--- trunk/COonPt/firstTry.tex	2013/03/13 14:57:09	3874
+++ trunk/COonPt/firstTry.tex	2013/03/15 12:51:01	3876
@@ -1,4 +1,13 @@
-\documentclass[11pt]{article}
+\documentclass[journal = jpccck, manuscript = article]{achemso}
+\setkeys{acs}{usetitle = true}
+\usepackage{achemso}
+\usepackage{caption}
+\usepackage{float}
+\usepackage{geometry}
+\usepackage{natbib}
+\usepackage{setspace}
+\usepackage{xkeyval}
+%%%%%%%%%%%%%%%%%%%%%%%
 \usepackage{amsmath}
 \usepackage{amssymb}
 \usepackage{times}
@@ -6,13 +15,14 @@
 \usepackage{setspace}
 \usepackage{endfloat}
 \usepackage{caption}
-%\usepackage{tabularx}
+\usepackage{tabularx}
+\usepackage{longtable}
 \usepackage{graphicx}
 \usepackage{multirow}
-%\usepackage{booktabs}
-%\usepackage{bibentry}
-%\usepackage{mathrsfs}
-\usepackage[square, comma, sort&compress]{natbib}
+\usepackage{multicol}
+
+\usepackage[version=3]{mhchem}  % this is a great package for formatting chemical reactions
+% \usepackage[square, comma, sort&compress]{natbib}
 \usepackage{url}
 \pagestyle{plain} \pagenumbering{arabic} \oddsidemargin 0.0cm
 \evensidemargin 0.0cm \topmargin -21pt \headsep 10pt \textheight
@@ -22,13 +32,27 @@
 %\AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
 \setlength{\abovecaptionskip}{20 pt}
 \setlength{\belowcaptionskip}{30 pt}
+% \bibpunct{}{}{,}{s}{}{;}
 
-\bibpunct{}{}{,}{s}{}{;}
-\bibliographystyle{achemso}
+%\citestyle{nature}
+% \bibliographystyle{achemso}
 
-\begin{document}
+\title{Molecular Dynamics simulations of the surface reconstructions
+  of Pt(557) and Au(557) under exposure to CO}
 
+\author{Joseph R. Michalka}
+\author{Patrick W. McIntyre}
+\author{J. Daniel Gezelter}
+\email{gezelter@nd.edu}
+\affiliation[University of Notre Dame]{251 Nieuwland Science Hall\\
+  Department of Chemistry and Biochemistry\\ University of Notre
+  Dame\\ Notre Dame, Indiana 46556}
 
+\keywords{}
+
+\begin{document}
+
+ 
 %%
 %Introduction
 %	Experimental observations
@@ -47,26 +71,7 @@
 %Summary
 %%
 
-%Title
-\title{Molecular Dynamics simulations of the surface reconstructions
-  of Pt(557) and Au(557) under exposure to CO}
 
-\author{Joseph R. Michalka, Patrick W. McIntyre and J. Daniel
-Gezelter\footnote{Corresponding author. \ Electronic mail: gezelter@nd.edu} \\
-Department of Chemistry and Biochemistry,\\
-University of Notre Dame\\
-Notre Dame, Indiana 46556}
-
-%Date
-\date{Mar 5, 2013}
-
-%authors
-
-% make the title
-\maketitle
-
-\begin{doublespace}
-
 \begin{abstract}
 We examine surface reconstructions of Pt and Au(557) under
 various CO coverages using molecular dynamics in order to 
@@ -300,7 +305,7 @@ zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxe
 performed until the energy difference between subsequent steps 
 was less than $10^{-8}$ Ry.   Nonspin-polarized supercell calculations 
 were performed with a 4~x~4~x~4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
-zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxed gold slab was
+zone.\cite{Monkhorst:1976} The relaxed gold slab was
 then used in numerous single point calculations with CO at various
 heights (and angles relative to the surface) to allow fitting of the
 empirical force field.
@@ -346,7 +351,7 @@ future work.
   \multirow{2}{*}{\textbf{Pt-CO}} & \multirow{2}{*}{-1.9} & -1.4 \bibpunct{}{}{,}{n}{}{,}
   (Ref. \protect\cite{Kelemen:1979}) \\
  & &  -1.9 \bibpunct{}{}{,}{n}{}{,} (Ref. \protect\cite{Yeo}) \\ \hline
-  \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPD_Gold}) \\
+  \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPDGold}) \\
   \hline
 \end{tabular}
 \label{tab:co_energies}
@@ -364,8 +369,8 @@ The different bulk melting temperatures (1337~K for Au
 1200~K were performed to confirm the relative
 stability of the surfaces without a CO overlayer.  
 
