--- trunk/COonPt/firstTry.tex	2012/12/10 14:53:16	3807
+++ trunk/COonPt/firstTry.tex	2012/12/19 21:37:51	3826
@@ -1,11 +1,34 @@
-\documentclass[a4paper,12pt]{article}
-
+\documentclass[11pt]{article}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{times}
+\usepackage{mathptm}
 \usepackage{setspace}
-\usepackage{float}
-\usepackage{cite}
-\usepackage[pdftex]{graphicx}
-\usepackage[font=small,labelfont=bf]{caption}
+\usepackage{endfloat}
+\usepackage{caption}
+%\usepackage{tabularx}
+\usepackage{graphicx}
+\usepackage{multirow}
+%\usepackage{booktabs}
+%\usepackage{bibentry}
+%\usepackage{mathrsfs}
+\usepackage[square, comma, sort&compress]{natbib}
+\usepackage{url}
+\pagestyle{plain} \pagenumbering{arabic} \oddsidemargin 0.0cm
+\evensidemargin 0.0cm \topmargin -21pt \headsep 10pt \textheight
+9.0in \textwidth 6.5in \brokenpenalty=10000
 
+% double space list of tables and figures
+%\AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
+\setlength{\abovecaptionskip}{20 pt}
+\setlength{\belowcaptionskip}{30 pt}
+
+\bibpunct{}{}{,}{s}{}{;}
+\bibliographystyle{achemso}
+
+\begin{document}
+
+
 %%
 %Introduction
 %	Experimental observations
@@ -24,22 +47,33 @@
 %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}
 
-\begin{document}
-%Title
-\title{Investigation of the Pt and Au 557 Surface Reconstructions under a CO Atmosphere}
 %Date
-\date{Dec 15,  2012}
+\date{Dec 15, 2012}
+
 %authors
-\author{Joseph R.~Michalka, Patrick W. McIntyre, \& J.~Daniel Gezelter}
+
 % make the title
 \maketitle
 
-\doublespacing
+\begin{doublespace}
 
+\begin{abstract}
 
+\end{abstract}
 
+\newpage
+
+
 \section{Introduction}
 % Importance: catalytically active metals are important
 % 	Sub: Knowledge of how their surface structure affects their ability to catalytically facilitate certain reactions is growing, but is more reactionary than predictive
@@ -48,75 +82,214 @@
 %	Sub: Also, easier to observe what is going on and provide reasons and explanations
 %
 
+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 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}
 
-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. 
+This work an effort to understand the mechanism and timescale for
+surface restructuring using molecular simulations.  Since the dynamics
+of the process is of particular interest, we utilize classical force
+fields that represent a compromise between chemical accuracy and the
+computational efficiency necessary to observe the process of interest.
 
+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}
-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
+The challenge in modeling any solid/gas interface problem is the
+development of a sufficiently general yet computationally tractable
+model of the chemical interactions between the surface atoms and
+adsorbates.  Since the interfaces involved are quite large (10$^3$ -
+10$^6$ atoms) and respond slowly to perturbations, {\it ab initio}
+molecular dynamics
+(AIMD),\cite{KRESSE:1993ve,KRESSE:1993qf,KRESSE:1994ul} Car-Parrinello
+methods,\cite{CAR:1985bh,Izvekov:2000fv,Guidelli:2000fy} and quantum
+mechanical potential energy surfaces remain out of reach.
+Additionally, the ``bonds'' between metal atoms at a surface are
+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 used classical molecular
+dynamics with potential energy surfaces that are specifically tuned
+for transition metals.  In particular, we used the EAM potential for
+Au-Au and Pt-Pt interactions, while modeling the CO using a rigid
+three-site model developed by Straub and Karplus for studying
+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 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
+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,
+\begin{equation*}
+\bar{\rho}_i = \sum_{j\neq i} \rho_j(r_{ij})
+\end{equation*}
+Here, $\rho_j(r_{ij})$ is the function that describes the distance
+dependence of the valence electron distribution of atom $j$. The
+contribution to the potential that comes from placing atom $i$ at that
+location is then
+\begin{equation*}
+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.  
 
+% 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.
 
