 55
4.4 速度自相關函數 60
第五章 結論與建議 68
5.1 結論 68
5.2 未來展望與建議 71
參考文獻 72
作 者 77

[1]Brend Gromol, “Micro cooling systems for high density packaging”. Rev. Gen. Therm, 37 781-787 (1997).
[2]N.S. Ong, Y.H. Koh, Y.Q. Fu, “microlens array produced using hot embossing process”, Microelectronic engineering, 60 365-379 (2002).
[3]H. Takaba, M. Katagiri, M. Kubo, R. Vetrivel, and A. Miyamoto, Microporous Materials, 3, 449-455, (1995).
[4]R. E. Tuzun, D. W. Noid, B. G. Sumpter, and R. C. Merkle, Nanotechnology 7, 241-246, (1996).
[5]M. C. Gordillo, and J. Marti, Chemical Physics Letters, 329, 341-345, (2000).
[6]G. Hummer, J. C. Rasaiah, and J. P. Noworyta, Nature, 414, 188-190.
[7]M. C. Gordillo, and J. Marti, Chemical Physics Letters, 341, 250-254, (2001).
[8]M. Wirtz, S. Yu, and C. R. Martin, Analyst, 127, 871-879, (2002).
[9]Y.C. Lin and Q. Wang, “Transport behavior of water confined in carbon nanotubes,” Phys. Rev. B., vol. 72, 085420 (2005).
[10]Jie Zheng and Erin M. Lennon, “Transport of a liquid water and methanol mixture through carbonnanotubes under a chemical potential gradient” The Journal of Chemical Physics, 122, 214702 (2005).
[11]R. Wan, J. Li, H. Lu, H. Fang, “Controllable water channel gating of nanometer dimensions” JACS, 127, 7166-7170 (2005).
[12]Cavallaro, G.; Fresta, M.; Giammona, G. ; Puglisi, G. ; Villari,A. “Entrapment of-Lactams Antibiotics in Poly(ethyl cyanoacrylate) Nanoparticles : Studies on the Possible in Vivo Application of this Colloidal Delivery system. “ International Journal of Pharmaceutics, 111, 31-41, (1994).
[13]Rosi, N.L. and Mirkin, C.A. “Nanostructures in Biodiagnostics”, Chem Rev., 105, 1547-1562 (2005).
[14]M. Haruta, T. Kobayashi, H. Sano, and N. Yamada “Novel Gold Catalysts for the Oxidation of Carbon Monoxide at a Temperature far below 0 degree C”. Chemistry Letter 2,405-408 (1987).
[15]M. Wirtz, Shufang Yu, Charles R. martin. “Template synthesized gold nanotube membranes for chemical separation and sensing” Analyst, 127, 871-879 (2002).
[16]M. Wirtz, M. Parker, Y. Kobayashi, C. R. Martin, “Molecular sieving and sensing with gold nanotube membranes” The chemical record, Vol. 2, 259-267 (2002).
[17]Alyautdin, R ; Gothier, D.; Petrov, V.; Kharkevich, D.; Kreuter, Joerg. “Analgesic Activity of the Hexapeptide Dalargin Adsorbed on the Surface of Polysorbate 80-coated Poly(butyl cyanoacrylate ) Nanoparticles “.European Journal of Pharmaceutics and Biopharmaceutics, 41, 44-48, (1995).
[18]S. P. Ju, J. G. Chang, “A molecular dynamics simulation investigation into the behavior of water molecules inside au nanotubes of various sizes” Microporous and Mesoporous Materials, 75, 81-87 (2004).
[19]J. Duchet, R. Legras, S. Demoustier-Champagne, Chemical synthesis of polypyrrole: structure-properties relationship, Synth. Met., 98, 113-122 (1998).
[20]N.K. Chaki, K. Vijayamohanan, Self-assembled monolayers as a tuneable platform for biosensor applications, Biosensors. Bioelectron. 171-12(2002).
[21]Wolynes, P.G. and J.A. McCammon, “Hydrodynamic Effect on the Coagulation of Porous Biopolymers,” Macromolecules, vol. 10, pp.86-87. (1977).
[22]McCammon, J.A. and P.G. Wolynes, 1977, “Nonsteady Hydrodynamics of Biopolymer Motions,” The Journal of Chemical Physics, vol. 66,pp.1452-1456.
[23]McCammon, J. A., “Molecular Dynamics Study of the Bovine Pancreatic Trysin Inhibitor, in "Report of the 1976 Workshop, “Models for Protein Dynamics," H. J. C. Berendsen Edit, Centre Europeen de CalculAtomique et Moleculaire”, Universite de Paris IX, France, pp.137-152. (1977).
[24]McCammon, J. A., , B. R. Gelin, and M. Karplus, “Dynamics of Folded Proteins,” Nature, vol. 267, pp.585-590. (1977).
[25]McCammon, J. A. and M. Karplus, “Internal Motions of Antibody Molecules,” Nature, vol. 268, pp.765-766, (1977).
