--- trunk/COonPt/firstTry.tex	2012/12/10 16:46:27	3808
+++ trunk/COonPt/firstTry.tex	2013/03/05 22:54:02	3869
@@ -1,6 +1,8 @@
 \documentclass[11pt]{article}
 \usepackage{amsmath}
 \usepackage{amssymb}
+\usepackage{times}
+\usepackage{mathptm}
 \usepackage{setspace}
 \usepackage{endfloat}
 \usepackage{caption}
@@ -10,7 +12,6 @@
 %\usepackage{booktabs}
 %\usepackage{bibentry}
 %\usepackage{mathrsfs}
-%\usepackage[ref]{overcite}
 \usepackage[square, comma, sort&compress]{natbib}
 \usepackage{url}
 \pagestyle{plain} \pagenumbering{arabic} \oddsidemargin 0.0cm
@@ -18,12 +19,11 @@
 9.0in \textwidth 6.5in \brokenpenalty=10000
 
 % double space list of tables and figures
-\AtBeginDelayedFloats{\renewcommand{\baselinestretch}{1.66}}
+%\AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
 \setlength{\abovecaptionskip}{20 pt}
 \setlength{\belowcaptionskip}{30 pt}
 
-%\renewcommand\citemid{\ } % no comma in optional reference note
-\bibpunct{[}{]}{,}{n}{}{;}
+\bibpunct{}{}{,}{s}{}{;}
 \bibliographystyle{achemso}
 
 \begin{document}
@@ -48,15 +48,18 @@
 %%
 
 %Title
-\title{Investigation of the Pt and Au 557 Surface Reconstructions
-  under a CO Atmosphere}
-\author{Joseph R. Michalka, Patrick W. MacIntyre and J. Daniel
+\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}
+\date{Mar 5, 2013}
+
 %authors
 
 % make the title
@@ -65,6 +68,18 @@ Notre Dame, Indiana 46556}
 \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}
 
@@ -79,45 +94,43 @@ Industrial catalysts usually consist of small particle
 %	Sub: Also, easier to observe what is going on and provide reasons and explanations
 %
 
-Industrial catalysts usually consist of small particles exposing
-different atomic terminations that exhibit a high concentration of
-step, kink sites, and vacancies at the edges of the facets.  These
-sites are thought to be the locations catalytic
+Industrial catalysts usually consist of small particles that exhibit a
+high concentration of steps, kink sites, and vacancies at the edges of
+the facets.  These sites are thought to be the locations of catalytic
 activity.\cite{ISI:000083038000001,ISI:000083924800001} There is now
-significant evidence to demonstrate that solid surfaces are often
-structurally, compositionally, and chemically {\it modified} by
-reactants under operating conditions.\cite{Tao2008,Tao:2010,Tao2011}
-The coupling between surface oxidation state and catalytic activity
-for CO oxidation on Pt, for instance, is widely
-documented.\cite{Ertl08,Hendriksen:2002} Despite the well-documented
-role of these effects on reactivity, the ability to capture or predict
-them in atomistic models is currently somewhat limited.  While these
-effects are perhaps unsurprising on the highly disperse, multi-faceted
-nanoscale particles that characterize industrial catalysts, they are
-manifest even on ordered, well-defined surfaces. The Pt(557) surface,
-for example, exhibits substantial and reversible restructuring under
-exposure to moderate pressures of carbon monoxide.\cite{Tao:2010}
+significant evidence that solid surfaces are often structurally,
+compositionally, and chemically modified by reactants under operating
+conditions.\cite{Tao2008,Tao:2010,Tao2011} The coupling between
+surface oxidation states and catalytic activity for CO oxidation on
+Pt, for instance, is widely documented.\cite{Ertl08,Hendriksen:2002}
+Despite the well-documented role of these effects on reactivity, the
+ability to capture or predict them in atomistic models is somewhat
+limited.  While these effects are perhaps unsurprising on the highly
+disperse, multi-faceted nanoscale particles that characterize
+industrial catalysts, they are manifest even on ordered, well-defined
+surfaces. The Pt(557) surface, for example, exhibits substantial and
+reversible restructuring under exposure to moderate pressures of
+carbon monoxide.\cite{Tao:2010}
 
