由於分子動力學模擬有受限於能量的局部最小值以及無法長時間的模擬以獲得高分子的穩定結構的缺點。因此，本論文中，係利用粗殼粒子結構趨勢蒙地卡羅法來克服上述的缺點並探討甲基丙烯酸甲酯寡聚物吸附於具有凹槽結構之基板上的結構行為。其中，根據寡聚物與凹槽的相對位置可將其分為三種類型，分別為：類型1為寡聚物完全在凹槽內部、類型2為寡聚物部份在凹槽內、及類型3為寡聚物完全不在凹槽內部。類型1及類型2的秩序參數會隨著凹槽寬度的增加而遞減，然而類型3的秩序參數則大約維持在0.1。另外，當類型1的寡聚物與不同作用強度的基板顯示，其秩序參數亦隨著凹槽寬度的增加而遞減。而我們也探討了凹槽的深度對於寡聚物在最窄(20 Å)及最寬(35 Å)的凹槽內之影響。對於寡聚物在最窄的凹槽內而言，類型1的寡聚物之排列會受到凹槽寬度的影響。然而，對於寡聚物最寬的凹槽內，類型1的寡聚物之秩序參數會大約為持在0.2。期望能藉由此研究讓研究者們能更深入了解分子的物理吸附特徵與現象，更能在近代的科技應用上有所貢獻。

The coarse-grained configurational-bias Monte Carlo (CG-CBMC) simulation was employed to study the structural behaviors of methyl methacrylate (MMA) oligomers adsorbed on grooved substrate due to molecular dynamics (MD) simulation is probably trapped at some local energy minima and difficult to carry out over a long enough time to allow relaxation of chain motion for an enormous polymeric system. Therefore, the CG-CBMC simulation was adopted in the present study. In this study, three types of chains are classified according to their positions relative to the groove. Type 1, Type 2, and Type 3 represent the entire MMA-oligomer within the groove, the MMA-oligomer partially within the groove, and the oligomer outside the groove, respectively. The orientational order parameters of Type 1 and Type 2 oligomers decrease with the increase of groove width, but the orientational order parameter of Type 3 oligomers is approximately equal to 0.1. In addition, observation of the orientational order parameters of Type 1 oligomers interacting with the grooved substrate at different interaction strengths decrease with increasing the groove width. Furthermore, the orientational order parameters of Type 1 oligomers within the narrowest (20 Å) and the widest (35 Å) groove with different depths were determined. For the narrowest groove, the arrangement of Type 1 oligomers will be influenced by the groove width. However, in the case of the widest groove, the orientational order parameter of Type 1 oligomers is approximately equal to 0.2. This study can help engineers clarify the characteristics and phenomena of physical adsorption of the molecules, as well as contributing to the application of recent technology.

Contents I
List of Figures IV
List of Tables VI
List of Symbols VII
List of Abbreviations XII
Chapter 1 Introduction 1
1-1 Introduction to Confinement Effect 1
1-2 Introduction to Surface Adsorption of Molecules on Substrate 2
1-2-1 Application and Experimental Studies 2
1-2-2 Review of Molecular Modeling for Surface Adsorption of Molecules on Substrate 5
1-3 Introduction to Surface Adsorption of Molecules on Cylindrical Tube 8
1-3-1 Application and Experimental Studies 8
1-3-2 Reviewing of Molecular Modeling for Surface Adsorption of Molecules on Cylindrical Surface 10
1-3-3 Experimental and Theoretical Studies of Confinement Effect of Au Nanotube 12
1-4 Outline of the Dissertation 13
Chapter 2 Molecular Dynamics Modeling 15
2-1 Introduction 15
2-2 Equations of Motion 15
2-3 Empirical Force Field Model 17
2-3-1 Development and Outline of Force Field for Bio-molecule and Polymer System 17
2-3-2 Energy Calculation and Dynamics Force Field 18
2-3-3 Tight-Binding Potential 19
2-3-4 Dreiding Force Field 20
2-4 Thermodynamic Ensembles 21
2-5 Constant Temperature Dynamics 22
2-5-1 Rescaling of Velocity 22
2-5-2 Heat Bath: Weak coupling method 23
2-5-3 Heat Bath: Stochastic collision method 24
2-5-4 Heat Bath: Extended system coupling method 25
2-6 Constant Pressure Dynamics 26
Chapter 3 Numerical Methodology of Molecular Dynamics 28
3-1 Periodic Boundary Conditions and Minimum Image Convention 28
3-2 Treatment of non-bonded interaction 30
3-3 Non-bonded Neighbor Lists 34
3-4 Flow Chart of Molecular Dynamics 36
Chapter 4 Monte Carlo Simulation 37
4-1 Metropolis Monte Carlo Algorithm 37
4-2 The Detailed Balance 39
4-3 Metropolis Monte Carlo Simulation 40
4-4 Flow Chart of Metropolis Monte Carlo simulation 41
4-5 Configurational-bias Monte Carlo Simulation 42
4-6 Flow Chart of Configurational-bias Monte Carlo Simulation 45
Chapter 5 Coarse-grained model 46
5-1 Introduction to Coarse-grained Model 46
5-2 United Atom Model 47
5-2-1 Mapping Scheme 47
5-2-2 Interaction Energy of United Atom Model 48
5-2-3 Iterative Boltzmann Inversion 49
5-3 Structured-based Model 50
5-3-1 Mapping Scheme 50
5-3-2 Inverse Mapping of Structured-based Model 51
5-4 Bead-spring Model 51
5-5 Linked-vector Model 53
5-5-1 Mapping Scheme 53
5-5-2 Interaction Energy of Linked-vector Model 54
5-5-3 Reverse-mapping of Linked-vector Model 55
Chapter 6 Results and Discussion 56
6-1 Dynamic Properties of Water Molecules within Au Nanotube with Different Bulk Densities 56
6-2 Why Use Coarse-Grained Simulation 61
6-3 Investigation of MMA-oligomer Adsorbed on Grooved Substrate of Different Aspect Ratios by Coarse-grained Configurational-bias Monte Carlo Simulation 62
6-3-1 Poly (methyl methacrylate) 62
6-3-2 Simulation Model 63
6-3-3 Equilibrium Conformations of MMA-oligomers on Grooved Substrate of Different Widths 69
6-3-4 Order Parameters of MMA-oligomers on the Substrate 71
6-3-5 Order Parameters of MMA-oligomers on the Substrate of Different Interaction Strengths 74
6-3-6 Bond Fraction of MMA-oligomers around the Groove of Different Widths 75
6-3-7 Equilibrium Conformations of MMA-oligomers on the Substrate of Different Depths 77
6-3-8 Comparison of the Order Parameters of MMA-oligomers within the Narrowest and the Widest Grooves 79
6-3-9 Bond Fraction of MMA-oligomers around the Groove of Different Depths 81
6-3-10 Number of MMA-oligomers within Groove with Different Interaction Strengths 82
6-4 Preliminary Result: The Structural Behaviors of MMA-oligomers and Cylindrical Nanotube Nanocomposite 84
Chapter 7 Conclusion and Future Works 90
7-1 Conclusion of the Study of MMA-oligomer Adsorbed on Grooved Substrate of Different Aspect Ratios 90
7-2 Future Work 91
Appendix A Parameters in force field 92
References 96

[1] P. Rittigstein and J. M. Torkelson, "Polymer-
nanoparticle interfacial interactions in polymer nanocomposites: Confinement effects on glass transition temperature and suppression of physical aging", J. Poly. Sci. : Part B: Poly. Phys., vol. 44, pp. 2935, 2006.