-The different bulk melting temperatures (1337~K for Au\cite{Au:melting}
-and 2045~K for Pt\cite{Pt:melting}) suggest that any possible reconstruction should happen at
+The different bulk melting temperatures (1345~$\pm$~10~K for Au\cite{Au:melting}
+and $\sim$~2045~K for Pt\cite{Pt:melting}) suggest that any possible reconstruction should happen at
 different temperatures for the two metals.  The bare Au and Pt surfaces were
 initially run in the canonical (NVT) ensemble at 800~K and 1000~K
 respectively for 100 ps. The two surfaces were relatively stable at these 
@@ -392,9 +397,9 @@ to undergo remodeling that was not observed in the bar
 \section{Results}
 \subsection{Structural remodeling}
 The surfaces of both systems, upon dosage of CO, began 
-to undergo remodeling that was not observed in the bare 
-metal system. The surfaces which were not exposed to CO 
-did experience minor roughening of the step-edge because 
+to undergo extensive remodeling that was not observed in the bare 
+systems. The bare metal surfaces 
+experienced minor roughening of the step-edge because 
 of the elevated temperatures, but the 
 (557) lattice was well-maintained throughout the simulation 
 time. The Au systems were limited to greater amounts of 
@@ -411,33 +416,33 @@ adatoms and step-edges alike, also increased. Addition
 The 0\% coverage surfaces for both metals showed minimal 
 movement at their respective run temperatures. As the CO 
 coverage increased however, the mobility of the surface, 
-adatoms and step-edges alike, also increased. Additionally, 
-at the higher coverages on both metals, there was more 
-step-wandering. Except for the 50\% Pt system, the step-edges 
-did not coalesce in any of the other simulations, instead preferring 
-to keep nearly the same distance between steps as in the 
-original (557) lattice. Previous work by Williams et al.\cite{Williams:1991, Williams:1994} 
+described through adatom diffusion and step-edge wandering, 
+also increased.  Except for the 50\% Pt system, the step-edges 
+did not coalesce in any of the other simulations, instead 
+preferring to keep nearly the same distance between steps 
+as in the original (557) lattice, $\sim$13\AA for Pt and $\sim$14\AA for Au. 
+Previous work by Williams et al.\cite{Williams:1991, Williams:1994} 
 highlights the repulsion that exists between step-edges even 
 when no direct interactions are present in the system. This 
-repulsion arises because the entropy of the step-edges is constrained, 
-since step-edge crossing is not allowed. This entropic repulsion 
-does not completely define the interactions between steps, 
-which is why some surfaces will undergo step coalescence, 
-where additional attractive interactions can overcome the 
-repulsion\cite{Williams:1991} and others will not. The presence and concentration
-of adsorbates, as shown in this work, can affect these step interactions, potentially 
-leading to a new surface structure as the thermodynamic minimum.
+repulsion arises because step-edge crossing is not allowed 
+which constrains the entropy. This entropic repulsion does 
+not completely define the interactions between steps, which 
+is why some surfaces will undergo step coalescence, where 
+additional attractive interactions can overcome the repulsion.\cite{Williams:1991} 
+The presence and concentration of adsorbates, as shown in 
+this work, can affect these step interactions, potentially leading 
+to a new surface structure as the thermodynamic minimum.
 
