--- trunk/COonPt/firstTry.tex	2012/12/19 21:37:51	3826
+++ trunk/COonPt/COonPtAu.tex	2013/03/21 15:28:49	3887
@@ -1,34 +1,30 @@
-\documentclass[11pt]{article}
-\usepackage{amsmath}
-\usepackage{amssymb}
-\usepackage{times}
-\usepackage{mathptm}
-\usepackage{setspace}
-\usepackage{endfloat}
-\usepackage{caption}
-%\usepackage{tabularx}
-\usepackage{graphicx}
+\documentclass[journal = jpccck, manuscript = article]{achemso}
+\setkeys{acs}{usetitle = true}
+\usepackage{achemso}
+\usepackage{natbib}
 \usepackage{multirow}
-%\usepackage{booktabs}
-%\usepackage{bibentry}
-%\usepackage{mathrsfs}
-\usepackage[square, comma, sort&compress]{natbib}
+\usepackage{wrapfig}
+%\mciteErrorOnUnknownfalse
+
+\usepackage[version=3]{mhchem}  % this is a great package for formatting chemical reactions
 \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
-%\AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
-\setlength{\abovecaptionskip}{20 pt}
-\setlength{\belowcaptionskip}{30 pt}
+\title{Molecular Dynamics simulations of the surface reconstructions
+  of Pt(557) and Au(557) under exposure to CO}
 
-\bibpunct{}{}{,}{s}{}{;}
-\bibliographystyle{achemso}
+\author{Joseph R. Michalka}
+\author{Patrick W. McIntyre}
+\author{J. Daniel Gezelter}
+\email{gezelter@nd.edu}
+\affiliation[University of Notre Dame]{251 Nieuwland Science Hall\\
+  Department of Chemistry and Biochemistry\\ University of Notre
+  Dame\\ Notre Dame, Indiana 46556}
 
+\keywords{}
+
 \begin{document}
 
-
+ 
 %%
 %Introduction
 %	Experimental observations
@@ -47,28 +43,23 @@
 %Summary
 %%
 
-%Title
-\title{Molecular Dynamics simulations of the surface reconstructions
-  of Pt(557) and Au(557) under exposure to CO}
 
-\author{Joseph R. Michalka, Patrick W. McIntyre and J. Daniel
-Gezelter\footnote{Corresponding author. \ Electronic mail: gezelter@nd.edu} \\
-Department of Chemistry and Biochemistry,\\
-University of Notre Dame\\
-Notre Dame, Indiana 46556}
-
-%Date
-\date{Dec 15, 2012}
-
-%authors
-
-% make the title
-\maketitle
-
-\begin{doublespace}
-
 \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
+  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
@@ -100,28 +91,42 @@ This work an effort to understand the mechanism and ti
 reversible restructuring under exposure to moderate pressures of
 carbon monoxide.\cite{Tao:2010}
 
-This work an effort to understand the mechanism and timescale for
-surface restructuring using molecular simulations.  Since the dynamics
-of the process is of particular interest, we utilize classical force
-fields that represent a compromise between chemical accuracy and the
-computational efficiency necessary to observe the process of interest.
+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.
 
-Since restructuring occurs as a result of specific interactions of the
-catalyst with adsorbates, two metal systems exposed to carbon monoxide
-were examined in this work. The Pt(557) surface has already been shown
-to reconstruct under certain conditions. The Au(557) surface, because
-of a weaker interaction with CO, is less likely to undergo this kind
-of reconstruction.  MORE HERE ON PT AND AU PREVIOUS WORK.
-
 %Platinum molecular dynamics
 %gold molecular dynamics
 
 \section{Simulation Methods}
-The challenge in modeling any solid/gas interface problem 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
@@ -133,8 +138,8 @@ Au-Au and Pt-Pt interactions, while modeling the CO us
 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, while modeling the CO 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.
   
@@ -146,13 +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.} 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*}
@@ -164,8 +169,8 @@ $\phi_{ij}(r_{ij})$ is an pairwise term that is meant 
 V_i =  F[ \bar{\rho}_i ]  + \sum_{j \neq i} \phi_{ij}(r_{ij})
 \end{equation*}
 where $F[ \bar{\rho}_i ]$ is an energy embedding functional, and
-$\phi_{ij}(r_{ij})$ is an pairwise term that is meant to represent the
-overlap of the two positively charged cores.  
+$\phi_{ij}(r_{ij})$ is a pairwise term that is meant to represent the
+repulsive overlap of the two positively charged cores.  
 
