--- trunk/COonPt/firstTry.tex	2013/03/20 17:50:18	3885
+++ trunk/COonPt/COonPtAu.tex	2013/03/21 15:28:49	3887
@@ -1,45 +1,14 @@
 \documentclass[journal = jpccck, manuscript = article]{achemso}
 \setkeys{acs}{usetitle = true}
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-
 \title{Molecular Dynamics simulations of the surface reconstructions
   of Pt(557) and Au(557) under exposure to CO}
 
@@ -78,7 +47,7 @@
 \begin{abstract}
   The mechanism and dynamics of surface reconstructions of Pt(557) and
   Au(557) exposed to various coverages of carbon monoxide (CO) were
-  investigated using molecular dynamics simulations. Metal-CO
+  investigated using molecular dynamics simulations.  Metal-CO
   interactions were parameterized from experimental data and
   plane-wave Density Functional Theory (DFT) calculations.  The large
   difference in binding strengths of the Pt-CO and Au-CO interactions
@@ -87,7 +56,10 @@
   wandering and step doubling were investigated on the Pt(557)
   surface.  We find that the energetics of CO adsorbed to the surface
   can explain the step-doubling reconstruction observed on Pt(557) and
-  the lack of such a reconstruction on the Au(557) surface.
+  the lack of such a reconstruction on the Au(557) surface.  However,
+  more complicated reconstructions into triangular clusters that have
+  been seen in recent experiments were not observed in these
+  simulations.
 \end{abstract}
 
 \newpage
@@ -119,39 +91,42 @@ This work is an investigation into the mechanism and t
 reversible restructuring under exposure to moderate pressures of
 carbon monoxide.\cite{Tao:2010}
 
-This work is an investigation into the mechanism and timescale for the Pt(557) \& Au(557)
-surface restructuring using molecular simulations.  Since the dynamics
-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.
-Since restructuring typically occurs 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
-to undergo a large scale reconstruction under certain conditions.\cite{Tao:2010} 
-The Au(557) surface, because of a weaker interaction with CO, is less 
-likely to undergo this kind of reconstruction. However, Peters {\it et al}.\cite{Peters:2000} 
-and Piccolo {\it et al}.\cite{Piccolo:2004} have both observed CO-induced 
-reconstruction of a Au(111) surface. Peters {\it et al}. saw a relaxation to the 
-22 x $\sqrt{3}$ cell. They argued that only a few Au atoms
-become adatoms, limiting the stress of this reconstruction, while 
-allowing the rest to relax and approach the ideal (111) 
-configuration. They did not see the usual herringbone pattern on Au(111) being greatly 
-affected by this relaxation. Piccolo {\it et al}. on the other hand, did see a 
-disruption of the herringbone pattern as CO was adsorbed to the 
-surface. Both groups suggested that the preference CO shows for 
-low-coordinated Au atoms was the primary driving force for the reconstruction.
+This work is an investigation into the mechanism and timescale for the
+Pt(557) \& Au(557) surface restructuring using molecular simulation.
+Since the dynamics 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.  Since restructuring typically
+occurs 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 to undergo a
+large scale reconstruction under certain conditions.\cite{Tao:2010}
+The Au(557) surface, because of weaker interactions with CO, is less
+likely to undergo this kind of reconstruction. However, Peters {\it et
+  al}.\cite{Peters:2000} and Piccolo {\it et al}.\cite{Piccolo:2004}
+have both observed CO-induced modification of reconstructions to the
+Au(111) surface. Peters {\it et al}. observed the Au(111)-($22 \times
+\sqrt{3}$) ``herringbone'' reconstruction relaxing slightly under CO
+adsorption. They argued that only a few Au atoms become adatoms,
+limiting the stress of this reconstruction, while allowing the rest to
+relax and approach the ideal (111) configuration.  Piccolo {\it et
+  al}. on the other hand, saw a more significant disruption of the
+Au(111)-($22 \times \sqrt{3}$) herringbone pattern as CO adsorbed on
+the surface. Both groups suggested that the preference CO shows for
+low-coordinated Au atoms was the primary driving force for the
+relaxation.  Although the Au(111) reconstruction was not the primary
+goal of our work, the classical models we have fit may be of future
+use in simulating this reconstruction.
 
