--- trunk/COonPt/firstTry.tex	2013/02/27 21:15:17	3866
+++ trunk/COonPt/firstTry.tex	2013/03/05 00:18:33	3867
@@ -58,7 +58,7 @@ Notre Dame, Indiana 46556}
 Notre Dame, Indiana 46556}
 
 %Date
-\date{Dec 15, 2012}
+\date{Mar 4, 2013}
 
 %authors
 
@@ -68,7 +68,19 @@ We examine potential surface reconstructions of Pt and
 \begin{doublespace}
 
 \begin{abstract}
-We examine potential surface reconstructions of Pt and Au (557) under various CO coverages using molecular dynamics in order to find possible mechanisms and dynamics for the restructuring. The metal-CO interactions were parameterized as part of this work so that a large scale treatment of this system could be undertaken. The relative binding strengths of the metal-CO interactions were found to play a large role with regards to step edge stability and adatom diffusion. A small correlation between coverage and the size of the diffusion constant was also determined. These results appear sufficient to explain the reconstructions observed on the Pt systems and the lack of reconstructions on the Au systems.
+We examine potential surface reconstructions of Pt and Au(557)
+under various CO coverages using molecular dynamics in order
+to explore possible mechanisms for any observed reconstructions and their dynamics.
+The metal-CO interactions were parameterized as part of this 
+work so that an efficient large-scale treatment of this system could be
+undertaken. The relative binding strengths of the metal-CO 
+interactions were found to play a large role with regards to 
+step-edge stability and adatom diffusion. A small correlation 
+between coverage and the size of the diffusion constant was 
+also determined. An in-depth examination of the energetics of CO
+adsorbed to the surface provides results that appear sufficient to explain the 
+reconstructions observed on the Pt systems and the corresponding lack  
+on the Au systems.
 \end{abstract}
 
 \newpage
@@ -105,7 +117,6 @@ computational efficiency necessary to simulate the pro
 of the process are of particular interest, we employ classical force
 fields that represent a compromise between chemical accuracy and the
 computational efficiency necessary to simulate the process of interest.
-
 Restructuring can occur as a result of specific interactions of the
 catalyst with adsorbates. In this work, two metal systems exposed 
 to carbon monoxide were examined. The Pt(557) surface has already been shown
@@ -146,7 +157,7 @@ parameter sets. The glue model of Ercolessi {\it et al
 methods,\cite{Daw84,Foiles86,Johnson89,Daw89,Plimpton93,Voter95a,Lu97,Alemany98}
 but other models like the Finnis-Sinclair\cite{Finnis84,Chen90} and
 the quantum-corrected Sutton-Chen method\cite{QSC,Qi99} have simpler
-parameter sets. The glue model of Ercolessi {\it et al.} is among the
+parameter sets. The glue model of Ercolessi et al. is among the
 fastest of these density functional approaches.\cite{Ercolessi88} In
 all of these models, atoms are conceptualized as a positively charged
 core with a radially-decaying valence electron distribution. To
@@ -206,7 +217,7 @@ mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCO
 \begin{table}[H]
   \caption{Positions, Lennard-Jones parameters ($\sigma$ and
     $\epsilon$), and charges for the CO-CO 
-    interactions borrowed from Ref. \bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA~, energies are 
+    interactions borrowed from Ref.\bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA, energies are 
     in kcal/mol, and charges are in atomic units.}
 \centering
 \begin{tabular}{| c | c | ccc |}
@@ -223,7 +234,7 @@ Since the adsorption of CO onto a platinum surface has
 
 \subsection{Cross-Interactions between the metals and carbon monoxide}
 
-Since the adsorption of CO onto a platinum surface has been the focus
+Since the adsorption of CO onto a Pt surface has been the focus
 of much experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979}
 and theoretical work
 \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
@@ -234,7 +245,7 @@ than the experimentally-reported values as shown in Ta
 position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}
 This resulted in binding energies that are slightly higher
 than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
-{\it et al.},\cite{Pons:1986} the Pt-C interaction was fit to a deep
+et al.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
 Lennard-Jones interaction to mimic strong, but short-ranged partial
 binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
 Pt-O interaction was parameterized to a Morse potential at a larger
@@ -278,15 +289,15 @@ a future work.\cite{Deshlahra:2012,StreitzMintmire}
 (111) surfaces are displayed in Table~\ref{co_energies}.  Charge transfer
 and polarization are neglected in this model, although these effects are likely to
 affect binding energies and binding site preferences, and will be added in
-a future work.\cite{Deshlahra:2012,StreitzMintmire}
+a future work.\cite{Deshlahra:2012,StreitzMintmire:1994}
 
