--- trunk/COonPt/firstTry.tex	2013/03/15 12:51:01	3876
+++ trunk/COonPt/firstTry.tex	2013/03/15 13:18:17	3877
@@ -161,7 +161,7 @@ Au-Au and Pt-Pt interactions\cite{EAM}. The CO was mod
 Coulomb potential.  For this work, we have used classical molecular
 dynamics with potential energy surfaces that are specifically tuned
 for transition metals.  In particular, we used the EAM potential for
-Au-Au and Pt-Pt interactions\cite{EAM}. The CO was modeled using a rigid
+Au-Au and Pt-Pt interactions.\cite{EAM} The CO was modeled using a rigid
 three-site model developed by Straub and Karplus for studying
 photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
 Pt-CO cross interactions were parameterized as part of this work.
@@ -475,8 +475,8 @@ with the energetics and structures at different condit
 
 \subsection{Dynamics}
 Previous atomistic simulations of stepped surfaces dealt largely
-with the energetics and structures at different conditions
-\cite{Williams:1991,Williams:1994}. Consequently, the most common 
+with the energetics and structures at different conditions.
+\cite{Williams:1991,Williams:1994} Consequently, the most common 
 technique utilized to date has been Monte Carlo sampling. Monte Carlo approaches give an efficient 
 sampling of the equilibrium thermodynamic landscape at the expense 
 of ignoring the dynamics of the system. Previous experimental work by Pearl and 
@@ -499,7 +499,7 @@ on the surface. For certain distributions of CO, see F
 energetic penalty around $\sim$~45 kcal/mol, but this is easier than lifting 
 the same metal atom vertically out of the surface,  \textgreater~60 kcal/mol. 
 The penalty lowers significantly when CO is present in sufficient quantities 
-on the surface. For certain distributions of CO, see Figures \ref{fig:sketchGraphic} and \ref{fig:sketchEnergies}, the penalty can fall to as low as 
+on the surface. For certain distributions of CO, see Figures \ref{fig:SketchGraphic} and \ref{fig:SketchEnergies}, the penalty can fall to as low as 
 $\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for 
 diffusion is negligible ( \textless~4 kcal/mol for a Pt adatom). These adatoms are then
 able to explore the terrace before rejoining either their original step-edge or 
@@ -547,11 +547,12 @@ stability strongly and is no longer a good source for 
 definite trend marred by the highest coverage surface. Two 
 explanations arise for this drop. First, upon a visual inspection of 
 the system, after a double layer has been formed, it maintains its 
-stability strongly and is no longer a good source for adatoms and so 
-atoms that had been tracked for mobility data have now been buried. By 
-performing the same diffusion calculation but on a shorter run time 
-(20~ns), only including data before the formation of the double layer, we obtain 
-the larger values for both $\mathbf{D}_{\parallel}$ and $\mathbf{D}_{\perp}$ at the 50\% coverage.
+stability strongly and many atoms that had been tracked for mobility 
+data have now been buried. By performing the same diffusion 
+calculation but on a shorter run time (20~ns), only including data 
+before the formation of the first double layer, we obtain the larger 
+values for both $\mathbf{D}_{\parallel}$ and $\mathbf{D}_{\perp}$ 
+at the 50\% coverage as seen in Figure \ref{fig:diff}.
 This places the parallel diffusion constant more closely in line with the 
 expected trend, while the perpendicular diffusion constant does not 
 drop as far. A secondary explanation arising from our analysis of the 
@@ -559,7 +560,7 @@ arrangements of CO on the surface allowing the formati
 surface has with respect to overcoming surface diffusion of Pt. If the 
 coverage is too sparse, the Pt engages in minimal interactions and 
 thus minimal diffusion. As coverage increases, there are more favorable 
-arrangements of CO on the surface allowing the formation of a path, 
+arrangements of CO on the surface allowing for the formation of a path, 
 a minimum energy trajectory, for the adatom to explore the surface. 
 As the CO is constantly moving on the surface, this path is constantly 
 changing. If the coverage becomes too great, the paths could 
@@ -569,15 +570,17 @@ The increased diffusion on Pt at the higher 
 
 
 \subsubsection{Dynamics of double layer formation}
-The increased diffusion on Pt at the higher 
-CO coverages plays a primary role in double layer formation. However, this is not 
-a complete explanation -- the 33\%~Pt system 
-has higher diffusion constants but did not show 
-any signs of edge doubling in the observed run time. On the 
-50\%~Pt system, one layer formed within the first 40~ns of simulation time, while two more were formed as the system was run for an additional
-110~ns (150~ns total). Previous experimental 
-work gives insight into the upper bounds of the 
-time required for step coalescence.\cite{Williams:1991,Pearl} 
+The increased diffusion on Pt at the higher CO coverages 
+plays a primary role in double layer formation. However, 
+this is not a complete explanation -- the 33\%~Pt system 
+has higher diffusion constants but did not show any signs 
+of edge doubling in the observed run time. On the 
+50\%~Pt system, one layer formed within the first 40~ns 
+of simulation time, while two more were formed as the 
+system was allowed to run for an additional
+110~ns (150~ns total). This suggests that this reconstruction is 
+a rapid process and that the previously mentioned upper bound
+will be lowered as experimental techniques continue to improve.\cite{Williams:1991,Pearl} 
 In this system, as seen in Figure \ref{fig:reconstruct}, the first 
 appearance of a double layer, appears at 19~ns 
 into the simulation. Within 12~ns of this nucleation event, nearly half of the step has 
@@ -587,12 +590,13 @@ The other two layers in this simulation formed over pe
 appearance of the first nucleation event to the first observed double layer, the process took $\sim$20~ns. Another 
 $\sim$40~ns was necessary for the layer to completely straighten. 
 The other two layers in this simulation formed over periods of
-22~ns and 42~ns respectively. Comparing this to the upper 
-bounds of the image scan, it is likely that most aspects of this 
-reconstruction occur very rapidly. A possible explanation 
+22~ns and 42~ns respectively. A possible explanation 
 for this rapid reconstruction is the elevated temperatures 
 under which our systems were simulated. It is probable that the process would 
-take longer at lower temperatures.
+take longer at lower temperatures. Additionally, our measured times for completion 
+of the doubling after the appearance of a nucleation site are likely affected by our 
+constrained axes. A longer step-edge will likely take longer to ``zipper''. However, 
+the first appearance of a nucleation site will likely occur more quickly due to its stochastic nature.
 
 
 
@@ -696,9 +700,9 @@ configurations are displayed in Figure \ref{fig:lambda
 Pt atoms. To test this hypothesis, numerous configurations of 
 CO in varying quantities were arranged on the higher and lower plateaus
 around a step on a otherwise clean Pt(557) surface. A few sample 
-configurations are displayed in Figure \ref{fig:lambdaTable}, with 
+configurations are displayed in Figure \ref{fig:SketchGraphic}, with 
 energies at various positions along the path displayed in Table 
-\ref{tab:rxcoord}. Certain configurations of CO, cases B and D for 
+NO TABLE. Certain configurations of CO, cases B and D for 
 example, can have quite strong energetic reasons for breaking 
 away from the step-edge. Although the packing of these configurations 
 is unlikely until CO coverage has reached a high enough value.