Mesoscopic models of lipid bilayers and bilayers with embedded ...

More documents

Recommendations

Info

$Learning LATEX by Doing$

120 Mesoscopic model for lipid bilayers with embedded proteins [28] Groot, R.; Warren, P. J. Chem. Phys. 1997, 107, 4423–4435. [29] Cantor, R. Biochemistry 1997, 36, 2339–2344. [30] Cantor, R. J. Phys. Chem. B 1997, 101, 1723–1725. [31] Coveney, P.; Novik, K. Phys. Rev. E 1996, 54, 5134–5141. [32] Coveney, P.; Novik, K. Phys. Rev. E 1997, 55, 4831. [33] Novik, K.; Coveney, P. Int. J. Mod. Phys. C 1997, 8, 909–918. [34] Groot, R.; Madden, T. J. Chem. Phys. 1998, 108, 8713–8724. [35] Groot, R.; Madden, T.; Tildesley, D. J. Chem. Phys. 1999, 110, 9739–9749. [36] Schlijper, A.; Hoogerbrugge, P.; Manke, C. J. Rehol. 1995, 39, 567–579. [37] Schlijper, P.; Manke, C.; Madden, W.; Kong, Y. Int. J. Mod. Phys. C 1997, 8, 919–929. [38] Kong, Y.; Manke, C.; Madden, W.; Schlijper, A. J. Chem. Phys. 1997, 107, 592–602. [39] Spenley, N. Europhys. Lett. 2000, 49, 534–540. [40] Koelman, J.; Hoogerbrugge, P. Europhys. Lett. 1993, 21, 363–368. [41] Boek, E.; Coveney, P.; Lekkerkekker, H. J.Phys.: Condens. Matter 1996, 8, 9509–9512. [42] Boek, E.; Coveney, P.; Lekkerkekker, H.; van Schoot, P. Phys. Rev. E 1997, 55, 3124–3133. [43] Wijmans, C.; Smit, B.; Groot, R. J. Chem. Phys. 2001, 114, 7644–7654. [44] Wijmans, C.; Smit, B. Macromolecules 2002, 35, 7138–7148. [45] Jury, S.; Bladon, P.; Cates, M.; Krishna, S.; Hagen, M.; Ruddock, N.; Warren, P. Phys. Chem. Chem. Phys. 1999, 1, 2051–2056. [46] Groot, R. Langmuir 2000, 16, 7493–7502. [47] Warren, P. Curr. Opin. Colloid. Interf. Sci. 1998, 3, 620–624. [48] Español, P. SIMU, Challenges in molecular simulations 2002, 4, 59–77. [49] Willemsen, S.; Vlugt, T.; Hoefsloot, H.; Smit, B. J. Comp. Phys. 1998, 147, 507–517. [50] Shillcock, J.; Lipowsky, R. J. Chem. Phys. 2002, 117, 5048–5061. [51] Gibson, J.; Chen, K.; Chynoweth, S. J. Colloid Interface Sci. 1998, 206, 464–474. [52] Alberts, B.; Johnson, A.; Lewis, J.; Raff, M.; Roberts, K.; Walters, P. Molecular biology of the cell; Garlan Science: New York, 2002. [53] Rowlinson, J.; Widom, B. Molecular Theory of Capillarity; Clarendon Press: Oxford, 1982. [54] Jähnig, F. Biophys. J. 1996, 71, 1348–1349. [55] Kwok, R.; Evans, E. Biophys. J. 1981, 35, 637–652. [56] Chiu, S.; Clark, M.; Balaji, V.; Subramaniam, S.; Scott, H.; Jakobsson, E. Biophys. J. 1995, 69, 1230–1245. [57] Zhang, Y.; Feller, S.; Brooks, B.; Pastor, R. J. Chem. Phys. 1995, 103, 10252–10266. [58] Feller, S.; Pastor, R. Biophys. J. 1996, 71, 1350–1355. [59] Feller, S.; Pastor, R. J. Chem. Phys. 1999, 111, 1281–1287. [60] Marrink, S.; Mark, A. J. Phys. Chem. B 2001, 105, 6122–6127. [61] Feller, S.; Zhang, Y.; Pastor, R. J. Chem. Phys. 1995, 103, 10267–10276. [62] Tieleman, D.; Berendsen, H. J. Chem. Phys. 1996, 105, 4871–4880. [63] Chiu, S.; Jakobsson, E.; Subramaniam, S.; Scott, H. Biophys. J. 1999, 77, 2462–2469. [64] Venable, R.; Brooks, R.; Pastor, R. J. Chem. Phys. 2000, 112, 4822–4832. [65] Sun, F. Biophys. J. 2002, 85, 2511 –2519. [66] Varnik, F.; Baschnagel, J.; Binder, K. J. Chem. Phys. 2000, 113, 4444–4453. [67] Kirkwood, J.; Buff, F. J. Chem. Phys. 1949, 17, 338.
