--- trunk/COonPt/firstTry.tex	2012/12/05 22:20:07	3805
+++ trunk/COonPt/firstTry.tex	2012/12/07 19:16:39	3806
@@ -49,21 +49,21 @@ High-index surfaces of catalytically active metals are
 %
 
 
-High-index surfaces of catalytically active metals are an important area of exploration because they are typically more reactive than an ideal surface of the same metal. The greater number of low-coordinated surface atoms is likely responsible for this increased reactivity \cite{}. Additionally, the activity and specificity of many metals towards certain chemical processes has been shown to strongly depend on the structure of the surface \cite{}. Prior work has also shown that reaction conditions, such as high pressures and high temperatures are able to cause reconstructions of the metallic surface, either through changing the displayed surface facets or by changing the number and types of high-index sites available for reactions \cite{doi:10.1126/science.1197461,doi:10.1021/nn3015322, doi:10.1021/jp302379x}. A greater understanding of these high-index surfaces and the restructuring processes they undergo is needed as a prerequisite for more intelligent catalyst design. While current experimental work has started exploring systems at \emph{in situ} conditions, for a long time such experiments were limited to ideal surfaces in high vacuum. New techniques, such as ambient pressure XPS (AP-XPS) \cite{}, high-pressure XPS (HP-XPS) \cite{}, high-pressure STM \cite{}, environmental transmission electron microscopy (E-TEM) \cite{} and many others, are providing clearer pictures of the processes that are occurring on metal surfaces under these conditions. Nevertheless, all of these techniques still have limitations, especially in observing what is occurring at an atomic level. Theoretical models and simulations in combination with experiment have proven their worth in explaining the underlying reasons for some of these reconstructions \cite{}. 
+High-index surfaces of catalytically active metals are an important area of exploration because they are typically more reactive than an ideal surface of the same metal. The greater number of low-coordinated surface atoms is believed responsible for this increased reactivity \cite{}. Additionally, the activity and specificity of many metals towards certain chemical processes has been shown to strongly depend on the structure of the surface \cite{}. Prior work has also shown that reaction conditions, such as high pressures and high temperatures are able to cause reconstructions of the metallic surface, either through changing the displayed surface facets or by changing the number and types of high-index sites available for reactions \cite{doi:10.1126/science.1197461,doi:10.1021/nn3015322, doi:10.1021/jp302379x}. A greater understanding of these high-index surfaces and the restructuring processes they undergo is needed as a prerequisite for more intelligent catalyst design. While current experimental work has started exploring systems at \emph{in situ} conditions, for a long time such experiments were limited to ideal surfaces in high vacuum. New techniques, such as ambient pressure XPS (AP-XPS) \cite{}, high-pressure XPS (HP-XPS) \cite{}, high-pressure STM \cite{}, environmental transmission electron microscopy (E-TEM) \cite{} and many others, are providing clearer pictures of the processes that are occurring on metal surfaces under these conditions. Nevertheless, all of these techniques still have limitations, especially in observing what is occurring at an atomic level. Theoretical models and simulations in combination with experiment have proven their worth in explaining the underlying reasons for some of these reconstructions \cite{}. 
 \\
-By examining two different metal-CO systems the effect that the metal and the metal-CO interaction plays can be elucidated. Our first system is composed of Platinum and CO and has been the subject of many experimental and theoretical studies primarily because of Platinum's strong reactivity toward CO oxidation. The focus has primarily been on adsorption energies, preferred adsorption sites, and catalytic activities. The second system we examined is composed of Gold and CO. The Gold-CO interaction is much weaker than the Platinum-CO interaction and it seems likely that this difference in attraction would lead to differences in any potential surface reconstructions.
+By examining two different metal-CO systems the effect that the metal and the metal-CO interaction plays can be elucidated. Our first system is composed of platinum and CO and has been the subject of many experimental and theoretical studies primarily because of platinum's strong reactivity toward CO oxidation. The focus has primarily been on adsorption energies, preferred adsorption sites, and catalytic activities. The second system we examined is composed of gold and CO. The gold-CO interaction is much weaker than the platinum-CO interaction and it seems likely that this difference in attraction would lead to differences in any potential surface reconstructions.
 %It has also been a good test for new quantum methods because of the difficulty with modeling the preference CO has for the atop binding site \cite{doi:10.1021/jp002302t}. 
-%Now that dynamic surface events are known to play a role in many catalytic systems, additional research is being done to more closely examine many systems. Recent work by Tao et al. \cite{doi:10.1126/science.1182122} shows that a high-index platinum surface undergoes surface reconstructions when exposed to a small amount of CO, $\sim$~1 torr. Unexpectedly,  the reconstruction was metastable and reverted upon removal of the CO. Work by McCarthy et al. \cite{doi:10.1021/jp302379x} examined temperature programmed desorption's of CO from various Platinum samples and saw that species which had large amounts of low-coordinated surface atoms, highly sputtered surfaces or small nano particles, developed a higher temperature desorption peak, suggesting that binding of CO to the Platinum surface is strongly dependent on local geometry. 
+%Now that dynamic surface events are known to play a role in many catalytic systems, additional research is being done to more closely examine many systems. Recent work by Tao et al. \cite{doi:10.1126/science.1182122} shows that a high-index platinum surface undergoes surface reconstructions when exposed to a small amount of CO, $\sim$~1 torr. Unexpectedly,  the reconstruction was metastable and reverted upon removal of the CO. Work by McCarthy et al. \cite{doi:10.1021/jp302379x} examined temperature programmed desorption's of CO from various platinum samples and saw that species which had large amounts of low-coordinated surface atoms, highly sputtered surfaces or small nano particles, developed a higher temperature desorption peak, suggesting that binding of CO to the platinum surface is strongly dependent on local geometry. 
 
