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1 < \documentclass[11pt]{article}
1 > \documentclass[journal = jpccck, manuscript = article]{achemso}
2 > \setkeys{acs}{usetitle = true}
3 > \usepackage{achemso}
4 > \usepackage{caption}
5 > \usepackage{float}
6 > \usepackage{geometry}
7 > \usepackage{natbib}
8 > \usepackage{setspace}
9 > \usepackage{xkeyval}
10 > %%%%%%%%%%%%%%%%%%%%%%%
11   \usepackage{amsmath}
12   \usepackage{amssymb}
13   \usepackage{times}
# Line 6 | Line 15
15   \usepackage{setspace}
16   \usepackage{endfloat}
17   \usepackage{caption}
18 < %\usepackage{tabularx}
18 > \usepackage{tabularx}
19 > \usepackage{longtable}
20   \usepackage{graphicx}
21   \usepackage{multirow}
22 < %\usepackage{booktabs}
23 < %\usepackage{bibentry}
24 < %\usepackage{mathrsfs}
25 < \usepackage[square, comma, sort&compress]{natbib}
22 > \usepackage{multicol}
23 > \mciteErrorOnUnknownfalse
24 > %\usepackage{epstopdf}
25 >
26 > \usepackage[version=3]{mhchem}  % this is a great package for formatting chemical reactions
27 > % \usepackage[square, comma, sort&compress]{natbib}
28   \usepackage{url}
29   \pagestyle{plain} \pagenumbering{arabic} \oddsidemargin 0.0cm
30   \evensidemargin 0.0cm \topmargin -21pt \headsep 10pt \textheight
31 < 9.0in \textwidth 6.5in \brokenpenalty=10000
31 > 9.0in \textwidth 6.5in \brokenpenalty=1110000
32  
33   % double space list of tables and figures
34   %\AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
35   \setlength{\abovecaptionskip}{20 pt}
36   \setlength{\belowcaptionskip}{30 pt}
37 + % \bibpunct{}{}{,}{s}{}{;}
38  
39 < \bibpunct{}{}{,}{s}{}{;}
40 < \bibliographystyle{achemso}
39 > %\citestyle{nature}
40 > % \bibliographystyle{achemso}
41  
42 < \begin{document}
42 > \title{Molecular Dynamics simulations of the surface reconstructions
43 >  of Pt(557) and Au(557) under exposure to CO}
44  
45 + \author{Joseph R. Michalka}
46 + \author{Patrick W. McIntyre}
47 + \author{J. Daniel Gezelter}
48 + \email{gezelter@nd.edu}
49 + \affiliation[University of Notre Dame]{251 Nieuwland Science Hall\\
50 +  Department of Chemistry and Biochemistry\\ University of Notre
51 +  Dame\\ Notre Dame, Indiana 46556}
52  
53 + \keywords{}
54 +
55 + \begin{document}
56 +
57 +
58   %%
59   %Introduction
60   %       Experimental observations
# Line 47 | Line 73
73   %Summary
74   %%
75  
50 %Title
51 \title{Molecular Dynamics simulations of the surface reconstructions
52  of Pt(557) and Au(557) under exposure to CO}
76  
54 \author{Joseph R. Michalka, Patrick W. McIntyre and J. Daniel
55 Gezelter\footnote{Corresponding author. \ Electronic mail: gezelter@nd.edu} \\
56 Department of Chemistry and Biochemistry,\\
57 University of Notre Dame\\
58 Notre Dame, Indiana 46556}
59
60 %Date
61 \date{Dec 15, 2012}
62
63 %authors
64
65 % make the title
66 \maketitle
67
68 \begin{doublespace}
69
77   \begin{abstract}
78 < We examine potential surface reconstructions of Pt and Au (557) under various CO coverages using molecular dynamics in order to find possible mechanisms and dynamics for the restructuring. The metal-CO interactions were parameterized as part of this work so that a large scale treatment of this system could be undertaken. The relative binding strengths of the metal-CO interactions were found to play a large role with regards to step edge stability and adatom diffusion. A small correlation between coverage and the size of the diffusion constant was also determined. These results appear sufficient to explain the reconstructions observed on the Pt systems and the lack of reconstructions on the Au systems.
78 >  The mechanism and dynamics of surface reconstructions of Pt(557) and
79 >  Au(557) exposed to various coverages of carbon monoxide (CO) were
80 >  investigated using molecular dynamics simulations. Metal-CO
81 >  interactions were parameterized from experimental data and
82 >  plane-wave Density Functional Theory (DFT) calculations.  The large
83 >  difference in binding strengths of the Pt-CO and Au-CO interactions
84 >  was found to play a significant role in step-edge stability and
85 >  adatom diffusion constants.  Various mechanisms for CO-mediated step
86 >  wandering and step doubling were investigated on the Pt(557)
87 >  surface.  We find that the energetics of CO adsorbed to the surface
88 >  can explain the step-doubling reconstruction observed on Pt(557) and
89 >  the lack of such a reconstruction on the Au(557) surface.