 % The {\it modified} embedded atom method (MEAM) adds angular terms to
 % the electron density functions and an angular screening factor to the
@@ -176,28 +181,35 @@ The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen 
 % metals,\cite{Lee:2001qf} and also interfaces.\cite{Beurden:2002ys})
 % MEAM presents significant additional computational costs, however.
 
-The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen potentials
+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} All of these potentials have their
-strengths and weaknesses.  One of the strengths common to all of the
-methods is the relatively large library of metals for which these
-potentials have been
-parameterized.\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}
-Since previous explanations for the surface rearrangements center on
-the large linear quadrupole moment of carbon monoxide, the model
-chosen for this molecule exhibits this property in an efficient
-manner. We used a model first proposed by Karplus and Straub to study
-the photodissociation of CO from myoglobin.\cite{Straub} The Straub
-and Karplus model is a rigid linear three site model which places a
-massless (M) site at the center of mass along the CO bond.  The
-geometry and interaction parameters are reproduced in Table 1. The
+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
@@ -205,38 +217,43 @@ mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCO
 %CO Table
 \begin{table}[H]
   \caption{Positions, Lennard-Jones parameters ($\sigma$ and
-    $\epsilon$), and charges for the CO-CO 
-    interactions borrowed from Ref. \bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA~, energies are 
-    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
 &  {\it z} & $\sigma$ & $\epsilon$ & q\\
 \hline
-\textbf{C} & -0.6457 &  0.0262  & 3.83   &   -0.75 \\
-\textbf{O} &  0.4843 &   0.1591 &   3.12 &   -0.85 \\
+\textbf{C} & -0.6457 &  3.83 & 0.0262   &   -0.75 \\
+\textbf{O} &  0.4843 &  3.12 &  0.1591  &   -0.85 \\
 \textbf{M} & 0.0 & -  &  -  &    1.6 \\
 \hline
 \end{tabular}
+\label{tab:CO}
 \end{table}
 
 \subsection{Cross-Interactions between the metals and carbon monoxide}
 
-Since the adsorption of CO onto a platinum surface has been the focus
+Since the adsorption of CO onto a Pt surface has been the focus
 of much experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979}
 and theoretical work
 \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
 there is a significant amount of data on adsorption energies for CO on
-clean metal surfaces. Parameters reported by Korzeniewski {\it et
-  al.}\cite{Pons:1986} were a starting point for our fits, which were
+clean metal surfaces. An earlier model by Korzeniewski {\it et
+  al.}\cite{Pons:1986} served as a starting point for our fits. The parameters were
 modified to ensure that the Pt-CO interaction favored the atop binding
-position on Pt(111). This resulting binding energies are on the higher
-side of the experimentally-reported values. Following Korzeniewski
-{\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
+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
+{\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 parameterized to a Morse potential with a large
-range parameter ($r_o$).  In most cases, this contributes a weak
+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 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
@@ -245,45 +262,44 @@ The Au-C and Au-O cross-interactions were fit using Le
 %where did you actually get the functionals for citation?
 %scf calculations, so initial relaxation was of the four layers, but two layers weren't kept fixed, I don't think
 %same cutoff for slab and slab + CO ? seems low, although feibelmen had values around there...
-The Au-C and Au-O cross-interactions were fit using Lennard-Jones and
+The Au-C and Au-O cross-interactions were also fit using Lennard-Jones and
 Morse potentials, respectively, to reproduce Au-CO binding energies.
-
-The fits were refined against gas-surface DFT calculations with a
+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 are
+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
 computed with the PBE implementation of the generalized gradient
 approximation (GGA) for gold, carbon, and oxygen that was constructed
 by Rappe, Rabe, Kaxiras, and Joannopoulos.\cite{Perdew_GGA,RRKJ_PP}
-Ionic relaxations were performed until the energy difference between
-subsequent steps was less than $10^{-8}$ Ry.  In testing the CO-Au
-interaction, Au(111) supercells were constructed of four layers of 4
+In testing the Au-CO interaction, Au(111) supercells were constructed of four layers of 4
 Au x 2 Au surface planes and separated from vertical images by six
-layers of vacuum space. The surface atoms were all allowed to relax.
-Supercell calculations were performed nonspin-polarized with a 4 x 4 x
-4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
-zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxed gold slab was
+layers of vacuum space. The surface atoms were all allowed to relax 
+before CO was added to the system. Electronic relaxations were 
+performed until the energy difference between subsequent steps 
+was less than $10^{-8}$ Ry.   Nonspin-polarized supercell calculations 
+were performed with a 4~x~4~x~4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
+zone.\cite{Monkhorst:1976} The relaxed gold slab was
 then used in numerous single point calculations with CO at various
 heights (and angles relative to the surface) to allow fitting of the
 empirical force field.
 