 
 
 
 
 \section{Simulation Methods}
-Our model systems are composed of approximately 4000 metal atoms cut along the 557 plane. This cut creates a stepped surface of 6x(111) surface plateaus separated by a single (100) atomic step height. The large number of low-coordination atoms along the step edges provide a suitable model for industrial catalysts which tend to have a prevalence of lower CN, i.e. more reactive, sites. Drawing from experimental conclusions, the reconstructions seen for the Pt 557 surface involve doubling of the step height and the formation of triangular motifs along the steps \cite{doi:10.1126/science.1182122}. To properly observe these changes, our system size needs to be greater than the periodic phenomena we are examining. The large size and the long time scales needed precluded us from using expensive quantum approaches. Thus, a forcefield describing the Metal-Metal, CO-CO, and CO-Metal interactions was parameterized. 
+Our model systems are composed of approximately 4000 metal atoms cut along the 557 plane. This cut creates a stepped surface of 6x(111) surface plateaus separated by a single (100) atomic step height. The abundance of low-coordination atoms along the step edges acts as a suitable model for industrial catalysts which tend to have a high concentration of high-index sites. Experimental work has shown that such surfaces are notable for reconstructing upon adsorption\cite{}. Reconstructions have been seen for the Pt 557 surface that involve doubling of the step height and further formation of nano clusters with a triangular motif \cite{doi:10.1126/science.1182122}. To shed insight on whether this reconstruction is limited to the platinum surface, simulations of gold under similar conditions will also be examined. To properly observe these changes, our system size needs to be greater than the periodic phenomena we are examining. The large size and the long time scales needed precluded us from using quantum approaches. Thus, a forcefield describing the Metal-Metal, CO-CO, and CO-Metal interactions was parameterized and the simulations were run using OpenMD\cite{} an open-source molecular dynamics package.
 %Metal
 \subsection{Metal}
-Recent metallic forcefields, inspired by density-functional theory, including EAM\cite{doi:10.1103/PhysRevB.29.6443, doi:10.1103/PhysRevB.33.7983} and QSC\cite{} have become very popular for modeling novel metallic systems.  What makes these forcefields more suitable for metals than their pair-wise predecessors is that they work with the total electron density of the system in a manner akin to DFT. The energy contributed by a single atom is a function of the total background electron density at the point where the atom is to be embedded. The density at any given point is well-approximated by a linear superposition of the electron density as contributed by all the other atoms in the system. This description of the embedding energy allows this method to more accurately treat surfaces, alloys, and other non-bulk systems. The function describing the energy as related to the density is parameterized for each element, rather than by solving the Kohn-Sham equations which is what allows this method to be used for large systems. The embedding energy is completely enclosed within the functional $F_i[\rho_{h,i}]$ which is dependent on the host density $\rho_{h}$ at atom $i$. The density at $i$ is the sum of the density as generated by the rest of the metal. The $\phi_{ij}$ term is a purely repulsive pair-pair interaction parameterized from effective charge repulsions. 
