--- trunk/COonPt/firstTry.tex	2013/03/15 12:51:01	3876
+++ trunk/COonPt/COonPtAu.tex	2013/03/21 15:28:49	3887
@@ -1,42 +1,14 @@
 \documentclass[journal = jpccck, manuscript = article]{achemso}
 \setkeys{acs}{usetitle = true}
 \usepackage{achemso}
-\usepackage{caption}
-\usepackage{float}
-\usepackage{geometry}
 \usepackage{natbib}
-\usepackage{setspace}
-\usepackage{xkeyval}
-%%%%%%%%%%%%%%%%%%%%%%%
-\usepackage{amsmath}
-\usepackage{amssymb}
-\usepackage{times}
-\usepackage{mathptm}
-\usepackage{setspace}
-\usepackage{endfloat}
-\usepackage{caption}
-\usepackage{tabularx}
-\usepackage{longtable}
-\usepackage{graphicx}
 \usepackage{multirow}
-\usepackage{multicol}
+\usepackage{wrapfig}
+%\mciteErrorOnUnknownfalse
 
 \usepackage[version=3]{mhchem}  % this is a great package for formatting chemical reactions
-% \usepackage[square, comma, sort&compress]{natbib}
 \usepackage{url}
-\pagestyle{plain} \pagenumbering{arabic} \oddsidemargin 0.0cm
-\evensidemargin 0.0cm \topmargin -21pt \headsep 10pt \textheight
-9.0in \textwidth 6.5in \brokenpenalty=10000
 
-% double space list of tables and figures
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-% \bibliographystyle{achemso}
-
 \title{Molecular Dynamics simulations of the surface reconstructions
   of Pt(557) and Au(557) under exposure to CO}
 
@@ -73,19 +45,21 @@ We examine surface reconstructions of Pt and Au(557) u
 
 
 \begin{abstract}
-We examine 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 large difference in binding 
-strengths of the metal-CO interactions was found to play a significant 
-role with regards to step-edge stability and adatom diffusion. A 
-small correlation between coverage and the diffusion constant 
-was also determined. The energetics of CO adsorbed to the surface 
-is sufficient to explain the reconstructions observed on the Pt 
-systems and the lack  of reconstruction of the Au systems.
-
+  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
+  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
+  was found to play a significant role in step-edge stability and
+  adatom diffusion constants.  Various mechanisms for CO-mediated step
+  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.  However,
+  more complicated reconstructions into triangular clusters that have
+  been seen in recent experiments were not observed in these
+  simulations.
 \end{abstract}
 
 \newpage
@@ -117,39 +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
-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 seen as less 
-likely to undergo this kind of reconstruction. However, Peters et al.\cite{Peters:2000} 
-and Piccolo et al.\cite{Piccolo:2004} have both observed CO-induced 
-reconstruction of a Au(111) surface. Peters 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 being greatly 
-affected by this relaxation. Piccolo 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$^6$ 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
@@ -161,8 +138,8 @@ Au-Au and Pt-Pt interactions\cite{EAM}. The CO was mod
 Coulomb potential.  For this work, we have used classical molecular
 dynamics with potential energy surfaces that are specifically tuned
 for transition metals.  In particular, we used the EAM potential for
-Au-Au and Pt-Pt interactions\cite{EAM}. The CO was modeled using a rigid
-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.
   