 %Hint at future work
-The parameters employed in this work are shown in Table 2 and the
-binding energies on the 111 surfaces are displayed in Table 3.  To
-speed up the computations, charge transfer and polarization are not
-being treated in this model, although these effects are likely to
-affect binding energies and binding site
-preferences.\cite{Deshlahra:2012}
+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 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 potential, while the
-    (mostly-repulsive) 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 |}
@@ -295,12 +311,13 @@ preferences.\cite{Deshlahra:2012}
 
 \hline
 \end{tabular}
+\label{tab:co_parameters}
 \end{table}
 
 %Table of energies
 \begin{table}[H]
-  \caption{Adsorption energies for CO on M(111) using the potentials
-    described in this work.  All values are in eV}
+  \caption{Adsorption energies for a single CO at the atop site on M(111) at the atop site using the potentials
+    described in this work.  All values are in eV.}
 \centering
 \begin{tabular}{| c | cc |}
   \hline
@@ -309,191 +326,514 @@ preferences.\cite{Deshlahra:2012}
   \multirow{2}{*}{\textbf{Pt-CO}} & \multirow{2}{*}{-1.9} & -1.4 \bibpunct{}{}{,}{n}{}{,}
   (Ref. \protect\cite{Kelemen:1979}) \\
  & &  -1.9 \bibpunct{}{}{,}{n}{}{,} (Ref. \protect\cite{Yeo}) \\ \hline
-  \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPD_Gold}) \\
+  \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPDGold}) \\
   \hline
 \end{tabular}
+\label{tab:co_energies}
 \end{table}
 
 \subsection{Pt(557) and Au(557) metal interfaces}
-
-Our model systems are composed of 3888 Pt atoms and XXXX Au atoms in a
-FCC crystal that have been cut along the 557 plane so that they are
-periodic in the {\it x} and {\it y} directions, and have been rotated
-to expose two parallel 557 cuts along the positive and negative {\it
-  z}-axis.  Simulations of the bare metal interfaces at temperatures
-ranging from 300~K to 1200~K were done to observe the relative
+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. 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
+(557) cuts along the extended {\it z}-axis.  Simulations of the 
+bare metal interfaces at temperatures ranging from 300~K to
+1200~K were performed to confirm the relative
 stability of the surfaces without a CO overlayer.  
 
-The different bulk (and surface) melting temperatures (1337~K for Au
-and 2045~K for Pt) suggest that the reconstruction may happen at
-different temperatures for the two metals.  To copy experimental
-conditions for the CO-exposed surfaces, the bare surfaces were
-initially run in the canonical (NVT) ensemble at 800~K and 1000~K
-respectively for 100 ps.  Each surface was exposed to a range of CO
-that was initially placed in the vacuum region.  Upon full adsorption,
-these amounts correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
-coverage.  Because of the difference in binding energies, the platinum
-systems very rarely had CO that was not bound to the surface, while
-the gold surfaces often had a significant CO population in the gas
-phase.  These systems were allowed to reach thermal equilibrium (over
-5 ns) before being shifted to the microcanonical (NVE) ensemble for
-data collection. All of the systems examined had at least 40 ns in the
-data collection stage, although simulation times for some of the
-systems exceeded 200ns.  All simulations were run using the open
-source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,OpenMD}
+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}
 
-% Just results, leave discussion for discussion section
+
+% RESULTS
+%
 \section{Results}
-Tao {\it et al.} showed experimentally that the Pt(557) surface
-undergoes two separate reconstructions upon CO
-adsorption.\cite{Tao:2010} The first reconstruction involves a
-doubling of the step edge height which is accomplished by a doubling
-of the plateau length. The second reconstruction led to the formation
-of triangular clusters that arrange themselves along the lengthened
-plateaus.
+\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 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}
 
-The primary observation and results of our simulation is that the
-presence of CO overlayer on Pt(557) causes the same kind of
-reconstruction observed experimentally. The 6-atom 111 facets
-initially become disordered, and after 20-40 ns, a double-layer (with
-a 2-atom step between terraces) forms.  However, we did not observe
-the triangular cluster formation that was observed at longer times in
-the experiments.  Without the CO present on the Pt(557) surface, there
-was some disorder at the step edges, but no significant restructuring
-was observed.
+\subsubsection{Step wandering}
+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.
 