-This work is part of an ongoing effort to understand the causes,
-mechanisms and timescales for surface restructuring using molecular
-simulation methods.  Since the dynamics of the process is of
-particular interest, we utilize classical molecular dynamic methods
-with force fields that represent a compromise between chemical
-accuracy and the computational efficiency necessary to observe the
-process of interest.
+This work is an attempt to understand the mechanism and timescale for
+surface restructuring by using molecular simulations.  Since the dynamics
+of the process are of particular interest, we employ classical force
+fields that represent a compromise between chemical accuracy and the
+computational efficiency necessary to simulate the process of interest.
+Since restructuring typically occurs as a result of specific interactions of the
+catalyst with adsorbates, in this work, two metal systems exposed 
+to carbon monoxide were examined. The Pt(557) surface has already been shown
+to reconstruct under certain conditions. The Au(557) surface, because
+of a weaker interaction with CO, is less likely to undergo this kind
+of reconstruction.  
 
-High-index surfaces of catalytically active metals are an important area of exploration because they are typically more reactive than an ideal surface of the same metal. The greater number of low-coordinated surface atoms is believed responsible for this increased reactivity \cite{}. Additionally, the activity and specificity of many metals towards certain chemical processes has been shown to strongly depend on the structure of the surface \cite{}. Prior work has also shown that reaction conditions, such as high pressures and high temperatures are able to cause reconstructions of the metallic surface, either through changing the displayed surface facets or by changing the number and types of high-index sites available for reactions \cite{doi:10.1126/science.1197461,doi:10.1021/nn3015322, doi:10.1021/jp302379x}. A greater understanding of these high-index surfaces and the restructuring processes they undergo is needed as a prerequisite for more intelligent catalyst design. While current experimental work has started exploring systems at \emph{in situ} conditions, for a long time such experiments were limited to ideal surfaces in high vacuum. New techniques, such as ambient pressure XPS (AP-XPS) \cite{}, high-pressure XPS (HP-XPS) \cite{}, high-pressure STM \cite{}, environmental transmission electron microscopy (E-TEM) \cite{} and many others, are providing clearer pictures of the processes that are occurring on metal surfaces under these conditions. Nevertheless, all of these techniques still have limitations, especially in observing what is occurring at an atomic level. Theoretical models and simulations in combination with experiment have proven their worth in explaining the underlying reasons for some of these reconstructions \cite{}. 
-\\
-By examining two different metal-CO systems the effect that the metal and the metal-CO interaction plays can be elucidated. Our first system is composed of platinum and CO and has been the subject of many experimental and theoretical studies primarily because of platinum's strong reactivity toward CO oxidation. The focus has primarily been on adsorption energies, preferred adsorption sites, and catalytic activities. The second system we examined is composed of gold and CO. The gold-CO interaction is much weaker than the platinum-CO interaction and it seems likely that this difference in attraction would lead to differences in any potential surface reconstructions.
-%It has also been a good test for new quantum methods because of the difficulty with modeling the preference CO has for the atop binding site \cite{doi:10.1021/jp002302t}. 
-%Now that dynamic surface events are known to play a role in many catalytic systems, additional research is being done to more closely examine many systems. Recent work by Tao et al. \cite{doi:10.1126/science.1182122} shows that a high-index platinum surface undergoes surface reconstructions when exposed to a small amount of CO, $\sim$~1 torr. Unexpectedly,  the reconstruction was metastable and reverted upon removal of the CO. Work by McCarthy et al. \cite{doi:10.1021/jp302379x} examined temperature programmed desorption's of CO from various platinum samples and saw that species which had large amounts of low-coordinated surface atoms, highly sputtered surfaces or small nano particles, developed a higher temperature desorption peak, suggesting that binding of CO to the platinum surface is strongly dependent on local geometry. 
 