@@ -174,13 +151,13 @@ parameter sets. The glue model of Ercolessi et al. is 
 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 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
-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*}
@@ -207,45 +184,44 @@ properties,\cite{Chui:2003fk,Wang:2005qy,Medasani:2007
 The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen (QSC) potentials
 have all been widely used by the materials simulation community for
 simulations of bulk and nanoparticle
-properties,\cite{Chui:2003fk,Wang:2005qy,Medasani:2007uq}
+properties,\cite{Chui:2003fk,Wang:2005qy,Medasani:2007uq,mishin99:_inter}
 melting,\cite{Belonoshko00,sankaranarayanan:155441,Sankaranarayanan:2005lr}
-fracture,\cite{Shastry:1996qg,Shastry:1998dx} crack
-propagation,\cite{BECQUART:1993rg} and alloying
-dynamics.\cite{Shibata:2002hh} One of EAM's strengths
-is its sensitivity to small changes in structure. This arises
-from the original parameterization, where the interactions
-up to the third nearest neighbor were taken into account.\cite{Voter95a}
-Comparing that to the glue model of Ercolessi 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 EAMs functional 
-treatment of the embedding energy to standard density functional 
-theory (DFT) makes fitting DFT-derived cross potentials with adsorbates somewhat easier.
-\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
+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 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
@@ -272,12 +248,12 @@ et al.,\cite{Pons:1986} the Pt-C interaction was fit t
 position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}.
 The modified parameters yield binding energies that are slightly higher
 than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
-et al.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
-Lennard-Jones interaction to mimic strong, but short-ranged partial
+{\it 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 modeled with a Morse potential with a large
 equilibrium distance, ($r_o$).  These choices ensure that the C is preferred
-over O as the surface-binding atom. In most cases, the Pt-O parameterization contributes a weak
+over O as the surface-binding atom. In most geometries, the Pt-O parameterization contributes a weak
 repulsion which favors the atop site.  The resulting potential-energy
 surface suitably recovers the calculated Pt-C separation length
 (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
@@ -291,7 +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
@@ -314,17 +290,16 @@ and polarization are neglected in this model, although
 The parameters employed for the metal-CO cross-interactions in this work 
 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 are likely to
-affect binding energies and binding site preferences, and will be addressed in
-future work.
+and polarization are neglected in this model, although these effects could have 
+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 |}
@@ -360,7 +335,9 @@ dimensions of 57.4~x~51.9285~x~100~\AA.
 \subsection{Pt(557) and Au(557) metal interfaces}
 Our Pt system is an orthorhombic periodic box of dimensions
 54.482~x~50.046~x~120.88~\AA~while our Au system has 
-dimensions of 57.4~x~51.9285~x~100~\AA.
+dimensions of 57.4~x~51.9285~x~100~\AA. The metal slabs 
+are 9 and 8 atoms deep respectively, corresponding to a slab 
+thickness of $\sim$21~\AA~ for Pt and $\sim$19~\AA~for Au.
 The systems are arranged in a FCC crystal that have been cut
 along the (557) plane so that they are periodic in the {\it x} and
 {\it y} directions, and have been oriented to expose two aligned
@@ -369,104 +346,100 @@ The different bulk melting temperatures (1345~$\pm$~10
 1200~K were performed to confirm the relative
 stability of the surfaces without a CO overlayer.  
 
