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

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$Learning LATEX by Doing$

Promotiecommissie: Promotor: • prof. dr. ir. B. Smit Overige leden: • prof. dr. G. Ciccotti • prof. dr. D. Frenkel • prof. dr. K.J. Hellingwerf • prof. dr. J.A. Killian • prof. dr. B. de Kruijff • dr. E.J. Meijer • dr. M.M. Sperotto Faculteit der Natuurwetenschappen, Wiskunde en Informatica The research reported in this thesis was carried out at the Department of Chemical Engineering, Faculty of Science, University of Amsterdam (Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands). Financial support was provided by FOM (Stichting voor Fundamenteel Onderzoek der Materie).
Contents 1 Introduction 1 1.1 The cell membrane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.2 Study of lipid bilayers with computer simulations . . . . . . . . . . . . . 3 1.3 This thesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2 Simulation method for coarse-grained lipids 7 2.1 Dissipative Particle Dynamics . . . . . . . . . . . . . . . . . . . . . . . . 8 2.2 Coarse-grained model of lipids . . . . . . . . . . . . . . . . . . . . . . . 12 2.3 Self-assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 3 Surface tension in lipid bilayers 21 3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 3.2 Method of calculation of surface tension . . . . . . . . . . . . . . . . . . 23 3.3 Constant surface tension ensemble . . . . . . . . . . . . . . . . . . . . . 27 3.4 Surface tension in lipid bilayers . . . . . . . . . . . . . . . . . . . . . . . 30 3.5 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 4 Structural characterization of lipid bilayers 37 4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 4.2 Structural quantities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 4.3 Computational details . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 4.4 Results and discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 4.4.1 Density profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 4.4.2 Effect of chain length . . . . . . . . . . . . . . . . . . . . . . . . . 45 4.4.3 Lateral pressure profiles in tensionless bilayers . . . . . . . . . . 45 4.4.4 Double-tail lipids . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 5 Phase behavior of coarse-grained lipid bilayers 57 5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 5.2 Single-tail lipid bilayers . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 5.2.1 Computational details . . . . . . . . . . . . . . . . . . . . . . . . 59 5.2.2 Results and Discussion . . . . . . . . . . . . . . . . . . . . . . . . 60
Page 1: Mesoscopic models of lipid bilayers
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 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 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
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4.4 Results and discussion 49 Shill
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4.4 Results and discussion 51 chain
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4.4 Results and discussion 53 4.4.4
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4.4 Results and discussion 55 headg
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58 Phase behavior of coarse-grained
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VI Interaction of small molecules w
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6.2 Computational details 81 For re
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6.3 Results and Discussion 83 withi
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6.3 Results and Discussion 85 ρ(z)
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6.3 Results and Discussion 87 ρ(z)
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6.3 Results and Discussion 89 S m 0
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6.3 Results and Discussion 91 π(z)
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6.3 Results and Discussion 93 the l
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96 Mesoscopic model for lipid bilay
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98 Mesoscopic model for lipid bilay
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100 Mesoscopic model for lipid bila
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References [1] Tanford, C. Science
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7.4 Conclusion 121 [68] Ono, S.; Ko
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7.4 Conclusion 123 [139] Lee, A. Bi
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Summary Biological membranes, as th
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agreement we find gives us confiden
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Samenvatting Biologische membranen,
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de lage temperatuur gel fase of Lβ
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ied dat het dichtst bij het hydrofo
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This thesis is based on the followi
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