 
+%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$^3$ -
@@ -130,29 +143,29 @@ Coulomb potential.  For this work, we have been using 
 typically not well represented in terms of classical pairwise
 interactions in the same way that bonds in a molecular material are,
 nor are they captured by simple non-directional interactions like the
-Coulomb potential.  For this work, we have been using classical
-molecular dynamics with potential energy surfaces that are
-specifically tuned for transition metals.  In particular, we use the
-EAM potential for Au-Au and Pt-Pt interactions, while modeling the CO
-using a 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.
+Coulomb potential.  For this work, we have used classical molecular
+dynamics with potential energy surfaces that are specifically tuned
+for transition metals.  In particular, we used the EAM potential for
+Au-Au and Pt-Pt interactions\cite{EAM}. The CO was modeled using a rigid
+three-site model developed by Straub and Karplus for studying
+photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
+Pt-CO cross interactions were parameterized as part of this work.
   
 \subsection{Metal-metal interactions}
-Many of the potentials used for classical simulation of transition
-metals are based on a non-pairwise additive functional of the local
-electron density. The embedded atom method (EAM) is perhaps the best
-known of these
+Many of the potentials used for modeling transition metals are based
+on a non-pairwise additive functional of the local electron
+density. The embedded atom method (EAM) is perhaps the best known of
+these
 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 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, 
+atomic sites is computed at atom $i$'s location,
 \begin{equation*}
 \bar{\rho}_i = \sum_{j\neq i} \rho_j(r_{ij})
 \end{equation*}
@@ -164,19 +177,19 @@ $\phi_{ij}(r_{ij})$ 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
-pairwise interaction between two
-atoms.\cite{BASKES:1994fk,Lee:2000vn,Thijsse:2002ly,Timonova:2011ve}
-MEAM has become widely used to simulate systems in which angular
-interactions are important (e.g. silicon,\cite{Timonova:2011ve} bcc
-metals,\cite{Lee:2001qf} and also interfaces.\cite{Beurden:2002ys})
-MEAM presents significant additional computational costs, however.
+% The {\it modified} embedded atom method (MEAM) adds angular terms to
+% the electron density functions and an angular screening factor to the
+% pairwise interaction between two
+% atoms.\cite{BASKES:1994fk,Lee:2000vn,Thijsse:2002ly,Timonova:2011ve}
+% MEAM has become widely used to simulate systems in which angular
+% interactions are important (e.g. silicon,\cite{Timonova:2011ve} bcc
+% metals,\cite{Lee:2001qf} and also interfaces.\cite{Beurden:2002ys})
+% MEAM presents significant additional computational costs, however.
 
-The EAM, Finnis-Sinclair, MEAM, 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}
@@ -184,146 +197,453 @@ strengths and weaknesses.  One of the strengths common
 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} 
+strengths and weaknesses.  \cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
 
-\subsection{CO}
-Since one explanation for the strong surface CO repulsion on metals is
-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 three site model which places a massless M
-site WHERE?  GEOMETRY NEEDED. The effective dipole moment is still
-small (WHAT VALUE) while the linear quadrupole (WHAT VALUE) is close
-to the quantum mechanical predicition (WHAT VALUE).
+\subsection{Carbon Monoxide model}
+Previous explanations for the surface rearrangements center on
+the large linear quadrupole moment of carbon monoxide.\cite{Tao:2010}  
+We used a model first proposed by Karplus and Straub to study
+the photodissociation of CO from myoglobin because it reproduces 
+the quadrupole moment well.\cite{Straub} The Straub and
+Karplus model, treats CO as a rigid three site molecule with a massless M
+site at the molecular center of mass. The geometry and interaction 
+parameters are reproduced in Table~\ref{tab:CO}. The effective 
+dipole moment, calculated from the assigned charges, is still
+small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is close
+to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum 
+mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCOCalc}.
 %CO Table
 \begin{table}[H]
-\caption{$\sigma$, $\epsilon$ and charges for CO self-interactions\cite{}. Distances are in \AA~, energies are in kcal/mol, and charges are in $e$.}
+  \caption{Positions, Lennard-Jones parameters ($\sigma$ and
+    $\epsilon$), and charges for the CO-CO 
+    interactions in Ref.\bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA, energies are 
+    in kcal/mol, and charges are in atomic units.}
 \centering
-\begin{tabular}{| c | ccc |}
+\begin{tabular}{| c | c | ccc |}
 \hline
-\multicolumn{4}{|c|}{\textbf{Self-Interactions}}\\
+&  {\it z} & $\sigma$ & $\epsilon$ & q\\
 \hline
-&  $\sigma$ & $\epsilon$ & q\\
+\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
-\textbf{C} &  0.0262  & 3.83   &   -0.75 \\
-\textbf{O} &   0.1591 &   3.12 &   -0.85 \\
-\textbf{M} & -  &  -  &    1.6 \\
-\hline
 \end{tabular}
+\label{tab:CO}
 \end{table}
 
