1 |
\chapter{\label{chapt:lipid}LIPID MODELING} |
2 |
|
3 |
\section{\label{lipidSection:introduction}Introduction} |
4 |
|
5 |
Under biologically relevant conditions, phospholipids are solvated |
6 |
in aqueous solutions at a roughly 25:1 ratio. Solvation can have a |
7 |
tremendous impact on transport phenomena in biological membranes |
8 |
since it can affect the dynamics of ions and molecules that are |
9 |
transferred across membranes. Studies suggest that because of the |
10 |
directional hydrogen bonding ability of the lipid headgroups, a |
11 |
small number of water molecules are strongly held around the |
12 |
different parts of the headgroup and are oriented by them with |
13 |
residence times for the first hydration shell being around 0.5 - 1 |
14 |
ns\cite{Ho1992}. In the second solvation shell, some water molecules |
15 |
are weakly bound, but are still essential for determining the |
16 |
properties of the system. Transport of various molecular species |
17 |
into living cells is one of the major functions of membranes. A |
18 |
thorough understanding of the underlying molecular mechanism for |
19 |
solute diffusion is crucial to the further studies of other related |
20 |
biological processes. All transport across cell membranes takes |
21 |
place by one of two fundamental processes: Passive transport is |
22 |
driven by bulk or inter-diffusion of the molecules being transported |
23 |
or by membrane pores which facilitate crossing. Active transport |
24 |
depends upon the expenditure of cellular energy in the form of ATP |
25 |
hydrolysis. As the central processes of membrane assembly, |
26 |
translocation of phospholipids across membrane bilayers requires the |
27 |
hydrophilic head of the phospholipid to pass through the highly |
28 |
hydrophobic interior of the membrane, and for the hydrophobic tails |
29 |
to be exposed to the aqueous environment\cite{Sasaki2004}. A number |
30 |
of studies indicate that the flipping of phospholipids occurs |
31 |
rapidly in the eukaryotic ER and the bacterial cytoplasmic membrane |
32 |
via a bi-directional, facilitated diffusion process requiring no |
33 |
metabolic energy input. Another system of interest would be the |
34 |
distribution of sites occupied by inhaled anesthetics in membrane. |
35 |
Although the physiological effects of anesthetics have been |
36 |
extensively studied, the controversy over their effects on lipid |
37 |
bilayers still continues. Recent deuterium NMR measurements on |
38 |
halothane in POPC lipid bilayers suggest the anesthetics are |
39 |
primarily located at the hydrocarbon chain region\cite{Baber1995}. |
40 |
Infrared spectroscopy experiments suggest that halothane in DMPC |
41 |
lipid bilayers lives near the membrane/water |
42 |
interface\cite{Lieb1982}. |
43 |
|
44 |
Molecular dynamics simulations have proven to be a powerful tool for |
45 |
studying the functions of biological systems, providing structural, |
46 |
thermodynamic and dynamical information. Unfortunately, much of |
47 |
biological interest happens on time and length scales well beyond |
48 |
the range of current simulation technologies. |
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%review of coarse-grained modeling |
50 |
Several schemes are proposed in this chapter to overcome these |
51 |
difficulties. |
52 |
|
53 |
\section{\label{lipidSection:model}Model} |
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|
55 |
\subsection{\label{lipidSection:SSD}The Soft Sticky Dipole Water Model} |
56 |
|
57 |