-
-
 %Platinum molecular dynamics
 %gold molecular dynamics
 
 \section{Simulation Methods}
-The challenge in modeling any solid/gas interface is the
-development of a sufficiently general yet computationally tractable
-model of the chemical interactions between the surface atoms and
-adsorbates.  Since the interfaces involved are quite large (10$^3$ -
-10$^4$ atoms) and respond slowly to perturbations, {\it ab initio}
+The challenge in modeling any solid/gas interface is the development
+of a sufficiently general yet computationally tractable model of the
+chemical interactions between the surface atoms and adsorbates.  Since
+the interfaces involved are quite large (10$^3$ - 10$^4$ atoms), have
+many electrons, and respond slowly to perturbations, {\it ab initio}
 molecular dynamics
 (AIMD),\cite{KRESSE:1993ve,KRESSE:1993qf,KRESSE:1994ul} Car-Parrinello
 methods,\cite{CAR:1985bh,Izvekov:2000fv,Guidelli:2000fy} and quantum
@@ -163,8 +138,8 @@ Au-Au and Pt-Pt interactions.\cite{Foiles86} The CO wa
 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{Foiles86} The CO was modeled using a rigid
-three-site model developed by Straub and Karplus for studying
+Au-Au and Pt-Pt interactions.\cite{Foiles86} 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.
   
@@ -176,13 +151,13 @@ 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}.\cite{Ercolessi88} is among the
-fastest of these density functional approaches. In
-all of these models, atoms are treated as a positively charged
-core with a radially-decaying valence electron distribution. To
-calculate the energy for embedding the core at a particular location,
-the electron density due to the valence electrons at all of the other
-atomic sites is computed at atom $i$'s location,
+parameter sets. The glue model of Ercolessi {\it et
+  al}.\cite{Ercolessi88} is among the fastest of these density
+functional approaches. In all of these models, atoms are treated as a
+positively charged core with a radially-decaying valence electron
+distribution. To calculate the energy for embedding the core at a
+particular location, the electron density due to the valence electrons
+at all of the other atomic sites is computed at atom $i$'s location,
 \begin{equation*}
 \bar{\rho}_i = \sum_{j\neq i} \rho_j(r_{ij})
 \end{equation*}
@@ -213,41 +188,40 @@ dynamics.\cite{Shibata:2002hh,mishin02:b2nial,zope03:t
 melting,\cite{Belonoshko00,sankaranarayanan:155441,Sankaranarayanan:2005lr}
 fracture,\cite{Shastry:1996qg,Shastry:1998dx,mishin01:cu} crack
 propagation,\cite{BECQUART:1993rg,Rifkin1992} and alloying
-dynamics.\cite{Shibata:2002hh,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni} One of EAM's strengths
-is its sensitivity to small changes in structure. This arises
-because interactions
-up to the third nearest neighbor were taken into account in the parameterization.\cite{Voter95a}
-Comparing that to the glue model of Ercolessi {\it et al}.\cite{Ercolessi88}
-which is only parameterized up to the nearest-neighbor
-interactions, EAM is a suitable choice for systems where 
-the bulk properties are of secondary importance to low-index 
-surface structures. Additionally, the similarity of EAM's functional 
-treatment of the embedding energy to standard density functional 
-theory (DFT) makes fitting DFT-derived cross potentials with adsorbates somewhat easier.
+dynamics.\cite{Shibata:2002hh,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}
+One of EAM's strengths is its sensitivity to small changes in
+structure. This is due to the inclusion of up to the third nearest
+neighbor interactions during fitting of the parameters.\cite{Voter95a}
+In comparison, the glue model of Ercolessi {\it et
+  al}.\cite{Ercolessi88} was only parameterized to include
+nearest-neighbor interactions, EAM is a suitable choice for systems
+where the bulk properties are of secondary importance to low-index
+surface structures. Additionally, the similarity of EAM's functional
+treatment of the embedding energy to standard density functional
+theory (DFT) makes fitting DFT-derived cross potentials with
+adsorbates somewhat easier.
 