-\subsection{Cross-Interactions}
-The cross-interactions between the metals and the CO needed to be parameterized. Previous attempts at parameterization have used two different functional forms to model these interactions\cite{}. A LJ model was fit for the Metal-Carbon interaction and a Morse potential was parameterized for the Metal-Oxygen interaction. The parameter sets chosen, as shown in Table 2, did a suitable job at reproducing experimental adsorption energies as shown in Table 3, but more importantly, they were able to capture the binding site preference. The Pt-CO parameters show a slight preference for the atop binding site which matches the experimental observations.
+\subsection{Cross-Interactions between the metals and carbon monoxide}
 
-\subsection{Construction and Equilibration of 557 Metal interfaces}
+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. 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). These parameters are reproduced in Table~\ref{tab:co_parameters}.
+The modified parameters yield binding energies that are slightly higher
+than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
+et al.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
+Lennard-Jones interaction to mimic strong, but short-ranged partial
+binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
+Pt-O interaction was modeled with a Morse potential with a large
+equilibrium distance, ($r_o$).  These choices ensure that the C is preferred
+over O as the surface-binding atom. In most cases, the Pt-O parameterization contributes a weak
+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
+position.\cite{Deshlahra:2012, Hopster:1978}
 
-Our model systems are composed of approximately 4000 metal atoms cut along the 557 plane. The bare crystals were initially run in the Canonical ensemble at 1000K and 800K respectively for Pt and Au. The difference in temperature is necessary because of the two metals different melting points. Various amounts of CO were added to the simulation box and allowed to absorb to the metal surfaces over a short period of 100 ps. After further thermal relaxation the simulations were all run for at least 40 ns. A subset of the runs that showed interesting effects were allowed to run longer. The system
+%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 also fit using Lennard-Jones and
+Morse potentials, respectively, to reproduce Au-CO binding energies.
+The limited experimental data for CO adsorption on Au required refining the fits against plane-wave DFT calculations.
+Adsorption energies were obtained from gas-surface DFT calculations with a
+periodic supercell plane-wave basis approach, as implemented in the
+{\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores were
+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}
+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 
+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,PhysRevB.13.5188} 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 for the metal-CO cross-interactions in this work 
+are shown in Table~\ref{tab:co_parameters} and the binding energies on the 
+(111) surfaces are displayed in Table~\ref{tab:co_energies}.  Charge transfer
+and polarization are neglected in this model, although these effects are likely to
+affect binding energies and binding site preferences, and will be addressed in
+a future work.\cite{Deshlahra:2012,StreitzMintmire:1994}
 
