--- trunk/COonPt/firstTry.tex	2012/12/19 21:37:51	3826
+++ trunk/COonPt/firstTry.tex	2013/03/18 21:20:12	3879
@@ -1,4 +1,13 @@
-\documentclass[11pt]{article}
+\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}
@@ -6,13 +15,14 @@
 \usepackage{setspace}
 \usepackage{endfloat}
 \usepackage{caption}
-%\usepackage{tabularx}
+\usepackage{tabularx}
+\usepackage{longtable}
 \usepackage{graphicx}
 \usepackage{multirow}
-%\usepackage{booktabs}
-%\usepackage{bibentry}
-%\usepackage{mathrsfs}
-\usepackage[square, comma, sort&compress]{natbib}
+\usepackage{multicol}
+
+\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
@@ -22,13 +32,27 @@
 %\AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
 \setlength{\abovecaptionskip}{20 pt}
 \setlength{\belowcaptionskip}{30 pt}
+% \bibpunct{}{}{,}{s}{}{;}
 
-\bibpunct{}{}{,}{s}{}{;}
-\bibliographystyle{achemso}
+%\citestyle{nature}
+% \bibliographystyle{achemso}
 
-\begin{document}
+\title{Molecular Dynamics simulations of the surface reconstructions
+  of Pt(557) and Au(557) under exposure to CO}
 
+\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
@@ -47,27 +71,20 @@
 %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}
+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.
 
 \end{abstract}
 
@@ -100,28 +117,39 @@ 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
+This work is an investigation into the mechanism and timescale for the Pt(557) \& Au(557)
 surface restructuring using molecular simulations.  Since the dynamics
-of the process is of particular interest, we utilize classical force
+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 observe the process of interest.
+computational efficiency necessary to simulate the process of interest.
+Since restructuring typically occurs as a result of specific interactions of the
+catalyst with adsorbates, in this work, two metal systems exposed 
+to carbon monoxide were examined. The Pt(557) surface has already been shown
+to undergo a large scale reconstruction under certain conditions.\cite{Tao:2010} 
+The Au(557) surface, because of a weaker interaction with CO, is less 
+likely to undergo this kind of reconstruction. However, Peters {\it et al}.\cite{Peters:2000} 
+and Piccolo {\it et al}.\cite{Piccolo:2004} have both observed CO-induced 
+reconstruction of a Au(111) surface. Peters {\it et al}. saw a relaxation to the 
+22 x $\sqrt{3}$ cell. They argued that only a few Au atoms
+become adatoms, limiting the stress of this reconstruction, while 
+allowing the rest to relax and approach the ideal (111) 
+configuration. They did not see the usual herringbone pattern on Au(111) being greatly 
+affected by this relaxation. Piccolo {\it et al}. on the other hand, did see a 
+disruption of the herringbone pattern as CO was adsorbed to the 
+surface. Both groups suggested that the preference CO shows for 
+low-coordinated Au atoms was the primary driving force for the reconstruction.
 
-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
+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}
+10$^4$ atoms) 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
@@ -133,7 +161,7 @@ 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
+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
 photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
 Pt-CO cross interactions were parameterized as part of this work.
@@ -146,9 +174,9 @@ parameter sets. The glue model of Ercolessi {\it et al
 methods,\cite{Daw84,Foiles86,Johnson89,Daw89,Plimpton93,Voter95a,Lu97,Alemany98}
 but other models like the Finnis-Sinclair\cite{Finnis84,Chen90} and
 the quantum-corrected Sutton-Chen method\cite{QSC,Qi99} have simpler
-parameter sets. The glue model of Ercolessi {\it et al.} is among the
+parameter sets. The glue model of Ercolessi {\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
+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
@@ -164,8 +192,8 @@ $\phi_{ij}(r_{ij})$ 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
@@ -176,67 +204,80 @@ 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}
 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}  
+dynamics.\cite{Shibata:2002hh} One of EAM's strengths
+is its sensitivity to small changes in structure. This arises
+because interactions
+up to the third nearest neighbor were taken into account in the parameterization.\cite{Voter95a}
+Comparing that to the glue model of Ercolessi {\it et al}.\cite{Ercolessi88}
+which is only parameterized up to the nearest-neighbor
+interactions, EAM is a suitable choice for systems where 
+the bulk properties are of secondary importance to low-index 
+surface structures. Additionally, the similarity of EAM's functional 
+treatment of the embedding energy to standard density functional 
+theory (DFT) makes fitting DFT-derived cross potentials with adsorbates somewhat easier.
+\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
 