 %Table  of Parameters
 %Pt Parameter Set 9
 %Au Parameter Set 35
 \begin{table}[H]
-  \caption{Best fit parameters for metal-CO cross-interactions.   Metal-C
+  \caption{Best fit parameters for metal-CO cross-interactions. Metal-C
     interactions are modeled with Lennard-Jones potential, while the
-    (mostly-repulsive) metal-O interactions were fit to Morse
+    metal-O interactions were fit to Morse
     potentials.  Distances are given in \AA~and energies in kcal/mol. }
 \centering
 \begin{tabular}{| c | cc | c | ccc |}
@@ -303,8 +314,8 @@ a future work.\cite{Deshlahra:2012,StreitzMintmire}
 
 %Table of energies
 \begin{table}[H]
-  \caption{Adsorption energies for CO on M(111) using the potentials
-    described in this work.  All values are in eV}
+  \caption{Adsorption energies for CO on M(111) at the atop site using the potentials
+    described in this work.  All values are in eV.}
 \centering
 \begin{tabular}{| c | cc |}
   \hline
@@ -322,30 +333,33 @@ FCC crystal that have been cut along the 557 plane so 
 \subsection{Pt(557) and Au(557) metal interfaces}
 
 Our model systems are composed of 3888 Pt atoms and 3384 Au atoms in a
-FCC crystal that have been cut along the 557 plane so that they are
-periodic in the {\it x} and {\it y} directions, and have been rotated
-to expose two parallel 557 cuts along the positive and negative {\it
+FCC crystal that have been cut along the (557) plane so that they are
+periodic in the {\it x} and {\it y} directions, and have been oriented
+to expose two aligned (557) cuts along the extended {\it
   z}-axis.  Simulations of the bare metal interfaces at temperatures
-ranging from 300~K to 1200~K were done to observe the relative
+ranging from 300~K to 1200~K were performed to observe the relative
 stability of the surfaces without a CO overlayer.  
 
 The different bulk (and surface) melting temperatures (1337~K for Au
-and 2045~K for Pt) suggest that the reconstruction may happen at
-different temperatures for the two metals.  To copy experimental
-conditions for the CO-exposed surfaces, the bare surfaces were
+and 2045~K for Pt) suggest that any possible reconstruction may 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.  Each surface was exposed to a range of CO
+respectively for 100 ps. These temperatures were chosen because the 
+surfaces were relatively stable at these temperatures when no CO was 
+present, but experienced additional instability upon addition of CO in the time
+frames we were examining. Each surface was exposed to a range of CO
 that was initially placed in the vacuum region.  Upon full adsorption,
 these amounts correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
-coverage.  Because of the difference in binding energies, the platinum
+coverage. Higher coverages were tried, but the CO-CO repulsion was preventing
+a higher amount of adsorption.  Because of the difference in binding energies, the Pt
 systems very rarely had CO that was not bound to the surface, while
-the gold surfaces often had a significant CO population in the gas
+the Au surfaces often had a significant CO population in the gas
 phase.  These systems were allowed to reach thermal equilibrium (over
-5 ns) before being shifted to the microcanonical (NVE) ensemble for
+5 ns) before being run in the microcanonical (NVE) ensemble for
 data collection. All of the systems examined had at least 40 ns in the
 data collection stage, although simulation times for some of the
 systems exceeded 200ns.  All simulations were run using the open
-source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,OpenMD}
+source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE}
 