-Our model systems are composed of approximately 4000 metal atoms cut along the 557 plane. This cut creates a stepped surface of 6x(111) surface plateaus separated by a single (100) atomic step height. The abundance of low-coordination atoms along the step edges acts as a suitable model for industrial catalysts which tend to have a high concentration of high-index sites. Experimental work has shown that such surfaces are notable for reconstructing upon adsorption\cite{}. Reconstructions have been seen for the Pt 557 surface that involve doubling of the step height and further formation of nano clusters with a triangular motif \cite{doi:10.1126/science.1182122}. To shed insight on whether this reconstruction is limited to the platinum surface, simulations of gold under similar conditions will also be examined. To properly observe these changes, our system size needs to be greater than the periodic phenomena we are examining. The large size and the long time scales needed precluded us from using quantum approaches. Thus, a forcefield describing the Metal-Metal, CO-CO, and CO-Metal interactions was parameterized and the simulations were run using OpenMD\cite{} an open-source molecular dynamics package.
-
-
-
-
-%\subsection{System}
-%Once equilibration was reached, the systems were exposed to various sub-monolayer coverage of CO: $0, \frac{1}{10}, \frac{1}{4}, \frac{1}{3},\frac{1}{2}$. The CO was started many \AA~above the surface with random velocity and rotational velocity vectors sampling from a Gaussian distribution centered on the temperature of the equilibrated metal block.  Full adsorption occurred over the period of approximately 10 ps for Pt, while the binding energy between Au and CO is smaller and led to an incomplete adsorption. The metal-metal interactions were treated using the Embedded Atom Method while the Pt-CO and Au-CO interactions were fit to experimental data and quantum calculations. The raised temperature helped shorten the length of the simulations by allowing the activation barrier of reconstruction to be more easily overcome. A few runs at lower temperatures showed the very beginnings of reconstructions, but their simulation lengths limited their usefulness.
-
-
 %Table  of Parameters
 %Pt Parameter Set 9
 %Au Parameter Set 35
 \begin{table}[H]
-\caption{Best fit parameters for metal-adsorbate interactions. Distances are in \AA~and energies are in kcal/mol}
+  \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 |}
 \hline
-\multicolumn{7}{| c |}{\textbf{Cross-Interactions} }\\
+ &  $\sigma$ & $\epsilon$ & & $r$ & $D$ & $\gamma$ (\AA$^{-1}$) \\
 \hline
- &  $\sigma$ & $\epsilon$ & & $r$ & $D$ & $\gamma$ \\
-\hline
 \textbf{Pt-C} & 1.3 & 15  & \textbf{Pt-O} & 3.8 & 3.0 & 1 \\
 \textbf{Au-C} & 1.9 & 6.5  & \textbf{Au-O} & 3.8 & 0.37 & 0.9\\
 
 \hline
 \end{tabular}
+\label{tab:co_parameters}
 \end{table}
 
 %Table of energies
 \begin{table}[H]
-\caption{Adsorption energies 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
- & Calc. & Exp. \\
-\hline
-\textbf{Pt-CO} & -1.9 & -1.4~\cite{Kelemen}-- -1.9~\cite{Yeo} \\
-\textbf{Au-CO} & -0.39 & -0.44~\cite{TPD_Gold_CO} \\
-\hline
+  \hline
+  & Calculated & Experimental \\
+  \hline
+  \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}) \\
+  \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 3384 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 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 observe the relative
+stability of the surfaces without a CO overlayer.  
 
-
-
+The different bulk melting temperatures (1337~K for Au
+and 2045~K for Pt) suggest that any possible reconstruction should happen at
+different temperatures for the two metals.  The bare Au and Pt surfaces were
+initially run in the canonical (NVT) ensemble at 800~K and 1000~K
+respectively for 100 ps. The two surfaces were relatively stable at these 
+temperatures when no CO was present, but experienced increased surface 
+mobility on addition of CO. Each surface was then dosed with different concentrations of CO
+that was initially placed in the vacuum region.  Upon full adsorption,
+these concentrations correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
+coverage. Higher coverages resulted in CO double layer formation, 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 of the
+systems exceeded 200~ns.  Simulations were run using the open
+source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE}
 
 % Just results, leave discussion for discussion section
+% structure
+%	Pt: step wandering, double layers, no triangular motifs
+%	Au: step wandering, no double layers
+% dynamics
+% 	diffusion
+% 	time scale, formation, breakage
 \section{Results}
-\subsection{Diffusion}
-While an ideal metallic surface is unlikely to experience much surface diffusion, high-index surfaces have large numbers of low-coordinated atoms which have a much easier time overcoming the energetic barriers limiting diffusion, leading to easier surface reconstructions. Surface movement was divided between the parallel ($\parallel$) and perpendicular ($\perp$) directions relative to the step edge. We were then able to calculate diffusion constants as a function of CO coverage. As can be seen in Table 4, the presence and amount of CO directly affects the diffusion constants of surface platinum atoms. The presence of two 50\% coverage systems is to show how the diffusion process is affected by time. The majority of the systems were run for approximately 50 ns while the half monolayer system been running continuously. The lowered diffusion constant at longer run times will be examined in-depth in the discussion section.
+\subsection{Structural remodeling}
+Tao et al. have shown experimentally that the Pt(557) surface 
+undergoes two separate reconstructions upon CO 
+adsorption.\cite{Tao:2010} The first involves a doubling of 
+the step height and plateau length. Similar behavior has been 
+seen to occur on numerous surfaces at varying conditions: Ni(977), Si(111).
+\cite{Williams:1994,Williams:1991,Pearl} Of the two systems 
+we examined, the Pt system showed a larger amount of 
+reconstruction when compared to the Au system. The amount 
+of reconstruction is correlated to the amount of CO 
+adsorbed upon the surface.  This appears to be related to the 
+effect that adsorbate coverage has on edge breakup and on the surface 
+diffusion of metal adatoms. While both systems displayed step-edge 
+wandering, only the Pt surface underwent the doubling seen by 
+Tao et al. within the time scales studied here.  
+Only the 50~\% coverage Pt system exhibited
+a complete doubling in the time scales we 
+were able to monitor. Over longer periods (150~ns) two more double layers formed on this interface. 
+Although double layer formation did not occur in the other Pt systems, they show 
+more lateral movement of the step-edges
+compared to the Au systems. The 50\% Pt system is highlighted 
+in Figure \ref{fig:reconstruct} at various times along the simulation 
+showing the evolution of a step-edge.
 
