--- trunk/COonPt/firstTry.tex	2013/03/05 15:43:47	3868
+++ trunk/COonPt/firstTry.tex	2013/03/05 22:54:02	3869
@@ -68,19 +68,19 @@ We examine potential surface reconstructions of Pt and
 \begin{doublespace}
 
 \begin{abstract}
-We examine potential 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 magnitude of the diffusion constant was 
-also determined. An in-depth examination of the energetics of CO
-adsorbed to the surface provides results that appear sufficient to explain the 
-reconstructions observed on the Pt systems and the corresponding lack  
-on the Au systems.
+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}
 
 \newpage
@@ -130,7 +130,7 @@ The challenge in modeling any solid/gas interface prob
 %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$^3$ -
@@ -146,7 +146,7 @@ Au-Au and Pt-Pt interactions\cite{EAM}, while modeling
 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}, 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.
@@ -197,20 +197,17 @@ 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{Carbon Monoxide model}
 Previous explanations for the surface rearrangements center on
-the large linear quadrupole moment of carbon monoxide.  
+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 which places a massless M
-site at the center of mass position along the CO bond.  The geometry used along
-with the interaction parameters are reproduced in Table~\ref{tab:CO}. The effective 
+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 
@@ -219,15 +216,15 @@ 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}
@@ -241,18 +238,18 @@ clean metal surfaces. Parameters reported by Korzeniew
 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). These parameters are reproduced in Table~\ref{tab:co_parameters}
-This resulted in binding energies that are slightly higher
+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 at a larger
-minimum distance, ($r_o$).  This was chosen so that the C would be preferred
-over O as the binder to the surface. In most cases, this parameterization 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
@@ -263,10 +260,10 @@ The limited experimental data for CO adsorption on Au 
 %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 lead us to refine our fits against DFT.
+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
@@ -287,10 +284,10 @@ are shown in Table~\ref{co_parameters} and the binding
 
 %Hint at future work
 The parameters employed for the metal-CO cross-interactions in this work 
-are shown in Table~\ref{co_parameters} and the binding energies on the 
-(111) surfaces are displayed in Table~\ref{co_energies}.  Charge transfer
+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 added in
+affect binding energies and binding site preferences, and will be addressed in
 a future work.\cite{Deshlahra:2012,StreitzMintmire:1994}
 
 %Table  of Parameters
@@ -298,7 +295,7 @@ a future work.\cite{Deshlahra:2012,StreitzMintmire:199
 %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
+    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
@@ -316,7 +313,7 @@ a future work.\cite{Deshlahra:2012,StreitzMintmire:199
 
 %Table of energies
 \begin{table}[H]
-  \caption{Adsorption energies for CO on M(111) at the atop site using the potentials
+  \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 |}
@@ -342,25 +339,23 @@ The different bulk (and surface) melting 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 any possible reconstruction may happen at
+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. These temperatures were chosen because the 
-surfaces were relatively stable at these temperatures when no CO was 
-present, but experienced additional instability upon addition of CO in the time
-frames we were examining. 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. Higher coverages were tried, but the CO-CO repulsion was preventing
-a higher amount of adsorption.  Because of the difference in binding energies, the Pt
-systems very rarely had CO that was not bound to the surface, while
+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 200ns.  All simulations were run using the open
+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
@@ -372,39 +367,33 @@ Tao et al. showed experimentally that the Pt(557) surf
 % 	time scale, formation, breakage
 \section{Results}
 \subsection{Structural remodeling}
-Tao et al. showed experimentally that the Pt(557) surface 
+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, etc).
+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 appears to be correlated to the amount of CO 
-adsorbed upon the surface.  We believe this is related to the 
-effect that adsorbate coverage has on edge breakup and surface 
-diffusion of adatoms. While both systems displayed step-edge 
+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 we were modeling. Specifically, 
-only the 50~\% coverage Pt system was observed to have a 
-step-edge undergo a complete doubling in the time scales we 
-were able to monitor. This event encouraged us to allow that 
-specific system to run for much longer periods during which two 
-more double layers were created. The other systems, not displaying 
-any large scale changes of interest, were all stopped after running 
-for 40 ns in the microcanonical ensemble. Despite no observation 
-of double layer formation, the other Pt systems tended to show 
-more cumulative lateral movement of the step-edges when 
+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 the system.
+showing the evolution of a step-edge.
 
 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 
-our simulated time scales, experiences this reconstruction. A constructed 
-system in which the triangular motifs were constructed on the surface 
-will be explored in future work and is shown in the supporting information.
+the 40~ns time scale, experienced this reconstruction.
 
 \subsection{Dynamics}
 While atomistic-like simulations of stepped surfaces have been 