 % Just results, leave discussion for discussion section
 % structure
@@ -356,83 +370,118 @@ Tao {\it et al.} showed experimentally that the Pt(557
 % 	time scale, formation, breakage
 \section{Results}
 \subsection{Structural remodeling}
-Tao {\it et al.} showed experimentally that the Pt(557) surface undergoes
-two separate reconstructions upon CO adsorption.\cite{Tao:2010} The first 
-reconstruction involves a doubling of the step height and plateau length. Similar
-behavior has been seen to occur on numerous surfaces at varying conditions.\cite{Williams:1994,Williams:1991,Pearl}
-Of the two systems we examined, the Platinum system showed the most surface 
-reconstruction. Additionally, the amount of reconstruction appears to be 
-dependent on the amount of CO adsorbed upon the surface. This result is likely
-related to the effect that coverage has on surface diffusion. While both systems 
-displayed step edge wandering, only the Pt surface underwent doubling within 
-the time scales we were modeling. Specifically only the 50 \% coverage Pt system
-was observed to undergo a complete doubling in the time scales we were able to monitor. 
-This event encouraged us to allow that specific system to run continuously during which two
-more double layers were created. The other systems, not displaying any large scale changes
-of interest, were all stopped after 40 ns of simulation. Neverthless, the other Platinum systems tended to show 
-more cumulative lateral movement of the step edges when compared to the Gold systems. 
-The 50 \% Pt system is highlighted in figure \ref{fig:reconstruct} at various times along the 
-simulation showing the evolution of the system.
-
-The second reconstruction on the Pt(557) surface observed by Tao involved the 
-formation of triangular clusters that stretched across the plateau between two step edges.
-Neither system, within our simulated time scales, experiences this reconstruction. A constructed
-system in which the triangular motifs were constructed on the surface will be explored in future 
-work and is shown in the supporting information.
+Tao et al. showed 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 at varying conditions (Ni 977, Si 111, etc).
+\cite{Williams:1994,Williams:1991,Pearl} Of the two systems 
+we examined, the Pt system showed a larger amount of 
+reconstruction when compared to the Au system. The amount 
+of reconstruction appears to be correlated to the amount of CO 
+adsorbed upon the surface.  We believe this is related to the 
+effect that adsorbate coverage has on edge breakup and surface 
+diffusion of adatoms. While both systems displayed step-edge 
+wandering, only the Pt surface underwent the doubling seen by 
+Tao et al., within the time scales we were modeling. Specifically, 
+only the 50~\% coverage Pt system was observed to have a 
+step-edge undergo a complete doubling in the time scales we 
+were able to monitor. This event encouraged us to allow that 
+specific system to run for much longer periods during which two 
+more double layers were created. The other systems, not displaying 
+any large scale changes of interest, were all stopped after running 
+for 40 ns in the microcanonical ensemble. Despite no observation 
+of double layer formation, the other Pt systems tended to show 
+more cumulative lateral movement of the step-edges when 
+compared to the Au systems. The 50\% Pt system is highlighted 
+in Figure \ref{fig:reconstruct} at various times along the simulation 
+showing the evolution of the system.
 
+The second reconstruction on the Pt(557) surface observed by 
+Tao involved the formation of triangular clusters that stretched 
+across the plateau between two step-edges. Neither system, within 
+our simulated time scales, experiences this reconstruction. A constructed 
+system in which the triangular motifs were constructed on the surface 
+will be explored in future work and is shown in the supporting information.
+
 \subsection{Dynamics}
-While atomistic-like simulations of stepped surfaces have been performed before \cite{}, they tend to be
-performed using Monte Carlo techniques\cite{Williams:1991,Williams:1994}. This allows them to efficiently sample the thermodynamic
-landscape but at the expense of ignoring the dynamics of the system. Previous work, using STM \cite{Pearl},
-has been able to visualize the coalescing of steps of (system). The time scale of the image acquisition, ~ 70 s/image 
-provides an upper bounds for the time required for the doubling to actually occur. While statistical treatments
-of step edges are adept at analyzing such systems, it is important to remember that the edges are made
-up of individual atoms and thus can be examined in numerous ways.
+While atomistic-like simulations of stepped surfaces have been 
+performed before, they tend to be performed using Monte Carlo 
+techniques\cite{Williams:1991,Williams:1994}. This allows them 
+to efficiently sample the equilibrium thermodynamic landscape 
+but at the expense of ignoring the dynamics of the system. Previous
+work by Pearl and Sibener\cite{Pearl}, using STM, has been able to 
+visualize the coalescing of steps of Ni(977). The time scale of the image 
+acquisition, $\sim$70 s/image provides an upper bounds for the time 
+required for the doubling to actually occur. Statistical treatments of step-edges
+are adept at analyzing such systems. However, in a system where 
+the number of steps is limited, examining the individual atoms that make 
+up the steps can provide useful information as well. 
 