90   \end{abstract}
91  
92   \newpage
# Line 100 | Line 118 | This work is an attempt to understand the mechanism an
118   reversible restructuring under exposure to moderate pressures of
119   carbon monoxide.\cite{Tao:2010}
120  
121 < This work is an attempt to understand the mechanism and timescale for
121 > This work is an investigation into the mechanism and timescale for the Pt(557) \& Au(557)
122   surface restructuring using molecular simulations.  Since the dynamics
123   of the process are of particular interest, we employ classical force
124   fields that represent a compromise between chemical accuracy and the
125   computational efficiency necessary to simulate the process of interest.
126 <
127 < Restructuring can occur as a result of specific interactions of the
110 < catalyst with adsorbates. In this work, two metal systems exposed
126 > Since restructuring typically occurs as a result of specific interactions of the
127 > catalyst with adsorbates, in this work, two metal systems exposed
128   to carbon monoxide were examined. The Pt(557) surface has already been shown
129 < to reconstruct under certain conditions. The Au(557) surface, because
130 < of a weaker interaction with CO, is less likely to undergo this kind
131 < of reconstruction.  MORE HERE ON PT AND AU PREVIOUS WORK.
129 > to undergo a large scale reconstruction under certain conditions.\cite{Tao:2010}
130 > The Au(557) surface, because of a weaker interaction with CO, is less
131 > likely to undergo this kind of reconstruction. However, Peters {\it et al}.\cite{Peters:2000}
132 > and Piccolo {\it et al}.\cite{Piccolo:2004} have both observed CO-induced
133 > reconstruction of a Au(111) surface. Peters {\it et al}. saw a relaxation to the
134 > 22 x $\sqrt{3}$ cell. They argued that only a few Au atoms
135 > become adatoms, limiting the stress of this reconstruction, while
136 > allowing the rest to relax and approach the ideal (111)
137 > configuration. They did not see the usual herringbone pattern on Au(111) being greatly
138 > affected by this relaxation. Piccolo {\it et al}. on the other hand, did see a
139 > disruption of the herringbone pattern as CO was adsorbed to the
140 > surface. Both groups suggested that the preference CO shows for
141 > low-coordinated Au atoms was the primary driving force for the reconstruction.
142  
143 +
144 +
145   %Platinum molecular dynamics
146   %gold molecular dynamics
147  
148   \section{Simulation Methods}
149 < The challenge in modeling any solid/gas interface problem is the
149 > The challenge in modeling any solid/gas interface is the
150   development of a sufficiently general yet computationally tractable
151   model of the chemical interactions between the surface atoms and
152   adsorbates.  Since the interfaces involved are quite large (10$^3$ -
153 < 10$^6$ atoms) and respond slowly to perturbations, {\it ab initio}
153 > 10$^4$ atoms) and respond slowly to perturbations, {\it ab initio}
154   molecular dynamics
155   (AIMD),\cite{KRESSE:1993ve,KRESSE:1993qf,KRESSE:1994ul} Car-Parrinello
156   methods,\cite{CAR:1985bh,Izvekov:2000fv,Guidelli:2000fy} and quantum
# Line 133 | Line 162 | Au-Au and Pt-Pt interactions\cite{EAM}, while modeling
162   Coulomb potential.  For this work, we have used classical molecular
163   dynamics with potential energy surfaces that are specifically tuned
164   for transition metals.  In particular, we used the EAM potential for
165 < Au-Au and Pt-Pt interactions\cite{EAM}, while modeling the CO using a rigid
165 > Au-Au and Pt-Pt interactions.\cite{Foiles86} The CO was modeled using a rigid
