| 57 |
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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 |
| 60 |
> |
model\cite{Chandra1999,Fennell2004} 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 |
| 115 |
|
|
| 116 |
|
\begin{figure} |
| 117 |
|
\centering |
| 118 |
< |
\includegraphics[width=\linewidth]{coarse_grained.eps} |
| 118 |
> |
\includegraphics[width=3in]{coarse_grained.eps} |
| 119 |
|
\caption[A representation of coarse-grained phospholipid model]{} |
| 120 |
|
\label{lipidFigure:coarseGrained} |
| 121 |
|
\end{figure} |
| 152 |
|
|
| 153 |
|
\begin{figure} |
| 154 |
|
\centering |
| 155 |
< |
\includegraphics[width=\linewidth]{charge_dipole.eps} |
| 155 |
> |
\includegraphics[width=3in]{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} |
| 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, |
| 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}} |
| 315 |
|
\label{lipidFigure:bilayer} |
| 316 |
|
\end{figure} |
| 317 |
|
|
| 318 |
< |
\subsubsection{Electron Density Profile (EDP)} |
| 318 |
> |
\subsubsection{\textbf{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, |
| 351 |
|
\label{lipidFigure:electronDensity} |
| 352 |
|
\end{figure} |
| 353 |
|
|
| 354 |
< |
\subsubsection{$\text{S}_{\text{{\sc cd}}}$ Order Parameter} |
| 354 |
> |
\subsubsection{\textbf{$\text{S}_{\text{{\sc cd}}}$ 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 |