[2] Y. S. Lipatov, T. T. Alekseeva, L. A. Sorochinskaya, and G. V. Dudarenko, "Confinement effects on the kinetics of formation of sequential semi-interpenetrating polymer networks", Poly. Bull., vol. 59, pp. 739, 2008.
[3] S. Ok, M. Steinhart, A. Serbescu, C. Franz, F. V. Chávez, and K. Saalwächter, "Confinement effects on chain dynamics and local chain order in entangled polymer melts", Macromolecules, vol. 43, pp. 4429, 2010.
[4] M. Malvaldi, S. Bruzzone, and F. Picchioni, "Confinement effect in diffusion-controlled stepwise polymerization by Monte Carlo simulation", J. Phys. Chem. B, vol. 110, pp. 12281, 2006.
[5] I. Nakamura and A. Shi, "Conformation of a tethered polymer in a leaky nanocavity", J. Chem. Phys., vol. 132, pp. 174102, 2010.
[6] Nan Li and Chih-Ming Ho, "Patterning functional proteins with high selectivity for biosensor applications", J. Assoc. Lab. Autom., vol. 13, pp. 237, 2008.
[7] J. W. Choi, S. J. Park, Y. S. Nam, W. H. Lee, and M. Fujihira, "Molecular pattern formation using chemically modified cytochrome c", Coll. Surf. B: Biointerfaces, vol. 23, pp. 295, 2002.
[8] J. B. Lee, S. H. Um, J. W. Choi, and K. K. Koo, "Surface modification of a self-assembled ferredoxin monolayer on a gold substrate by CHAPS", Langmuir, vol. 19, pp. 8744, 2003.
[9] A. E. Kamholz, B. H. Weigl, B. A. Finlayson, and P. Yager, "Quantitative analysis of molecular interaction in a microfluidic channel: The T-Sensor", Anal. Chem., vol. 71, pp. 5340, 1999.
[10] A. E. Kamholz, E. A. Schilling, and P. Yager, "Optical measurement of transverse molecular diffusion in a microchannel", Biophys. J., vol. 80, pp. 1967, 2001.
[11] K. Macounavá, C. R. Cabrera, M. R. Holl, and P. Yager, "Generation of natural pH gradients in microfluidic channels for use in isoelectric focusing", Anal. Chem., vol. 72, pp. 3745, 2000.
[12] N. P. Westcott, and M. N. Yousaf, "Synergistic microfluidic and electrochemical strategy to activate and pattern surfaces selectively with ligands and cells", Langmuir, vol. 24, pp. 2261, 2008.
[13] X. F. Wu and G. Q. Shi, "Fabrication of a lotus-like micro-nanoscale binary structured surface and wettability modulation from superhydrophilic to superhydrophobic", Nanotech., vol. 16, pp. 2056, 2005.
[14] D. Panja, G. T. Barkema, and A. B. Kolomeisky, "Non-equilibrium dynamics of single polymer adsorption to solid surfaces", J. Phys.: Condens. Matter, vol. 21, pp. 242101, 2009.
[15] B. Zappone, M. Ruths, G. W. Greene, G. D. Jay, and J. N. Israelachvili, "Adsorption, lubrication, and wear of lubricin on model surfaces: polymer brush-like behavior of a glycoprotein", Biophys. J., vol. 92, pp. 1693, 2007.
[16] X. Yan, S. S. Perry, N. D. Spencer, S. Pasche, S. M. De Paul, M. Textor, and M. S. Lim, "Reduction of friction at oxide interfaces upon polymer adsorption from aqueous solutions", Langmuir, vol. 20, pp. 423, 2004.
[17] J. C. Meredith and K. P. Johnston, "Theory of polymer adsorption and colloid stabilization in supercritical fluids. 1. Homopolymer stabilizers", Macromol., vol. 31, pp. 5507, 1998.
[18] E. Martinez, E. Engel, J. A. Planell, and J. Samitier, "Effects of artificial micro- and nano-structured surfaces on cell behavior", Ann. Anat., vol. 191, pp. 126, 2009.
[19] J. J. Gray, "The interaction of proteins with solid surface", Cur. Opin. Struc. Bio., vol. 14, pp. 110, 2004.
[20] F. Darain, K. L. Gan, and S. C. Tjin, "Antibody immobilization on to polystyrene substrate-on-chip immunoassay for horse IgG based on fluorescence", Biomed. Microdevices, vol. 11, pp. 623, 2009.
[21] M. E. Vlachopoulou, P. S. Petrou, S. E. Kakabakos, A. Tserepi, K. Beltsios, and E. Gogolides, "Effect of surface nanostructuring of PDMS on wetting properties, ydrophobic recovery and protein adsorption", Microelec. Eng., vol. 86, pp. 1321, 2009.
