--- trunk/COonPt/firstTry.tex	2012/12/20 21:36:33	3839
+++ trunk/COonPt/firstTry.tex	2013/03/08 22:06:22	3870
@@ -58,7 +58,7 @@ Notre Dame, Indiana 46556}
 Notre Dame, Indiana 46556}
 
 %Date
-\date{Dec 15, 2012}
+\date{Mar 5, 2013}
 
 %authors
 
@@ -68,6 +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}
 
@@ -100,24 +112,35 @@ This work an effort to understand the mechanism and ti
 reversible restructuring under exposure to moderate pressures of
 carbon monoxide.\cite{Tao:2010}
 
-This work an effort to understand the mechanism and timescale for
-surface restructuring using molecular simulations.  Since the dynamics
-of the process is of particular interest, we utilize classical force
+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 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 seen as less 
+likely to undergo this kind of reconstruction. However, Peters et al.\cite{Peters:2000} 
+and Piccolo et al.\cite{Piccolo:2004} have both observed CO induced 
+reconstruction of a Au(111) surface. Peters et al. saw a relaxing of the 
+22 x $\sqrt{3}$ cell. They argued that a very small number of Au atoms
+would become adatoms, limiting the stress of this reconstruction while 
+allowing the rest of the row to relax and approach the ideal (111) 
+configuration. They did not see the ``herringbone'' pattern being greatly 
+affected by this relaxation. Piccolo et al. on the other hand, did see a 
+disruption of the ``herringbone'' pattern as CO was adsorbed to the 
+surface. Both groups suggested that the preference CO shows for 
+low-coordinated Au particles was the primary driving force for these reconstructions.
 
-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$^3$ -
@@ -133,7 +156,7 @@ 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.
@@ -146,7 +169,7 @@ 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 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
@@ -164,8 +187,8 @@ $\phi_{ij}(r_{ij})$ is an pairwise term that is meant 
 V_i =  F[ \bar{\rho}_i ]  + \sum_{j \neq i} \phi_{ij}(r_{ij})
 \end{equation*}
 where $F[ \bar{\rho}_i ]$ is an energy embedding functional, and
-$\phi_{ij}(r_{ij})$ is an pairwise term that is meant to represent the
-overlap of the two positively charged cores.  
+$\phi_{ij}(r_{ij})$ is a pairwise term that is meant to represent the
+repulsive overlap of the two positively charged cores.  
 
 % The {\it modified} embedded atom method (MEAM) adds angular terms to
 % the electron density functions and an angular screening factor to the
@@ -176,28 +199,38 @@ 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
+from the original parameterization, where the interactions
+up to the third nearest-neighbor were taken into account.\cite{Voter95a}
+Comparing that to the glue model of Ercolessi et al.\cite{Ercolessi88}
+which only parameterized up to the nearest-neighbor
+interactions, EAM is a suitable choice for systems where 
+the bulk properties are of secondary importance to low-index 
+surface structures. Additionally, the similarity of EAMs functional 
+treatment of the embedding energy to standard density functional 
+theory (DFT) approaches gives EAM, and conclusions derived, a firm theoretical footing.
+\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 three site model which places a massless M
-site at the center of mass along the CO bond.  The geometry used along
-with the interaction parameters are reproduced in Table~1. The effective 
+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 
@@ -206,37 +239,40 @@ mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCO
 \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
+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 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 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
@@ -245,45 +281,45 @@ 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
+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 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 are likely to
+affect binding energies and binding site preferences, and will be addressed in
+a future work.\cite{Deshlahra:2012,StreitzMintmire:1994}
 
 %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 +331,13 @@ 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
@@ -312,185 +349,313 @@ preferences.\cite{Deshlahra:2012}
   \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 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 has dimensions of 18~x~24~x~9 in a box of size
+54.482~x~50.046~x~120.88~\AA while our Au system has 
+dimensions of 18~x~24~x~8 in a box of size 57.4~x~51.9285~x~100~\AA.
+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 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
+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.  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 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 shifted to the microcanonical (NVE) ensemble for
+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 200ns.  All simulations were run using the open
-source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,OpenMD}
+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}
-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}
+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 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 step-edge.
 
-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.
+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.
 
