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 ...
24 Surface tension in lipid bilayers with From equations 3.1 and 3.2 we have Pxx(r) = Pyy(r). (3.3) ∂Pxx ∂x ex + ∂Pyy ∂y ey + ∂Pzz ∂z ez = 0 (3.4) where eα (α = x, y, z) are the orthogonal basis vectors in the Cartesian space. From equations 3.4 and 3.3 results that the lateral (also called tangential) components of the pressure tensor are function of z only: PL(z) = Pxx(z) = Pyy(z). The normal component is constant throughout the system and equal to the external pressure: PN(z) = Pzz(z) = Pext. The lateral components are also equal to the external pressure in the bulk phases. The surface tension is defined as the integral over the interface of the difference between the normal and lateral components of the pressure tensor [67, 68] γ = z2 z1 dz [PN(z) − PL(z)] = z2 z1 dγ(z) (3.5) where z1 and z2 are positions in the bulk phases and γ(z) is the local surface tension at position z. In molecular simulations, statistical mechanics is used to relate thermodynamic quantities to ensemble averages over microscopic degrees of freedom. For an homogeneous system the pressure is a scalar and it can be expressed by the virial equa- tion [69, 70] P = ρkBT + 1 N ri · Fi 3V i=1 (3.6) where Fi is the total internal force on particle i and the brackets indicate an ensemble average. If the intermolecular forces are pairwise additive, the above may be written as P = ρkBT + 1 3V i j>i where Fij is the force on particle i due to particle j. rij · Fij (3.7) For an inhomogeneous system the pressure tensor at position r can still be expressed in a tensorial form of the virial equation and it can be split in a kinetic P K and a potential part P U [66], P(r) = P K (r) + P U (r) (3.8)
3.2 Method of calculation of surface tension 25 The kinetic part can be expressed as a generalization of the ideal gas contribution P K (r) = kBT ρ(r)^1 (3.9) where ρ(r) is density at position r and ^1 is the 3x3 unit matrix. This kinetic part is a single particle property and it is well localized in space. Conversely, there is no unambiguous way of expressing the potential part of the pressure tensor. P U (r) can be defined as the force acting across a microscopic element of area located at r. Because the force depends on the position of two particles (for pair additive potentials), there is no unique way to determine which pairs of particles should contribute to the pressure across the microscopic element of area at r [71], and to reduce the non local two-particles force to a local force at r. Irving and Kirkwood [72] derived the equations of hydrodynamics by means of classical statistical mechanics and obtained the expression of the pressure tensor in terms of molecular variables. They required that, in any definition of the pressure tensor, the local virial should be located near the line connecting the two interacting particles. Different methods have been proposed to compute the potential part of the pressure tensor, like the Irving and Kirkwood method [72] or the Harashima method [73]. The various definitions correspond to different choices of the contour which connects the position in which the microscopic pressure tensor is calculated with the particles position. It is important to underline that all methods give the same expression for the total pressure and interfacial tension when integrated over the whole system, while the expression of the local pressure depends on the applied method. For a detailed description of these different methods see [66]. In our simulations we use the Kirkwood-Buff convention [67, 74], which takes as a contour a straight line. The simulation box of sizes Lx, Ly and Lz, is divided into Ns slabs parallel to the interface (xy-plane) and the contribution of each pair of interacting particles to the local pressure tensor is evenly split through all the slabs which intersect the line the connects the two particles (line of centers). The normal and lateral components of the local pressure tensor in slab k, including the kinetic contribution, are then given by PL(k) = kBT 〈ρ(k)〉 − 1 2Vs (i,j) PN(k) = kBT 〈ρ(k)〉 − 1 Vs (k) x2 ij + y2 ij u rij ′ (rij) (k) z (i,j) 2 ij u rij ′ (rij) (3.10) (3.11) where ρ(k) is the average density in slab k, Vs = LxLyLz/Ns is the volume of a slab, u ′ (r) is the derivative of the intramolecular potential, and the brackets denote an ensemble average. (k) (i,j) means that the summation runs over all pairs of particles (i, j) of which the slab k (partially) contains the line of centers. A slab k gets a contribu-
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- 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
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- Page 27 and 28: III Surface tension in lipid bilaye
- Page 29: 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
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- 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
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24 Surface tension in <strong>lipid</strong> <strong>bilayers</strong><br />
<strong>with</strong><br />
From equations 3.1 <strong>and</strong> 3.2 we have<br />
Pxx(r) = Pyy(r). (3.3)<br />
∂Pxx<br />
∂x ex + ∂Pyy<br />
∂y ey + ∂Pzz<br />
∂z ez = 0 (3.4)<br />
where eα (α = x, y, z) are the orthogonal basis vectors in the Cartesian space. From<br />
equations 3.4 <strong>and</strong> 3.3 results that the lateral (also called tangential) components <strong>of</strong><br />
the pressure tensor are function <strong>of</strong> z only: PL(z) = Pxx(z) = Pyy(z). The normal<br />
component is constant throughout the system <strong>and</strong> equal to the external pressure:<br />
PN(z) = Pzz(z) = Pext. The lateral components are also equal to the external pressure<br />
in the bulk phases.<br />
The surface tension is defined as the integral over the interface <strong>of</strong> the difference<br />
between the normal <strong>and</strong> lateral components <strong>of</strong> the pressure tensor [67, 68]<br />
γ =<br />
z2<br />
z1<br />
dz [PN(z) − PL(z)] =<br />
z2<br />
z1<br />
dγ(z) (3.5)<br />
where z1 <strong>and</strong> z2 are positions in the bulk phases <strong>and</strong> γ(z) is the local surface tension<br />
at position z.<br />
In molecular simulations, statistical mechanics is used to relate thermodynamic<br />
quantities to ensemble averages over microscopic degrees <strong>of</strong> freedom. For an homogeneous<br />
system the pressure is a scalar <strong>and</strong> it can be expressed by the virial equa-<br />
tion [69, 70]<br />
P = ρkBT + 1<br />
<br />
N<br />
<br />
ri · Fi<br />
3V<br />
i=1<br />
(3.6)<br />
where Fi is the total internal force on particle i <strong>and</strong> the brackets indicate an ensemble<br />
average. If the intermolecular forces are pairwise additive, the above may be written<br />
as<br />
P = ρkBT + 1<br />
3V<br />
<br />
<br />
i<br />
j>i<br />
where Fij is the force on particle i due to particle j.<br />
rij · Fij<br />
<br />
(3.7)<br />
For an inhomogeneous system the pressure tensor at position r can still be expressed<br />
in a tensorial form <strong>of</strong> the virial equation <strong>and</strong> it can be split in a kinetic P K<br />
<strong>and</strong> a potential part P U [66],<br />
P(r) = P K (r) + P U (r) (3.8)