-The different bulk melting temperatures (1345~$\pm$~10~K for Au\cite{Au:melting}
-and $\sim$~2045~K for Pt\cite{Pt:melting}) suggest that any possible reconstruction should happen at
-different temperatures for the two metals.  The bare Au and Pt surfaces were
-initially run in the canonical (NVT) ensemble at 800~K and 1000~K
-respectively for 100 ps. The two surfaces were relatively stable at these 
-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}
+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 surfaces of both systems, upon dosage of CO, began 
-to undergo extensive remodeling that was not observed in the bare 
-systems. The bare metal surfaces 
-experienced minor roughening of the step-edge because 
-of the elevated temperatures, but the 
-(557) lattice was well-maintained throughout the simulation 
-time. The Au systems were limited to greater amounts of 
-roughening, i.e. breakup of the step-edge, and some step 
-wandering. The lower coverage Pt systems experienced 
-similar restructuring but to a greater extent when 
-compared to the Au systems. The 50\% coverage 
-Pt system was unique among our simulations in that it 
-formed numerous double layers through step coalescence, 
-similar to results reported by Tao 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 
-movement at their respective run temperatures. As the CO 
-coverage increased however, the mobility of the surface, 
-described through adatom diffusion and step-edge wandering, 
-also increased.  Except for the 50\% Pt system, the step-edges 
-did not coalesce in any of the other simulations, instead 
-preferring to keep nearly the same distance between steps 
-as in the original (557) lattice, $\sim$13\AA for Pt and $\sim$14\AA for Au. 
-Previous work by Williams et al.\cite{Williams:1991, Williams:1994} 
-highlights the repulsion that exists between step-edges even 
-when no direct interactions are present in the system. This 
-repulsion arises because step-edge crossing is not allowed 
-which constrains the entropy. This entropic repulsion does 
-not completely define the interactions between steps, which 
-is why some surfaces will undergo step coalescence, where 
-additional attractive interactions can overcome the repulsion.\cite{Williams:1991} 
-The presence and concentration of adsorbates, as shown in 
-this work, can affect these step interactions, potentially leading 
-to a new surface structure as the thermodynamic minimum.
+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 et al.\cite{Tao:2010} have shown experimentally that the Pt(557) surface 
-undergoes two separate reconstructions upon CO adsorption.\cite{Tao:2010} 
-The first involves a doubling of the step height and plateau length. 
-Similar behavior has been seen on numerous surfaces 
-at varying conditions: Ni(977), Si(111).\cite{Williams:1994,Williams:1991,Pearl} 
-Of the two systems we examined, the Pt system showed a greater 
-propensity for reconstruction when compared to the Au system 
-because of the larger surface mobility and extent of step wandering. 
-The amount of reconstruction is strongly correlated to the amount of CO 
-adsorbed upon the surface.  This appears to be related to the 
-effect that adsorbate coverage has on edge breakup and on the 
-surface diffusion of metal adatoms. While both systems displayed 
-step-edge wandering, only the 50\% Pt surface underwent the 
-doubling seen by Tao et al.\cite{Tao:2010} within the time scales studied here. 
-Over longer periods, (150~ns) two more double layers formed 
-on this interface. Although double layer formation did not occur 
-in the other Pt systems, they show more step-wandering and 
-general roughening compared to their Au counterparts. The 
-50\% Pt system is highlighted in Figure \ref{fig:reconstruct} at 
-various times along the simulation showing the evolution of a 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 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 
-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]{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
+\includegraphics[width=\linewidth]{EPS_ProgressionOfDoubleLayerFormation}
+\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.}
@@ -474,278 +447,314 @@ Previous atomistic simulations of stepped surfaces dea
 \end{figure}
 
 \subsection{Dynamics}
-Previous atomistic simulations of stepped surfaces dealt largely
-with the energetics and structures at different conditions
-\cite{Williams:1991,Williams:1994}. Consequently, the most common 
-technique utilized to date has been Monte Carlo sampling. Monte Carlo approaches give an efficient 
-sampling of the equilibrium thermodynamic landscape at the expense 
-of ignoring the dynamics of the system. Previous experimental work by Pearl and 
-Sibener\cite{Pearl}, using STM, has been able to capture the coalescing 
-of steps on Ni(977). The time scale of the image acquisition, 
-$\sim$70~s/image provides an upper bound for the time required for 
-the doubling to occur. By utilizing Molecular Dynamics we were able to probe the dynamics of these reconstructions and in this section we give data on dynamic and 
-transport properties, e.g. diffusion, layer formation time, etc.
+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 movement or 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. 
-Breaking away from the 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 Figures \ref{fig:sketchGraphic} and \ref{fig:sketchEnergies}, the penalty can fall to as low as 
-$\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for 
-diffusion is negligible ( \textless~4 kcal/mol for a Pt adatom). These adatoms are then
-able to explore the terrace before rejoining either their original step-edge or 
-becoming a part of a different edge. It is a difficult process for an atom 
-to traverse to a separate terrace although the presence of CO can lower the 
-energy barrier required to lift or lower 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, dynamically breaking apart and rejoining the 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). An atom that was 
-truly mobile 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]{DiffusionComparison_errorXY_remade_20ns.pdf}
+\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}
 