[22] Y. Zhao, Q. Lu, M. Li, and X. Li, "Anisotropic wetting characteristics on submicrometer-scale periodic grooved surface", Langmuir, vol. 23, pp. 6212, 2007.
[23] M. Ball, D. M. Grant, W. J. Lo, and C. A. Scotchford, " The effect of different surface morphology and roughness on osteoblast-like cells", J. Biomed. Mat. Res. Part A, vol. 86, pp. 637, 2007.
[24] H. Hori, K. Tawa, K. Kintaka, J. Nishii, and Y. Tatsu, "Influence of groove and surface profile on fluorescence enhancement by grating-coupled surface plasmon resonance", Optical Review, vol. 16, pp. 216, 2009.
[25] S. Fujuta, M. Ohshima, and H. Iwata, "Time-lapse observation of cell alignment on nanogrooved patterns", J. R. Soc. Interface, vol. 6, pp. S269, 2009.
[26] Y. Yi, G. Lombardo, N. Ashby, R. Barberi, J. E. Maclennan, and N. A. Clark, "Topographic-pattern-induced homeotropic alignment of liquid crystals", Phys. Rev. E, vol. 79, pp. 041701, 2009.
[27] M. Hirtz, H. Fuchs, and L. Chi, "Influence of substrate treatment on self-organized pattern formation by langmuir-Blodgett transfer", J. Phys. Chem. B, vol. 112, pp. 824, 2008.
[28] W. Wang, X. Mei, G. Jiang, S. Lei, and C. Yang, "Effect of two typical focus positions on microstructure shape and morphology in femtosecond laser multi-pulse ablation of metals", App. Surf. Sci., vol. 255, pp. 2303, 2008.
[29] J. Lim, M. Popall, and S. Kang, "Application of organic/inorganic hybrid photopolymer to fabricate ultra-high-density patterned substrate", IEEE Trans. Magn., vol. 45, pp. 2300, 2009.
[30] H. Oshima, H. Tamura, M. Takeuchi, A. Inomata, Y. Yanaida, N. Matsushita, H. Komoriya, T. Uzumaki, and A. Tanaka, "Nanopattern transfer from high-density self-assembled nanosphere arrays on prepatterned substrates", Nanotech., vol. 20, pp. 455303, 2009.
[31] S. Watanabe, K. Inukai, S. Mizuta, and M. T. Miyahara, "Mechanism for stripe pattern formation on hydrophilic surfaces by using convective self-assembly", Langmuir, vol. 25, pp. 7287, 2009.
[32] B. Zdyrko, O. Hoy, M. K. Kinnan, G. Chumanov, and I. Luzinov, "Nano-patterning with polymer brushes via solvent-assisted polymer grafting", Soft Matter, vol. 4, pp. 2213, 2008.
[33] J. H. Kim, M. Seo, and S. Y. Kim, "Lithographically patterned breath figure of photoresponsive small molecules: Dual-patterned honeycomb lines from a combination of bottom-up and top-down lithography", Adv. Mater., vol. 21, pp. 1, 2009.
[34] S. J. Jeong, J. E. Kim, H. S. Moon, B. H. Kim, S. M. Kim, J. B. Kim, and S. O. Kim, "Soft graphoepitaxy of block copolymer assembly with disposable photoresist confinement", Nano Letters, vol. 9, pp. 2300, 2009.
[35] A. Bardea and R. Naaman, "Submicrometer chemical patterning with high throughput using magnetolithography, Langmuir, vol. 25, pp. 5451, 2009."
[36] J. G. Kim, N. Takama, B. J. Kim, and H. Fujita, "Optical-softlithographic technology for patterning on curved surfaces", J. Micromech. Microeng., vol. 19, pp. 055017, 2009.
[37] A. Zelcer, A. Wolosiuk, and G. J. A. A. Soler-Illia, "Carbonaceous submicro sized islands: a surface patterning route to hierarchical macro/mesoporous thin films", J. Mater. Chem., vol. 19, pp. 4191, 2009.
[38] J. Shi, X. F. Ni, and Y. Chen, "Patterning biomolecules with a water-soluble release and protection interlayer", Langmuir, vol. 23, pp. 11377, 2007.
[39] K. Arimoto, G. Kawaguchi, K. Shimizu, M. Watanabe, J. Yamanaka, K. Nakagawa, N. Usami, K. Nakajima, K. Sawano, and Y. Shiraki, "Structural and transport properties of strained SiGe grown on V-groove patterned Si (110) substrates", J. Crys. Grow., vol. 311, pp. 814, 2009.
[40] D. S. Kim, B. K. Lee, J. Yeo, M. J. Choi, W. Yang, and T. H. Kwon, "Fabrication of PDMS micro/nano hybrid surface for increasing hydrophobicity", Microele. Eng., vol. 86, pp. 1375, 2009.
[41] W. Zhang, G. Liu, J. Xu, and Y. Yang, "Effect of channel surface wettability and temperature gradients on the boiling flow pattern in a single microchannel", J. Micromech. Microeng., vol. 19, pp. 055012, 2009.
[42] C. C. Chen, P. C. H. Hsieh, G. M. Wang, W. C. Chen, and M. L. Yeh, "The influence of surface morphology and rigidity of the substrata on cell motility", Mat. Lett., vol. 63, pp. 1872, 2009.
[43] L. Wang, L. Lei, X. F. Ni, J. Shi, and Y. Chen, "Patterning bio-molecules for cell attachment at single cell levels in PDMS microfluidic chips", Microele. Eng., vol. 86, pp. 1462, 2009."
[44] S. Chen and L. M. Smith, "Photopatterned thiol surfaces for biomolecule immobilization", Langmuir, vol. 25, pp. 12275, 2009.
[45] J. T. Hirvi and T. A. Pakkanen, "Molecular dynamics simulations of water droplets on polymer surfaces", J. Chem. Phys, vol. 125, pp. 144712, 2006.
[46] J. T. Hirvi and T. A. Pakkanen, "Wetting of Nanogrooved polymer surfaces", Langmuir, vol. 23, pp. 7724, 2007.
[47] J. T. Hirvi and T. A. Pakkanen, "Enhanced hydrophobicity of rough polymer surfaces", J. Phys. Chem. B, vol. 111, pp. 3336, 2007.