+
 \subsubsection{Transport of surface metal atoms}
 %forcedSystems/stepSeparation
-The movement of a step edge is a cooperative effect arising from the individual movements of the atoms
-making up the step. An ideal metal surface displaying a low index facet (111, 100, 110) is unlikely to
-experience much surface diffusion because of the large energetic barrier to lift an atom out of the surface.
-For our surfaces however, the presence of step edges provide a source for mobile metal atoms. Breaking away
-from the step edge still imposes an energetic penalty around 40 kcal/mole, but is much less than lifting the same metal
-atom out from the surface,  > 60 kcal/mole, and the penalty lowers even further when CO is present in sufficient quantities
-on the surface, ~20 kcal/mole. Once an adatom exists on the surface, its barrier for diffusion is negligible ( < 4 kcal/mole)
-and is well able to explore its terrace. Atoms traversing terraces is more difficult, but can be overcome through a joining and lifting stage.
-By tracking the mobility of individual metal atoms on the Platinum and Gold surfaces we were able to determine
-the relative diffusion rates and how varying coverages of CO affected the rates. Close
-observation of the mobile metal atoms showed that they were typically in equilibrium with the
-step edges, constantly breaking apart and rejoining. Additionally, at times their motion was concerted and
-two or more atoms would be observed moving together across the surfaces. The primary challenge in quantifying
-the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
+The movement or wandering of a step-edge is a cooperative effect 
+arising from the individual movements, primarily through surface 
+diffusion, of the atoms making up the step. An ideal metal surface 
+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 
+on higher-index surfaces provide a source for mobile metal atoms. 
+Breaking away from the step-edge on a clean surface still imposes an 
+energetic penalty around $\sim$~40 kcal/mole, but is much less than lifting 
+the same metal atom out from the surface,  \textgreater~60 kcal/mole, and 
+the penalty lowers even further when CO is present in sufficient quantities 
+on the surface. For certain tested distributions of CO, the penalty was lowered 
+to $\sim$~20 kcal/mole. Once an adatom exists on the surface, its barrier for 
+diffusion is negligible ( \textless~4 kcal/mole) and is well able to explore the 
+terrace before potentially rejoining its original step-edge or becoming a part 
+of a different edge. Atoms traversing separate terraces is a more difficult 
+process, but can be overcome through a joining and lifting stage which is 
+examined in the discussion section. By tracking the mobility of individual 
+metal atoms on the Pt and Au surfaces we were able to determine the relative 
+diffusion rates and how varying coverages of CO affected the rates. Close 
+observation of the mobile metal atoms showed that they were typically in 
+equilibrium with the step-edges, constantly breaking apart and rejoining. 
+At times their motion was concerted and two or more adatoms would be 
+observed moving together across the surfaces. The primary challenge in 
+quantifying the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
 
-A particle was considered mobile once it had traveled more than 2~\AA~ between saved configurations
-of the system (10-100 ps). An atom that was truly mobile would typically travel much greater than this, but
-the 2~\AA~ cutoff was to prevent the in-place vibrational movement of atoms from being included in the analysis.
-Since diffusion on  a surface is strongly affected by local structures, in this case the presence of single and double
-layer step edges, the diffusion parallel to the step edges was determined separately from the diffusion perpendicular
-to these edges. The parallel and perpendicular diffusion constants are shown in figure \ref{fig:diff}.
+A particle was considered mobile once it had traveled more than 2~\AA~
+between saved configurations of the system (10-100 ps). An atom that was 
+truly mobile would typically travel much greater than this, but the 2~\AA~ cutoff 
+was to prevent the in-place vibrational movement of non-surface atoms from 
+being included in the analysis. 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. This led us to compute 
+those diffusions separately as seen in Figure \ref{fig:diff}.
 