-
-
-
-
 \subsection{Carbon Monoxide model}
-Previous explanations for the surface rearrangements center on
-the large linear quadrupole moment of carbon monoxide.\cite{Tao:2010}  
-We used a model first proposed by Karplus and Straub to study
-the photodissociation of CO from myoglobin because it reproduces 
-the quadrupole moment well.\cite{Straub} The Straub and
-Karplus model treats CO as a rigid three site molecule with a massless M
-site at the molecular center of mass. The geometry and interaction 
-parameters are reproduced in Table~\ref{tab:CO}. The effective 
-dipole moment, calculated from the assigned charges, is still
-small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is close
-to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum 
+Previous explanations for the surface rearrangements center on the
+large linear quadrupole moment of carbon monoxide.\cite{Tao:2010} We
+used a model first proposed by Karplus and Straub to study the
+photodissociation of CO from myoglobin because it reproduces the
+quadrupole moment well.\cite{Straub} The Straub and Karplus model
+treats CO as a rigid three site molecule with a massless
+charge-carrying ``M'' site at the center of mass. The geometry and
+interaction parameters are reproduced in Table~\ref{tab:CO}. The
+effective dipole moment, calculated from the assigned charges, is
+still small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is
+close to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum
 mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCOCalc}.
 %CO Table
 \begin{table}[H]
   \caption{Positions, Lennard-Jones parameters ($\sigma$ and
-    $\epsilon$), and charges for the CO-CO 
-    interactions in Ref.\bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA, energies are 
-    in kcal/mol, and charges are in atomic units.}
+    $\epsilon$), and charges for CO-CO 
+    interactions. Distances are in \AA, energies are 
+    in kcal/mol, and charges are in atomic units.  The CO model
+    from Ref.\bibpunct{}{}{,}{n}{}{,}
+    \protect\cite{Straub} was used without modification.}
 \centering
 \begin{tabular}{| c | c | ccc |}
 \hline
@@ -293,7 +267,7 @@ periodic supercell plane-wave basis approach, as imple
 The limited experimental data for CO adsorption on Au required refining the fits against plane-wave DFT calculations.
 Adsorption energies were obtained from gas-surface DFT calculations with a
 periodic supercell plane-wave basis approach, as implemented in the
-{\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores were
+Quantum ESPRESSO package.\cite{QE-2009} Electron cores were
 described with the projector augmented-wave (PAW)
 method,\cite{PhysRevB.50.17953,PhysRevB.59.1758} with plane waves
 included to an energy cutoff of 20 Ry. Electronic energies are
@@ -317,15 +291,15 @@ an effect on  binding energies and binding site prefer
 are shown in Table~\ref{tab:co_parameters} and the binding energies on the 
 (111) surfaces are displayed in Table~\ref{tab:co_energies}.  Charge transfer
 and polarization are neglected in this model, although these effects could have 
-an effect on  binding energies and binding site preferences.
+an effect on binding energies and binding site preferences.
 
 %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
-    interactions are modeled with Lennard-Jones potentials. While the
-    metal-O interactions were fit to Morse
+  \caption{Parameters for the metal-CO cross-interactions. Metal-C
+    interactions are modeled with Lennard-Jones potentials, while the
+    metal-O interactions were fit to broad Morse
     potentials.  Distances are given in \AA~and energies in kcal/mol. }
 \centering
 \begin{tabular}{| c | cc | c | ccc |}
@@ -372,100 +346,100 @@ The different bulk melting temperatures predicted by E
 1200~K were performed to confirm the relative
 stability of the surfaces without a CO overlayer.  
 
-The different bulk melting temperatures predicted by EAM (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 
-temperatures when no CO was present, but experienced increased surface 
-mobility on addition of CO. Each surface was then dosed with different concentrations of CO
-that was initially placed in the vacuum region.  Upon full adsorption,
-these concentrations correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
-coverage. Higher coverages resulted in the formation of a double layer of CO,
-which introduces artifacts that are not relevant to (557) reconstruction.
-Because of the difference in binding energies, nearly all of the CO was bound to the Pt surface, while
-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 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 Pt of the
-systems exceeded 200~ns.  Simulations were carried out using the open
-source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,openmd}
+The different bulk melting temperatures predicted by EAM
+(1345~$\pm$~10~K for Au\cite{Au:melting} and $\sim$~2045~K for
+Pt\cite{Pt:melting}) suggest that any reconstructions 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 temperatures when no CO was present, but experienced
+increased surface mobility on addition of CO. Each surface was then
+dosed with different concentrations of CO that was initially placed in
+the vacuum region.  Upon full adsorption, these concentrations
+correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface coverage. Higher
+coverages resulted in the formation of a double layer of CO, which
+introduces artifacts that are not relevant to (557) reconstruction.
+Because of the difference in binding energies, nearly all of the CO
+was bound to the Pt surface, while 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 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 Pt of the systems exceeded 200~ns.
+Simulations were carried out using the open source molecular dynamics
+package, OpenMD.\cite{Ewald,OOPSE,openmd}
 