7.4 Conclusion 121 [68] Ono, S.; Kondo, S. Encyclopedia of physics, Vol. 10; S. Flugge, Springer: Berlin, 1960. [69] Hansen, J.; McDonald, I. Theory of Simple Liquids; Academic Press: London, 2nd ed., 1986. [70] Allen, M.; Tildesley, D. Computer Simulation of Liquids; Clarendon Press: Oxford, 1987. [71] Walton, J.; Tildesley, D.; Rowlinson, J. Mol. Phys. 1983, 48, 1357–1368. [72] Irving, J.; Kirkwood, J. J. Chem. Phys. 1950, 18, 817–829. [73] Harasima, A. Adv. Chem. Phys. 1958, 1, 203. [74] Nijmeijer, M.; Bakker, A.; Bruin, C.; Sikkenk, J. J. Chem. Phys. 1988, 89, 3789–3792. [75] Venturoli, M.; Smit, B. Phys.Chem.Comm. 1999, 10, 45–49. [76] Frenkel, D.; Smit, B. Understanding Molecular Simulations: from Algorithms to Applications; Academic Press: San Diego, 2002. [77] Lindahl, E.; Edholm, O. J. Chem. Phys. 2000, 113, 3882–3893. [78] Rawicz, W.; Olbrich, K.; McIntosh, T.; Needham, D.; Evans, E. Biophys. J. 2000, 79, 328– 339. [79] Miller, D. M. Biochim. Biophys. Acta 1986, 856, 27–35. [80] Templer, R.; Castle, S.; Curran, A.; Rumbles, G.; Klug, D. Faraday Discuss. 1998, 111, 41–53. [81] Gullingsrud, J.; Schulten, K. Biophys. J. 2004, 86, 3496–3509. [82] Harries, D.; Ben-Shaul, A. J. Chem. Phys. 1997, 106, 1609–1619. [83] Seelig, J.; Seelig, A. Q. Rev. Biophys. 1980, 13, 19–61. [84] Wiener, M.; White, S. Biophys. J. 1992, 61, 434–447. [85] Nagle, J.; Zhang, R.; Tristram-Nagle, S.; Sun, W.; Petrache, H.; Suter, R. Biophys. J. 1996, 70, 1419–1431. [86] Nagle, J. Biophys. J. 1993, 64, 1476–1481. [87] Petrache, H.; Feller, S.; Nagle, J. Biophys. J. 1997, 70, 2237–2242. [88] Petrache, H.; Tu, K.; Nagle, J. Biophys. J. 1999, 76, 2749–2487. [89] Takaoka, Y.; Pasenkiewicz-Gierula, M.; ¡iyagawa, H.; Kitamura, K.; Tamura, Y.; Kusumi, A. Biophys. J. 2000, 79, 3118–3138. [90] McIntosh, T.; McDaniel, R.; Simon, S. Biochim. Biophys. Acta 1983, 731, 109–114. [91] Simon, S.; McIntosh, T. Biochim. Biophys. Acta 1984, 773, 169–172. [92] Petrache, H.; Dodd, S.; Brown, M. Biophys. J. 2000, 79, 3172–3192. [93] Marrink, S.; Berendsen, H. J. Phys. Chem. 1994, 98, 4155–4168. [94] Cantor, R. Biophys. J. 1999, 76, 2625–2639. [95] Cantor, S. Biophys. J. 2001, 80, 2284–2297. [96] Koynova, R.; Caffrey, M. Biochim. Biophys. Acta 1998, 1376, 91–145. [97] Katsaras, J.; Gutberlet, T. Lipid Bilayers. Structure and interactions; Springer-Verlag: New York, 2001. [98] Slater, J.; Huang, C.-H. Prog. Lipid. Res. 1988, 27, 325–359. [99] Furuike, S.; Levadny, V.; Li, S.; Yamazaki, M. Biophys. J. 1999, 77, 2015–2023. [100] McIntosh, T.; Lin, H.; Li, S.; Huang, C.-H. Biochim. Biophys. Acta 2001, 1510, 219–230. [101] Adachi, T.; Takahashi, H.; Ohki, K.; Hatta, I. Biophys. J. 1995, 68, 1850–1855. [102] Hata, T.; Matsuki, H.; Kaneshina, S. Biophys. Chem. 2000, 87, 25–36. [103] Lewis, R.; Winter, I.; Kriechbaum, M.; Lohner, K.; McElhaney, R. Biophys. J. 2001, 80, 1329–1342.
