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Revision 3947 by gezelter, Wed Sep 4 20:54:02 2013 UTC vs.
Revision 3948 by gezelter, Fri Sep 6 20:29:20 2013 UTC

# Line 438 | Line 438 | eq. \eqref{C(t)1}, $P_{2}$ is the second-order Legendr
438   molecules.  The rate at which the function decays provides information
439   about hindered motions and the timescales for relaxation.  In
440   eq. \eqref{C(t)1}, $P_{2}$ is the second-order Legendre polynomial,
441 < the vector $\mathbf{u}$ is usually taken as HOH bisector, although
442 < slightly different behavior is observed when $\mathbf{u}$ is the
441 > the vector $\mathbf{u}$ is often taken as HOH bisector, although
442 > slightly different behavior can be observed when $\mathbf{u}$ is the
443   vector along one of the OH bonds.  The angle brackets denote an
444   ensemble average over all water molecules in a given spatial region.
445  
# Line 447 | Line 447 | in the decay behavior as a function of the $z$ coordin
447   have computed $C_{2}(z,t)$ for molecules that are present within a
448   particular slab along the $z$- axis at the initial time.  The change
449   in the decay behavior as a function of the $z$ coordinate is another
450 < measure of the change of how the environment changes as we traverse
451 < the ice/water interface.  To compute these correlation functions, each
452 < of the 0.5 ns simulations was followed by a shorter 200 ps simulation
453 < where the positions of every molecule in the system were recorded
454 < every 0.1 ps. The systems were then divided into 30 bins and $C_2(t)$
455 < was evaluated for each bin.
450 > measure of the change of how the local environment changes across the
451 > ice/water interface.  To compute these correlation functions, each of
452 > the 0.5 ns simulations was followed by a shorter 200 ps microcanonical
453 > (NVE) simulation in which the positions and orientations of every
454 > molecule in the system were recorded every 0.1 ps. The systems were
455 > then divided into 30 bins and $C_2(t)$ was evaluated for each bin.
456  
457 < In simulations at biological interfaces, it has been shown that
458 < $C_2(t)$ for water can be fit by a triexponential decay\cite{Furse08},
459 < where the three components of the decay correspond to a fast (<200 fs)
460 < reorientational piece driven by the restoring forces of existing
461 < hydrogen bonds, a middle (on the order of several ps) piece describing
462 < the large angle jumps that occur during the breaking and formation of
463 < new hydrogen bonds,\cite{Laage08,Laage11} and a slow (on the order of
464 < tens of ps) contribution describing the translational motion of the
465 < molecules. We have similarly fit our correlation functions
457 > In simulations of water at biological interfaces, Furse {\em et al.}
458 > fit $C_2(t)$ functions for water with triexponential
459 > functions,\cite{Furse08} where the three components of the decay
460 > correspond to a fast (<200 fs) reorientational piece driven by the
461 > restoring forces of existing hydrogen bonds, a middle (on the order of
462 > several ps) piece describing the large angle jumps that occur during
463 > the breaking and formation of new hydrogen bonds,and a slow (on the
464 > order of tens of ps) contribution describing the translational motion
465 > of the molecules.  The model for orientational decay presented
466 > recently by Laage and Hynes {\em et al.}\cite{Laage08,Laage11} also
467 > includes three similar decay constants, although two of the time
468 > constants are linked, and the resulting decay curve has two parameters
469 > governing the dynamics of decay.
470 >
471 > In our ice/water interfaces, we are at substantially lower
472 > temperatures, and the water molecules are further perturbed by the
473 > presence of the ice phase nearby.  We have obtained the most
474 > reasonable fits using triexponential functions with three distinct
475 > time domains, as well as a constant piece that accounts for the water
476 > stuck in the ice phase that does not experience any long-time
477 > orientational decay,
478   \begin{equation}
479   C_{2}(t) \approx a e^{-t/\tau_\mathrm{short}} + b e^{-t/\tau_\mathrm{middle}} + c
480   e^{-t/\tau_\mathrm{long}} + (1-a-b-c)
481   \end{equation}
482 < An average value and standard deviation for each $\tau$ was obtained
483 < for each bin from the four runs.  To improve statistics, the data is
484 < shown as a function of distance from the center of the ice slab in
485 < figures \ref{fig:basal_Tau_comic_strip} and
486 < \ref{fig:prismatic_Tau_comic_strip}.
482 > Average values for the three decay constants (and error estimates)
483 > were obtained for each bin. In figures \ref{fig:basal_Tau_comic_strip}
484 > and \ref{fig:prismatic_Tau_comic_strip}, the three orientational decay
485 > times are shown as a function of distance from the center of the ice
486 > slab.
487  
488   \begin{figure}
489   \includegraphics[width=\linewidth]{basal_Tau_comic_strip.pdf}

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