 
-
-
 % RESULTS
 %
 \section{Results}
 \subsection{Structural remodeling}
-The bare metal surfaces experienced minor roughening of the 
-step-edge because of the elevated temperatures, but the (557) 
-face was stable throughout the simulations. The surface of both 
-systems, upon dosage of CO, began to undergo extensive remodeling 
-that was not observed in the bare systems. Reconstructions of 
-the Au systems were limited to breakup of the step-edges and 
-some step wandering. The lower coverage Pt systems experienced 
-similar restructuring but to a greater extent. The 50\% coverage 
-Pt system was unique among our simulations in that it formed 
-well-defined and stable double layers through step coalescence, 
-similar to results reported by Tao {\it et al}.\cite{Tao:2010}
+The bare metal surfaces experienced minor roughening of the step-edge
+because of the elevated temperatures, but the (557) face was stable
+throughout the simulations. The surfaces of both systems, upon dosage
+of CO, began to undergo extensive remodeling that was not observed in
+the bare systems. Reconstructions of the Au systems were limited to
+breakup of the step-edges and some step wandering. The lower coverage
+Pt systems experienced similar step edge wandering but to a greater
+extent. The 50\% coverage Pt system was unique among our simulations
+in that it formed well-defined and stable double layers through step
+coalescence, similar to results reported by Tao {\it et
+  al}.\cite{Tao:2010}
 
-
 \subsubsection{Step wandering}
-The 0\% coverage surfaces for both metals showed minimal 
-step-wandering at their respective temperatures. As the CO 
-coverage increased however, the mobility of the surface atoms, 
-described through adatom diffusion and step-edge wandering, 
-also increased.  Except for the 50\% Pt system where step 
-coalescence occurred, the step-edges in the other simulations 
-preferred 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 {\it 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 is caused by an entropic barrier that arises from 
-the fact that steps cannot cross over one another. This entropic 
-repulsion does not completely define the interactions between 
-steps, however, so it is possible to observe step coalescence 
-on some surfaces.\cite{Williams:1991} The presence and 
-concentration of adsorbates, as shown in this work, can 
-affect step-step interactions, potentially leading to a new 
-surface structure as the thermodynamic equilibrium.
+The bare surfaces for both metals showed minimal step-wandering at
+their respective temperatures. As the CO coverage increased however,
+the mobility of the surface atoms, described through adatom diffusion
+and step-edge wandering, also increased.  Except for the 50\% Pt
+system where step coalescence occurred, the step-edges in the other
+simulations preferred 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 {\it 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 is caused by an entropic barrier
+that arises from the fact that steps cannot cross over one
+another. This entropic repulsion does not completely define the
+interactions between steps, however, so it is possible to observe step
+coalescence on some surfaces.\cite{Williams:1991} The presence and
+concentration of adsorbates, as shown in this work, can affect
+step-step interactions, potentially leading to a new surface structure
+as the thermodynamic equilibrium.
 
 \subsubsection{Double layers}
-Tao {\it et al}.\cite{Tao:2010} have shown experimentally that the Pt(557) surface 
-undergoes two separate reconstructions upon CO adsorption.
-The first involves a doubling of the step height and plateau length. 
-Similar behavior has been seen on a number of surfaces 
-at varying conditions, including Ni(977) and Si(111).\cite{Williams:1994,Williams:1991,Pearl} 
-Of the two systems we examined, the Pt system showed a greater 
-propensity for reconstruction  
-because of the larger surface mobility and the greater extent of step wandering. 
-The amount of reconstruction was 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. Only the 50\% Pt surface underwent the 
-doubling seen by Tao {\it et al}.\cite{Tao:2010} within the time scales studied here. 
-Over a longer time scale (150~ns) two more double layers formed 
-on this surface. Although double layer formation did not occur 
-in the other Pt systems, they exhibited more step-wandering and 
-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 double layer step-edge.
+Tao {\it et al}.\cite{Tao:2010} have shown experimentally that the
+Pt(557) surface undergoes two separate reconstructions upon CO
+adsorption.  The first involves a doubling of the step height and
+plateau length.  Similar behavior has been seen on a number of
+surfaces at varying conditions, including Ni(977) and
+Si(111).\cite{Williams:1994,Williams:1991,Pearl} Of the two systems we
+examined, the Pt system showed a greater propensity for reconstruction
+because of the larger surface mobility and the greater extent of step
+wandering.  The amount of reconstruction was 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. Only the 50\% Pt surface
+underwent the doubling seen by Tao {\it et al}.\cite{Tao:2010} within
+the time scales studied here.  Over a longer time scale (150~ns) two
+more double layers formed on this surface. Although double layer
+formation did not occur in the other Pt systems, they exhibited more
+step-wandering and 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 double
+layer step-edge.
 