+
+
+
 \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
-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 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 
 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 borrowed from Ref. \bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA~, energies are 
+    interactions in Ref.\bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA, energies are 
     in kcal/mol, and charges are in atomic units.}
 \centering
 \begin{tabular}{| c | c | ccc |}
 \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 +286,44 @@ 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
+{\sc 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{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
     potentials.  Distances are given in \AA~and energies in kcal/mol. }
 \centering
 \begin{tabular}{| c | cc | c | ccc |}
@@ -295,12 +335,13 @@ 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 +350,462 @@ 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
+The different bulk melting temperatures predicted by EAM (1345~$\pm$~10~K for Au\cite{Au:melting}
+and $\sim$~2045~K for Pt\cite{Pt:melting}) suggest that any possible reconstruction should happen at
+different temperatures for the two metals.  The bare Au and Pt surfaces were
 initially run in the canonical (NVT) ensemble at 800~K and 1000~K
-respectively for 100 ps.  Each surface was exposed to a range of CO
+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 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
+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 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}
+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}
 
-% 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 surface of both 
+systems, upon dosage of CO, began to undergo extensive remodeling 
+that was not observed in the bare systems. Reconstructions of 
+the Au systems were limited to breakup of the step-edges and 
+some step wandering. The lower coverage Pt systems experienced 
+similar restructuring but to a greater extent. The 50\% coverage 
+Pt system was unique among our simulations in that it formed 
+well-defined and stable double layers through step coalescence, 
+similar to results reported by Tao {\it et al}.\cite{Tao:2010}
 
-The 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.
 
-In these simulations, the Au(557) surface did not exhibit any
-significant restructuring either with or without the presence of a CO
-overlayer.
+\subsubsection{Step wandering}
+The 0\% coverage surfaces for both metals showed minimal 
+step-wandering at their respective temperatures. As the CO 
+coverage increased however, the mobility of the surface atoms, 
+described through adatom diffusion and step-edge wandering, 
+also increased.  Except for the 50\% Pt system where step 
+coalescence occurred, the step-edges in the other simulations 
+preferred to keep nearly the same distance between steps as in 
+the original (557) lattice, $\sim$13\AA~for Pt and $\sim$14\AA~for Au. 
+Previous work by Williams {\it et al}.\cite{Williams:1991, Williams:1994} 
+highlights the repulsion that exists between step-edges even 
+when no direct interactions are present in the system. This 
+repulsion is caused by an entropic barrier that arises from 
+the fact that steps cannot cross over one another. This entropic 
+repulsion does not completely define the interactions between 
+steps, however, so it is possible to observe step coalescence 
+on some surfaces.\cite{Williams:1991} The presence and 
+concentration of adsorbates, as shown in this work, can 
+affect step-step interactions, potentially leading to a new 
+surface structure as the thermodynamic equilibrium.
 
-\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.
+\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.
 
-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}.
+The second reconstruction observed by 
+Tao {\it et al}.\cite{Tao:2010} involved the formation of triangular clusters that stretched 
+across the plateau between two step-edges. Neither metal, within 
+the 40~ns time scale or the extended simulation time of 150~ns for 
+the 50\% Pt system, experienced this reconstruction.
 
-%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.
+%Evolution of surface
+\begin{figure}[H]
+\includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
+\caption{The Pt(557) / 50\% CO system at a sequence of times after
+  initial exposure to the CO: (a) 258~ps, (b) 19~ns, (c) 31.2~ns, and
+  (d) 86.1~ns. Disruption of the (557) step-edges occurs quickly.  The
+  doubling of the layers appears only after two adjacent step-edges
+  touch.  The circled spot in (b) nucleated the growth of the double
+  step observed in the later configurations.}
+  \label{fig:reconstruct}
+\end{figure}
 
