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

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60 Phase behavior of coarse-grained lipid bilayers ht 6 ht7 ht8 ht9 Figure 5.2: Schematic drawing of the model lipids used in this study with their nomenclature. The black particles represent the head beads and the white particles the tail beads. The repulsion parameters used are aww = att = 25, a wh = 15, and awt = 80 (see equation 2.2, Chapter 2). In addition, we vary the head-head interaction parameter (a hh) to study the effect of changing the interactions between the hydrophilic segments of a lipid. In a real system the head-head interactions can be changed by, for example, adding salt to the system. All our simulations are performed on tensionless bilayers of 200 lipids. The total number of particles was 3500. The overall density of the system is ρ = 3. We initialize our system by distributing lipids randomly in water and we observe the self-assembly of a bilayer using DPD simulation only. After the bilayer is formed, we perform, in addition to the DPD moves, Monte Carlo moves in which we change the area as well. A typical simulation required 100,000 cycles of which 20,000 cycles were needed for equilibration. All the results are expressed in the usual reduced units, i.e. using Rc as the unit of length and kBTo = 1, with To room temperature, as unit of the energy. In the following we will denote as T ∗ the temperature expressed in this unit. 5.2.2 Results and Discussion In this section we first describe in detail the different phases of a bilayer formed by single tail lipids consisting of one head bead and nine tail beads (ht9), which we study at different reduced temperatures, from T ∗ = 0.8 to T ∗ = 1.5. At a fixed head-head repulsion of a hh = 35 an interdigitated gel phase is formed at low temperatures, while at a hh = 15 the non-interdigitated Lβ phase is formed. We then investigate the influence of changing the interactions between the headgroups and we show that we obtain the non-interdigitated Lβ phase or the interdigitated LβI phase dependent on the head-head repulsion parameter (see figure 5.3). Finally, we investigate the influence of tail length and we compare our results with experimental data on single-tail lipids.
5.2 Single-tail lipid bilayers 61 ahh 40 30 20 L EI L E 10 0.7 0.8 0.9 1.0 1.1 Figure 5.3: Computed phase diagram of the lipid ht9 as function of head-head repulsion parameter ahh and reduced temperature T ∗ . At high values of the head-head repulsion parameters the interdigitated LβI phase is formed, while at low values the non-interdigitated Lβ phase is formed. Increasing temperature causes the melting of the bilayer to the Lα phase. The lipid ht9 Head-head repulsion a hh = 35 In figure 5.4 the average area per lipid AL and the bilayer thickness, Dc, are plotted as function of temperature. The error bars have been calculated with the block averages method [76, 105]. In all the other plots of the area per lipid or bilayer thickness, we will not include error bars, which, however, have been estimated as ≤ 5%. A L 0.95 0.90 0.85 0.80 0.8 1.0 1.2 T* 1.4 1.6 (a) D c T* 8.20 7.80 7.40 L D 7.00 0.8 1.0 1.2 T* 1.4 1.6 Figure 5.4: Area per lipid AL and (b) bilayer thickness Dc as function of reduced temperature T ∗ for lipid type ht9. (b)
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Mesoscopic models of lipid bilayers
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Promotiecommissie: Promotor: • pr
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ii CONTENTS 5.3 Double-tail lipid b
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2 Introduction 1.1 The cell membran
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4 Introduction between the beads, a
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6 Introduction whether the preferre
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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
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 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
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110 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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