[26]J. Irving, and J. Kirkwood , “The statistical mechanical theory of transport properties. IV. The equations of hydrodynamics,” Journal of Chemical Physics, Vol.18, pp. 817-829 (1950).
[27]Lewis E. Kay and Kevin H. Gardner, “Current Opinion in Structrual Biology” 7, 722-731, (1997).
[28]Robert M. Cooke, “Current Opinion in Chemical Biology”, 1, 359-364, (1997).
[29]Timothy Cardozo, Serge Batalov, Ruben Abagyan, “Estimating local backbone Structural deviation in homology models”,Computer and Chemistry, Vol.24, p.p.13-31 (2000).
[30]Chothia C, Lesk AM, “Relationship between The divergence of sequence and structure in proteins”,EMBO J, Vol.5, p.p.823-827 (1986).
[31]John Moult, “The current state of the art In protein structure prediction”,Current Opinion in Biotechnology, Vol.7, p.p.422-427, (1996).
[32]J. Haile, Molecular Dynamics Simulation: Elementary Methods, John Wiley & Sons, Inc., New York. (1997).
[33] D. Rapaport, The Art of Molecular Dynamics Simulation, Cambridge University Press, London. (1997).
[34]M. P. Allen et al, Computer Simulation of Liquid, Oxford press(1994).
[35]W. A. Wallqvist, and O. Teleman, Molecular Physics 74, 515 (1991).
[36]T.I. Mizan. Et al, Comparison of rigid and flexible simple point charge water models at supercritical conditions, Journal of computational chemistry, 17, 1757 (1996).
[37]T.I. Mizan. Et al, Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution, J. Phys. Chem. B, 101, 5051 (1997).
[38]J. Bocker et al, Molecular dynamics simulation studies of the mercury-water interface, surface science, 335,372 (1995).
[39]F. Cleri, and V. Rosato, “Tight-binding potentials for transition metals and alloys,” Phys. Rev. B, Vol. 48, Issue. 1, pp.22-33 (1993).
[40]E. A. Jagla, “Boundary Lubrication Properties of Materials with Expansive Freezing.” Phys. Rev. Lett., 88(24),245504 (2002).
[41]M. P, Allen and D. J. Tildesley, Computer Simulation of Liquids, Clarendon press, Oxford. (1991).
[42]Haile, Molecular Dynamics Simulation: Elementary Methods, John Wiley & Sons, Inc., New York. (1997).
[43]Rapaport, The Art of Molecular Dynamics Simulation, Cambridge University Press, London. (1997).
[44]Kallinteris. G. C, Papanicolaou. N. I, and Evangelakis. G. A, Phys. Rev. B., Vol.55, 2150 (1997).
[45]Lynn. L. W, Smith. H. G, and Nicklow. R. M, Phys. Rev. B., Vol.8, 3493(1973).
[46]M.C. Gordillo, J. Marti, Chemical Physics Letters, 329, 341-345 (2000).
[47]Young In Jhon, Kyoung Tai No, Mu Shik Jhon, Fluid phase Equilibria, 224 ,160-166 (2006).
[48]Jie Zheng and Erin M. Lennon, Heng-Kwong Tsao, Yu-Jane Sheng, Shaoyi Jiang, The Journal of Chemical Physics, 122, 2147702 (2005).
[49]D. Bertolini, M. Cassettari, M. Ferrario, P. Grigolini, and G. Salveti, Adv. Chem. Phys., 62, 277 (1985).
[50]H. Chen and J. Teixeira, Adv. Chem. Phys., 64, 1 (1986).
[51]E.W. Castner, Y.J. Chang, Y.C. Chu, and G.E. Walrafen, J. Chem. Phys., 102, 653 (1995).
[52]M.F. Kropman and H.J. Bakker, Science, 291, 2118 (2001).
[53]H.J. Bakker, H.-K. Nienhuys, G.Gallot, N.Lascoux, G..M. Gale, J.C. Leicknam, and S. Bratos, J. Chem. Phys., 116, 2592 (2002) .
[54]A. Luzar and D. Chandler, Nature, 379, 53 (1996).
[55]A. Luzar, J. Chem. Phys., 113, 10663 (2000).
[56]H. Xu, H.A. Stern, and B.J. Berne, J. Phys. Chem. B, 106, 2054, (2002).
[57]G. Sutmann and R. Vallauri, Journal of Molecular Liquids, 213, 98-99 (2002).
[58]F. Starr, J. Nielsen, and H.E. Stanley, Phys. Rev. E: Stat. Phys. Plasmas, Fluids, Relat. Interdiscip. Top, 62, 579 (2000).
[59]A. Chandra, J. Phys. Chem. B, 107, 3899 (2003).
[60]J.Marti. J.A. Padro, and E. Guardia, J. Chem. Phys., 105, 639 (1996).
[61] A. Chandra, Phys. Rev, Lett., 85, 768 (2000)
[62]Z. Zhou, B.D. Todd, K.P. Travis, and R.J. Sadus, J. Chem. Phys., 123,051505(2005)
[63]R. Messina, C.Holm, and K. Kremer, J. Chem. Phys., 117, 2947 (2002)