模擬脂質雙層膜上的分子機器

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姓名

黃慕傑(Mu-Jie Huang) 查詢紙本館藏

畢業系所

物理學系

論文名稱

模擬脂質雙層膜上的分子機器
(Simulating active machines in a lipid bilayer)

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摘要(中)

本論文提出一個在介觀層次模擬脂質雙層膜上分子馬達（機器）的新方法，其中分子機器以一彈性網路來模擬，脂質分子則以由彈簧和球所組成的鏈狀分子來表示，並利用多粒子碰撞來呈現溶液的動力學。這個模擬的方法可以重現液態和膠態的脂質雙層膜。模擬中所測得液態細胞膜的彎曲和拉伸的彈性模數接近實驗的測量值。從分析兩個脂質區塊間速度的相關性，我們發現脂質雙層膜在模擬的空間尺度下可以被看作一個二維的流體。當把一個簡單的奈米游泳機器放在這個二維流體上時，它在熱擾動下仍能自我推進。模擬亦探討了主動和被動的分子機器對細胞膜的影響。當此分子機器為被動且沒有配體時，它使得細胞膜有較劇烈的形變。模擬主動的分子機器在細胞膜中時，細胞膜形狀的擾動被此機器所影響。另一有趣的現象是這樣循環轉換狀態的分子機器會造成一個長距離的脂質流場。本論文為生物膜上分子馬達的大尺度模擬指出了全新的研究方向。

摘要(英)

This thesis discusses an efficient method to simulate the dynamics of active molecular machines in a lipid bilayer embedded in a solvent. A molecular machine is modeled as an elastic network (EN) that can change its conformations, a lipid chain is modeled by a single bead-spring chain, and the dynamics of the solvent is carried out using multiparticle collision dynamics. This simulation method reproduces liquid and gel phases of a lipid membrane. In the liquid phase, the bending and stretching moduli are found to be comparable to the experimental measurements. Analyzing velocity correlation between two lipid domains at different separations, lipid bilayers are found to indeed behave as two-dimensional (2D) fluids. Simulations of a toy machine representing nano swimmer in such 2D fluid have been performed. We find that this swimmer propels itself over long distances against thermal nosies. Using EN model, the effects of both passive and active molecular machines on the membrane are investigated. For passive machine, the membranes are found to be strongly deformed when the machine is in its ligand-free conformation state. When the active machine is considered, we find that the membrane shape fluctuations modified by machine activities. Moreover, the cyclic conformation transitions of the machine induces a long-ranged lipid flow field.

關鍵字(中)

★ 膜物理

關鍵字(英)

★ Membrane physics

論文目次

1 Introduction 1
2 Lipid bilayer self-assembly and dynamics 6
2.1 Mesoscopic Model for Lipid Bilayer Dynamics . . . . . . . . . 6
2.1.1 Lipid Interactions . . . . . . . . . . . . . . . . . . . . . 7
2.1.2 Lipid-solvent interactions . . . . . . . . . . . . . . . . . 11
2.1.3 MD-MPC dynamics . . . . . . . . . . . . . . . . . . . . 11
2.1.4 Simulation details . . . . . . . . . . . . . . . . . . . . . 13
2.2 Membrane properties at different temperatures . . . . . . . . . 14
2.2.1 Membrane structures . . . . . . . . . . . . . . . . . . . 15
2.2.2 Orientational order parameter . . . . . . . . . . . . . . 16
2.2.3 In-plane radial distribution function . . . . . . . . . . . 18
2.2.4 Vertical density profile . . . . . . . . . . . . . . . . . . 20
2.2.5 Lipid diffusion . . . . . . . . . . . . . . . . . . . . . . . 21
2.3 Self-assembly of the membrane . . . . . . . . . . . . . . . . . . 25
2.4 Macroscopic membrane properties . . . . . . . . . . . . . . . . 26
2.4.1 Membrane stretching modulus . . . . . . . . . . . . . . 28
2.4.2 Membrane bending modulus . . . . . . . . . . . . . . . 30
2.4.3 Velocity correlation functions . . . . . . . . . . . . . . 33
2.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3 Nano-swimmers in two dimensions 39
3.1 Low Reynolds number dynamics of a two dimensional swimmer 40
3.2 Membrane swimmer simulations . . . . . . . . . . . . . . . . 47
3.3 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
4 Active machines in lipid bilayers 60
4.1 The model machine . . . . . . . . . . . . . . . . . . . . . . . . 61
4.2 Interactions with the solvent . . . . . . . . . . . . . . . . . . . 66
4.3 Parameter values . . . . . . . . . . . . . . . . . . . . . . . . . 67
4.4 Results of numerical simulations . . . . . . . . . . . . . . . . . 68
4.4.1 Effects of passive inclusions on the membrane . . . . . 70
4.4.2 Effects of active inclusions . . . . . . . . . . . . . . . . 76
4.4.3 Lipid flows induced by an active machine . . . . . . . . 83
4.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
5 Conclusion and Outlook 88
Bibliography 92