-The second reconstruction observed by 
-Tao {\it et al}.\cite{Tao:2010} involved the formation of triangular clusters that stretched 
-across the plateau between two step-edges. Neither metal, within 
-the 40~ns time scale or the extended simulation time of 150~ns for 
-the 50\% Pt system, experienced this reconstruction.
+The second reconstruction observed by Tao {\it et al}.\cite{Tao:2010}
+involved the formation of triangular clusters that stretched across
+the plateau between two step-edges. Neither of the simulated metal
+interfaces, within the 40~ns time scale or the extended time of 150~ns
+for the 50\% Pt system, experienced this reconstruction.
 
 %Evolution of surface
 \begin{figure}[H]
 \includegraphics[width=\linewidth]{EPS_ProgressionOfDoubleLayerFormation}
-\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
+\caption{The Pt(557) / 50\% CO interface upon exposure to the CO: (a)
+  258~ps, (b) 19~ns, (c) 31.2~ns, and (d) 86.1~ns after
+  exposure. 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.}
@@ -473,65 +447,74 @@ Previous experimental work by Pearl and Sibener\cite{P
 \end{figure}
 
 \subsection{Dynamics}
-Previous experimental work by Pearl and Sibener\cite{Pearl}, 
-using STM, has been able to capture the coalescence 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. By utilizing Molecular Dynamics we are able to probe 
-the dynamics of these reconstructions at elevated temperatures 
-and in this section we provide data on the timescales for transport 
-properties, e.g. diffusion and layer formation time.
+Previous experimental work by Pearl and Sibener\cite{Pearl}, using
+STM, has been able to capture the coalescence 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. By
+utilizing Molecular Dynamics we are able to probe the dynamics of
+these reconstructions at elevated temperatures and in this section we
+provide data on the timescales for transport properties,
+e.g. diffusion and layer formation time.
 
 
 \subsubsection{Transport of surface metal atoms}
 %forcedSystems/stepSeparation
-The wandering of a step-edge is a cooperative effect 
-arising from the individual movements of the atoms making up the steps. 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 and other surface features
-on higher-index facets provides a lower energy source for mobile metal atoms. 
-Single-atom break-away from a step-edge on a clean surface still imposes an 
-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 Discussion, 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 
-becoming a part of a different edge. It is an energetically unfavorable process with a high barrier for an atom 
-to traverse to a separate terrace although the presence of CO can lower the 
-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 
-equilibrium with the step-edges. 
-At times, their motion was concerted and two or more adatoms would be 
-observed moving together across the surfaces. 
 
-A particle was considered ``mobile'' once it had traveled more than 2~\AA~
-between saved configurations of the system (typically 10-100 ps). A mobile atom 
-would typically travel much greater distances than this, but the 2~\AA~cutoff 
-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 larger than 
-the diffusion perpendicular to these edges. Parallel and perpendicular
-diffusion constants are shown in Figure \ref{fig:diff}.
+The wandering of a step-edge is a cooperative effect arising from the
+individual movements of the atoms making up the steps. 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 and other surface features on higher-index
+facets provides a lower energy source for mobile metal atoms.  Using
+our potential model, single-atom break-away from a step-edge on a
+clean surface still imposes an energetic penalty around
+$\sim$~45~kcal/mol, but this is certainly 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
+energetic penalty can fall to as low as $\sim$~20~kcal/mol. The
+configurations that create these lower barriers are detailed in the
+discussion section below.
 
+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 becoming a part of a different edge. It is an
+energetically unfavorable process with a high barrier for an atom to
+traverse to a separate terrace although the presence of CO can lower
+the 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 equilibrium
+with the step-edges.  At times, their motion was concerted, and two or
+more adatoms would be observed moving together across the surfaces.
+
+A particle was considered ``mobile'' once it had traveled more than
+2~\AA~ between saved configurations of the system (typically 10-100
+ps). A mobile atom would typically travel much greater distances than
+this, but the 2~\AA~cutoff 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 the presence
+of single and double layer 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}.  Diffusion parallel to the step-edge is higher
+than diffusion perpendicular to the edge because of the lower energy
+barrier associated with sliding along an edge compared to breaking
+away to form an isolated adatom.
+
 %Diffusion graph
 \begin{figure}[H]
 \includegraphics[width=\linewidth]{Portrait_DiffusionComparison_1}
 \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 }
+  surface coverage.  The two reported diffusion constants for the 50\%
+  Pt system correspond to a 20~ns period before the formation of the
+  double layer (upper points), and to the full 40~ns sampling period
+  (lower points).}
 \label{fig:diff}
 \end{figure}
 
@@ -543,13 +526,12 @@ now been buried resulting in a smaller reported diffus
 at the earliest times in the simulations. Following double layer formation, 
 however, there is a precipitous drop in adatom diffusion. As the double 
 layer forms, many atoms that had been tracked for mobility data have 
-now been buried resulting in a smaller reported diffusion constant. A
+now been buried, resulting in a smaller reported diffusion constant. A
 secondary effect of higher coverages is CO-CO cross interactions that
 lower the effective mobility of the Pt adatoms that are bound to each CO.
 This effect would become evident only at higher coverages. A detailed
 account of Pt adatom energetics follows in the Discussion.
  