[48] C. C. Hwang, Y. R. Jeng, Y. L. Hsu, and J. G. Chang, "Molecular dynamics simulation of microscopic droplet spread on rough surfaces", Journal of the Physical Society of Japan, vol. 70, pp. 2626, 2001.
[49] T. Kimura and S. Maruyama, "A molecular dynamics simulation of water droplet in contact with a platinum surface", The 6th ASME-JSME Thermal Engineering Joint Conference, March16-20, pp. TED-AJ03-183, 2003.
[50] X. Yong and L. T. Zhang, "Nanoscale wetting on groove-patterned surfaces", Langmuir, vol. 25, pp. 5045, 2009.
[51] S. Balasubraian, M. L. Klein, and J. llja Siepmann, "Monte carlo investigations of hexadecane films on a metal substrate", J. Chem. Phys., vol. 103, pp. 3184, 1995.
[52] A. Chemos, E. Glynos, V. Koutsos, and P. Caompus, "Adsorption and self-assembly of linear polymers on substrate: a computer simulation study", Soft Matter, vol. 5, pp. 637, 2009.
[53] S. Elli, G. Raffaini, and F. Ganazzoli, "Surface adsorption of comb polymers by Monte Carlo Simulation", Polymer, vol. 49, pp. 1716, 2008.
[54] N. Källrot, M. Daiqvist, and P, Linse, "Dynamics of polymer adsorption from bulk solution onto plannar", Nanotech., vol. 42, pp. 3641, 2009.
[55] S. F. Edwards and Y. Chen, "The statistics of polymers on rough surfaces", J. Phys. A: Math. Gen., vol. 21, pp. 2963, 1988.
[56] J. F. Douglas, "How does surface roughness affect polymer-surface interactions?", Macromolecules, vol. 22, pp. 3707, 1989.
[57] A. C. Balazs, K. Huang, and C. W. Lantman, "Adsorption of triblock copolymers on rough surfaces", Macromolecules, vol. 23, pp. 4641, 1990.
[58] A. Baumgärtner and M. Muthukumar, "Effects of surface roughness on adsorbed polymers", J. Chem. Phys., vol. 94, pp. 4062, 1991.
[59] A. C. Balazs, K. Huang, P. McElwain, and J. E. Brady, "Polymer adsorption on laterally heterogenerous surfaces: a Monte Carlo computer model", Macromolecules, vol. 24, pp. 714, 1991.
[60] M. R. Wattenbarger, V. A. Bloomfield, and D. F. Evans, " Monte Carlo simulation of chain molecule adsorption on a line defect", Macromolecules, vol. 25, pp. 261, 1992.
[61] D. Kim and E. Darve, "Molecular dynamics simulation of electro-osmotic flows in rough wall nanochannels", Phys. Rev. E, vol. 73, pp. 051203, 2006.
[62] K. Kiyohara, K. Asaka, H. Monobe, N. Terasawa, and Y. Shimizu, "Surface anchoring of rodlike molecules on corrugated substrates", J. Chem. Phys., vol. 124, pp. 034704, 2006.
[63] X. L. Wang, Z. Y. Lu, Z. S. Li, and C. C. Sun, "Molecular dynamics simulation study on controlling the adsorption behavior of polyethylene by fine tuning the surface nanodecoration of graphite", Langmuir, vol. 23, pp. 802, 2007.
[64] A. Niavarani and N. V. Priezjev, "Rheological study of polymer flow past rough surfaces with slip boundary conditions", J. Chem. Phys., vol. 129, pp. 144902, 2008.
[65] L. D. Site, S. Leon, and K. Kremer, "Specific interaction of polymers with surface defects: structure formation of polycarbonate on nickel", J. Phys.: Condens. Matter, vol. 17, pp. L53, 2005.
[66] M. Patra and P. Linse, "Simulation of grafted polymers on nanopatterned surfaces", Nano Letters, vol. 6, pp. 133, 2006.
[67] A. G. Koutsioubas and A. G. Vanakaras, "Polymer brushes on periodically nanopatterned surfaces", Langmuir, vol. 24, pp. 13717, 2008.
[68] T. Zehl, M. Wahab, P. Schiller, and H. J. Mögel, "Monte Carlo simulation of surfactant adsorption on hydrophilic surfaces", Langmuir, vol. 25, pp. 2090, 2009.
[69] P. Adamczyk, P. Romiszowski, and A. Sikorski, "Adsorption of homopolymer chains on a strip-patterned surface: A Monte Carlo study", Catal. Lett., vol. 129, pp. 130, 2009.
[70] B. E. Kibride, J. N. Coleman, J. Fraysse, P. Fournet, M. Cadek, A. Drury, S. Jutzler, S. Roth, and W. J. Blau, "Experimental observation of scaling laws for alternating current and direct current conductiveity in polymer-carbon nanotune composite thin fikms", J. Appl. Phys., vol. 92, pp. 4024, 2002.
[71] R. Ramasubramaniam, J. Chen, and H. Liu, "Homogeneous carbon nanotube/polymer composites for electrical applications", App. Phys. Lett., vol. 83, pp. 2928, 2003.
[72] B. Kim, J. Lee, and I. Yu, "Electrical properties of single-wall carbon nanotube and epoxy composites", J. Appl. Phys., vol. 94, pp. 6724, 2003.
[73] L. S. Schadler, S. C. Giannaris, and P. M. Ajayan, "Load transfer in carbon nanotube epoxy composites", Appl. Phys. Lett., vol. 73, pp. 3842, 1998.
[74] H. D. Wagner, O. Lourie, Y. Feldman, and R. Tenne, "Stress-induced fragmentation of multiwall carbon nanotubein a polymer matrix", Appl. Phys. Lett., vol. 72, pp. 188, 1998.
[75] R. Andrews, D. Jacques, A. M. Rao, T. Rantell, and F. Derbyshire, "Nanotube composite carbon fibers", Appl. Phys. Lett., vol. 75, pp. 1329, 1999.
[76] P. A. Ajayan, L. S. Schadler, C. Giannaris, and A. Rubio, "Single-walled carbon nanotube-polymer composites: Strength and weakness", Adv. Mater., vol. 12, pp. 750, 2000.