 \subsubsection{Double layer formation}
-The increased amounts of diffusion on Pt at the higher CO coverages appears to play a role in the
-formation of double layers, seeing as how that was the only system within our observed simulation time
-that showed the formation. Despite this being the only system where this reconstruction occurs, three separate layers
-were formed over the extended run time of this system. As mentioned earlier, previous experimental work has given some insight into
-the upper bounds of the time required for enough atoms to move around to allow two steps to coalesce\cite{Williams:1991,Pearl}.
-As seen in figure \ref{fig:reconstruct}, the first appearance of a double layer, a nodal site, appears at 19 ns into
-the simulation. Within 12 ns, nearly half of the step has formed the double layer and by 86 ns, a smooth complete
-layer has formed. The double layer is complete by 37 ns but is a bit rough. 
-From the appearance of the first node to the initial doubling of the layers ignoring their roughness took ~20 ns.
-Another ~40 ns was necessary for the layer to completely straighten. The other two layers in this simulation form
-over a period of 22 ns and 42 ns respectively.
+The increased amounts of diffusion on Pt at the higher CO coverages appears
+to play a primary role in the formation of double layers, although this conclusion
+does not explain the 33\% coverage Pt system. On the 50\% system, three
+separate layers were formed over the extended run time of this system. As 
+mentioned earlier, previous experimental work has given some insight into the 
+upper bounds of the time required for enough atoms to move around to allow two 
+steps to coalesce\cite{Williams:1991,Pearl}. As seen in Figure \ref{fig:reconstruct},
+the first appearance of a double layer, a nodal site, appears at 19 ns into the 
+simulation. Within 12 ns, nearly half of the step has formed the double layer and 
+by 86 ns, a smooth complete layer has formed. The double layer is ``complete" by 
+37 ns but is a bit rough. From the appearance of the first node to the initial doubling 
+of the layers ignoring their roughness took $\sim$~20 ns. Another ~40 ns was 
+necessary for the layer to completely straighten. The other two layers in this 
+simulation form over a period of 22 ns and 42 ns respectively. Comparing this to 
+the upper bounds of the image scan, it is likely that aspects of this reconstruction 
+occur very quickly.
 
 %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
+  (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}
@@ -442,15 +491,14 @@ over a period of 22 ns and 42 ns respectively.
 \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
+  ($\mathbf{D}_{\perp}$) 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 going from approximately 7 nearest neighbors
-  to 5, as compared to the 3 of an adatom. Additionally, the observed
+  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 platinum atoms around and more importantly across
-  the surface. }
+  movement of the Pt atoms around and across the surface. }
 \label{fig:diff}
 \end{figure}
 
@@ -460,85 +508,86 @@ Pt (557) surface upon CO adsorption as shown by Tao et
 %Discussion
 \section{Discussion}
 In this paper we have shown that we were able to accurately 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 capture the dynamic processes inherent within this reconstruction. 
+Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
+were able to observe the dynamic processes necessary for this reconstruction. 
 
 \subsection{Mechanism for restructuring}
-The increased computational cost to examine this system using molecular dynamics rather than
-a Monte Carlo based approach was necessary so that our predictions on possible mechanisms
-and driving forces would have support not only from thermodynamic arguments but also from the 
-actual dynamics of the system.
+Comparing the results from simulation to those reported previously by 
+Tao et al.\cite{Tao:2010} the similarities in the Pt-CO system are quite 
+strong. As shown in Figure \ref{fig:reconstruct}, the simulated Pt 
+system under a CO atmosphere will restructure by doubling the terrace 
+heights. The restructuring occurs slowly, one to two Pt atoms at a time. 
+Looking at individual configurations of the system, the adatoms either 
+break away from the step-edge and stay on the lower terrace or they lift 
+up onto the higher terrace. Once ``free'' they will diffuse on the terrace 
+until reaching another step-edge or coming back to 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 meeting point tends to act as a focus 
+or growth point for the rest of the edge to meet up, akin to that of a zipper. 
+From the handful of cases where a double layer was formed during the 
+simulation, measuring from the initial appearance of a growth point, the 
+double layer tends to be fully formed within $\sim$~35 ns.
 
-Comparing the results from simulation to those reported previously by
-Tao et al. the similarities in the platinum and CO system are quite
-strong. As shown in figure \ref{fig:reconstruct}, the simulated platinum system under a CO
-atmosphere will restructure slightly by doubling the terrace
-heights. The restructuring appears to occur slowly, one to two
-platinum atoms at a time. Looking at individual snapshots, these
-adatoms tend to either rise on top of the plateau or break away from
-the step edge and then diffuse perpendicularly to the step direction
-until reaching another step edge. This combination of growth and decay
-of the step edges appears to be in somewhat of a state of dynamic
-equilibrium. However, once two previously separated edges meet as
-shown in figure 1.B, this point tends to act as a focus or growth
-point for the rest of the edge to meet up, akin to that of a
-zipper. From the handful of cases where a double layer was formed
-during the simulation, measuring from the initial appearance of a
-growth point, the double layer tends to be fully formed within
-$\sim$~35 ns.
+A number of possible mechanisms exist to explain the role of adsorbed 
+CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent 
+CO molecules adsorbed on the surface is one likely possibility.  However, 
+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 perhaps, this explanation 
+gains some weight.  The energetic repulsion between two CO located a 
+distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in 
+a  vertical orientation is 8.62 kcal/mole. 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/mole. Allowing the CO's to leave a purely vertical orientation 
+also quickly drops the repulsion, a minimum is reached at $\sim$24 degrees 
+of 6.2 kcal/mole. As mentioned above, the energy barrier for surface diffusion 
+of a Pt adatom is only 4 kcal/mole. So this repulsion between CO can help 
+increase the surface diffusion. However, the residence time of CO was 
+examined and while the majority of the CO is on or near the surface throughout 
+the run, it is extremely mobile. This mobility suggests that the CO are more 
+likely to shift their positions without necessarily dragging the Pt along with them.
 