-
 \subsubsection{Dynamics of double layer formation}
 The increased diffusion on Pt at the higher CO coverages is the primary 
 contributor to double layer formation. However, this is not a complete 
@@ -609,22 +591,25 @@ adsorption for example, this explanation would gain cr
 possibility.  However, the quadrupole-quadrupole interaction is
 short-ranged and is attractive for some orientations.  If the CO
 molecules are ``locked'' in a vertical orientation, through atop
-adsorption for example, this explanation would gain credence. The
-calculated energetic repulsion between two CO molecules 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 to the
-second nearest-neighbor distance of 4.8~\AA~drops the repulsion to
-nearly 0. Allowing the CO to rotate away from a purely vertical
-orientation also lowers the repulsion. When the carbons are locked at
-a distance of 2.77~\AA, a minimum of 6.2 kcal/mol is reached when the
-angle between the 2 CO is $\sim$24\textsuperscript{o}.  The calculated
+adsorption for example, this explanation would gain credence. Within
+the framework of our classical potential, the calculated energetic
+repulsion between two CO molecules 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 to the second
+nearest-neighbor distance of 4.8~\AA~drops the repulsion to nearly
+0. Allowing the CO to rotate away from a purely vertical orientation
+also lowers the repulsion. When the carbons are locked at a distance
+of 2.77~\AA, a minimum of 6.2 kcal/mol is reached when the angle
+between the 2 CO is $\sim$24\textsuperscript{o}.  The calculated
 barrier for surface diffusion of a Pt adatom is only 4 kcal/mol, so
-repulsion between adjacent CO molecules bound to Pt could increase the
-surface diffusion. However, the residence time of CO on Pt suggests
-that the CO molecules are extremely mobile, with diffusion constants 40
-to 2500 times larger than surface Pt atoms. This mobility suggests
-that the CO molecules jump between different Pt atoms throughout the
-simulation, but can stay bound for significant periods of time.
+repulsion between adjacent CO molecules bound to Pt could indeed
+increase the surface diffusion. However, the residence time of CO on
+Pt suggests that the CO molecules are extremely mobile, with diffusion
+constants 40 to 2500 times larger than surface Pt atoms. This mobility
+suggests that the CO molecules jump between different Pt atoms
+throughout the simulation.  However, they do stay bound to individual
+Pt atoms for long enough to modify the local energy landscape for the
+mobile adatoms.
 