In a typical bilayer simulation, the dominant portion of the |
58 |
computation time will be spent calculating water-water interactions. |
59 |
As an efficient solvent model, the Soft Sticky Dipole (SSD) water |
60 |
model\cite{Chandra1999,Fennel2004} is used as the explicit solvent |
61 |
in this project. Unlike other water models which have partial |
62 |
charges distributed throughout the whole molecule, the SSD water |
63 |
model consists of a single site which is a Lennard-Jones interaction |
64 |
site, as well as a point dipole. A tetrahedral potential is added to |
65 |
correct for hydrogen bonding. The following equation describes the |
66 |
interaction between two water molecules: |
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\[ |
68 |
V_{SSD} = V_{LJ} (r_{ij} ) + V_{dp} (r_{ij} ,\Omega _i ,\Omega _j ) |
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+ V_{sticky} (r_{ij} ,\Omega _i ,\Omega _j ) |
70 |
\] |
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where $r_{ij}$ is the vector between molecule $i$ and molecule $j$, |
72 |
$\Omega _i$ and $\Omega _j$ are the orientational degrees of freedom |
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for molecule $i$ and molecule $j$ respectively. |
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\[ |
75 |
V_{LJ} (r_{ij} ) = 4\varepsilon _{ij} \left[ {\left( {\frac{{\sigma |
76 |
_{ij} }}{{r_{ij} }}} \right)^{12} - \left( {\frac{{\sigma _{ij} |
77 |
}}{{r_{ij} }}} \right)^6 } \right] |
78 |
\] |
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\[ |
80 |
V_{dp} (r_{ij} ,\Omega _i ,\Omega _j ) = \frac{1}{{4\pi \varepsilon |
81 |
_0 }}\left[ {\frac{{\mu _i \cdot \mu _j }}{{r_{ij}^3 }} - |
82 |
\frac{{3\left( {\mu _i \cdot r_{ij} } \right)\left( {\mu _i \cdot |
83 |
r_{ij} } \right)}}{{r_{ij}^5 }}} \right] |
84 |
\] |
85 |
\[ |
86 |
V_{sticky} (r_{ij} ,\Omega _i ,\Omega _j ) = v_0 [s(r_{ij} )w(r_{ij} |
87 |
,\Omega _i ,\Omega _j ) + s'(r_{ij} )w'(r_{ij} ,\Omega _i ,\Omega _j |
88 |
)] |
89 |
\] |
90 |
where $v_0$ is a strength parameter, $s$ and $s'$ are cubic |
91 |
switching functions, while $w$ and $w'$ are responsible for the |
92 |
tetrahedral potential and the short-range correction to the dipolar |
93 |
interaction respectively. |
94 |
\[ |
95 |
\begin{array}{l} |
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w(r_{ij} ,\Omega _i ,\Omega _j ) = \sin \theta _{ij} \sin 2\theta _{ij} \cos 2\phi _{ij} \\ |
97 |
w'(r_{ij} ,\Omega _i ,\Omega _j ) = (\cos \theta _{ij} - 0.6)^2 (\cos \theta _{ij} + 0.8)^2 - w_0 \\ |
98 |
\end{array} |
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\] |
100 |
Although dipole-dipole and sticky interactions are more |
101 |
mathematically complicated than Coulomb interactions, the number of |
102 |
pair interactions is reduced dramatically both because the model |
103 |
only contains a single-point as well as "short range" nature of the |
104 |
higher order interaction. |
105 |
|
106 |
\subsection{\label{lipidSection:coarseGrained}The Coarse-Grained Phospholipid Model} |
107 |
|
108 |
Fig.~\ref{lipidFigure:coarseGrained} shows a schematic for our |
109 |
coarse-grained phospholipid model. The lipid head group is modeled |
110 |
by a linear rigid body which consists of three Lennard-Jones spheres |
111 |
and a centrally located point-dipole. The backbone atoms in the |
112 |
glycerol motif are modeled by Lennard-Jones spheres with dipoles. |
113 |
Alkyl groups in hydrocarbon chains are replaced with unified |
114 |
$\text{{\sc CH}}_2$ or $\text{{\sc CH}}_3$ atoms. |
115 |
|
116 |
\begin{figure} |
117 |