 \subsubsection{Double layers}
-Tao et al. have shown experimentally that the Pt(557) surface 
+Tao et al.\cite{Tao:2010} have shown experimentally that the Pt(557) surface 
 undergoes two separate reconstructions upon CO adsorption.\cite{Tao:2010} 
 The first involves a doubling of the step height and plateau length. 
-Similar behavior has been seen to occur on numerous surfaces 
+Similar behavior has been seen on numerous surfaces 
 at varying conditions: Ni(977), Si(111).\cite{Williams:1994,Williams:1991,Pearl} 
 Of the two systems we examined, the Pt system showed a greater 
 propensity for reconstruction when compared to the Au system 
 because of the larger surface mobility and extent of step wandering. 
-The amount of reconstruction is correlated to the amount of CO 
+The amount of reconstruction is strongly correlated to the amount of CO 
 adsorbed upon the surface.  This appears to be related to the 
 effect that adsorbate coverage has on edge breakup and on the 
 surface diffusion of metal adatoms. While both systems displayed 
@@ -448,7 +453,7 @@ various times along the simulation showing the evoluti
 in the other Pt systems, they show more step-wandering and 
 general roughening compared to their Au counterparts. The 
 50\% Pt system is highlighted in Figure \ref{fig:reconstruct} at 
-various times along the simulation showing the evolution of a step-edge.
+various times along the simulation showing the evolution of a double layer step-edge.
 
 The second reconstruction on the Pt(557) surface observed by 
 Tao involved the formation of triangular clusters that stretched 
@@ -456,17 +461,29 @@ the 50\% Pt system, experienced this reconstruction.
 the 40~ns time scale or the extended simulation time of 150~ns for 
 the 50\% Pt system, experienced this reconstruction.
 
+%Evolution of surface
+\begin{figure}[H]
+\includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
+\caption{The Pt(557) / 50\% CO system at a sequence of times after
+  initial exposure to the CO: (a) 258~ps, (b) 19~ns, (c) 31.2~ns, and
+  (d) 86.1~ns. Disruption of the (557) step-edges occurs quickly.  The
+  doubling of the layers appears only after two adjacent step-edges
+  touch.  The circled spot in (b) nucleated the growth of the double
+  step observed in the later configurations.}
+  \label{fig:reconstruct}
+\end{figure}
+
 \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 
-technique utilized to date has been Monte Carlo sampling. Monte Carlo gives an efficient 
+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 
 Sibener\cite{Pearl}, using STM, has been able to capture the coalescing 
 of steps on Ni(977). The time scale of the image acquisition, 
 $\sim$70~s/image provides an upper bound for the time required for 
-the doubling to occur. In this section we give data on dynamic and 
+the doubling to occur. By utilizing Molecular Dynamics we were able to probe the dynamics of these reconstructions and in this section we give data on dynamic and 
 transport properties, e.g. diffusion, layer formation time, etc.
 
 
@@ -477,18 +494,18 @@ on higher-index facets provide a lower energy source f
 displaying a low index facet, (111) or (100), is unlikely to experience 
 much surface diffusion because of the large energetic barrier that must 
 be overcome to lift an atom out of the surface. The presence of step-edges and other surface features
-on higher-index facets provide a lower energy source for mobile metal atoms. 
+on higher-index facets provides a lower energy source for mobile metal atoms. 
 Breaking away from the step-edge on a clean surface still imposes an 
-energetic penalty around $\sim$~40 kcal/mol, but this is significantly easier than lifting 
+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, the penalty can fall 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 
-able to explore the terrace before rejoining either the original step-edge or 
-becoming a part of a different edge. It is a more difficult process for an atom 
+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 
+becoming a part of a different edge. It is a difficult process for an atom 
 to traverse to a separate terrace although the presence of CO can lower the 
-energy barrier required to lift or lower the adatom. By tracking the mobility of individual 
+energy barrier required to lift or lower an adatom. By tracking the mobility of individual 
 metal atoms on the Pt and Au surfaces we were able to determine the relative 
 diffusion constants, as well as how varying coverages of CO affect the diffusion. Close 
 observation of the mobile metal atoms showed that they were typically in 
@@ -502,27 +519,43 @@ step-edges causes the diffusion parallel to the step-e
 was used to prevent swamping the diffusion data with the in-place vibrational 
 movement of buried atoms. Diffusion on a surface is strongly affected by 
 local structures and in this work, the presence of single and double layer 
-step-edges causes the diffusion parallel to the step-edges to be different 
-from the diffusion perpendicular to these edges. Parallel and perpendicular
+step-edges causes the diffusion parallel to the step-edges to be larger than 
+the diffusion perpendicular to these edges. Parallel and perpendicular
 diffusion constants are shown in Figure \ref{fig:diff}.
 