-There are a number of possible mechanisms to explain the role of
-adsorbed CO in restructuring the Pt surface. Quadrupolar repulsion
-between adjacent CO molecules adsorbed on the surface is one
-possibility.  However, 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 however,
-this explanation gains some weight.  The energetic repulsion between two CO 
-located a distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in a 
-vertical orientation is 8.62 kcal/mole. 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/mole. SHOW A NUMBER FOR ROTATION.
-As mentioned above, the energy barrier for surface diffusion of a platinum adatom is only 4 kcal/mole. So this
-repulsion between CO can help increase the surface diffusion. However, the residence time of CO was examined
-and while the majority of the CO is on or near the surface throughout the run, it is extremely mobile. This mobility
-suggests that the CO are more likely to shift their positions without necessarily dragging the platinum 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 could have the effect of increasing surface mobility
+Pt atoms.  This would then have the effect of increasing surface mobility
 of these 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 platinum atoms was then examined to determine possible barriers. Because
-of the forced movement along a pre-defined reaction coordinate that may differ
+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:energies}. The presence of CO at suitable
-sites can lead to lowered barriers for platinum breaking apart from the step edge.
-Additionally, as highlighted in figure \ref{fig:lambda}, the presence of CO makes the
-burrowing and lifting nature favorable, whereas without CO, the process is neutral
+are displayed in Table \ref{tab:energies}. 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.
 
 %lambda progression of Pt -> shoving its way into the step
 \begin{figure}[H]
 \includegraphics[width=\linewidth]{lambdaProgression_atopCO.png}
-\caption{A model system of the Pt 557 surface was used as the framework for a reaction coordinate.
-Various numbers, placements, and rotations of CO were examined. The one displayed was a 
-representative sample. As shown in Table , relative to the energy at 0\% there is a slight decrease
-upon insertion of the platinum atom into the step edge along with the resultant lifting of the other
-platinum atom.}
+\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
+ 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}
 
 
 
 \subsection{Diffusion}
-As shown in the results section, the diffusion parallel to the step edge tends to be 
-much faster than that perpendicular to the step edge. Additionally, the coverage 
-of CO appears to play a slight role in relative rates of diffusion, as shown in figure \ref{fig:diff}
+As shown in the results section, the diffusion parallel to the step-edge tends to be 
+much larger than that perpendicular to the step-edge, likely because of 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 
+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. 
@@ -548,7 +597,11 @@ 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}
-\caption{Hi}
+%:
+\caption{(A)  0 ps, (B) 100 ps, (C) 1 ns, after the removal of CO. The presence of the CO
+ helped maintain the stability of the double layer and upon removal the two layers break
+ and begin separating. The separation is not a simple pulling apart however, rather 
+ there is a mixing of the lower and upper atoms at the edge.}
 \label{fig:breaking}
 \end{figure}
 
@@ -558,20 +611,26 @@ more likely a growth point is to be formed. 
 %Peaks!
 \begin{figure}[H]
 \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
-\caption{}
+\caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
+ of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with 
+ aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
 \label{fig:peaks}
 \end{figure}
 
+
+%Don't think I need this
 %clean surface...
-\begin{figure}[H]
-\includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
-\caption{}
+%\begin{figure}[H]
+%\includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
+%\caption{}
 
-\end{figure}
-\label{fig:clean}
-\section{Conclusion}
+%\end{figure}
+%\label{fig:clean}
 
 
+\section{Conclusion}
+In this work we have shown the reconstruction of the Pt(557) crystalline surface upon adsorption of CO in < $\mu s$. Only the highest coverage Pt system showed this initial reconstruction similar to that seen previously. The strong interaction between Pt and CO and the limited interaction between Au and CO helps explain the differences between the two systems. 
+
 %Things I am not ready to remove yet
 
 %Table of Diffusion Constants