\centering |
118 |
\includegraphics[width=\linewidth]{coarse_grained.eps} |
119 |
\caption[A representation of coarse-grained phospholipid model]{} |
120 |
\label{lipidFigure:coarseGrained} |
121 |
\end{figure} |
122 |
|
123 |
Accurate and efficient computation of electrostatics is one of the |
124 |
most difficult tasks in molecular modeling. Traditionally, the |
125 |
electrostatic interaction between two molecular species is |
126 |
calculated as a sum of interactions between pairs of point charges, |
127 |
using Coulomb's law: |
128 |
\[ |
129 |
V = \sum\limits_{i = 1}^{N_A } {\sum\limits_{j = 1}^{N_B } |
130 |
{\frac{{q_i q_j }}{{4\pi \varepsilon _0 r_{ij} }}} } |
131 |
\] |
132 |
where $N_A$ and $N_B$ are the number of point charges in the two |
133 |
molecular species. Originally developed to study ionic crystals, the |
134 |
Ewald summation method mathematically transforms this |
135 |
straightforward but conditionally convergent summation into two more |
136 |
complicated but rapidly convergent sums. One summation is carried |
137 |
out in reciprocal space while the other is carried out in real |
138 |
space. An alternative approach is a multipole expansion, which is |
139 |
based on electrostatic moments, such as charge (monopole), dipole, |
140 |
quadruple etc. |
141 |
|
142 |
Here we consider a linear molecule which consists of two point |
143 |
charges $\pm q$ located at $ ( \pm \frac{d}{2},0)$. The |
144 |
electrostatic potential at point $P$ is given by: |
145 |
\[ |
146 |
\frac{1}{{4\pi \varepsilon _0 }}\left( {\frac{{ - q}}{{r_ - }} + |
147 |
\frac{{ + q}}{{r_ + }}} \right) = \frac{1}{{4\pi \varepsilon _0 |
148 |
}}\left( {\frac{{ - q}}{{\sqrt {r^2 + \frac{{d^2 }}{4} + rd\cos |
149 |
\theta } }} + \frac{q}{{\sqrt {r^2 + \frac{{d^2 }}{4} - rd\cos |
150 |
\theta } }}} \right) |
151 |
\] |
152 |
|
153 |
\begin{figure} |
154 |
\centering |
155 |
\includegraphics[width=\linewidth]{charge_dipole.eps} |
156 |
\caption[Electrostatic potential due to a linear molecule comprising |
157 |
two point charges]{Electrostatic potential due to a linear molecule |
158 |
comprising two point charges} \label{lipidFigure:chargeDipole} |
159 |
\end{figure} |
160 |
|
161 |
The basic assumption of the multipole expansion is $r \gg d$ , thus, |
162 |
$\frac{{d^2 }}{4}$ inside the square root of the denominator is |
163 |
neglected. This is a reasonable approximation in most cases. |
164 |
Unfortunately, in our headgroup model, the distance of charge |
165 |
separation $d$ (4.63 $\AA$ in PC headgroup) may be comparable to |
166 |
$r$. Nevertheless, we could still assume $ \cos \theta \approx 0$ |
167 |
in the central region of the headgroup. Using Taylor expansion and |
168 |
associating appropriate terms with electric moments will result in a |
169 |
"split-dipole" approximation: |
170 |
\[ |
171 |
V(r) = \frac{1}{{4\pi \varepsilon _0 }}\frac{{r\mu \cos \theta |
172 |
}}{{R^3 }} |
173 |
\] |
174 |
where$R = \sqrt {r^2 + \frac{{d^2 }}{4}}$ Placing a dipole at point |
175 |
$P$ and applying the same strategy, the interaction between two |
176 |
split-dipoles is then given by: |
177 |
\[ |
178 |
V_{sd} (r_{ij} ,\Omega _i ,\Omega _j ) = \frac{1}{{4\pi \varepsilon |
179 |
_0 }}\left[ {\frac{{\mu _i \cdot \mu _j }}{{R_{ij}^3 }} - |
180 |
\frac{{3\left( {\mu _i \cdot r_{ij} } \right)\left( {\mu _i \cdot |
181 |
r_{ij} } \right)}}{{R_{ij}^5 }}} \right] |
182 |
\] |
183 |
where $\mu _i$ and $\mu _j$ are the dipole moment of molecule $i$ |
184 |
and molecule $j$ respectively, $r_{ij}$ is vector between molecule |
185 |