-The lack of a definite trend in the Au diffusion data in Figure \ref{fig:diff} is likely due 
-to the weaker bonding between Au and CO. This leads to a lower observed
-coverage ({\it x}-axis) when compared to dosage amount, which 
-then further limits the effect the CO can have on surface diffusion. The correlation 
-between coverage and Pt diffusion rates conversely shows a 
-definite trend marred by the highest coverage surface. Two 
-explanations arise for this drop. First, upon a visual inspection of 
-the system, after a double layer has been formed, it maintains its 
-stability strongly and is no longer a good source for adatoms and so 
-atoms that had been tracked for mobility data have now been buried. By 
-performing the same diffusion calculation but on a shorter run time 
-(20~ns), only including data before the formation of the double layer, we obtain 
-the larger values for both $\mathbf{D}_{\parallel}$ and $\mathbf{D}_{\perp}$ at the 50\% coverage.
-This places the parallel diffusion constant more closely in line with the 
-expected trend, while the perpendicular diffusion constant does not 
-drop as far. A secondary explanation arising from our analysis of the 
-mechanism of double layer formation focuses on the effect that CO on the 
-surface has with respect to overcoming surface diffusion of Pt. If the 
-coverage is too sparse, the Pt engages in minimal interactions and 
-thus minimal diffusion. As coverage increases, there are more favorable 
-arrangements of CO on the surface allowing the formation of a path, 
-a minimum energy trajectory, for the adatom to explore the surface. 
-As the CO is constantly moving on the surface, this path is constantly 
-changing. If the coverage becomes too great, the paths could 
-potentially be clogged leading to a decrease in diffusion despite 
-their being more adatoms and step-wandering.
-
-
-
+The weaker Au-CO interaction is evident in the weak CO-coverage 
+dependance of Au diffusion. This weak interaction leads to lower 
+observed coverages when compared to dosage amounts. This further 
+limits the effect the CO can have on surface diffusion. The correlation 
+between coverage and Pt diffusion rates shows a near linear relationship 
+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
+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 plays a primary role in double layer formation. However, this is not 
-a complete explanation -- the 33\%~Pt system 
-has higher diffusion constants but did not show 
-any signs of edge doubling in the observed run time. On the 
-50\%~Pt system, one layer formed within the first 40~ns of simulation time, while two more were formed as the system was run for an additional
-110~ns (150~ns total). Previous experimental 
-work gives insight into the upper bounds of the 
-time required for step coalescence.\cite{Williams:1991,Pearl} 
-In this system, as seen in Figure \ref{fig:reconstruct}, the first 
-appearance of a double layer, appears at 19~ns 
-into the simulation. Within 12~ns of this nucleation event, nearly half of the step has 
-formed the double layer and by 86~ns, the complete layer 
-has been flattened out. The double layer could be considered 
-``complete" by 37~ns but remains a bit rough. From the 
-appearance of the first nucleation event to the first observed double layer, the process took $\sim$20~ns. Another 
-$\sim$40~ns was necessary for the layer to completely straighten. 
-The other two layers in this simulation formed over periods of
-22~ns and 42~ns respectively. Comparing this to the upper 
-bounds of the image scan, it is likely that most aspects of this 
-reconstruction occur very rapidly. A possible explanation 
-for this rapid reconstruction is the elevated temperatures 
-under which our systems were simulated. It is probable that the process would 
-take longer at lower temperatures.
+The increased diffusion on Pt at the higher CO coverages is the primary 
+contributor to double layer formation. However, this is not a complete 
+explanation -- the 33\%~Pt system has higher diffusion constants, but 
+did not show any signs of edge doubling in 40~ns. On the 50\%~Pt 
+system, one double layer formed within the first 40~ns of simulation time, 
+while two more were formed as the system was allowed to run for an 
+additional 110~ns (150~ns total). This suggests that this reconstruction 
+is a rapid process and that the previously mentioned upper bound is a 
+very large overestimate.\cite{Williams:1991,Pearl} In this system the first 
+appearance of a double layer appears at 19~ns into the simulation. 
+Within 12~ns of this nucleation event, nearly half of the step has formed 
+the double layer and by 86~ns the complete layer has flattened out. 
+From the appearance of the first nucleation event to the first observed 
+double layer, the process took $\sim$20~ns. Another $\sim$40~ns was 
+necessary for the layer to completely straighten. The other two layers in 
+this simulation formed over periods of 22~ns and 42~ns respectively. 
+A possible explanation for this rapid reconstruction is the elevated 
+temperatures under which our systems were simulated. The process 
+would almost certainly take longer at lower temperatures. Additionally, 
+our measured times for completion of the doubling after the appearance 
+of a nucleation site are likely affected by our periodic boxes. A longer 
+step-edge will likely take longer to ``zipper''. 
 
