| 121 |
|
protein like hen egg white lysozyme (PDB code: 1LYZ) yields an |
| 122 |
|
effective protein concentration of 100 mg/mL.\cite{Asthagiri20053300} |
| 123 |
|
|
| 124 |
< |
{\it Yotal} protein concentrations in the cell are typically on the |
| 124 |
> |
{\it Total} protein concentrations in the cell are typically on the |
| 125 |
|
order of 160-310 mg/ml,\cite{Brown1991195} and individual proteins |
| 126 |
|
have concentrations orders of magnitude lower than this in the |
| 127 |
|
cellular environment. The effective concentrations of single proteins |
| 431 |
|
)_{T}. |
| 432 |
|
\label{eq:BMN} |
| 433 |
|
\end{equation} |
| 434 |
< |
The region we used is a spherical volume of 10 \AA\ radius centered in |
| 434 |
> |
The region we used is a spherical volume of 20 \AA\ radius centered in |
| 435 |
|
the middle of the cluster. $N$ is the average number of molecules |
| 436 |
|
found within this region throughout a given simulation. The geometry |
| 437 |
|
and size of the region is arbitrary, and any bulk-like portion of the |
| 518 |
|
temperature respond to the Langevin Hull for nanoparticles that were |
| 519 |
|
initialized far from the target pressure and temperature. As |
| 520 |
|
expected, the rate at which thermal equilibrium is achieved depends on |
| 521 |
< |
the total surface area of the cluter exposed to the bath as well as |
| 521 |
> |
the total surface area of the cluster exposed to the bath as well as |
| 522 |
|
the bath viscosity. Pressure that is applied suddenly to a cluster |
| 523 |
|
can excite breathing vibrations, but these rapidly damp out (on time |
| 524 |
|
scales of 30 -- 50 ps). |
| 545 |
|
and previous simulation work throughout the 1 -- 1000 atm pressure |
| 546 |
|
regime. Compressibilities computed using the Hull volume, however, |
| 547 |
|
deviate dramatically from the experimental values at low applied |
| 548 |
< |
pressures. The reason for this deviation is quite simple; at low |
| 548 |
> |
pressures. The reason for this deviation is quite simple: at low |
| 549 |
|
applied pressures, the liquid is in equilibrium with a vapor phase, |
| 550 |
|
and it is entirely possible for one (or a few) molecules to drift away |
| 551 |
|
from the liquid cluster (see Fig. \ref{fig:coneOfShame}). At low |
| 575 |
|
different pressures must be done to compute the first derivatives. It |
| 576 |
|
is also possible to compute the compressibility using the fluctuation |
| 577 |
|
dissipation theorem using either fluctuations in the |
| 578 |
< |
volume,\cite{Debenedetti1986}, |
| 578 |
> |
volume,\cite{Debenedetti1986} |
| 579 |
|
\begin{equation} |
| 580 |
|
\kappa_{T} = \frac{\left \langle V^{2} \right \rangle - \left \langle |
| 581 |
|
V \right \rangle ^{2}}{V \, k_{B} \, T}, |
| 613 |
|
hydrophobic boundary, or orientational or radial constraints. |
| 614 |
|
Therefore, the orientational correlations of the molecules in water |
| 615 |
|
clusters are of particular interest in testing this method. Ideally, |
| 616 |
< |
the water molecules on the surfaces of the clusterss will have enough |
| 616 |
> |
the water molecules on the surfaces of the clusters will have enough |
| 617 |
|
mobility into and out of the center of the cluster to maintain |
| 618 |
|
bulk-like orientational distribution in the absence of orientational |
| 619 |
|
and radial constraints. However, since the number of hydrogen bonding |