 A different interpretation of the above mechanism which takes the
 large mobility of the CO into account, would be in the destabilization
@@ -641,17 +626,17 @@ step-edge atoms. Step-edge breakup by continuous singl
 populations. The roughening is present to a lesser extent on surfaces
 with lower CO coverage (and even on the bare surfaces), although in
 these cases it is likely due to random fluctuations that squeeze out
-step-edge atoms. Step-edge breakup by continuous single-atom
-translations (as suggested by these energy curves) is probably a
-worst-case scenario.  Multistep mechanisms in which an adatom moves
-laterally on the surface after being ejected would be more
-energetically favorable.  This would leave the adatom alongside the
-ledge, providing it with 5 nearest neighbors.  While fewer than the 7
-neighbors it had as part of the step-edge, it keeps more Pt neighbors
-than the 3 an isolated adatom would have on the terrace. In this
-proposed mechanism, the CO quadrupolar repulsion still plays a role in
-the initial roughening of the step-edge, but not in any long-term
-bonds with individual Pt atoms.  Higher CO coverages create more
+step-edge atoms. Step-edge breakup by direct single-atom translations
+(as suggested by these energy curves) is probably a worst-case
+scenario.  Multistep mechanisms in which an adatom moves laterally on
+the surface after being ejected would be more energetically favorable.
+This would leave the adatom alongside the ledge, providing it with
+five nearest neighbors.  While fewer than the seven neighbors it had
+as part of the step-edge, it keeps more Pt neighbors than the three
+neighbors an isolated adatom has on the terrace. In this proposed
+mechanism, the CO quadrupolar repulsion still plays a role in the
+initial roughening of the step-edge, but not in any long-term bonds
+with individual Pt atoms.  Higher CO coverages create more
 opportunities for the crowded CO configurations shown in Figure
 \ref{fig:SketchGraphic}, and this is likely to cause an increased
 propensity for step-edge breakup.
@@ -660,12 +645,12 @@ propensity for step-edge breakup.
 \begin{figure}[H]
 \includegraphics[width=\linewidth]{COpaths}
 \caption{Configurations used to investigate the mechanism of step-edge
-  breakup on Pt(557). In each case, the central (starred) atom is
+  breakup on Pt(557). In each case, the central (starred) atom was
   pulled directly across the surface away from the step edge.  The Pt
   atoms on the upper terrace are colored dark grey, while those on the
   lower terrace are in white.  In each of these configurations, some
-  number of the atoms (highlighted in blue) had a CO molecule bound in
-  a vertical atop position.  The energies of these configurations as a
+  of the atoms (highlighted in blue) had CO molecules bound in the
+  vertical atop position.  The energies of these configurations as a
   function of central atom displacement are displayed in Figure
   \ref{fig:SketchEnergies}.}
 \label{fig:SketchGraphic}
@@ -677,10 +662,10 @@ propensity for step-edge breakup.
 \caption{Energies for displacing a single edge atom perpendicular to
   the step edge as a function of atomic displacement. Each of the
   energy curves corresponds to one of the labeled configurations in
-  Figure \ref{fig:SketchGraphic}, and are referenced to the
-  unperturbed step-edge.  Certain arrangements of bound CO (notably
-  configurations g and h) can lower the energetic barrier for creating
-  an adatom relative to the bare surface (configuration a).}
+  Figure \ref{fig:SketchGraphic}, and the energies are referenced to
+  the unperturbed step-edge.  Certain arrangements of bound CO
+  (notably configurations g and h) can lower the energetic barrier for
+  creating an adatom relative to the bare surface (configuration a).}
 \label{fig:SketchEnergies}
 \end{figure}
 
@@ -695,20 +680,20 @@ original edge atom onto the higher terrace. A number o
 displacement of Pt atoms at the step edge. Figure \ref{fig:lambda}
 shows four points along a reaction coordinate in which a CO-bound
 adatom along the step-edge ``burrows'' into the edge and displaces the
-original edge atom onto the higher terrace. A number of events similar
-to this mechanism were observed during the simulations.  We predict an
-energetic barrier of 20~kcal/mol for this process (in which the
-displaced edge atom follows a curvilinear path into an adjacent 3-fold
-hollow site).  The barrier heights we obtain for this reaction
+original edge atom onto the higher terrace.  A number of events
+similar to this mechanism were observed during the simulations.  We
+predict an energetic barrier of 20~kcal/mol for this process (in which
+the displaced edge atom follows a curvilinear path into an adjacent
+3-fold hollow site).  The barrier heights we obtain for this reaction
 coordinate are approximate because the exact path is unknown, but the
 calculated energy barriers would be easily accessible at operating
 conditions.  Additionally, this mechanism is exothermic, with a final
 energy 15~kcal/mol below the original $\lambda = 0$ configuration.
 When CO is not present and this reaction coordinate is followed, the
-process is endothermic by 3~kcal/mol.  The difference in the relative 
+process is endothermic by 3~kcal/mol.  The difference in the relative
 energies for the $\lambda=0$ and $\lambda=1$ case when CO is present
 provides strong support for CO-mediated Pt-Pt interactions giving rise
-to the doubling reconstruction. 
+to the doubling reconstruction.
 
 %lambda progression of Pt -> shoving its way into the step
 \begin{figure}[H]
@@ -718,7 +703,7 @@ to the doubling reconstruction. 
   step edge and displaces an edge atom onto the upper terrace along a
   curvilinear path.  The approximate barrier for the process is
   20~kcal/mol, and the complete process is exothermic by 15~kcal/mol
-  in the presence of CO, but is endothermic by 3~kcal/mol without.}
+  in the presence of CO, but is endothermic by 3~kcal/mol without CO.}
 \label{fig:lambda}
 \end{figure}
 
@@ -726,7 +711,7 @@ by travelling to the terraces above of below their ori
 the cooperation of at least two distinct processes. For complete
 doubling of a layer to occur there must be a breakup of one
 terrace. These atoms must then ``disappear'' from that terrace, either
-by travelling to the terraces above of below their original levels.
+by travelling to the terraces above or below their original levels.
 The presence of CO helps explain mechanisms for both of these
 situations. There must be sufficient breakage of the step-edge to
 increase the concentration of adatoms on the surface and these adatoms
@@ -735,37 +720,36 @@ Once a double layer had formed on the 50\%~Pt system, 
 mechanisms working in concert lead to the formation of a double layer.
 