-The lack of a definite trend in the Au diffusion data is likely due 
-to the weaker bonding between Au and CO. This leads to a lower 
+%Diffusion graph
+\begin{figure}[H]
+\includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade_20ns.pdf}
+\caption{Diffusion constants for mobile surface atoms along directions
+  parallel ($\mathbf{D}_{\parallel}$) and perpendicular
+  ($\mathbf{D}_{\perp}$) to the (557) step-edges as a function of CO
+  surface coverage.  Diffusion parallel to the step-edge is higher
+  than that perpendicular to the edge because of the lower energy
+  barrier associated with traversing along the edge as compared to
+  completely breaking away. The two reported diffusion constants for
+  the 50\% Pt system arise from different sample sets. The lower values
+  correspond to the same 40~ns amount that all of the other systems were
+  examined at, while the larger values correspond to a 20~ns period }
+\label{fig:diff}
+\end{figure}
+
+The lack of a definite trend in the Au diffusion data in Figure \ref{fig:diff} is likely due 
+to the weaker bonding between Au and CO. This leads to a lower observed
 coverage ({\it x}-axis) when compared to dosage amount, which 
-then further limits the affects of the surface diffusion. The correlation 
+then further limits the effect the CO can have on surface diffusion. The correlation 
 between coverage and Pt diffusion rates conversely shows a 
 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. By 
+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, 
-provides a $\mathbf{D}_{\perp}$ diffusion constant of $1.69~\pm~0.08$ 
-and a $\mathbf{D}_{\parallel}$ diffusion constant of $6.30~\pm~0.08$. 
+(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.
 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 
-mechanism of double layer formation show the affect that CO on the 
+mechanism of double layer formation focuses on the effect that CO on the 
 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 
@@ -533,6 +566,8 @@ their being more adatoms and step-wandering.
 potentially be clogged leading to a decrease in diffusion despite 
 their being more adatoms and step-wandering.
 
+
+
 \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 
@@ -559,59 +594,80 @@ take longer at lower temperatures.
 under which our systems were simulated. It is probable that the process would 
 take longer at lower temperatures.
 
-%Evolution of surface
+
+
+
+
+
+%Sketch graphic of different configurations
 \begin{figure}[H]
-\includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
-\caption{The Pt(557) / 50\% CO system at a sequence of times after
-  initial exposure to the CO: (a) 258~ps, (b) 19~ns, (c) 31.2~ns, and
-  (d) 86.1~ns. Disruption of the (557) step-edges occurs quickly.  The
-  doubling of the layers appears only after two adjacent step-edges
-  touch.  The circled spot in (b) nucleated the growth of the double
-  step observed in the later configurations.}
-  \label{fig:reconstruct}
+\includegraphics[width=0.8\linewidth, height=0.8\textheight]{COpathsSketch.pdf}
+\caption{The dark grey atoms refer to the upper ledge, while the white atoms are 
+the lower terrace. The blue highlighted atoms had a CO in a vertical atop position 
+upon them. These are a sampling of the configurations examined to gain a more 
+complete understanding of the effects CO has on surface diffusion and edge breakup. 
+Energies associated with each configuration are displayed in Figure \ref{fig:SketchEnergies}.}
+\label{fig:SketchGraphic}
 \end{figure}
 