參考文獻

[1] M.-J. Huang, R. Kapral, A. S. Mikhailov, and H.-Y. Chen. J. Chem. Phys. 137, 055101 (2012).
[2] M.-J Huang, H.-Y. Chen, and A. S. Mikhailov. Eur. Phys. J. E 35, 119 (2012).
[3] M.-J. Huang, R. Kapral, A. S. Mikhailov, and H.-Y. Chen. In preparation.
[4] M. D. El Alaoui Faris, D. Lacoste, J. Pécréaux, J.-F Joanny, J. Prost, and P. Bassereau. Phys. Rev. Lett. 102, 038102 (2009).
[5] M. Bagnat, Sirkka Kera¨nen, Anna Shevchenko, Andrej Shevchenko, and Kai Simons. Proc. Natl. Acad. Sci. U.S.A. 97, 3254 (2000).
[6] H. Lodish, A. Berk, C. A. Kaiser, M. Krieger, M. P. Scott, A. Bretscher, H. Ploegh, and P. Matsudaira. Molecular cell biology. W. H. Freeman, 6 edition, (2007).
[7] D. P. Tieleman, S. J. Marrink, and H J. C. Berendsen. Biochim. Biophys. Acta 1331, 235 (1997).
[8] S. E. Feller. Curr. Opin. Colloid Interface Sci. 5, 217 (2000).
[9] Bert L. de Groot and Helmut Grubmuller. Science 294, 2353 (2001).
[10] L. Saiz and M. L. Klein. Acc. Chem. Res. 35, 482 (2002).
[11] A. N. Dickey and R. Faller. Biophys. J. 95, 2636 (2008).
[12] B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter. Molecular Biology of the Cell. Garland, New York, 4 edition, (2002).
[13] S. O. Nielsen, C. F. Lopez, G. Srinivas, and M. L. Klein. J. Phys.: Condens. Matter 16, R481 (2004).
[14] R. Goetz, G. Gompper, and R. Lipowsky. Phys. Rev. Lett. 82, 221 (1999).
[15] A. P. Lyubartsev. Eur. Biophys. J. 35, 53 (2005).
[16] M. Venturoli, M. M. Sperotto, M. Kranenburg, and B. Smit. Phys. Repts. 437, 1 (2006).
[17] G. A. Voth. Coarse-Graining of Condensed Phase and Biomolecular Systems. CRC Press, Boca Raton, (2008).
[18] S. V. Bennun, M. I. Hoopes, C. Xing, and R. Faller. Chem. Phys. Lipids 159, 59 (2009).
[19] M. Orsi, J. Michel, and J. W. Essex. J. Phys.: Condens. Matter 22, 155106 (2010).
[20] R. Lipowsky. Nature Mater. 3, 589 (2004).
[21] J. C. Shillcock and R. Lipowsky. J. Chem. Phys. 117, 5048 (2002).
[22] M. Laradji and P.B. S. Kumar. Phys. Rev. Lett 93, 198105 (2004).
[23] L. Gao, J. Shillcock, and R. Lipowsky. J. Chem. Phys. 126, 015101 (2007).
[24] N. Malevanets and R. Kapral. J. Chem. Phys. 110, 8605 (1999).
[25] N. Malevanets and R. Kapral. J. Chem. Phys. 112, 7260 (1999).
[26] U. Schmidt, G. Guigas, and M. Weiss. Phys. Rev. Lett. 101, 128104 (2008).
[27] F. J.-M. de Meyer, M. Venturoli, and B. Smit. Biophys. J. 95, 1851 (2008).
[28] D. Morozova, M. Weiss, and G. Guigas. Soft Matter 8, 11905 (2012).
[29] Y. Togashi and A. S. Mikhailov. Proc. Natl. Acad. Sci. U.S.A. 104, 8697 (2007).
[30] Carlos Echeverria, Yuichi Togashi, Alexander S. Mikhailovc, and Raymond Kapral. Phys. Chem. Chem. Phys. 13, 10527 (2011).
[31] Holger Flechsig and Alexander S. Mikhailov. Proc. Natl. Acad. Sci. U.S.A. 107, 20875 (2010).
