| 101 |
|
|
| 102 |
|
\subsection{\label{lipidSection:coarseGrained}The Coarse-Grained Phospholipid Model} |
| 103 |
|
|
| 104 |
< |
Figure 1 shows a schematic for our coarse-grained phospholipid |
| 105 |
< |
model. The lipid head group is modeled by a linear rigid body which |
| 106 |
< |
consists of three Lennard-Jones spheres and a centrally located |
| 107 |
< |
point-dipole. The backbone atoms in the glycerol motif are modeled |
| 108 |
< |
by Lennard-Jones spheres with dipoles. Alkyl groups in hydrocarbon |
| 109 |
< |
chains are replaced with unified CH2 or CH3 atoms. |
| 104 |
> |
Fig.~\ref{lipidFigure:coarseGrained} shows a schematic for our |
| 105 |
> |
coarse-grained phospholipid model. The lipid head group is modeled |
| 106 |
> |
by a linear rigid body which consists of three Lennard-Jones spheres |
| 107 |
> |
and a centrally located point-dipole. The backbone atoms in the |
| 108 |
> |
glycerol motif are modeled by Lennard-Jones spheres with dipoles. |
| 109 |
> |
Alkyl groups in hydrocarbon chains are replaced with unified |
| 110 |
> |
$\text{{\sc CH}}_2$ or $\text{{\sc CH}}_3$ atoms. |
| 111 |
|
|
| 112 |
+ |
\begin{figure} |
| 113 |
+ |
\centering |
| 114 |
+ |
\includegraphics[width=\linewidth]{coarse_grained.eps} |
| 115 |
+ |
\caption[A representation of coarse-grained phospholipid model]{} |
| 116 |
+ |
\label{lipidFigure:coarseGrained} |
| 117 |
+ |
\end{figure} |
| 118 |
+ |
|
| 119 |
|
Accurate and efficient computation of electrostatics is one of the |
| 120 |
|
most difficult tasks in molecular modeling. Traditionally, the |
| 121 |
|
electrostatic interaction between two molecular species is |
| 145 |
|
\theta } }} + \frac{q}{{\sqrt {r^2 + \frac{{d^2 }}{4} - rd\cos |
| 146 |
|
\theta } }}} \right) |
| 147 |
|
\] |
| 148 |
+ |
|
| 149 |
+ |
\begin{figure} |
| 150 |
+ |
\centering |
| 151 |
+ |
\includegraphics[width=\linewidth]{charge_dipole.eps} |
| 152 |
+ |
\caption[Electrostatic potential due to a linear molecule comprising |
| 153 |
+ |
two point charges]{Electrostatic potential due to a linear molecule |
| 154 |
+ |
comprising two point charges} \label{lipidFigure:chargeDipole} |
| 155 |
+ |
\end{figure} |
| 156 |
|
|
| 157 |
|
The basic assumption of the multipole expansion is $r \gg d$ , thus, |
| 158 |
|
$\frac{{d^2 }}{4}$ inside the square root of the denominator is |
| 275 |
|
\hline |
| 276 |
|
% after \\: \hline or \cline{col1-col2} \cline{col3-col4} ... |
| 277 |
|
Atom type & Mass & $\sigma$ & $\epsilon$ & charge & Dipole \\ |
| 262 |
– |
|
| 278 |
|
$\text{{\sc CH}}_2$ & 14.03 & 3.95 & 0.0914 & 0 & 0 \\ |
| 279 |
|
$\text{{\sc CH}}_3$ & 15.04 & 3.75 & 0.195 & 0 & 0 \\ |
| 280 |
< |
$\text{{\sc CE}}$ & 28.01 & 3.427& 0.294 & 0 & 1.693 |
| 280 |
> |
$\text{{\sc CE}}$ & 28.01 & 3.427& 0.294 & 0 & 1.693 \\ |
| 281 |
|
$\text{{\sc CK}}$ & 28.01 & 3.592& 0.311 & 0 & 2.478 \\ |
| 282 |
|
$\text{{\sc PO}}_4$ & 108.995& 3.9 & 1.88 & -1& 0 \\ |
| 283 |
|
$\text{{\sc HDP}}$ & 14.03 & 4.0 & 0.13 & 0 & 0 \\ |
| 391 |
|
(blue) and DMPC\cite{petrache00} (black) near 300~K.} |
| 392 |
|
\label{lipidFigure:Scd} |
| 393 |
|
\end{figure} |
| 394 |
+ |
|
| 395 |
+ |
%\subsection{Bilayer Simulations Using Gay-Berne Ellipsoid Model} |