-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.
+\subsection{Dynamics}
+Previous atomistic simulations of stepped surfaces were largely 
+concerned with the energetics and structures at different conditions
+\cite{Williams:1991,Williams:1994}. Consequently, the most common 
+technique has been Monte Carlo. Monte Carlo gives an efficient 
+sampling of the equilibrium thermodynamic landscape at the expense 
+of ignoring the dynamics of the system. Previous work by Pearl and 
+Sibener\cite{Pearl}, using STM, has been able to show the coalescing 
+of steps on Ni(977). The time scale of the image acquisition, 
+$\sim$70 s/image provides an upper bound for the time required for 
+the doubling to occur. In this section we give data on dynamic and 
+transport properties, e.g. diffusion, layer formation time, etc.
 
+
+\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 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 
+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/mol, but is much less than lifting 
+the same metal atom vertically out of the surface,  \textgreater~60 kcal/mol. 
+The penalty lowers significantly when CO is present in sufficient quantities 
+on the surface. For certain distributions of CO, the penalty can be as low as 
+$\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for 
+diffusion is negligible ( \textless~4 kcal/mol) and these adatoms are well 
+able to explore the terrace before rejoining either the 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 constants, as well as how varying coverages of CO affect the diffusion. Close 
+observation of the mobile metal atoms showed that they were typically in 
+equilibrium with the step-edges, dynamically breaking apart and rejoining the edges. 
+At times, their motion was concerted and two or more adatoms would be 
+observed moving together across the surfaces. 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 (10-100 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}.
+between saved configurations of the system (typically 10-100 ps). An atom that was 
+truly mobile would typically travel much greater distances than this, but the 2~\AA~ cutoff 
+was 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 different 
+from the diffusion perpendicular to these edges. Parallel and perpendicular
+diffusion constants 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.
+\subsubsection{Double layer formation dynamics}
+The increased amounts of diffusion on Pt at the higher CO coverages plays a primary role in the formation of the double layers observed on Pt. However, this is not a complete explanation as seen by the 33\% Pt system which has higher diffusion constants but did not show any signs of undergoing the doubling. This difference will be explored more fully in the discussion. On the 50\% Pt system, three separate layers were formed over the extended run time of this system. Previous experimental work has given some insight into the upper bounds of the time required for step coalescing.\cite{Williams:1991,Pearl} In this system, 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, the complete layer has been smoothed. The double layer could be considered ``complete" by 37 ns but is a bit rough or wavy. From the appearance of the first node to the first observed double layer, ignoring roughening, 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 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. A possible explanation for this rapid reconstruction is the elevated temperatures our systems were run at. It is likely that the process would take longer at lower temperatures and is an area of exploration for future work.
 
+%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
+  ($\mathbf{D}_{\perp}$) 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
+  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 platinum atoms around and more importantly across
-  the surface. }
+  movement of the Pt atoms around and 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(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}
 
+
+
 %Discussion
 \section{Discussion}
+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. 
 
-Mechanism for restructuring
+\subsection{Mechanism for restructuring}
+Since the Au surface showed no large scale restructuring throughout
+our simulation time our discussion will focus on the 50\% Pt-CO system
+which did undergo the doubling featured in Figure \ref{fig:reconstruct}.
+Comparing the results from this 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 exposed to a large dosage of CO will restructure by doubling the terrace 
+widths and step heights. The restructuring occurs in a piecemeal fashion, one to two Pt atoms at a time and as such is a fairly stochastic event. 
+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 rejoining their original edge.  
+This combination of growth and decay of the step-edges is in a state of 
+dynamic equilibrium. However, once two previously separated edges 
+meet as shown in Figure 1.B, this 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.
 
-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.  
+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 for example, 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/mol. Moving the CO apart to the second 
+nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to 
+nearly 0 kcal/mol. Allowing the CO's to leave a purely vertical orientation 
+also quickly drops the repulsion, a minimum of 6.2 kcal/mol is reached at $\sim$24 degrees between the 2 CO when the carbons are locked at a distance of 2.77 \AA apart.
+As mentioned above, the energy barrier for surface diffusion 
+of a Pt adatom is only 4 kcal/mol. So this repulsion between CO can help 
+increase the surface diffusion. However, the residence time of CO on Pt was 
+examined and while the majority of the CO is on or near the surface throughout 
+the run, 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 mechanism for the restructuring is in the
+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 could have the effect of increasing surface mobility
-of these atoms.  
+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.
 
-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.
+%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[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]{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{}
+\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}
-\begin{figure}[H]
-\includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
-\caption{}
-\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
 
+%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