-%Table of Diffusion Constants
-%Add gold?M
-\begin{table}[H]
-\caption{Platinum diffusion constants parallel and perpendicular to the 557 step edge. As the coverage increases, the diffusion constants parallel and  perpendicular to the step edge both initially increase and then decrease slightly. There were two approaches of analysis. One looking at the surface atoms that had moved more than a prescribed amount over the run time and the other looking at all surface atoms. Units are \AA\textsuperscript{2}/ns}
-\centering
-\begin{tabular}{| c | ccc | ccc | c |}
-\hline
-\textbf{System Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & \textbf{Atoms} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & \textbf{Atoms} & \textbf{Time (ns)}\\
-\hline
-&\multicolumn{3}{c|}{\textbf{Mobile}}&\multicolumn{3}{c|}{\textbf{Surface Atoms}} & \\
-\hline
-50\% & 3.74 & 0.89 & 497 & 2.05 & 0.49 & 912 & 116 \\
-50\% & 5.81 & 1.59 & 365 & 2.41 & 0.68 & 912 & 46   \\
-33\% & 6.73 & 2.47 & 332 & 2.51 & 0.93 & 912 & 46   \\
-25\% & 5.38 & 2.04 & 361 & 2.18 & 0.84 & 912 & 46  \\
-5\% & 5.54 & 0.63 & 230 & 1.44 & 0.19 & 912 & 46  \\
-0\% & 3.53 & 0.61 & 282 & 1.11 & 0.22 & 912 & 56  \\
-\hline
-50\%-r & 6.91 & 2.00 & 198 & 2.23 & 0.68  & 925 & 25\\
-0\%-r  & 4.73 & 0.27 & 128 & 0.72 & 0.05 & 925 & 43\\
-\hline 
-\end{tabular}
-\end{table}
+The second reconstruction on the Pt(557) surface observed by 
+Tao involved the formation of triangular clusters that stretched 
+across the plateau between two step-edges. Neither system, within 
+the 40~ns time scale, experienced this reconstruction.
 
+\subsection{Dynamics}
+While atomistic-like simulations of stepped surfaces have been 
+performed before, they tend to be performed using Monte Carlo 
+techniques\cite{Williams:1991,Williams:1994}. This allows them 
+to efficiently sample the equilibrium thermodynamic landscape 
+but at the expense of ignoring the dynamics of the system. Previous
+work by Pearl and Sibener\cite{Pearl}, using STM, has been able to 
+visualize the coalescing of steps of Ni(977). The time scale of the image 
+acquisition, $\sim$70 s/image provides an upper bounds for the time 
+required for the doubling to actually occur. Statistical treatments of step-edges
+are adept at analyzing such systems. However, in a system where 
+the number of steps is limited, examining the individual atoms that make 
+up the steps can provide useful information as well. 
 