[77] M. Cadek, J. N. Coleman, K. P. Ryan, V. Nicolosi, G. Bister, A. Fonseca, J. B. Nagy, K. Szostak, F. Béguin, and W. J. Blau, "Reinforcement of polymers with carbon nanotubes: The role of nanotube surface area", Nano Letters, vol. 4, pp. 353, 2004.
[78] C. Wei, D. Srivastava, and K. Cho, "Thermal expansion and diffusion coefficients of carbon nanotube-polymer composites", Nano Letters, vol. 2, pp. 647, 2002.
[79] J. Q. Pham, C. A. Mitchell, J. L. Bahr, J. M. Tour, R. Krishanamoorti, and P. F. Green, "Glass transition of polymer.single-walled carbon nanotune", J. Poly. Sci.: Part B: Poly. Phys., vol. 41, pp. 3339, 22003.
[80] E. Kymakis and G. A. J. Amaratunga, "Single-wall carbon nanotube/conjugated polymer photovoltaic devices", Appl. Phys. Lett., vol. 80, pp. 112, 2002.
[81] B. Philip, J. K. Abraham, A. Chandrasekhar, and V. K. Varadan, "Carbon nanotube/PMMA composite thin films for gas-sensing applications", Smart Mater. Struct., vol. 12, pp. 935, 2003.
[82] S. M. Khamis, R. R. Johnson, Z. Luo, and A. T. C. Johnson, "Homo-DNA functionalized carbon nanotube chemical sensors", J. Phys. Chem. Sol., vol. 71, pp. 476, 2010.
[83] Y. Cheng, Q. X. Pei, and H. Gao, "Molecular-dynamics studies of competitive replacement in peptide-nanotube assembly for control of drug release", Nanotech., vol. 20, pp. 145101, 2009.
[84] T. A. Hilder and J. M. Hill, "Modelling the encapsulation of the anticancer drug cisplatin into carbon nanotubes", Nanotech., vol. 18, pp. 275704, 2007.
[85] K. Besteman, J. O. Lee, F. G. M. Wiertz, H. A. Heering, and C. Dekker, "Enzyme-coated carbon nanotubes as single-molecule biosensors", Nano Letters, vol. 3, pp. 727, 2003.
[86] M. J. O'Connell, P. Boul, L. M. Ericson, C. Huffman, Y. Wang, E. Haroz, C. Kuper, J. Tour, K. D. Ausman, and R. E. Smalley, "Reversible water-solubilization of single-walled carbon nanotubes by polymer wrapping", Chem. Phys. Lett., vol. 342, pp. 265, 2001.
[87] C. A. Cooper, D. Ravich, D. Lips, J. Mayer, and H. D. Wagner, "Distribution and alignment of carbon nanotubes and nanofibrils in a polymer matrix", Comp. Sci. Tech., vol. 62, pp. 1105, 2002.
[88] V. V. Didenko, V. C. Moore, D. S. Baskin, and R. E. Smalley, "Visualization of individual single-walled carbon nanotubes by fluorescent polymer wrapping", Nano Letters, vol. 5, pp. 1563, 2005.
[89] S. Zhang, L. Zhu, C. P. Wong, and S. Kumar, "Polymer-infiltrated aligned carbon nanotube fibers by in situ polymerization", Macromol. Rapid Commun., vol. 30, pp. 1936, 2009.
[90] Y. K. Kang, O. S. Lee, P. Deria, S. H. Kim, T. H. Park, D. A. Bonnell, J. G. Saven, and M. J. Therien, "Helical wrapping of single-walled carbon nanotubes by water soluble poly(p-phenyleneethynylene)", Nano Letters, vol. 9, pp. 1414, 2009.
[91] G. Wang and Y. Liu, "Self-assembly of carbon nanotube modified by amphiphilic block polymers in selective solvent", Macromol. Chem. Phys., vol. 210, pp. 2070, 2009.
[92] Z. K. Chen, J. P. Yang, Q. Q. Ni, S. Y. Fu, and Y. G. Huang, "Reinforcement of epoxy resins with multi-walled carbon nanotubes for enhancing cryogenic mechanical properties", Polymer, vol. 50, pp. 4753, 2009.
[93] J. H. Lim, N. Phiboolsirichit, S. Mubeen, M. A. Deshusses, A. Mulchandani, and N. V. Myung, "Electrical and gas sensing properties of polyaniline functionalized single-walled carbon nanotubes", Nanotech., vol. 21, pp. 075502, 2010.
[94] C. Wei, D. Srivastava, and K. Cho, "Structural ordering in nanotube polymer composites", Nano Letters, vol. 4, pp. 1949, 2004.
[95] M. Yang, V. Koutsos, and M. Zaiser, "Interactions between polymers and carbon nanoes : A molecular dynamics study", J. Phys. Chem. B, vol. 109, pp. 10009, 2005.
[96] C. Wei, "Radius and chirality dependent conformation of polymer molecule at nanotube interface", Nano Letters, vol. 6, pp. 1627, 2006.
[97] I. Kusner and S. Srebnik, "Conformational behavior of semi-flexible polymers confined to a cylindrical surface", Chem. Phys. Lett., vol. 430, pp. 84, 2006.
[98] I, Gurevitch and S. Srebnik, "Monte Carlo simulation of polymer wrapping of nanotubes", Chem. Phys. Lett., vol. 444, pp. 96, 2007.
[99] E. J. Wallace and M. S. P. Sansom, "Carbon nanotube/detergent interactions via coarse-grained molecular dynamics", Nano Letters, vol. 7, pp. 1923, 2007.
[100] I. Gurevitch and S. Srebnik, "Conformational behavior of polymers adsorbed on nanotubes", J. Chem. Phys., vol. 128, pp. 144901, 2008.
[101] C. Wei, "Adsorption of an alkane mixture on carbon nanotubes: Selectivity and kinetics", Phys. Rev. B, vol. 80, pp. 085409, 2009.
[102] C. Liu, Y. Y. Fan, M. Liu, H. T. Cong, H. M. Cheng, and M. S. Dresselhaus, "Hydrogen storage in single-walled carbon nanotubes at room temperature", Science, vol. 286, pp. 1127, 1999.