-In these simulations, the Au(557) surface did not exhibit any
-significant restructuring either with or without the presence of a CO
-overlayer.
+\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.
 
-\subsection{Transport of surface metal atoms}
-An ideal metal surface displaying a low energy (111) face is unlikely
-to experience much surface diffusion because of the large vacancy
-formation energy for atoms at the surface.  This implies that
-significant energy must be expended to lift an atom out of the flat
-face so it can migrate on the surface.  Rougher surfaces and those
-that already contain numerous adatoms, step edges, and kinks, are
-expected to have higher surface diffusion rates.  Metal atoms that are
-mobile on the surface were observed to leave and then rejoin step
-edges or other formations. They may travel together or as isolated
-atoms.  The primary challenge of quantifying the overall surface
-mobility is in defining ``mobile'' vs. ``static'' atoms.
+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.
 
-A particle was considered mobile once it had traveled more than 2~\AA~
-between saved configurations (XX ps). Restricting the transport
-calculations to only mobile atoms eliminates all of the bulk metal as
-well as any surface atoms that remain fixed for a significant length
-of time.  Since diffusion on a surface is strongly affected by local
-structures, the diffusion parallel to the step edges was determined
-separately from the diffusion perpendicular to these edges.  The
-parallel and perpendicular diffusion constants (determined using
-linear fits to the mean squared displacement) are shown in figure \ref{fig:diff}.
+%Evolution of surface
+\begin{figure}[H]
+\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.}
+  \label{fig:reconstruct}
+\end{figure}
 
-%While an ideal metallic surface is unlikely to experience much surface diffusion, high-index surfaces have large numbers of low-coordinated atoms which have a much easier time overcoming the energetic barriers limiting diffusion, leading to easier surface reconstructions. Surface movement was divided between the parallel ($\parallel$) and perpendicular ($\perp$) directions relative to the step edge. We were then able to calculate diffusion constants as a function of CO coverage. As can be seen in Table 4, the presence and amount of CO directly affects the diffusion constants of surface platinum atoms. The presence of two 50\% coverage systems is to show how the diffusion process is affected by time. The majority of the systems were run for approximately 50 ns while the half monolayer system has been running continuously. The lowered diffusion constant at longer run times will be examined in-depth in the discussion section.
+\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.
 
+
+\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.  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[scale=0.6]{DiffusionComparison_error.png}
+\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 going from approximately 7 nearest neighbors
-  to 5, as compared to the 3 of an adatom. Additionally, the observed
-  maximum and subsequent decrease for the Pt system suggests that the
-  CO self-interactions are playing a significant role with regards to
-  movement of the platinum atoms around and more importantly across
-  the surface. }
+  ($\mathbf{D}_{\perp}$) to the (557) step-edges as a function of CO
+  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}
 
-%Table of Diffusion Constants
-%Add gold?M
-% \begin{table}[H]
-%   \caption{}
-%   \centering
-% \begin{tabular}{| c | cc | cc | }
-%   \hline
-%   &\multicolumn{2}{c|}{\textbf{Platinum}}&\multicolumn{2}{c|}{\textbf{Gold}} \\
-%   \hline
-%   \textbf{Surface Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  \\
-%   \hline
-%   50\% & 4.32(2) & 1.185 $\pm$ 0.008 & 1.72 $\pm$ 0.02 & 0.455 $\pm$ 0.006 \\
-%   33\% & 5.18 $\pm$ 0.03 & 1.999 $\pm$ 0.005 & 1.95 $\pm$ 0.02 & 0.337 $\pm$ 0.004  \\
-%   25\% & 5.01 $\pm$ 0.02 & 1.574 $\pm$ 0.004 & 1.26 $\pm$ 0.03 & 0.377 $\pm$ 0.006 \\
-%   5\%   & 3.61 $\pm$ 0.02 & 0.355 $\pm$ 0.002 & 1.84 $\pm$ 0.03 & 0.169 $\pm$ 0.004 \\
-%   0\%   & 3.27 $\pm$ 0.02 & 0.147 $\pm$ 0.004 & 1.50 $\pm$ 0.02 & 0.194 $\pm$ 0.002  \\
-%   \hline 
-% \end{tabular}
-% \end{table}
+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 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.
 
-Mechanism for restructuring
+\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.
 
-There are a number of possible mechanisms to explain the role of
-adsorbed CO in restructuring the Pt surface. Quadrupolar repulsion
-between adjacent CO molecules adsorbed on the surface is one
+\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 specific orientation relative to each other,
-this explanation gains some weight.  
+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.
 