 
+%Discussion
+\section{Discussion}
+We have shown that a classical potential is able to model the initial
+reconstruction of the Pt(557) surface upon CO adsorption, and have
+reproduced the double layer structure observed by Tao {\it et
+  al}.\cite{Tao:2010}. Additionally, this reconstruction appears to be
+rapid -- occurring within 100 ns of the initial exposure to CO.  Here
+we discuss the features of the classical potential that are
+contributing to the stability and speed of the Pt(557) reconstruction.
 
+\subsection{Diffusion}
+The perpendicular diffusion constant appears to be the most important
+indicator of double layer formation. As highlighted in Figure
+\ref{fig:reconstruct}, the formation of the double layer did not begin
+until a nucleation site appeared.  Williams {\it et
+  al}.\cite{Williams:1991,Williams:1994} cite an effective edge-edge
+repulsion arising from the inability of edge crossing.  This repulsion
+must be overcome to allow step coalescence.  A larger
+$\textbf{D}_\perp$ value implies more step-wandering and a larger
+chance for the stochastic meeting of two edges to create a nucleation
+point.  Diffusion parallel to the step-edge can help ``zipper'' up a
+nascent double layer. This helps explain the rapid time scale for
+double layer completion after the appearance of a nucleation site, while
+the initial appearance of the nucleation site was unpredictable.
 
+\subsection{Mechanism for restructuring}
+Since the Au surface showed no large scale restructuring in any of our
+simulations, our discussion will focus on the 50\% Pt-CO system which
+did exhibit doubling. 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
+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. 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 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
+of Pt-Pt interactions due to bound CO.  Destabilizing Pt-Pt bonds at
+the edges could lead to increased step-edge breakup and diffusion. On
+the bare Pt(557) surface the barrier to completely detach an edge atom
+is $\sim$43~kcal/mol, as is shown in configuration (a) in Figures
+\ref{fig:SketchGraphic} \& \ref{fig:SketchEnergies}. For certain
+configurations, cases (e), (g), and (h), the barrier can be lowered to
+$\sim$23~kcal/mol by the presence of bound CO molecules. In these
+instances, it becomes energetically favorable to roughen the edge by
+introducing a small separation of 0.5 to 1.0~\AA. This roughening
+becomes immediately obvious in simulations with significant CO
+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 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.
 
 %Sketch graphic of different configurations
 \begin{figure}[H]
-\includegraphics[width=0.8\linewidth, height=0.8\textheight]{COpathsSketch.pdf}
-\caption{The dark grey atoms refer to the upper ledge, while the white atoms are 
-the lower terrace. The blue highlighted atoms had a CO in a vertical atop position 
-upon them. These are a sampling of the configurations examined to gain a more 
-complete understanding of the effects CO has on surface diffusion and edge breakup. 
-Energies associated with each configuration are displayed in Figure \ref{fig:SketchEnergies}.}
+\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 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
+  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}
 \end{figure}
 
 %energy graph corresponding to sketch graphic
 \begin{figure}[H]
-\includegraphics[width=\linewidth]{stepSeparationComparison.pdf}
-\caption{The energy curves directly correspond to the labeled model 
-surface in Figure \ref{fig:SketchGraphic}. All energy curves are relative 
-to their initial configuration so the energy of a and h do not have the 
-same zero value. As is seen, certain arrangements of CO can lower 
-the energetic barrier that must be overcome to create an adatom. 
-However, it is the highest coverages where these higher-energy 
-configurations of CO will be more likely. }
+\includegraphics[width=\linewidth]{Portrait_SeparationComparison}
+\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 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}
 
-%Discussion
-\section{Discussion}
-We have shown that the classical potential models are able to model the initial reconstruction of the
-Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
-were able to observe features of the dynamic processes necessary for this reconstruction. 
+While configurations of CO on the surface are able to increase
+diffusion and the likelihood of edge wandering, this does not provide
+a complete explanation for the formation of double layers. If adatoms
+were constrained to their original terraces then doubling could not
+occur.  A mechanism for vertical displacement of adatoms at the
+step-edge is required to explain the doubling.
 