[103] C. Gu and G. H. Gao, "Path integral simulation of hydrogen adsorption in single-walled carbon nanotubes at low temperatures", Phys. Chem. Chem. Phys., vol. 4, pp. 4700, 2002.
[104] X. Zhang and W. Wang, "Adsorption of linear ethane molecules in single walled carbon nanotube arrays by molecular simulation", Phys. Chem. Chem. Phys., vol. 4, pp. 3048, 2002.
[105] Y. Gogotsi, J. A. Libera, A. G. Yazicioglu, and C. M. Megaridis, "In situ multiphase fluid experiments in hydrothermal carbon nanotubes", Appl. Phys. Lett., vol. 79, pp. 1021, 2001.
[106] S. Yu, S. B. Lee, M. Kang, and C. R. Martin, "Size-based protein separations in poly(ethylene glycol)-derivatized gold nanotube membranes", Nano Letters, vol. 1, pp. 495, 2001.
[107] M. Wirtz, S. Yu, and C. R. Martin, "Template synthesized gold nanotube membranes for chemical separations and sensing", Analyst (Cambridge, U.K.), vol. 127, pp. 871, 2002.
[108] M. Wirtz, M. Parker, Y. Kobayashi, and C.R. Martin, "Molecular sieving and sensing with gold nanotube membranes", Chem. Rec., vol. 2, pp. 259, 2002.
[109] A. Curulli , F. Valentini , G. Padeletti , A. Cusm`a , G.M. Ingo , S. Kaciulis , D. Caschera , and G. Palleschi, "Gold nanotubules arrays as new materials for sensing and biosensing: Synthesis and characterization", Sens. Actuators B, vol. 111-112, pp. 526, 2005.
[110] L. Liu, Y. Qiao, and X. Chen, "Pressure-driven water infiltration into carbon nanotube: The effect of applied charges", App. Phys. Lett., vol. 92, pp. 101927, 2008.
[111] Z. Siwy, E. Heins, C. C. Harrell, P. Kohli, and C. R. Martin, "Conical-nanotube ion-current rectifiers: The role of surface charge", J. Am. Chem. Soc., vol. 126, pp. 10850, 2004.
[112] P. Kohli, M. Wirtz, and C. R. Martin, "Nanotube membrane based biosensors", Electroanalysis, vol. 16, pp. 9, 2004.
[113] K. B. Jirage, J. C. Hulteen, and C. R. Martin, "Nanotubule-based molecular-filtration membranes", Science, vol. 278, pp. 655, 1997.
[114] X. Zhang, H. Wang, L. Bourgeois, R. Pan, D. Zhao and P. A. Webley, "Direct electrodeposition of gold nanotube arrays for sensing applications", J. Mater. Chem., vol. 18, pp. 463, 2008.
[115] J. Wang, Y. Zhu, J. Zhou and X. H. Lu, "Diameter and helicity effects on static properties of water molecules confined in carbon nanotubes", Phys. Chem. Chem. Phys., vol. 6, pp. 829, 2004.
[116] F. L. Liu and L. Peng, "DFT studies on coplanar poly-cage cubanes C8+4nH8 (n=1–5)", J. Mol. Struct.: THEOCHEM, vol. 709, pp. 163, 2004.
[117] H. Yang, Y. Liu, H. Zhang, Z. S. Li, "Diffusion of single alkane molecule in carbon nanotube studied by molecular dynamics simulation", Polymer, vol. 47, pp. 7607, 2006.
[118] D. Frenkel and B. Smit, "Understanding molecular simulation from algorithms to applications," (Academic, New York, 2002).
[119] A. R. Leach, "Molecular modeling, principles and applications," (2/E., Addison Wesley Longman Limited 2001).
[120] 楊小鎮, 分子模擬與高分子材料(北京: 科學出版社 2002).
[121] M. Levitt, M. Hirshberg, R. Sharon, and V. Daggett, "Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution," Com. Phys. Com., vol. 91, pp. 215, 1995.
[122] A. Hagler, P. Stern, R. Sharon, J. Becker, and F. Naider, "Computer simulation of conformational properties of oligopeptides. Comparison of theoretical methods and analysis of experimental results," J. Am. Chem. Soc., vol. 101, pp. 6842, 1979.
[123] S. Weiner, P. Kollman, D. Case, U. Singh, C. Ghio, G.Alagona, S. Profeta, and P. Weiner, "A new force field for molecular mechanical simulation of nucleic acids and proteins," J. Am. Chem. Soc., vol. 106, pp. 765, 1984.
[124] B. Brooks, R. Bruccoleri, B.Olafson, D. States, S.Swaminathan, and M. Karplus, "CHARMM: A program for macromolecular energy, minimization, and dynamics calculations," J. Comp. Chem., vol. 4, pp. 187, 1983.
[125] W. F. v. Gunsteren and H. J. C. Berendsen, "Groningen molecular simulation (GROMOS) library manual," Biomos, University of Groningen, Groningen, 1987.
[126] S. L. Mayo, B. D. Olafson, and W. A. Goddard, "Dreiding: A generic force field for molecular simulations," Journal of Phys. Chem., vol. 94, p. 8897, 1990.
[127] S. Lifson and A. Warshel, "Consistent force field for calculations of conformations, vibrational spectra, and enthalpies of cycloalkane and n-alkane molecules", J. Chem. Phys., vol. 49, pp. 5116, 1968.
[128] A. Warshel and S. Lifson, "Consistent force field calculations. II. Crystal structures, sublimation energies, molecular and lattice vibrations, molecular conformations, and enthalpies of alkanes," J. Chem. Phys., vol. 53, pp. 582, 1970.
[129] M. Levitt and S. Lifson, "Refinement of protein conformations using a macromolecular energy minimization procedure", J. Mol. Biol., vol. 46, pp. 269, 1969.
[130] C. L. I. Brooks, B. M. Pettitt, and M. Karplus, "Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids", J. Chem. Phys., vol. 83, pp. 5897, 1985.
[131] P. J. Steinbach and B. R. Brooks, "New spherical-cutoff methods for long-range forces in macromolecular simulation", J. Comp. Chem., vol. 15, pp. 667, 1994.
[132] M. Prevost, G. Lippens, and S. Wodak, "Computer simulations of liquid water: Treatment of long-range interactions", Mol. Phys., vol. 71, pp. 587, 1990.