Page 1:
Mesoscopic models of lipid bilayers
Page 4 and 5:
Promotiecommissie: Promotor: • pr
Page 6 and 7:
ii CONTENTS 5.3 Double-tail lipid b
Page 8 and 9:
2 Introduction 1.1 The cell membran
Page 10 and 11:
4 Introduction between the beads, a
Page 12 and 13:
6 Introduction whether the preferre
Page 14 and 15:
8 Simulation method for coarse-grai
Page 16 and 17:
10 Simulation method for coarse-gra
Page 18 and 19:
Page 20 and 21:
Page 22 and 23:
Page 24 and 25:
Page 27 and 28:
III Surface tension in lipid bilaye
Page 29 and 30:
3.2 Method of calculation of surfac
Page 31 and 32:
3.2 Method of calculation of surfac
Page 33 and 34:
3.3 Constant surface tension ensemb
Page 35 and 36:
3.3 Constant surface tension ensemb
Page 37 and 38:
3.4 Surface tension in lipid bilaye
Page 39 and 40:
Page 41 and 42:
Page 43 and 44:
IV Structural characterization of l
Page 45 and 46:
4.2 Structural quantities 39 been r
Page 47 and 48:
4.3 Computational details 41 lipid
Page 49 and 50:
4.4 Results and discussion 43 ρ(z)
Page 51 and 52:
4.4 Results and discussion 45 one l
Page 53 and 54:
4.4 Results and discussion 47 WH HT
Page 55 and 56:
4.4 Results and discussion 49 Shill
Page 57 and 58:
4.4 Results and discussion 51 chain
Page 59 and 60:
4.4 Results and discussion 53 4.4.4
Page 61:
4.4 Results and discussion 55 headg
Page 64 and 65:
58 Phase behavior of coarse-grained
Page 66 and 67:
Page 68 and 69:
Page 70 and 71:
Page 72 and 73:
Page 74 and 75:
Page 76 and 77: 70 Phase behavior of coarse-grained
Page 85 and 86: VI Interaction of small molecules w
Page 87 and 88: 6.2 Computational details 81 For re
Page 89 and 90: 6.3 Results and Discussion 83 withi
Page 91 and 92: 6.3 Results and Discussion 85 ρ(z)
Page 93 and 94: 6.3 Results and Discussion 87 ρ(z)
Page 95 and 96: 6.3 Results and Discussion 89 S m 0
Page 97 and 98: 6.3 Results and Discussion 91 π(z)
Page 99: 6.3 Results and Discussion 93 the l
Page 102 and 103: 96 Mesoscopic model for lipid bilay
Page 104 and 105: 98 Mesoscopic model for lipid bilay
Page 106 and 107: 100 Mesoscopic model for lipid bila
Page 125: References [1] Tanford, C. Science
Page 129 and 130: 7.4 Conclusion 123 [139] Lee, A. Bi
Page 131 and 132: Summary Biological membranes, as th
Page 133 and 134: agreement we find gives us confiden
Page 135 and 136: Samenvatting Biologische membranen,
Page 137 and 138: de lage temperatuur gel fase of Lβ
Page 139: ied dat het dichtst bij het hydrofo
Page 143: This thesis is based on the followi
show all

Mesoscopic models of lipid bilayers and bilayers with embedded ...

Create successful ePaper yourself

Delete template?

Save as template?