+Recent metallic forcefields, inspired by density-functional theory, including EAM\cite{doi:10.1103/PhysRevB.29.6443, doi:10.1103/PhysRevB.33.7983} and QSC\cite{} have become very popular for modeling novel metallic systems.  What makes these forcefields more suitable for metals than their pair-wise predecessors is that they work with the total electron density of the system in a manner akin to DFT. The energy contributed by a single atom is a function of the total background electron density at the point where the atom is to be embedded. The density at any given point is well-approximated by a linear superposition of the electron density as contributed by all the other atoms in the system. The function describing the energy as related to the density is parameterized for each element, rather than by solving the Kohn-Sham equations which is what allows this method to be used for large systems. The embedding energy is completely enclosed within the functional $F_i[\rho_{h,i}]$ which is dependent on the host density $\rho_{h}$ at atom $i$. The density at $i$ is the sum of the density as generated by the rest of the metal. The $\phi_{ij}$ term is a purely repulsive pair-pair interaction parameterized from effective charge repulsions. 
 %Can I increase the \sum size, not sure how...
 \begin{equation}
 E_{tot} = \sum_i F_i[\rho_{h,i}] + \frac{1}{2}\sum_i\sum_{j(\ne i)} \phi_{ij}(R_{ij})
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@@ -143,7 +143,7 @@ While an ideal metallic surface is unlikely to experie
 % Just results, leave discussion for discussion section
 \section{Results}
 \subsection{Diffusion}
-While an ideal metallic surface is unlikely to experience much surface diffusion, high-index surfaces have large numbers of low-coordinated atoms which have a much easier time overcoming the energetic barriers limiting diffusion, leading to easier surface reconstructions. Surface movement was divided between the parallel ($\parallel$) and perpendicular ($\perp$) directions relative to the step edge. We were then able to calculate diffusion constants as a function of CO coverage. As can be seen in Table 4, the presence and amount of CO directly affects the diffusion constants of surface Platinum atoms. The presence of two 50\% coverage systems is to show how the diffusion process is affected by time. The majority of the systems were run for approximately 50 ns while the half monolayer system been running continuously. The lowered diffusion constant at longer run times will be examined in-depth in the discussion section.
+While an ideal metallic surface is unlikely to experience much surface diffusion, high-index surfaces have large numbers of low-coordinated atoms which have a much easier time overcoming the energetic barriers limiting diffusion, leading to easier surface reconstructions. Surface movement was divided between the parallel ($\parallel$) and perpendicular ($\perp$) directions relative to the step edge. We were then able to calculate diffusion constants as a function of CO coverage. As can be seen in Table 4, the presence and amount of CO directly affects the diffusion constants of surface platinum atoms. The presence of two 50\% coverage systems is to show how the diffusion process is affected by time. The majority of the systems were run for approximately 50 ns while the half monolayer system been running continuously. The lowered diffusion constant at longer run times will be examined in-depth in the discussion section.
 
 %Table of Diffusion Constants
 %Add gold?M
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@@ -173,7 +173,7 @@ Comparing the results from simulation to those reporte
 
 %Discussion
 \section{Discussion}
-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 1, 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.
+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 1, 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.
 
 \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 Table 4. 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. One driving force behind this reconstruction appears to be the lowering of surface energy that occurs by doubling the terrace widths. (I'm not really proving this... I have the surface flatness to show it, but surface energy?)
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