[133] C. L. I. Brooks, B. M. Pettitt, and M. Karplus, "Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids", J. Chem. Phys., vol. 83, pp. 5897, 1985.
[134] M. Levitt, M. Hirshberg, R. Sharon, and V. Daggett, "Molecular dynamics of macromolecules in water", Chemica Scripta A, vol. 29, pp. 197, 1989.
[135] R.J. Loncharich and B.R. Brooks, "The effects of truncating long-range forces on protein dynamics", Proteins-Struc. Func. Genet, vol. 6, pp. 32, 1989.
[136] P.E. Smith and M.B. Pettitt, "Peptides in ionic solutions: A comparison of the ewald and switching function techniques", J. Chem. Phys., vol. 95, pp. 8430, 1991.
[137] M. Levitt, M. Hirshberg, R. Sharon, K. E. Laiding, and V. Daggett, "Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution", J. Phys. Chem. B, vol. 101, pp. 5051 1997.
[138] http://depts.washington.edu/daglab/downloads/Daggett_cv.pdf.
[139] V. Rosato, M. Guillope, and B. Legrand, "Thermodynamical and structural properties of f.c.c. transition metals using a simple tight-binding model", Philos. Mag. A, vol. 59, pp. 321, 1989.
[140] F. Cleri and V. Rosato, "Tight-binding potentials for transition metals and alloys," Phys. Rev. B, vol. 48, pp. 22, 1993.
[141] S. S. Jang, Y. H. Jang, Y. H. Kim, W. A. G. III, A. H. Flood, B. W. Laursen, H. R. Tseng, J. F. Stoddart, J. O. Jeppesen, J. W. Choi, D. W. Steuerman, E. DeIonno, and J. R. Heath, "Structures and properties of self-assembled monolayers of bistable rotaxanes on Au (111) surfaces from molecular dynamics simulations validated with experiment", J. Am. Chem. Soc., vol. 127, pp. 1563, 2005.
[142] J. Norberg and L. Nilsson, "Advances in biomolecular simulations: methodology and recent applications," Quarterly Reviews of Biophysics, vol. 36, pp. 257-306, 2003.
[143] D. A. C. Beck, R. S. Armen, and V. Daggett, "Cutoff size need not strongly influence moleuclar dynamics results for solvated polypeptides," Biochemistry, vol. 44, pp. 609-616, 2005.
[144] J. Norberg and L. Nilsson, "On the truncation of long range electrostatic interactionsin DNA," Biophysical Journal, vol. 79, pp. 1537-1553, 2000.
[145] J. M. Haile, "Molecular Dynamics Simulation : elementary methods," (John Wiley & Sons, New York, 1992).
[146] M. P. Allen and D. J. Tildesley, "Computer Simulation of Liquids," (Clarendon Press, Oxford, 1987).
[147] Y. Xie, J. Zhou, and S. Jiang, "Parallel tempering Monte Carlo simulation of lysozyme orientation on charged surface", J. Chem. Phys., vol. 132, pp. 065101, 2010.
[148] N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, and A. H. Teller, "Equation of state calculations by fast computing machines", J. Chem. Phys., vol. 21, pp. 1087, 1953.
[149] F. A. Escobedo and J. J. de Pablo, "Monte Carlo simulation of branched and crosslinked polymers", J. Chem. Phys., vol. 104, pp. 22, 1996.
[150] C. M. Chen and P. G. Higgs, "Monte Carlo simulation of polymer crystallization in dilute solution", J. Chem. Phys., vol. 108, pp. 4305, 1998.
[151] K. R. Haire and A. H. Windle, "Monte Carlo simulation of polymer welding", Com. Theo. Poly. Sci., vol. 11, pp. 227, 2001.
[152] D. T. Seaton, S. J. Mitchell, and D. P. Landau, "Monte Carlo simulation of a semi-flexible polymer chain: A first glance", Braz. J. Phys., vol. 36, pp. 623, 2006.
[153] K. Bolton, S. B. M. Bosio, W. L. Hase, W. F. Schneider, and K. C. Hass, "Comparison of explicit and united atom models for alkane chains physisorbed on α-Al2O3 (0001)", J. Phys. Chem. B, vol. 103, pp. 3885, 1999.
[154] A. Soldera, "Energetic analysis of the two PMMA chain tacticities and PMA through molecular dynamics simulations", Polymer, vol. 43, pp. 4269, 2002.
[155] C. Chen, P. Depa, J. K. Maranas, and V. G. Sakai, "Comparison of explicit atom, united atom, and coarse-grained simulations of poly(methyl methacrylate)", J. Chem. Phys., vol. 128, pp. 124906, 2008.
[156] X. Li, X. Ma, L. Huang, and H. Liang, "Developing coarse-grained force fields for cis-poly(1,4-butadiene) from the atomistic simulation", Polymer, vol. 46, pp. 6507, 2005.
[157] C. Peter, L. D. Site, and K. Kremer, "Classical simulations from the atomistic to the mesoscale and back: coarse graining an azobenzene liquid crystal", Soft Matter, vol. 4, pp. 859, 2008.
[158] H. J. Qian, P. Carbone, X. Chen, H. Ali, K. Varzaneh, C. C. Liew, and F. Müller-Plathe, "Temperature-transferable coarse-grained potentials for ethylbenzene, polystyrene, and their mixtures", Macromolecules, vol. 41, pp. 9919, 2008.
[159] A. Villa, C. Peter, and N, F, A, van der vegt, "Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation", Phys. Chem. Chem. Phys., vol. 11, pp. 2077, 2009.
[160] M. Isobe, H. Shimizu, and Y. Hiwatari, "A multicanonical molecular dynamics study on a simple bead-spring model for protein folding", J. Phys. Soc. Jap., vol. 70, pp. 1233, 2001.
[161] C. F. Abrams and K. Kremer, "The effect of bond length on the structure of dense bead-spring polymer melts", J. Chem. Phys., vol. 115, pp. 2776, 2001.
[162] X. Li, Y. Hu, L. Jiang, "Spreading dynamics of functional droplets", App. Surf. Sci., vol. 255, pp. 3336, 2008.