+\subsection{Dynamics}
+Previous experimental work by Pearl and Sibener\cite{Pearl}, 
+using STM, has been able to capture the coalescence of steps 
+on Ni(977). The time scale of the image acquisition, $\sim$70~s/image, 
+provides an upper bound for the time required for the doubling 
+to occur. By utilizing Molecular Dynamics we are able to probe 
+the dynamics of these reconstructions at elevated temperatures 
+and in this section we provide data on the timescales for transport 
+properties, e.g. diffusion and layer formation time.
+
+
+\subsubsection{Transport of surface metal atoms}
+%forcedSystems/stepSeparation
+The wandering of a step-edge is a cooperative effect 
+arising from the individual movements of the atoms making up the steps. An ideal metal surface 
+displaying a low index facet, (111) or (100), is unlikely to experience 
+much surface diffusion because of the large energetic barrier that must 
+be overcome to lift an atom out of the surface. The presence of step-edges and other surface features
+on higher-index facets provides a lower energy source for mobile metal atoms. 
+Single-atom break-away from a step-edge on a clean surface still imposes an 
+energetic penalty around $\sim$~45 kcal/mol, but this is easier than lifting 
+the same metal atom vertically out of the surface,  \textgreater~60 kcal/mol. 
+The penalty lowers significantly when CO is present in sufficient quantities 
+on the surface. For certain distributions of CO, see Discussion, the penalty can fall to as low as 
+$\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for 
+diffusion is negligible (\textless~4 kcal/mol for a Pt adatom). These adatoms are then
+able to explore the terrace before rejoining either their original step-edge or 
+becoming a part of a different edge. It is an energetically unfavorable process with a high barrier for an atom 
+to traverse to a separate terrace although the presence of CO can lower the 
+energy barrier required to lift or lower an adatom. By tracking the mobility of individual 
+metal atoms on the Pt and Au surfaces we were able to determine the relative 
+diffusion constants, as well as how varying coverages of CO affect the diffusion. Close 
+observation of the mobile metal atoms showed that they were typically in 
+equilibrium with the step-edges. 
+At times, their motion was concerted and two or more adatoms would be 
+observed moving together across the surfaces. 
+
+A particle was considered ``mobile'' once it had traveled more than 2~\AA~
+between saved configurations of the system (typically 10-100 ps). A mobile atom 
+would typically travel much greater distances than this, but the 2~\AA~cutoff 
+was used to prevent swamping the diffusion data with the in-place vibrational 
+movement of buried atoms. Diffusion on a surface is strongly affected by 
+local structures and in this work, the presence of single and double layer 
+step-edges causes the diffusion parallel to the step-edges to be larger than 
+the diffusion perpendicular to these edges. Parallel and perpendicular
+diffusion constants are shown in Figure \ref{fig:diff}.
+
+%Diffusion graph
 \begin{figure}[H]
-\includegraphics[scale=0.6]{DiffusionComparison_error.png}
+\includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade_20ns.pdf}
 \caption{Diffusion constants for mobile surface atoms along directions
   parallel ($\mathbf{D}_{\parallel}$) and perpendicular
-  ($\mathbf{D}_{\perp}$) to the 557 step edges as a function of CO
-  surface coverage.  Diffusion parallel to the step edge is higher
+  ($\mathbf{D}_{\perp}$) to the (557) step-edges as a function of CO
+  surface coverage.  Diffusion parallel to the step-edge is higher
   than that perpendicular to the edge because of the lower energy
-  barrier associated with going from approximately 7 nearest neighbors
-  to 5, as compared to the 3 of an adatom. Additionally, the observed
-  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. }
+  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 }
 \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 model is able to model the 
+initial reconstruction of the Pt(557) surface upon CO adsorption as 
+shown by Tao {\it et al}.\cite{Tao:2010}. More importantly, we were 
+able to observe features of the dynamic processes necessary for 
+this reconstruction. Here we discuss the features of the model that 
+give rise to the observed dynamical properties of the (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. And as mentioned by Williams {\it et al}.\cite{Williams:1991, Williams:1994}, 
+the inability for edges to cross leads to an effective edge-edge repulsion that 
+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 create a nucleation point. Parallel diffusion along the step-edge can help ``zipper'' up a nascent 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 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
-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.  
+\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 featured in Figure \ref{fig:reconstruct}. 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 would gain credence. The 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 barrier for surface diffusion of a Pt adatom is only 4 kcal/mol, so 
+repulsion between adjacent CO molecules bound to Pt could increase the surface 
+diffusion. However, the residence time of CO on Pt suggests that these 
+molecules are extremely mobile, with diffusion constants 40 to 2500 times 
+larger than surface Pt atoms. This mobility suggests that the CO are more 
+likely to shift their positions without dragging the Pt along with them.
 
-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, taking into account the large 
+mobility of the CO, looks at how instantaneous and short-lived configurations of 
+CO on the surface can destabilize Pt-Pt interactions leading 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/mole. In these instances, 
+it becomes quite 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, although it is present to a lesser extent 
+on lower coverage surfaces and even on the bare surfaces. In these cases it is likely 
+due to stochastic vibrational processes that squeeze out step-edge atoms. The mechanism 
+of step-edge breakup suggested by these energy curves is one the most difficult 
+processes, a complete break-away from the step-edge in one unbroken movement. 
+Easier multistep mechanisms likely exist where an adatom moves laterally on the surface 
+after being ejected so it is sitting on the edge. This provides the atom with 5 nearest 
+neighbors, which while lower than the 7 if it had stayed a part of the step-edge, is higher 
+than the 3 it could maintain located on the terrace. In this proposed mechanism, the CO 
+quadrupolar repulsion is still playing a primary role, but for its importance in roughening 
+the step-edge, rather than maintaining long-term bonds with a single Pt atom which is not 
+born out by their mobility data. The requirement for a large density of CO on the surface 
+for some of the more favorable suggested mechanisms in Figure \ref{fig:SketchGraphic} 
+correspond well with the increased mobility seen on higher coverage surfaces.
 