$i$ and molecule $j$, and $R_{ij{$ is given by, |
186 |
\[ |
187 |
R_{ij} = \sqrt {r_{ij}^2 + \frac{{d_i^2 }}{4} + \frac{{d_j^2 |
188 |
}}{4}} |
189 |
\] |
190 |
where $d_i$ and $d_j$ are the charge separation distance of dipole |
191 |
and respectively. This approximation to the multipole expansion |
192 |
maintains the fast fall-off of the multipole potentials but lacks |
193 |
the normal divergences when two polar groups get close to one |
194 |
another. |
195 |
%description of the comparsion |
196 |
\begin{figure} |
197 |
\centering |
198 |
\includegraphics[width=\linewidth]{split_dipole.eps} |
199 |
\caption[Comparison between electrostatic approximation]{Electron |
200 |
density profile along the bilayer normal.} |
201 |
\label{lipidFigure:splitDipole} |
202 |
\end{figure} |
203 |
|
204 |
%\section{\label{lipidSection:methods}Methods} |
205 |
|
206 |
\section{\label{lipidSection:resultDiscussion}Results and Discussion} |
207 |
|
208 |
\subsection{One Lipid in Sea of Water Molecules} |
209 |
|
210 |
To exclude the inter-headgroup interaction, atomistic models of one |
211 |
lipid (DMPC or DLPE) in sea of water molecules (TIP3P) were built |
212 |
and studied using atomistic molecular dynamics. The simulation was |
213 |
analyzed using a set of radial distribution functions, which give |
214 |
the probability of finding a pair of molecular species a distance |
215 |
apart, relative to the probability expected for a completely random |
216 |
distribution function at the same density. |
217 |
|
218 |
\begin{equation} |
219 |
g_{AB} (r) = \frac{1}{{\rho _B }}\frac{1}{{N_A }} < \sum\limits_{i |
220 |
\in A} {\sum\limits_{j \in B} {\delta (r - r_{ij} )} } > |
221 |
\end{equation} |
222 |
\begin{equation} |
223 |
g_{AB} (r,\cos \theta ) = \frac{1}{{\rho _B }}\frac{1}{{N_A }} < |
224 |
\sum\limits_{i \in A} {\sum\limits_{j \in B} {\delta (r - r_{ij} )} |
225 |
} \delta (\cos \theta _{ij} - \cos \theta ) > |
226 |
\end{equation} |
227 |
|
228 |
From figure 4(a), we can identify the first solvation shell (3.5 |
229 |
$\AA$) and the second solvation shell (5.0 $\AA$) from both plots. |
230 |
However, the corresponding orientations are different. In DLPE, |
231 |
water molecules prefer to sit around -NH3 group due to the hydrogen |
232 |
bonding. In contrast, because of the hydrophobic effect of the |
233 |
-N(CH3)3 group, the preferred position of water molecules in DMPC is |
234 |
around the -PO4 Group. When the water molecules are far from the |
235 |
headgroup, the distribution of the two angles should be uniform. The |
236 |
correlation close to center of the headgroup dipole (< 5 $\AA$) in |
237 |
both plots tell us that in the closely-bound region, the dipoles of |
238 |
the water molecules are preferentially anti-aligned with the dipole |
239 |
of headgroup. |
240 |
|
241 |
\begin{figure} |
242 |
\centering |
243 |
\includegraphics[width=\linewidth]{g_atom.eps} |
244 |
\caption[The pair correlation functions for atomistic models]{} |
245 |
\label{lipidFigure:PCFAtom} |
246 |
\end{figure} |
247 |
|
248 |
The initial configurations of coarse-grained systems are constructed |
249 |
from the previous atomistic ones. The parameters for the |
250 |
coarse-grained model in Table~\ref{lipidTable:parameter} are |
251 |
estimated and tuned using isothermal-isobaric molecular dynamics. |
252 |
Pair distribution functions calculated from coarse-grained models |
253 |
preserve the basic characteristics of the atomistic simulations. The |
254 |
water density, measured in a head-group-fixed reference frame, |
255 |