+%energy graph corresponding to sketch graphic
 \begin{figure}[H]
-\includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade.pdf}
-\caption{Diffusion constants for mobile surface atoms along directions
-  parallel ($\mathbf{D}_{\parallel}$) and perpendicular
-  ($\mathbf{D}_{\perp}$) to the (557) step-edges as a function of CO
-  surface coverage.  Diffusion parallel to the step-edge is higher
-  than that perpendicular to the edge because of the lower energy
-  barrier associated with traversing along the edge as compared to
-  completely breaking away. Additionally, the observed
-  maximum and subsequent decrease for the Pt system suggests that the
-  CO self-interactions are playing a significant role with regards to
-  movement of the Pt atoms around and across the surface. }
-\label{fig:diff}
+\includegraphics[width=\linewidth]{stepSeparationComparison.pdf}
+\caption{The energy curves directly correspond to the labeled model 
+surface in Figure \ref{fig:SketchGraphic}. All energy curves are relative 
+to their initial configuration so the energy of a and h do not have the 
+same zero value. As is seen, certain arrangements of CO can lower 
+the energetic barrier that must be overcome to create an adatom. 
+However, it is the highest coverages where these higher-energy 
+configurations of CO will be more likely. }
+\label{fig:SketchEnergies}
 \end{figure}
 
-
-
-
 %Discussion
 \section{Discussion}
 We have shown that the classical potential models are able to model the initial reconstruction of the
 Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
 were able to observe features of the dynamic processes necessary for this reconstruction. 
 
+\subsection{Diffusion}
+As shown in Figure \ref{fig:diff}, for the Pt systems, there 
+is a strong trend toward higher diffusion constants as 
+surface coverage of CO increases. The drop for the 50\% 
+case being explained as double layer formation already 
+beginning to occur in the analyzed 40~ns, which lowered 
+the calculated diffusion rates. Between the parallel and 
+perpendicular rates, the perpendicular diffusion constant 
+appears to be the most important indicator of double layer 
+formation. As highlighted in Figure \ref{fig:reconstruct}, the 
+formation of the double layer did not begin until a nucleation 
+site appeared. And as mentioned by Williams et al.\cite{Williams:1991, Williams:1994}, 
+the inability for edges to cross leads to an effective repulsion. 
+This repulsion must be overcome to allow step coalescence. 
+A greater $\textbf{D}_\perp$ implies more step-wandering 
+and a larger chance for the stochastic meeting of two edges 
+to form the nucleation point. Upon that appearance, parallel 
+diffusion along the step-edge can help ``zipper'' up the double 
+layer. This helps explain why the time scale for formation after 
+the appearance of a nucleation site was rapid, while the initial 
+appearance of said site was unpredictable. 
+
 \subsection{Mechanism for restructuring}
-Since the Au surface showed no large scale restructuring throughout
-our simulation time our discussion will focus on the 50\% Pt-CO system
-which did undergo the doubling featured in Figure \ref{fig:reconstruct}.
-Similarities of our results to those reported previously by 
-Tao et al.\cite{Tao:2010} are quite 
-strong. The simulated Pt 
-system exposed to a large dosage of CO readily restructures by doubling the terrace 
-widths and step heights. The restructuring occurs in a piecemeal fashion, one to two Pt atoms at a time, but is rapid on experimental timescales. 
-The adatoms either 
-break away from the step-edge and stay on the lower terrace or they lift 
-up onto a higher terrace. Once ``free'', they diffuse on the terrace 
-until reaching another step-edge or rejoining their original edge.  
-This combination of growth and decay of the step-edges is in a state of 
-dynamic equilibrium. However, once two previously separated edges 
-meet as shown in Figure 1.B, this nucleates the rest of the edge to meet up, forming a double layer.
-From simulations which exhibit a double layer, the time delay from the initial appearance of a nucleation point to a fully formed double layer is $\sim$35~ns.
+Since the Au surface showed no large scale restructuring throughout 
+our simulation time our discussion will focus on the 50\% Pt-CO system 
+which did undergo the doubling featured in Figure \ref{fig:reconstruct}. 
+Similarities of our results to those reported previously by Tao et al.\cite{Tao:2010} 
+are quite strong. The simulated Pt system exposed to a large dosage 
+of CO readily restructures by doubling the terrace widths and step heights. 
+The restructuring occurs in a piecemeal fashion, one to two Pt atoms at a 
+time, but is rapid on experimental timescales. The adatoms either break 
+away from the step-edge and stay on the lower terrace or they lift up onto 
+a higher terrace. Once ``free'', they diffuse on the terrace until reaching 
+another step-edge or rejoining their original edge. This combination of 
+growth and decay of the step-edges is in a state of dynamic equilibrium. 
+However, once two previously separated edges meet as shown in Figure 1.B, 
+this nucleates the rest of the edge to meet up, forming a double layer. 
+From simulations which exhibit a double layer, the time delay from the 
+initial appearance of a nucleation point to a fully formed double layer is $\sim$35~ns.
 