[163] S. Elli, G. Raffaini, F. Ganazzoli, E. G. Timoshenko, and Y. A. Kuznetsov, "Surface adsorption of comb polymers by Monte Carlo simulations", Polymer, vol. 49, pp. 1716, 2008.
[164] K. Tanaka, Y. Tateishi, Y. Okada, T. Nagamura, M. Doi, and H. Morita, "Interfacial mobility of polymers on inorganic solids", J. Phys. Chem. B, vol. 113, pp. 4571, 2009.
[165] T. C. Clancy, "Multi-scale modeling of polyimides", Polymer, vol. 45, pp. 7001, 2004.
[166] Y. Li, X. Chen, and N. Gu, "Computational investigation of interaction between nanoparticles and membranes: Hydrophobic/Hydrophilic effect", J. Phys. Chem. B, vol. 112, pp. 16647, 2008.
[167] G. S. Ayton and G. A. Voth, "Hybrid coarse-graining approach for lipid bilayers at large length and time scales", J. Phys. Chem. B, vol. 113, pp. 4413, 2009.
[168] A. Khalfa, W. Treptow, B. Maigret, and M. Tarek, "Self assembly of peptides near or within membranes using coarse grained MD simulations", Chem. Phys., vol. 358, pp. 161, 2009.
[169] N. Koga and S. Takada, "Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATpase ", Proc. Nat. Aca. Sci., vol. 103, pp. 5367, 2006.
[170] C. Hyeon and J. N. Onuchic, "Internal strain regulates the nucleotide binding site of the kinesin leading head ", Proc. Natl. Acad. Sci. USA., vol. 104, pp. 2175, 2007.
[171] T. N. Sasaki, H. Cein, and M. Sasai, "A coarse-grained langevin molecular dynamics approach to de novo protein structure prediction", Biochem. Biophys. Res. Comm., vol. 369, pp. 500, 2008.
[172] C. Clementi, "Coarse-grained models of protein folding: toy models or predictive tools?", Cur. Opin. Struc. Bio., vol. 18, pp. 10, 2008.
[173] J. D. Honeycutt and D. Thirumalai, "Metastability of the folded states of globular proteins", Proc. Natl. Acad. Sci. USA, vol. 87, pp. 3526, 1990.
[174] E. H. Yap, N. L. Fawzi, and T. H. Gordon, "A coarse-grained α-carbon protein model with anisotropic hydrogen-bonding", Proteins, vol. 70, pp. 626, 2008.
[175] D. Lu and Z. Liu, "Oscillatory molecular driving force for protein folding at high concentration: A molecular simulation", J. Phys. Chem. B, vol. 112, pp. 2686, 2008.
[176] H. Fukunaga, T. Aoyagi, J. Takimoto, and M. Doi, "Derivation of coarse grained potential for polyethylene", Comp, Phys. Comm., vol. 142, pp. 224, 2001.
[177] D. Reith, M. Pütz, and F. Müller-Plathe, "Deriving effective mesoscale potentials from atomistic simulations", J. Comput. Chem., vol. 24, pp. 1624, 2003.
[178] P. Nielaba, M. Mareschal, and G. Ciccotti, "Bridging time scales: Molecular simulations for the next decade," (Springer, Verlag Berlin Heidelberg, 2002).
[179] J. D. McCoy and J. G. Curro, "Mapping of explicit atom onto united atom potentials", Macromolecules, vol. 31, pp. 9362, 1998.
[180] S. P. Ju, C. Y. Chang, M. H. Weng, and N. K. Hsieh, "Dynamic properties of water molecules within an Au nanotube with different bulk densities", J. Phys. Chem. C, vol. 113, pp. 7484, 2009.
[181] Y. Y. Yan and C. Y. Ji, "Molecular dynamics simulation of behaviours of non-polar droplets merging and interactions with hydrophobic surfaces", J. Bionic Eng., vol. 5, pp. 271, 2008.
[182] W. L. Ash, M. R. Zlomislic, E. O. Oloo, and D. P. Tieleman, "Computer simulations of membrane proteins", Biochem. Biophys. Acta, vol. 1666, pp. 158, 2004.
[183] P. J.Bond, J. M. Cuthbertson, S. D. Deol, and M. S. P. Sansom, "MD simulations of spontaneous membrane protein/detergent micelle formation", J. Am. Chem. Soc., vol. 126, pp. 15948, 2004.
[184] R. Braun, D. M. Engelman, and K. Schulten, "Molecular dynamics simulations of micelle formation around dimeric glycophorin A transmembrane helices", Biophys. J., vol. 87, pp. 754, 2004.
[185] J. M. Zhang, D.H Zhang, D. Shen, "Orientation study of atactic poly(methyl methacrylate) thin film by SERS and RAIR spectra" Macromolecules, vol. 35, pp. 5140, 2002.
[186] K. T. Lu and K.L. Tung, "Molecular dynamics simulation study of the effect of PMMA tacticity on free volume morphology in membranes", Korean J. Chem. Eng., vol. 22, pp. 512, 2005.
[187] B. Prathab, V. Subramanian, and T. M. Aminabhavi, " Molecular dynamics simulations to investigate polymer–polymer and polymer–metal oxide interactions", Polymer, vol. 48, pp. 409, 2007.
[188] S. P. Ju, M. L. Liao, C. H. Cheng, W. J. Lee, and J. G. Chang, "Chain-length and tacticity effects on the conformational behavior of MMA-oligomer thin films on an Au (1 1 1) substrate", Comp. Mat. Sci., vol. 45, pp. 867, 2009.
[189] D. Zhang, Z. Liu, and R. Xu, "Monte Carlo simulatoion of the adsorption of C2-C7 linear alkanes in aluminophosphate AlPO4-11", Mol. Sim., vol. 33, pp. 1247, 2007.
[190] P. Adamczyk, P. Romiszowski, and A. Sikorski, "Adsorption of homopolymer chains on a strip-patterned surface: A Monte Carlo study", Catal. Lett., vol. 129, pp. 130, 2009.
[191] M. I. Capar and E. Cebe, "Molecuar dynamic study of the odd-even effect in some 4-n-alkyl-4'-cyanobiphenyls", Phys. Rev. E, vol. 73, pp. 061711, 2006.