surrounding two phospholipid headgroups is shown in |
256 |
Fig.~\ref{lipidFigure:PCFCoarse}. It is clear that the phosphate end |
257 |
in DMPC and the amine end in DMPE are the two most heavily solvated |
258 |
atoms. |
259 |
|
260 |
\begin{figure} |
261 |
\centering |
262 |
\includegraphics[width=\linewidth]{g_coarse.eps} |
263 |
\caption[The pair correlation functions for coarse-grained models]{} |
264 |
\label{lipidFigure:PCFCoarse} |
265 |
\end{figure} |
266 |
|
267 |
\begin{figure} |
268 |
\centering |
269 |
\includegraphics[width=\linewidth]{EWD_coarse.eps} |
270 |
\caption[Excess water density of coarse-grained phospholipids]{ } |
271 |
\label{lipidFigure:EWDCoarse} |
272 |
\end{figure} |
273 |
|
274 |
\begin{table} |
275 |
\caption{The Parameters For Coarse-grained Phospholipids} |
276 |
\label{lipidTable:parameter} |
277 |
\begin{center} |
278 |
\begin{tabular}{|l|c|c|c|c|c|} |
279 |
\hline |
280 |
% after \\: \hline or \cline{col1-col2} \cline{col3-col4} ... |
281 |
Atom type & Mass & $\sigma$ & $\epsilon$ & charge & Dipole \\ |
282 |
$\text{{\sc CH}}_2$ & 14.03 & 3.95 & 0.0914 & 0 & 0 \\ |
283 |
$\text{{\sc CH}}_3$ & 15.04 & 3.75 & 0.195 & 0 & 0 \\ |
284 |
$\text{{\sc CE}}$ & 28.01 & 3.427& 0.294 & 0 & 1.693 \\ |
285 |
$\text{{\sc CK}}$ & 28.01 & 3.592& 0.311 & 0 & 2.478 \\ |
286 |
$\text{{\sc PO}}_4$ & 108.995& 3.9 & 1.88 & -1& 0 \\ |
287 |
$\text{{\sc HDP}}$ & 14.03 & 4.0 & 0.13 & 0 & 0 \\ |
288 |
$\text{{\sc NC}}_4$ & 73.137 & 4.9 & 0.88 & +1& 0 \\ |
289 |
$\text{{\sc NH}}_3$ & 17.03 & 3.25 & 0.17 & +1& 0\\ |
290 |
\hline |
291 |
\end{tabular} |
292 |
\end{center} |
293 |
\end{table} |
294 |
|
295 |
\subsection{Bilayer Simulations Using Coarse-grained Model} |
296 |
|
297 |
A bilayer system consisting of 128 DMPC lipids and 3655 water |
298 |
molecules has been constructed from an atomistic coordinate |
299 |
file.[15] The MD simulation is performed at constant temperature, T |
300 |
= 300K, and constant pressure, p = 1 atm, and consisted of an |
301 |
equilibration period of 2 ns. During the equilibration period, the |
302 |
system was initially simulated at constant volume for 1ns. Once the |
303 |
system was equilibrated at constant volume, the cell dimensions of |
304 |
the system was relaxed by performing under NPT conditions using |
305 |
Nos¨¦-Hoover extended system isothermal-isobaric dynamics. After |
306 |
equilibration, different properties were evaluated over a production |
307 |
run of 5 ns. |
308 |
|
309 |
\begin{figure} |
310 |
\centering |
311 |
\includegraphics[width=\linewidth]{bilayer.eps} |
312 |
\caption[Image of a coarse-grained bilayer system]{A coarse-grained |
313 |
bilayer system consisting of 128 DMPC lipids and 3655 SSD water |
314 |
molecules.} |
315 |
\label{lipidFigure:bilayer} |
316 |
\end{figure} |
317 |
|
318 |
\subsubsection{Electron Density Profile (EDP)} |
319 |
|
320 |
Assuming a gaussian distribution of electrons on each atomic center |
321 |
with a variance estimated from the size of the van der Waals radius, |
322 |
the EDPs which are proportional to the density profiles measured |
323 |
along the bilayer normal obtained by x-ray scattering experiment, |
324 |
can be expressed by\cite{Tu1995} |
325 |
\begin{equation} |
326 |
\rho _{x - ray} (z)dz \propto \sum\limits_{i = 1}^N {\frac{{n_i |
327 |
}}{V}\frac{1}{{\sqrt {2\pi \sigma ^2 } }}e^{ - (z - z_i )^2 /2\sigma |
328 |
^2 } dz}, |
329 |
\end{equation} |
330 |
where $\sigma$ is the variance equal to the van der Waals radius, |
331 |
$n_i$ is the atomic number of site $i$ and $V$ is the volume of the |