 
+\subsubsection{Transport of surface metal atoms}
+%forcedSystems/stepSeparation
+The movement or wandering of a step-edge is a cooperative effect 
+arising from the individual movements, primarily through surface 
+diffusion, of the atoms making up the step. 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 
+on higher-index surfaces provide a source for mobile metal atoms. 
+Breaking away from the step-edge on a clean surface still imposes an 
+energetic penalty around $\sim$~40 kcal/mole, but is much less than lifting 
+the same metal atom out from the surface,  \textgreater~60 kcal/mole, and 
+the penalty lowers even further when CO is present in sufficient quantities 
+on the surface. For certain tested distributions of CO, the penalty was lowered 
+to $\sim$~20 kcal/mole. Once an adatom exists on the surface, its barrier for 
+diffusion is negligible ( \textless~4 kcal/mole) and is well able to explore the 
+terrace before potentially rejoining its original step-edge or becoming a part 
+of a different edge. Atoms traversing separate terraces is a more difficult 
+process, but can be overcome through a joining and lifting stage which is 
+examined in the discussion section. By tracking the mobility of individual 
+metal atoms on the Pt and Au surfaces we were able to determine the relative 
+diffusion rates and how varying coverages of CO affected the rates. Close 
+observation of the mobile metal atoms showed that they were typically in 
+equilibrium with the step-edges, constantly breaking apart and rejoining. 
+At times their motion was concerted and two or more adatoms would be 
+observed moving together across the surfaces. The primary challenge in 
+quantifying the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
+
+A particle was considered mobile once it had traveled more than 2~\AA~
+between saved configurations of the system (10-100 ps). An atom that was 
+truly mobile would typically travel much greater than this, but the 2~\AA~ cutoff 
+was to prevent the in-place vibrational movement of non-surface atoms from 
+being included in the analysis. 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 different 
+from the diffusion perpendicular to these edges. This led us to compute 
+those diffusions separately as seen in Figure \ref{fig:diff}.
+
+\subsubsection{Double layer formation}
+The increased amounts of diffusion on Pt at the higher CO coverages appears
+to play a primary role in the formation of double layers, although this conclusion
+does not explain the 33\% coverage Pt system. On the 50\% system, three
+separate layers were formed over the extended run time of this system. As 
+mentioned earlier, previous experimental work has given some insight into the 
+upper bounds of the time required for enough atoms to move around to allow two 
+steps to coalesce\cite{Williams:1991,Pearl}. As seen in Figure \ref{fig:reconstruct},
+the first appearance of a double layer, a nodal site, appears at 19 ns into the 
+simulation. Within 12 ns, nearly half of the step has formed the double layer and 
+by 86 ns, a smooth complete layer has formed. The double layer is ``complete" by 
+37 ns but is a bit rough. From the appearance of the first node to the initial doubling 
+of the layers ignoring their roughness took $\sim$~20 ns. Another ~40 ns was 
+necessary for the layer to completely straighten. The other two layers in this 
+simulation form over a period of 22 ns and 42 ns respectively. Comparing this to 
+the upper bounds of the image scan, it is likely that aspects of this reconstruction 
+occur very quickly.
+
+%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}
+
+\begin{figure}[H]
+\includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade.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
+  than that perpendicular to the edge because of the lower energy
+  barrier associated with traversing along the edge as compared to
+  completely breaking away. 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 Pt atoms around and across the surface. }
+\label{fig:diff}
+\end{figure}
+
+
+
+
 %Discussion
 \section{Discussion}
-Comparing the results from simulation to those reported previously by Tao et al. the similarities in the platinum and CO system are quite strong. As shown in figure 1, the simulated platinum system under a CO atmosphere will restructure slightly by doubling the terrace heights. The restructuring appears to occur slowly, one to two platinum atoms at a time. Looking at individual snapshots, these adatoms tend to either rise on top of the plateau or break away from the step edge and then diffuse perpendicularly to the step direction until reaching another step edge. This combination of growth and decay of the step edges appears to be in somewhat of a state of dynamic equilibrium. However, once two previously separated edges meet as shown in figure 1.B, this point tends to act as a focus or growth point for the rest of the edge to meet up, akin to that of a zipper. From the handful of cases where a double layer was formed during the simulation. Measuring from the initial appearance of a growth point, the double layer tends to be fully formed within $\sim$~35 ns.
+In this paper we have shown that we were able to accurately model the initial reconstruction of the
+Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
+were able to observe the dynamic processes necessary for this reconstruction. 
 