 \subsection{CO Removal and double layer stability}
-Once a double layer had formed on the 50\%~Pt system, it remained for
-the rest of the simulation time with minimal movement.  Random
-fluctuations that involved small clusters or divots were observed, but
-these features typically healed within a few nanoseconds.  Within our
-simulations, the formation of the double layer appeared to be
-irreversible and a double layer was never observed to split back into
-two single layer step-edges while CO was present. 
+Once the double layers had formed on the 50\%~Pt system, they remained
+stable for the rest of the simulation time with minimal movement.
+Random fluctuations that involved small clusters or divots were
+observed, but these features typically healed within a few
+nanoseconds.  Within our simulations, the formation of the double
+layer appeared to be irreversible and a double layer was never
+observed to split back into two single layer step-edges while CO was
+present.
 
 To further gauge the effect CO has on this surface, additional
 simulations were run starting from a late configuration of the 50\%~Pt
 system that had already formed double layers. These simulations then
-had their CO forcibly removed.  The double layer broke apart rapidly
-in these simulations, showing a well-defined edge-splitting after
-100~ps. Configurations of this system are shown in Figure
+had their CO molecules suddenly removed.  The double layer broke apart
+rapidly in these simulations, showing a well-defined edge-splitting
+after 100~ps. Configurations of this system are shown in Figure
 \ref{fig:breaking}. The coloring of the top and bottom layers helps to
-exhibit how much mixing the edges experience as they split. These
-systems were only examined for 10~ns, and within that time despite the
-initial rapid splitting, the edges only moved another few
-\AA~apart. It is possible that with longer simulation times, the (557)
-surface recovery observed by Tao {\it et al}.\cite{Tao:2010} could
-also be recovered.
+show how much mixing the edges experience as they split. These systems
+were only examined for 10~ns, and within that time despite the initial
+rapid splitting, the edges only moved another few \AA~apart. It is
+possible that with longer simulation times, the (557) surface recovery
+observed by Tao {\it et al}.\cite{Tao:2010} could also be recovered.
 
 %breaking of the double layer upon removal of CO
 \begin{figure}[H]
 \includegraphics[width=\linewidth]{EPS_doubleLayerBreaking}
-\caption{Dynamics of an established (111) double step after removal of
-  the adsorbed CO: (A) 0~ps, (B) 100~ps, and (C) 1~ns after the removal
-  of CO. The presence of the CO helped maintain the stability of the
-  double step.  Nearly immediately after the CO is removed, the step
-  edge reforms in a (100) configuration, which is also the step type
-  seen on clean (557) surfaces. The step separation involves
+\caption{Behavior of an established (111) double step after removal of
+  the adsorbed CO: (A) 0~ps, (B) 100~ps, and (C) 1~ns after the
+  removal of CO.  Nearly immediately after the CO is removed, the
+  step edge reforms in a (100) configuration, which is also the step
+  type seen on clean (557) surfaces. The step separation involves
   significant mixing of the lower and upper atoms at the edge.}
 \label{fig:breaking}
 \end{figure}
@@ -836,12 +820,20 @@ which are both necessary for double layer formation.
   Computing (CRC) at the University of Notre Dame.
 \end{acknowledgement}
 \newpage
-\bibliography{firstTryBibliography}
+\bibstyle{achemso}
+\bibliography{COonPtAu}
 %\end{doublespace}
 
 \begin{tocentry}
-A reconstructed Pt(557) surface after having been exposed to a dosage of CO equivalent to half a monolayer of coverage is observed to undergo a doubling of the step-edge height and terrace length.
-\includegraphics[height=3.5cm]{TOC_doubleLayer}
+\begin{wrapfigure}{l}{0.5\textwidth}
+\begin{center}
+\includegraphics[width=\linewidth]{TOC_doubleLayer}
+\end{center}
+\end{wrapfigure}
+A reconstructed Pt(557) surface after 86~ns exposure to a half a
+monolayer of CO.  The double layer that forms is a result of
+CO-mediated step-edge wandering as well as a burrowing mechanism that
+helps lift edge atoms onto an upper terrace.
 \end{tocentry}
 
 \end{document}