332 |
slab between $z$ and $z+dz$ . The highest density of total EDP |
333 |
appears at the position of lipid-water interface corresponding to |
334 |
headgroup, glycerol, and carbonyl groups of the lipids and the |
335 |
distribution of water locked near the head groups, while the lowest |
336 |
electron density is in the hydrocarbon region. As a good |
337 |
approximation to the thickness of the bilayer, the headgroup spacing |
338 |
, is defined as the distance between two peaks in the electron |
339 |
density profile, calculated from our simulations to be 34.1 $\AA$. |
340 |
This value is close to the x-ray diffraction experimental value 34.4 |
341 |
$\AA$\cite{Petrache1998}. |
342 |
|
343 |
\begin{figure} |
344 |
\centering |
345 |
\includegraphics[width=\linewidth]{electron_density.eps} |
346 |
\caption[The density profile of the lipid bilayers]{Electron density |
347 |
profile along the bilayer normal. The water density is shown in red, |
348 |
the density due to the headgroups in green, the glycerol backbone in |
349 |
brown, $\text{{\sc CH}}_2$ in yellow, $\text{{\sc CH}}_3$ in cyan, |
350 |
and total density due to DMPC in blue.} |
351 |
\label{lipidFigure:electronDensity} |
352 |
\end{figure} |
353 |
|
354 |
\subsubsection{$\text{S}_{\text{{\sc cd}}}$ Order Parameter} |
355 |
|
356 |
Measuring deuterium order parameters by NMR is a useful technique to |
357 |
study the orientation of hydrocarbon chains in phospholipids. The |
358 |
order parameter tensor $S$ is defined by: |
359 |
\begin{equation} |
360 |
S_{ij} = \frac{1}{2} < 3\cos \theta _i \cos \theta _j - \delta |
361 |
_{ij} > |
362 |
\end{equation} |
363 |
where $\theta$ is the angle between the $i$th molecular axis and |
364 |
the bilayer normal ($z$ axis). The brackets denote an average over |
365 |
time and molecules. The molecular axes are defined: |
366 |
\begin{itemize} |
367 |
\item $\mathbf{\hat{z}}$ is the vector from $C_{n-1}$ to $C_{n+1}$. |
368 |
\item $\mathbf{\hat{y}}$ is the vector that is perpendicular to $z$ and |
369 |
in the plane through $C_{n-1}$, $C_{n}$, and $C_{n+1}$. |
370 |
\item $\mathbf{\hat{x}}$ is the vector perpendicular to |
371 |
$\mathbf{\hat{y}}$ and $\mathbf{\hat{z}}$. |
372 |
\end{itemize} |
373 |
In coarse-grained model, although there are no explicit hydrogens, |
374 |
the order parameter can still be written in terms of carbon ordering |
375 |
at each point of the chain\cite{Egberts1988} |
376 |
\begin{equation} |
377 |
S_{ij} = \frac{1}{2} < 3\cos \theta _i \cos \theta _j - \delta |
378 |
_{ij} >. |
379 |
\end{equation} |
380 |
|
381 |
Fig.~\ref{lipidFigure:Scd} shows the order parameter profile |
382 |
calculated for our coarse-grained DMPC bilayer system at 300K. Also |
383 |
shown are the experimental data of Tu\cite{Tu1995}. The fact that |
384 |
$\text{S}_{\text{{\sc cd}}}$ order parameters calculated from |
385 |
simulation are higher than the experimental ones is ascribed to the |
386 |
assumption of the locations of implicit hydrogen atoms which are |
387 |
fixed in coarse-grained models at positions relative to the CC |
388 |
vector. |
389 |
|
390 |
\begin{figure} |
391 |
\centering |
392 |
\includegraphics[width=\linewidth]{scd.eps} |
393 |
\caption[$\text{S}_{\text{{\sc cd}}}$ order parameter]{A comparison |
394 |
of $|\text{S}_{\text{{\sc cd}}}|$ between coarse-grained model |
395 |
(blue) and DMPC\cite{petrache00} (black) near 300~K.} |
396 |
\label{lipidFigure:Scd} |
397 |
\end{figure} |
398 |
|
399 |
%\subsection{Bilayer Simulations Using Gay-Berne Ellipsoid Model} |