-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.
-%Metal
-\subsection{Metal}
-Recent metallic forcefields, inspired by density-functional theory, including EAM\cite{doi:10.1103/PhysRevB.29.6443, doi:10.1103/PhysRevB.33.7983} and QSC\cite{} have become very popular for modeling novel metallic systems.  What makes these forcefields more suitable for metals than their pair-wise predecessors is that they work with the total electron density of the system in a manner akin to DFT. The energy contributed by a single atom is a function of the total background electron density at the point where the atom is to be embedded. The density at any given point is well-approximated by a linear superposition of the electron density as contributed by all the other atoms in the system. The function describing the energy as related to the density is parameterized for each element, rather than by solving the Kohn-Sham equations which is what allows this method to be used for large systems. The embedding energy is completely enclosed within the functional $F_i[\rho_{h,i}]$ which is dependent on the host density $\rho_{h}$ at atom $i$. The density at $i$ is the sum of the density as generated by the rest of the metal. The $\phi_{ij}$ term is a purely repulsive pair-pair interaction parameterized from effective charge repulsions. 
-%Can I increase the \sum size, not sure how...
-\begin{equation}
-E_{tot} = \sum_i F_i[\rho_{h,i}] + \frac{1}{2}\sum_i\sum_{j(\ne i)} \phi_{ij}(R_{ij})
-\end{equation}
-\begin{equation}
-\rho_{h,i} = \sum_{j (\ne i)} \rho_j^a(R_{ij})
-\end{equation}
-The EAM functional forms are used to model the Au and Pt self-interactions in all of our simulations.
-%CO
-\subsection{CO}
-Our CO model was obtained from work done by Karplus and Straub\cite{}. In their description of the biological importance of CO they developed an accurate quadrupolar model of CO which we make use of in this work. It has been suggested that the strong electrostatic repulsion that arises from this linear quadrupole may play an important role in the restructuring of metal surfaces to which CO is bound\cite{}.
+The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen 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}  
+
+\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
+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 borrowed from 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 &  0.0262  & 3.83   &   -0.75 \\
+\textbf{O} &  0.4843 &   0.1591 &   3.12 &   -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}
 \end{table}
-%Cross
-\subsection{Cross-Interactions}
-To finish the forcefield, 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}
 
+Since the adsorption of CO onto a platinum 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
+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
+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
+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}
 
+%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
+Morse potentials, respectively, to reproduce Au-CO binding energies.
 
-%\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.
+The fits were refined against 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
+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
+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
+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}
 
 %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 potential, while the
+    (mostly-repulsive) 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\\
 
@@ -126,83 +299,201 @@ To finish the forcefield, the cross-interactions betwe
 
 %Table of energies
 \begin{table}[H]
-\caption{Adsorption energies in eV}
+  \caption{Adsorption energies for CO on M(111) 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}
 \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
+stability of the surfaces without a CO overlayer.  
 
+The different bulk (and surface) melting temperatures (1337~K for Au
+and 2045~K for Pt) suggest that the reconstruction may happen at
+different temperatures for the two metals.  To copy experimental
+conditions for the CO-exposed surfaces, the bare surfaces were
+initially run in the canonical (NVT) ensemble at 800~K and 1000~K
+respectively for 100 ps.  Each surface was exposed to a range of CO
+that was initially placed in the vacuum region.  Upon full adsorption,
+these amounts correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
+coverage.  Because of the difference in binding energies, the platinum
+systems very rarely had CO that was not bound to the surface, while
+the gold surfaces often had a significant CO population in the gas
+phase.  These systems were allowed to reach thermal equilibrium (over
+5 ns) before being shifted to the microcanonical (NVE) ensemble for
+data collection. All of the systems examined had at least 40 ns in the
+data collection stage, although simulation times for some of the
+systems exceeded 200ns.  All simulations were run using the open
+source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,OpenMD}
 
-
-
 % Just results, leave discussion for discussion section
 \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.
+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.
 
-%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 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.
 
+\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.
 
+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}.
+
+%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.
+
+\begin{figure}[H]
+\includegraphics[scale=0.6]{DiffusionComparison_error.png}
+\caption{Diffusion constants for mobile surface atoms along directions
+  parallel ($\mathbf{D}_{\parallel}$) and perpendicular
+  ($\mathbf{D}_{\perp}$) to the 557 step edges as a function of CO
+  surface coverage.  Diffusion parallel to the step edge is higher
+  than that perpendicular to the edge because of the lower energy
+  barrier associated with going from approximately 7 nearest neighbors
+  to 5, as compared to the 3 of an adatom. Additionally, the observed
+  maximum and subsequent decrease for the Pt system suggests that the
+  CO self-interactions are playing a significant role with regards to
+  movement of the platinum atoms around and more importantly across
+  the surface. }
+\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}
+
 %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.
 
+Mechanism for restructuring
+
+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.  
+
+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.  
+
+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.
+
 \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
 \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]{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.}
 \end{figure}
 
 
-
-
 %Peaks!
-\includegraphics[scale=0.25]{doublePeaks_noCO.png}
+\begin{figure}[H]
+\includegraphics[width=\linewidth]{doublePeaks_noCO.png}
+\caption{}
+\end{figure}
 \section{Conclusion}
 
 
+\section{Acknowledgments}
+Support for this project was provided by the National Science
+Foundation under grant CHE-0848243 and by the Center for Sustainable
+Energy at Notre Dame (cSEND). Computational time was provided by the
+Center for Research Computing (CRC) at the University of Notre Dame.
 
-
-
-
-
-
-
-
-
-\end{document}
\ No newline at end of file
+\newpage
+\bibliography{firstTryBibliography}
+\end{doublespace}
+\end{document}
