| 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 |
| 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 |
| 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 |
| 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 endoplasmic reticulum and the bacterial |
| 32 |
|
cytoplasmic membrane via a bi-directional, facilitated diffusion |
| 37 |
|
their effects on lipid bilayers still continues. Recent deuterium |
| 38 |
|
NMR measurements on halothane on POPC lipid bilayers suggest the |
| 39 |
|
anesthetics are primarily located at the hydrocarbon chain |
| 40 |
< |
region\cite{Baber1995}. However, infrared spectroscopy experiments |
| 40 |
> |
region.\cite{Baber1995} However, infrared spectroscopy experiments |
| 41 |
|
suggest that halothane in DMPC lipid bilayers lives near the |
| 42 |
< |
membrane/water interface\cite{Lieb1982}. |
| 42 |
> |
membrane/water 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, |
| 348 |
|
headgroup, glycerol, and carbonyl groups of the lipids and the |
| 349 |
|
distribution of water locked near the head groups, while the lowest |
| 350 |
|
electron density is in the hydrocarbon region. As a good |
| 351 |
< |
approximation to the thickness of the bilayer, the headgroup spacing $d$ |
| 352 |
< |
, is defined as the distance between two peaks in the electron |
| 353 |
< |
density profile, calculated from our simulations to be 34.1 $\rm{\AA}$. |
| 354 |
< |
This value is close to the x-ray diffraction experimental value 34.4 |
| 355 |
< |
\AA\cite{Petrache1998}. |
| 351 |
> |
approximation to the thickness of the bilayer, the headgroup spacing |
| 352 |
> |
$d$ , is defined as the distance between two peaks in the electron |
| 353 |
> |
density profile, calculated from our simulations to be 34.1 |
| 354 |
> |
$\rm{\AA}$. This value is close to the x-ray diffraction |
| 355 |
> |
experimental value 34.4 $\rm{\AA}$.\cite{Petrache1998} |
| 356 |
|
|
| 357 |
|
\begin{figure} |
| 358 |
|
\centering |
| 393 |
|
\end{equation} |
| 394 |
|
|
| 395 |
|
Fig.~\ref{lipidFigure:Scd} shows the order parameter profile |
| 396 |
< |
calculated for our coarse-grained DMPC bilayer system at 300K as well as the experimental data\cite{Tu1995}. The fact that |
| 396 |
> |
calculated for our coarse-grained DMPC bilayer system at 300K as |
| 397 |
> |
well as the experimental data.\cite{Tu1995} The fact that |
| 398 |
|
$\text{S}_{\text{{\sc cd}}}$ order parameters calculated from |
| 399 |
|
simulation are higher than the experimental ones is ascribed to the |
| 400 |
|
assumption of the locations of implicit hydrogen atoms which are |