 A number of possible mechanisms exist to explain the role of adsorbed 
 CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent 
@@ -619,34 +675,47 @@ gains some credence.  The energetic repulsion between 
 the quadrupole-quadrupole interaction is short-ranged and is attractive for 
 some orientations.  If the CO molecules are ``locked'' in a specific orientation 
 relative to each other, through atop adsorption for example, this explanation 
-gains some credence.  The energetic repulsion between two CO located a 
+gains some credence. The energetic repulsion between two CO located a 
 distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) and both in 
-a  vertical orientation, is 8.62 kcal/mol. Moving the CO apart to the second 
+a vertical orientation, is 8.62 kcal/mol. Moving the CO apart to the second 
 nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to 
-nearly 0 kcal/mol. Allowing the CO's to leave a purely vertical orientation 
-also quickly drops the repulsion, a minimum of 6.2 kcal/mol is reached at $\sim$24 degrees between the 2 CO when the carbons are locked at a distance of 2.77 \AA apart.
-As mentioned above, the energy barrier for surface diffusion 
-of a Pt adatom is only 4 kcal/mol. So this repulsion between neighboring CO molecules can 
-increase the surface diffusion. However, the residence time of CO on Pt was 
-examined and while the majority of the CO is on or near the surface throughout 
-the run, most molecules are mobile. This mobility suggests that the CO are more 
-likely to shift their positions without necessarily the Pt along with them.
+nearly 0 kcal/mol. Allowing the CO to rotate away from a purely vertical orientation 
+also lowers the repulsion. A minimum of 6.2 kcal/mol is reached at when the 
+angle between the 2 CO is $\sim$24\textsuperscript{o}, when the carbons are 
+locked at a distance of 2.77 \AA apart. As mentioned above, the energy barrier 
+for surface diffusion of a Pt adatom is only 4 kcal/mol. So this repulsion between 
+neighboring CO molecules can increase the surface diffusion. However, the 
+residence time of CO on Pt was examined and while the majority of the CO is 
+on or near the surface throughout the run, the molecules are extremely mobile, 
+with diffusion constants 40 to 2500 times larger, depending on coverage. This 
+mobility suggests that the CO are more likely to shift their positions without 
+necessarily the Pt along with them.
 
 Another possible and more likely mechanism for the restructuring is in the
 destabilization of strong Pt-Pt interactions by CO adsorbed on surface
-Pt atoms.  This would then have the effect of increasing surface mobility
-of these atoms.  To test this hypothesis, numerous configurations of 
+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. One representative
-configuration is displayed in Figure \ref{fig:lambda}. Single or concerted movement
-of Pt atoms was then examined to determine possible barriers. Because
-the movement was forced along a pre-defined reaction coordinate that may differ
-from the true minimum of this path, only the beginning and ending energies
-are displayed in Table \ref{tab:rxcoord} with the corresponding beginning and ending reaction coordinates in Figure \ref{fig:lambdaTable}. These values suggest that the presence of CO at suitable
-locations can lead to lowered barriers for Pt breaking apart from the step-edge.
-Additionally, as highlighted in Figure \ref{fig:lambda}, the presence of CO makes the
-burrowing and lifting of adatoms favorable, whereas without CO, the process is neutral
-in terms of energetics.
+around a step on a otherwise clean Pt(557) surface. A few sample 
+configurations are displayed in Figure \ref{fig:lambdaTable}, with 
+energies at various positions along the path displayed in Table 
+\ref{tab:rxcoord}. 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. 
+These examples are showing the most difficult cases, immediate 
+adatom formation through breakage away from the step-edge, which 
+is why their energies at large distances are relatively high. There are 
+mechanistic paths where an edge atom could get shifted to onto the 
+step-edge to form a small peak before fully breaking away. And again, 
+once the adatom is formed, the barrier for diffusion on the surface is 
+negligible. These sample configurations help explain CO's effect on 
+general surface mobility and step wandering, but they are lacking in 
+providing a mechanism for the formation of double layers. One possible 
+mechanism is elucidated in Figure \ref{fig:lambda}, where a burrowing 
+and lifting process of an adatom and step-edge atom respectively is 
+examined. The system, without CO present, is nearly energetically 
+neutral, whereas with CO present there is a $\sim$ 15 kcal/mol drop 
+in the energy of the system.
 
