Mesoscopic models of lipid bilayers and bilayers with embedded ...
Mesoscopic models of lipid bilayers and bilayers with embedded ... Mesoscopic models of lipid bilayers and bilayers with embedded ...
84 Interaction of small molecules with bilayers (a) dbA (b) dbH (c) dbN Figure 6.2: Snapshots of configurations taken from simulations of absorption of dumb-bell molecules in a bilayer of poly-unsaturated ht (L) t (K) 4 t (L) t lipids. (a) Amphiphilic, (b) hydrophobic, (c) neutral dumb-bells. The dumb-bells are represented as large spheres, the lipid tails as lines, the lipid headgroups as dark small spheres, and the water particles as light small spheres. The simulation box is periodic in all three Cartesian directions.
6.3 Results and Discussion 85 ρ(z) 0.3 0.2 0.1 0.0 −0.1 −6 −4 −2 0 Z 2 4 6 0.0 −0.1 (a) Pure bilayer −0.2 −6 −4 −2 0 Z 2 4 6 w h t (1,..,n−1) t n ρ tot 0.3 w h 0.2 t (1,..,n−1) tn db 0.1 π(z) (c) dbA 0.3 w h 0.2 t (1,..,n−1) tn db 0.1 π(z) 0.0 −0.1 −0.2 −6 −4 −2 0 Z 2 4 6 0.0 −0.1 (b) dbH 0.3 w h 0.2 t (1,..,n−1) tn db 0.1 π(z) −0.2 −6 −4 −2 0 Z 2 4 6 (d) dbN Figure 6.3: Density profiles for the pure ht (L) 6 t bilayer (a), and for the same bilayer with (b) hydrophobic (dbH), (c) amphiphilic (dbA), and (d) neutral dumb-bells (dbN). In figures (b), (c) and (d) the lateral pressure profile π(z) of the pure bilayer is also plotted. Note that the densities have been rescaled to fit in the same scale as the lateral pressure (hence the values on the graphs ordinate refer to π(z) only). The scaling factor for the density of the dumb-bells is two times smaller than the scaling for water and lipid densities. The densities refer to water (w), lipid headgroup (h), lipid hydrophobic tail-beads excluding the last one (t(1,...,n−1)), last tail-bead (tn), and dumb-bells (db). For the pure bilayer the total density ρtot is also plotted.
- Page 39 and 40: 3.4 Surface tension in lipid bilaye
- Page 41 and 42: 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 66 and 67: 60 Phase behavior of coarse-grained
- Page 68 and 69: 62 Phase behavior of coarse-grained
- Page 70 and 71: 64 Phase behavior of coarse-grained
- Page 72 and 73: 66 Phase behavior of coarse-grained
- Page 74 and 75: 68 Phase behavior of coarse-grained
- Page 76 and 77: 70 Phase behavior of coarse-grained
- Page 78 and 79: 72 Phase behavior of coarse-grained
- Page 80 and 81: 74 Phase behavior of coarse-grained
- Page 82 and 83: 76 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: 6.3 Results and Discussion 83 withi
- 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 108 and 109: 102 Mesoscopic model for lipid bila
- Page 110 and 111: 104 Mesoscopic model for lipid bila
- Page 112 and 113: 106 Mesoscopic model for lipid bila
- Page 114 and 115: 108 Mesoscopic model for lipid bila
- Page 116 and 117: 110 Mesoscopic model for lipid bila
- Page 118 and 119: 112 Mesoscopic model for lipid bila
- Page 120 and 121: 114 Mesoscopic model for lipid bila
- Page 122 and 123: 116 Mesoscopic model for lipid bila
- Page 125 and 126: References [1] Tanford, C. Science
- Page 127 and 128: 7.4 Conclusion 121 [68] Ono, S.; Ko
- 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
84 Interaction <strong>of</strong> small molecules <strong>with</strong> <strong>bilayers</strong><br />
(a) dbA (b) dbH<br />
(c) dbN<br />
Figure 6.2: Snapshots <strong>of</strong> configurations taken from simulations <strong>of</strong> absorption <strong>of</strong> dumb-bell<br />
molecules in a bilayer <strong>of</strong> poly-unsaturated ht (L) t (K)<br />
4 t (L) t <strong>lipid</strong>s. (a) Amphiphilic, (b) hydrophobic,<br />
(c) neutral dumb-bells. The dumb-bells are represented as large spheres, the <strong>lipid</strong> tails as<br />
lines, the <strong>lipid</strong> headgroups as dark small spheres, <strong>and</strong> the water particles as light small spheres.<br />
The simulation box is periodic in all three Cartesian directions.
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