+\subsection{Mechanism for restructuring}
+Comparing the results from simulation to those reported previously by 
+Tao et al.\cite{Tao:2010} the similarities in the Pt-CO system are quite 
+strong. As shown in Figure \ref{fig:reconstruct}, the simulated Pt 
+system under a CO atmosphere will restructure by doubling the terrace 
+heights. The restructuring occurs slowly, one to two Pt atoms at a time. 
+Looking at individual configurations of the system, the adatoms either 
+break away from the step-edge and stay on the lower terrace or they lift 
+up onto the higher terrace. Once ``free'' they will diffuse on the terrace 
+until reaching another step-edge or coming back to their original edge.  
+This combination of growth and decay of the step-edges is in a state of 
+dynamic equilibrium. However, once two previously separated edges 
+meet as shown in Figure 1.B, this meeting 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.
+
+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 likely 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 perhaps, this explanation 
+gains some weight.  The energetic repulsion between two CO located a 
+distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in 
+a  vertical orientation is 8.62 kcal/mole. Moving the CO apart to the second 
+nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to 
+nearly 0 kcal/mole. Allowing the CO's to leave a purely vertical orientation 
+also quickly drops the repulsion, a minimum is reached at $\sim$24 degrees 
+of 6.2 kcal/mole. As mentioned above, the energy barrier for surface diffusion 
+of a Pt adatom is only 4 kcal/mole. So this repulsion between CO can help 
+increase the surface diffusion. However, the residence time of CO was 
+examined and while the majority of the CO is on or near the surface throughout 
+the run, it is extremely mobile. This mobility suggests that the CO are more 
+likely to shift their positions without necessarily dragging the Pt along with them.
+
+Another possible and more likely mechanism for the restructuring is in the
+destabilization of strong Pt-Pt interactions by CO adsorbed on surface
+Pt atoms.  This would then have the effect of increasing surface mobility
+of these atoms.  To test this hypothesis, numerous configurations of 
+CO in varying quantities were arranged on the higher and lower plateaus
+around a step on a otherwise clean Pt(557) surface. One representative
+configuration is displayed in Figure \ref{fig:lambda}. Single or concerted movement
+of Pt atoms was then examined to determine possible barriers. Because
+the movement was forced along a pre-defined reaction coordinate that may differ
+from the true minimum of this path, only the beginning and ending energies
+are displayed in Table \ref{tab:energies}. These values suggest that the presence of CO at suitable
+locations can lead to lowered barriers for Pt breaking apart from the step-edge.
+Additionally, as highlighted in Figure \ref{fig:lambda}, the presence of CO makes the
+burrowing and lifting of adatoms favorable, whereas without CO, the process is neutral
+in terms of energetics.
+
+%lambda progression of Pt -> shoving its way into the step
+\begin{figure}[H]
+\includegraphics[width=\linewidth]{lambdaProgression_atopCO.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. As shown
+ in Table \ref{tab:rxcoord}, 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}
+
+
+
 \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?)
+As shown in the results section, the diffusion parallel to the step-edge tends to be 
+much larger than that perpendicular to the step-edge, likely because of the dynamic 
+equilibrium that is established between the step-edge and adatom interface. The coverage 
+of CO also appears to play a slight role in relative rates of diffusion, as shown in Figure \ref{fig:diff}.
+The 
+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. 
 \\
-\\
-%Evolution of surface
+
+
+%breaking of the double layer upon removal of CO
 \begin{figure}[H]
-\includegraphics[scale=0.5]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
-\caption{Four snapshots at various times a) 258 ps b) 19 ns c) 31.2 ns d) 86.1 ns. Slight disruption of the surface occurs fairly quickly. However, the doubling of the layers seems to be very dependent on the initial linking of two separate step edges. The focal point in b, appears to be a growth spot for the rest of the double layer.}
+\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!
-\includegraphics[scale=0.25]{doublePeaks_noCO.png}
+\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 < $\mu s$. 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
 
+%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}
+
 \section{Acknowledgments}
 Support for this project was provided by the National Science
 Foundation under grant CHE-0848243 and by the Center for Sustainable