-Another possible mechanism for the restructuring is in the
-destabilization of strong Pt-Pt interactions by CO adsorbed on surface
-Pt atoms.  This could have the effect of increasing surface mobility
-of these atoms.  
+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.
 
-Comparing the results from simulation to those reported previously by
-Tao et al. the similarities in the platinum and CO system are quite
-strong. As shown in figure, the simulated platinum system under a CO
-atmosphere will restructure slightly by doubling the terrace
-heights. The restructuring appears to occur slowly, one to two
-platinum atoms at a time. Looking at individual snapshots, these
-adatoms tend to either rise on top of the plateau or break away from
-the step edge and then diffuse perpendicularly to the step direction
-until reaching another step edge. This combination of growth and decay
-of the step edges appears to be in somewhat of a state of dynamic
-equilibrium. However, once two previously separated edges meet as
-shown in figure 1.B, this point tends to act as a focus or growth
-point for the rest of the edge to meet up, akin to that of a
-zipper. From the handful of cases where a double layer was formed
-during the simulation, measuring from the initial appearance of a
-growth point, the double layer tends to be fully formed within
-$\sim$~35 ns.
+%Sketch graphic of different configurations
+\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 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}
 
-\subsection{Diffusion}
-As shown in the results section, the diffusion parallel to the step edge tends to be much faster than that perpendicular to the step edge. Additionally, the coverage of CO appears to play a slight role in relative rates of diffusion, as shown in Table 4. Thus, the bottleneck of the double layer formation appears to be the initial formation of this growth point, which seems to be somewhat of a stochastic event. Once it appears, parallel diffusion, along the now slightly angled step edge, will allow for a faster formation of the double layer than if the entire process were dependent on only perpendicular diffusion across the plateaus. Thus, the larger $D_{\perp}$, the more likely a growth point is to be formed. One driving force behind this reconstruction appears to be the lowering of surface energy that occurs by doubling the terrace widths. (I'm not really proving this... I have the surface flatness to show it, but surface energy?)
-\\
-\\
-%Evolution of surface
+%energy graph corresponding to sketch graphic
 \begin{figure}[H]
-\includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
-\caption{The Pt(557) / 50\% CO system at a sequence of times after
-  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
-  (d) 86.1 ns. Disruption of the 557 step edges occurs quickly.  The
-  doubling of the layers appears only after two adjacent step edges
-  touch.  The circled spot in (b) nucleated the growth of the double
-  step observed in the later configurations.}
+\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}
 
+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.
 
-%Peaks!
+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.
+
+%lambda progression of Pt -> shoving its way into the step
 \begin{figure}[H]
-\includegraphics[width=\linewidth]{doublePeaks_noCO.png}
-\caption{}
+\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]{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}
+%\caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
+ %of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with 
+ %aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
+%\label{fig:peaks}
+%\end{figure}
+
+
+%Don't think I need this
+%clean surface...
+%\begin{figure}[H]
+%\includegraphics[width=\linewidth]{557_300K_cleanPDF}
+%\caption{}
+
+%\end{figure}
+%\label{fig:clean}
+
+
 \section{Conclusion}
+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.
 
-\section{Acknowledgments}
-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.
+%Things I am not ready to remove yet
 
+%Table of Diffusion Constants
+%Add gold?M
+% \begin{table}[H]
+%   \caption{}
+%   \centering
+% \begin{tabular}{| c | cc | cc | }
+%   \hline
+%   &\multicolumn{2}{c|}{\textbf{Platinum}}&\multicolumn{2}{c|}{\textbf{Gold}} \\
+%   \hline
+%   \textbf{Surface Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  \\
+%   \hline
+%   50\% & 4.32(2) & 1.185(8)  & 1.72(2) & 0.455(6) \\
+%   33\% & 5.18(3)  & 1.999(5)  & 1.95(2) & 0.337(4)   \\
+%   25\% & 5.01(2)  & 1.574(4)  & 1.26(3) & 0.377(6) \\
+%   5\%   & 3.61(2)  & 0.355(2)  & 1.84(3)  & 0.169(4)  \\
+%   0\%   & 3.27(2)  & 0.147(4)  & 1.50(2)  & 0.194(2)   \\
+%   \hline 
+% \end{tabular}
+% \end{table}
+
+\begin{acknowledgement}
+  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}
-\end{doublespace}
+\bibstyle{achemso}
+\bibliography{COonPtAu}
+%\end{doublespace}
+
+\begin{tocentry}
+\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}