-\subsection{Diffusion}
-As shown in Figure \ref{fig:diff}, for the Pt systems, there 
-is a strong trend toward higher diffusion constants as 
-surface coverage of CO increases. The drop for the 50\% 
-case being explained as double layer formation already 
-beginning to occur in the analyzed 40~ns, which lowered 
-the calculated diffusion rates. Between the parallel and 
-perpendicular rates, the perpendicular diffusion constant 
-appears to be the most important indicator of double layer 
-formation. As highlighted in Figure \ref{fig:reconstruct}, the 
-formation of the double layer did not begin until a nucleation 
-site appeared. And as mentioned by Williams et al.\cite{Williams:1991, Williams:1994}, 
-the inability for edges to cross leads to an effective repulsion. 
-This repulsion must be overcome to allow step coalescence. 
-A greater $\textbf{D}_\perp$ implies more step-wandering 
-and a larger chance for the stochastic meeting of two edges 
-to form the nucleation point. Upon that appearance, parallel 
-diffusion along the step-edge can help ``zipper'' up the double 
-layer. This helps explain why the time scale for formation after 
-the appearance of a nucleation site was rapid, while the initial 
-appearance of said site was unpredictable. 
+We have discovered one possible mechanism for a CO-mediated vertical
+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
+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
+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.
 
-\subsection{Mechanism for restructuring}
-Since the Au surface showed no large scale restructuring throughout 
-our simulation time our discussion will focus on the 50\% Pt-CO system 
-which did undergo the doubling featured in Figure \ref{fig:reconstruct}. 
-Similarities of our results to those reported previously by Tao et al.\cite{Tao:2010} 
-are quite strong. The simulated Pt system exposed to a large dosage 
-of CO readily restructures by doubling the terrace widths and step heights. 
-The restructuring occurs in a piecemeal fashion, one to two Pt atoms at a 
-time, but is rapid on experimental timescales. The adatoms either break 
-away from the step-edge and stay on the lower terrace or they lift up onto 
-a higher terrace. Once ``free'', they diffuse on the terrace until reaching 
-another step-edge or rejoining their original edge. This combination of 
-growth and decay of the step-edges is in a state of dynamic equilibrium. 
-However, once two previously separated edges meet as shown in Figure 1.B, 
-this nucleates the rest of the edge to meet up, forming a double layer. 
-From simulations which exhibit a double layer, the time delay from the 
-initial appearance of a nucleation point to a fully formed double layer is $\sim$35~ns.
-
-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 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 for example, this explanation 
-gains some credence. The energetic repulsion between two CO located a 
-distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) and both in 
-a vertical orientation, is 8.62 kcal/mol. Moving the CO apart to the second 
-nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to 
-nearly 0 kcal/mol. Allowing the CO to rotate away from a purely vertical orientation 
-also lowers the repulsion. A minimum of 6.2 kcal/mol is reached at when the 
-angle between the 2 CO is $\sim$24\textsuperscript{o}, when the carbons are 
-locked at a distance of 2.77 \AA apart. As mentioned above, the energy barrier 
-for surface diffusion of a Pt adatom is only 4 kcal/mol. So this repulsion between 
-neighboring CO molecules can increase the surface diffusion. However, the 
-residence time of CO on Pt was examined and while the majority of the CO is 
-on or near the surface throughout the run, the molecules are extremely mobile, 
-with diffusion constants 40 to 2500 times larger, depending on coverage. This 
-mobility suggests that the CO are more likely to shift their positions without 
-necessarily the Pt along with them.
-
-Another possible and more likely mechanism for the restructuring is in the
-destabilization of strong Pt-Pt interactions by CO adsorbed on surface
-Pt atoms. To test this hypothesis, numerous configurations of 
-CO in varying quantities were arranged on the higher and lower plateaus
-around a step on a otherwise clean Pt(557) surface. A few sample 
-configurations are displayed in Figure \ref{fig:lambdaTable}, with 
-energies at various positions along the path displayed in Table 
-\ref{tab:rxcoord}. Certain configurations of CO, cases B and D for 
-example, can have quite strong energetic reasons for breaking 
-away from the step-edge. Although the packing of these configurations 
-is unlikely until CO coverage has reached a high enough value. 
-These examples are showing the most difficult cases, immediate 
-adatom formation through breakage away from the step-edge, which 
-is why their energies at large distances are relatively high. There are 
-mechanistic paths where an edge atom could get shifted to onto the 
-step-edge to form a small peak before fully breaking away. And again, 
-once the adatom is formed, the barrier for diffusion on the surface is 
-negligible. These sample configurations help explain CO's effect on 
-general surface mobility and step wandering, but they are lacking in 
-providing a mechanism for the formation of double layers. One possible 
-mechanism is elucidated in Figure \ref{fig:lambda}, where a burrowing 
-and lifting process of an adatom and step-edge atom respectively is 
-examined. The system, without CO present, is nearly energetically 
-neutral, whereas with CO present there is a $\sim$ 15 kcal/mol drop 
-in the energy of the system.
-
 %lambda progression of Pt -> shoving its way into the step
 \begin{figure}[H]
-\includegraphics[width=\linewidth]{lambdaProgression_atopCO_withLambda.png}
-\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.  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.}
+\includegraphics[width=\linewidth]{EPS_rxnCoord}
+\caption{Points along a possible reaction coordinate for CO-mediated
+  edge doubling. Here, a CO-bound adatom burrows into an established
+  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 CO.}
 \label{fig:lambda}
 \end{figure}
 