-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=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}.}
+\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]{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. }
+\label{fig:SketchEnergies}
 \end{figure}
 
+While configurations of CO on the surface are able to increase diffusion, 
+this does not immediately provide an explanation for the formation of double 
+layers. If adatoms were constrained to their terrace then doubling would be 
+much less likely to occur. Nucleation sites could still potentially form, but there 
+would not be enough atoms to finish the doubling. Real materials, where the 
+step lengths can be taken as infinite, local doubling would be possible, but in 
+our simulations with our periodic treatment of the system, this is not possible. 
+Thus, there must be a mechanism that explains how adatoms are able to move 
+amongst terraces. Figure \ref{fig:lambda} shows points along a reaction coordinate 
+where an adatom along the step-edge with an adsorbed CO ``burrows'' into the 
+edge displacing an atom onto the higher terrace. This mechanism was chosen 
+because of similar events that were observed during the simulations. The barrier 
+heights we obtained are only approximations because we constrained the movement 
+of the highlighted atoms along a specific concerted path. The calculated $\Delta E$'s 
+are the more interesting results from this investigation. When CO is not present and 
+this reaction coordinate is followed, the $\Delta E > 3$~kcal/mol. The example shown 
+in the figure, where CO is present in the atop position, has a $\Delta E < -15$~kcal/mol. 
+While the barrier height is comparable to the non-CO case, that is a nearly a 20~kcal/mol 
+difference in energies and moves the process from slightly unfavorable to energetically favorable. 
 
-%Peaks!
+%lambda progression of Pt -> shoving its way into the step
 \begin{figure}[H]
-\includegraphics[width=\linewidth]{doublePeaks_noCO.png}
-\caption{}
+\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.}
+\label{fig:lambda}
 \end{figure}
+
+The mechanism for doubling on this surface appears to be a convolution of at least 
+these two described processes. For complete doubling of a layer to occur there must 
+be the equivalent removal of a separate terrace. For those atoms to ``disappear'' from 
+that terrace they must either rise up on the ledge above them or drop to the ledge below 
+them. The presence of CO helps with both of these situations. There must be sufficient 
+breakage of the step-edge to increase the concentration of adatoms on the surface. 
+These adatoms must then undergo the burrowing highlighted above or some comparable 
+mechanism to traverse the step-edge. Over time, these mechanisms working in concert 
+led to the formation of a double layer.
+
+\subsection{CO Removal and double layer stability}
+Once a double layer had formed on the 50\%~Pt system it 
+remained for the rest of the simulation time with minimal 
+movement. There were configurations that showed small 
+wells or peaks forming, but typically within a few nanoseconds 
+the feature would smooth away. Within our simulation time, 
+the formation of the double layer was 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 had on this system, additional simulations were run starting 
+from a late configuration of the 50\%~Pt system that had formed 
+double layers. These simulations then had their CO removed. 
+The double layer breaks rapidly in these simulations, already 
+showing a well-defined splitting after 100~ps. Configurations of 
+this system are shown in Figure \ref{fig:breaking}. The coloring 
+of the top and bottom layers helps to exhibit how much mixing 
+the edges experience as they split. These systems were only 
+examined briefly, 10~ns, and within that time despite the initial 
+rapid splitting, the edges only moved another few \AA~apart.
+It is possible with longer simulation times that the 
+(557) lattice could be recovered as seen by Tao {\it et al}.\cite{Tao:2010}
+
+
+
+%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.}
+\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.pdf}
+%\caption{}
+
+%\end{figure}
+%\label{fig:clean}
+
+
 \section{Conclusion}
+In this work we have shown the reconstruction of the Pt(557) crystalline surface upon adsorption of CO in 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. 
 
+%Things I am not ready to remove yet
 
-\section{Acknowledgments}
+%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}
 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}
+%\end{doublespace}
+
+\begin{tocentry}
+%\includegraphics[height=3.5cm]{timelapse}
+\end{tocentry}
+
 \end{document}