 %lambda progression of Pt -> shoving its way into the step
 \begin{figure}[H]
@@ -654,55 +723,16 @@ in terms of energetics.
 \caption{A model system of the Pt(557) surface was used as the framework
  for exploring energy barriers along a reaction coordinate. Various numbers,
  placements, and rotations of CO were examined as they affect Pt movement.
- The coordinate displayed in this Figure was a representative run. As shown
- in Table \ref{tab:rxcoord}, relative to the energy of the system at 0\%, there
+ The coordinate displayed in this Figure was a representative run.  relative to the energy of the system at 0\%, there
  is a slight decrease upon insertion of the Pt atom into the step-edge along
  with the resultant lifting of the other Pt atom when CO is present at certain positions.}
 \label{fig:lambda}
 \end{figure}
 
-\begin{figure}[H]
-\includegraphics[totalheight=0.9\textheight]{lambdaTable.png}
-\caption{}
-\label{fig:lambdaTable}
-\end{figure}
 
 
 
-\begin{table}[H]
-\caption{}
-\centering
-\begin{tabular}{| c || c | c | c | c |}
-\hline
-\textbf{System} & 0.5~\AA & 2~\AA & 4~\AA & 6~\AA \\
-\hline
-A & 6.38 & 38.34 & 44.65 & 47.60 \\
-B & -20.72 & 0.67 & 17.33 & 24.28 \\
-C & 4.92 & 27.02 & 41.05 & 47.43 \\
-D & -16.97 & 21.21 & 35.87 & 40.93 \\
-E & 5.92 & 30.96 & 43.69 & 49.23 \\
-F & 8.53 & 46.23 & 53.98 & 65.55 \\
-\hline 
-\end{tabular}
-\label{tab:rxcoord}
-\end{table}
 
-
-\subsection{Diffusion}
-The diffusion parallel to the step-edge tends to be 
-much larger than that perpendicular to the step-edge. The dynamic 
-equilibrium that is established between the step-edge and adatom interface. The coverage 
-of CO also appears to play a slight role in relative rates of diffusion, as shown in Figure \ref{fig:diff}.
-The 
-Thus, the bottleneck of the double layer formation appears to be the initial formation
-of this growth point, which seems to be somewhat of a stochastic event. Once it 
-appears, parallel diffusion, along the now slightly angled step-edge, will allow for 
-a faster formation of the double layer than if the entire process were dependent on 
-only perpendicular diffusion across the plateaus. Thus, the larger $D_{\perp}$, the 
-more likely a growth point is to be formed. 
-\\
-
-
 %breaking of the double layer upon removal of CO
 \begin{figure}[H]
 \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
@@ -761,13 +791,18 @@ In this work we have shown the reconstruction of the P
 % \end{tabular}
 % \end{table}
 
-\section{Acknowledgments}
+\begin{acknowledgement}
 Support for this project was provided by the National Science
 Foundation under grant CHE-0848243 and by the Center for Sustainable
 Energy at Notre Dame (cSEND). Computational time was provided by the
 Center for Research Computing (CRC) at the University of Notre Dame.
-
+\end{acknowledgement}
 \newpage
 \bibliography{firstTryBibliography}
-\end{doublespace}
+%\end{doublespace}
+
+\begin{tocentry}
+%\includegraphics[height=3.5cm]{timelapse}
+\end{tocentry}
+
 \end{document}