+The mechanism for doubling on the Pt(557) surface appears to require
+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 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
+must then undergo the burrowing highlighted above (or a comparable
+mechanism) to create the double layer.  With sufficient time, these
+mechanisms working in concert lead to the formation of a double layer.
 
+\subsection{CO Removal and double layer stability}
+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 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
+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]{doubleLayerBreaking_greenBlue_whiteLetters.png}
-\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.}
+\includegraphics[width=\linewidth]{EPS_doubleLayerBreaking}
+\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}
 
 
-
-
 %Peaks!
 %\begin{figure}[H]
 %\includegraphics[width=\linewidth]{doublePeaks_noCO.png}
@@ -759,7 +768,7 @@ in the energy of the system.
 %Don't think I need this
 %clean surface...
 %\begin{figure}[H]
-%\includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
+%\includegraphics[width=\linewidth]{557_300K_cleanPDF}
 %\caption{}
 
 %\end{figure}
@@ -767,8 +776,19 @@ In this work we have shown the reconstruction of the P
 
 
 \section{Conclusion}
-In this work we have shown the reconstruction of the Pt(557) crystalline surface upon adsorption of CO in less than a $\mu s$. 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. 
+The strength and directionality of the Pt-CO binding interaction, as
+well as the large quadrupolar repulsion between atop-bound CO
+molecules, help to explain the observed increase in surface mobility
+of Pt(557) and the resultant reconstruction into a double-layer
+configuration at the highest simulated CO-coverages.  The weaker Au-CO
+interaction results in significantly lower adataom diffusion
+constants, less step-wandering, and a lack of the double layer
+reconstruction on the Au(557) surface.
 
+An in-depth examination of the energetics shows the important role CO
+plays in increasing step-breakup and in facilitating edge traversal
+which are both necessary for double layer formation.
+
 %Things I am not ready to remove yet
 
 %Table of Diffusion Constants
@@ -792,17 +812,28 @@ Support for this project was provided by the National 
 % \end{table}
 
 \begin{acknowledgement}
-Support for this project was provided by the National Science
-Foundation under grant CHE-0848243 and by the Center for Sustainable
-Energy at Notre Dame (cSEND). Computational time was provided by the
-Center for Research Computing (CRC) at the University of Notre Dame.
+  We gratefully acknowledge conversations with Dr. William
+  F. Schneider and Dr. Feng Tao.  Support for this project was
+  provided by the National Science Foundation under grant CHE-0848243
+  and by the Center for Sustainable Energy at Notre Dame
+  (cSEND). Computational time was provided by the Center for Research
+  Computing (CRC) at the University of Notre Dame.
 \end{acknowledgement}
 \newpage
-\bibliography{firstTryBibliography}
+\bibstyle{achemso}
+\bibliography{COonPtAu}
 %\end{doublespace}
 
 \begin{tocentry}
-%\includegraphics[height=3.5cm]{timelapse}
+\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}