[32] Ira R. Cooke, Kurt Kremer, and Markus Deserno. Phys. Rev. E 72, 011506 (2005).
[33] K. Kremer and G. S. Grest. J. Chem. Phys. 92, 5057 (2004).
[34] G. Gompper, T. Ihle, D. M. Kroll, and R. G. Winkler. Adv. Polymer Sci. 221, 1 (2009).
[35] T. Ihle and D. M. Kroll. Phys. Rev. E 63, 020201 (2001).
[36] T. Ihle and D. M. Kroll. Phys. Rev. E 67, 066705 (2003).
[37] R. Kapral. Advances in Chemical Physics 140, 89 (2008).
[38] D. C. Rapaport. The Art of Molecular Dynamics Simulation. Cambridge U.P., 2 edition, (2004).
[39] M. Kranenburg, M. Venturoli, and B. Smit. J. Phys. Chem. B 107, 11491 (2003).
[40] T. Akimoto, E. Yamamoto, K. Yasuoka, Y. Hirano, and M. Yasui. Phys. Rev. Lett. 107, 178103 (2011).
[41] N. Kuccerka, M. A. Kiselev, and P. Balgavý. Eur. Biophys. J. 33, 328 (2004).
[42] J. Korlach, P. Scheille, W.W.Webb, and G.W. Feigenson. Proc. Natl. Acad. Sci. U.S.A. 96, 8461 (1999).
[43] A. F. Jakobsen. J. Chem. Phys. 122, 124901 (2005).
[44] R. Phillips, J. Kondev, and J. Theriot. Physical Biology of The Cell. Garland Science, (2009).
[45] D. R. Nelson, T. Piran, and S. Weinberg. Statistical Mechanics of Membranes and Surfaces. World Scientific, Singapore„ (2004).
[46] M. Deserno. Macromol. Rapid Commun. 30, 752–771 (2000).
[47] P. G. Saffman and M. Delbrück. Proc. Nat. Acad. Sci. USA 72, 3111 (1975).
[48] H. Diamant. J. Phys. Soc. Jpn. 78(4), 041002–1 (2009).
[49] A. Najafi and R. Golestanian. Phys. Rev. E 69, 062901 (2004).
[50] T. Sakaue, R. Kapral, and A. S. Mikhailov. Eur. Phys. J. B 75, 381 (2010).
[51] J.R. Howse, R.A.L. Jones, A.J. Ryan, T. Gough, R. Vahabakhsh, and R. Golestanian. Phys. Rev. Lett. 99, 048102 (2007).
[52] C. Echeverria, Y. Togashi, A.S. Mikhailov, and R. Kapral. Phys. Chem. Chem. Phys. 13, 10527 (2011).
[53] Y. Gambin, R. Lopez-Esparza, M. Reffay, E. Sierecki, N.S. Gov, M. Genest, R.S. Hodges, and W. Urbach. Proc. Natl. Acad. Sci. U.S.A. 103, 2098 (2006).
[54] R. Golestanian and A. Ajdari. Phys. Rev. Lett. 100, 038101 (2010).
[55] R. Golestanian. Phys. Rev. Lett. 105, 018103 (2010).
[56] Andrew Cressman, Yuichi Togashi, Alexander S. Mikhailov, and Raymond Kapral. Phys. Rev. E 77, 050901 (2008).
[57] R. Phillips, J. Kondev, and J. Theriot. Physical Biology of The Cell. Garland Science, (2009).
[58] D. Reeves, T. Ursell, P. Sens, J. Kondev, and R. Phillips. Phys. Rev. E 78, 041901 (2008).
[59] U. Schmidt, G. Guigas, and M. Weiss. Phys. Rev. Lett 101, 128104 (2008).
[60] J. S. Guasto, K. A. Johnson, and J. P. Gollub. Phys. Rev. Lett. 105, 168102 (2010).
[61] D. Morozova, M. Weiss, and G. Guigas. Soft Matter 8, 11905 (2012).

指導教授

陳宣毅(Hsuan-Yi Chen)

審核日期

2013-1-16

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