166   three-site model developed by Straub and Karplus for studying
167   photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
168   Pt-CO cross interactions were parameterized as part of this work.
# Line 146 | Line 175 | parameter sets. The glue model of Ercolessi {\it et al
175   methods,\cite{Daw84,Foiles86,Johnson89,Daw89,Plimpton93,Voter95a,Lu97,Alemany98}
176   but other models like the Finnis-Sinclair\cite{Finnis84,Chen90} and
177   the quantum-corrected Sutton-Chen method\cite{QSC,Qi99} have simpler
178 < parameter sets. The glue model of Ercolessi {\it et al.} is among the
179 < fastest of these density functional approaches.\cite{Ercolessi88} In
180 < all of these models, atoms are conceptualized as a positively charged
178 > parameter sets. The glue model of Ercolessi {\it et al}.\cite{Ercolessi88} is among the
179 > fastest of these density functional approaches. In
180 > all of these models, atoms are treated as a positively charged
181   core with a radially-decaying valence electron distribution. To
182   calculate the energy for embedding the core at a particular location,
183   the electron density due to the valence electrons at all of the other
# Line 183 | Line 212 | dynamics.\cite{Shibata:2002hh} All of these potentials
212   melting,\cite{Belonoshko00,sankaranarayanan:155441,Sankaranarayanan:2005lr}
213   fracture,\cite{Shastry:1996qg,Shastry:1998dx} crack
214   propagation,\cite{BECQUART:1993rg} and alloying
215 < dynamics.\cite{Shibata:2002hh} All of these potentials have their
216 < strengths and weaknesses.  One of the strengths common to all of the
217 < methods is the relatively large library of metals for which these
218 < potentials have been
219 < parameterized.\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
215 > dynamics.\cite{Shibata:2002hh} One of EAM's strengths
216 > is its sensitivity to small changes in structure. This arises
217 > because interactions
218 > up to the third nearest neighbor were taken into account in the parameterization.\cite{Voter95a}
219 > Comparing that to the glue model of Ercolessi {\it et al}.\cite{Ercolessi88}
220 > which is only parameterized up to the nearest-neighbor
221 > interactions, EAM is a suitable choice for systems where
222 > the bulk properties are of secondary importance to low-index
223 > surface structures. Additionally, the similarity of EAM's functional
224 > treatment of the embedding energy to standard density functional
225 > theory (DFT) makes fitting DFT-derived cross potentials with adsorbates somewhat easier.
226 > \cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
227  
228 +
229 +
230 +
231   \subsection{Carbon Monoxide model}
232   Previous explanations for the surface rearrangements center on
233 < the large linear quadrupole moment of carbon monoxide.  
233 > the large linear quadrupole moment of carbon monoxide.\cite{Tao:2010}  
234   We used a model first proposed by Karplus and Straub to study
235   the photodissociation of CO from myoglobin because it reproduces
236   the quadrupole moment well.\cite{Straub} The Straub and
237 < Karplus model, treats CO as a rigid three site molecule which places a massless M
238 < site at the center of mass position along the CO bond.  The geometry used along
239 < with the interaction parameters are reproduced in Table~\ref{tab:CO}. The effective
237 > Karplus model treats CO as a rigid three site molecule with a massless M
238 > site at the molecular center of mass. The geometry and interaction
239 > parameters are reproduced in Table~\ref{tab:CO}. The effective
240   dipole moment, calculated from the assigned charges, is still
241   small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is close
242   to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum
# Line 206 | Line 245 | mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCO
245   \begin{table}[H]
246    \caption{Positions, Lennard-Jones parameters ($\sigma$ and
247      $\epsilon$), and charges for the CO-CO
248 <    interactions borrowed from Ref. \bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA~, energies are
248 >    interactions in Ref.\bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA, energies are
249      in kcal/mol, and charges are in atomic units.}
250   \centering
251   \begin{tabular}{| c | c | ccc |}
252   \hline
253   &  {\it z} & $\sigma$ & $\epsilon$ & q\\
254   \hline
255 < \textbf{C} & -0.6457 &  0.0262  & 3.83   &   -0.75 \\
256 < \textbf{O} &  0.4843 &   0.1591 &   3.12 &   -0.85 \\
255 > \textbf{C} & -0.6457 &  3.83 & 0.0262   &   -0.75 \\
256 > \textbf{O} &  0.4843 &  3.12 &  0.1591  &   -0.85 \\
257   \textbf{M} & 0.0 & -  &  -  &    1.6 \\
258   \hline
259   \end{tabular}
# Line 223 | Line 262 | Since the adsorption of CO onto a platinum surface has
262  
263   \subsection{Cross-Interactions between the metals and carbon monoxide}
264  
265 < Since the adsorption of CO onto a platinum surface has been the focus
265 > Since the adsorption of CO onto a Pt surface has been the focus
266   of much experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979}
267   and theoretical work
268   \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
269   there is a significant amount of data on adsorption energies for CO on
270 < clean metal surfaces. Parameters reported by Korzeniewski {\it et
271 <  al.}\cite{Pons:1986} were a starting point for our fits, which were
270 > clean metal surfaces. An earlier model by Korzeniewski {\it et
271 >  al.}\cite{Pons:1986} served as a starting point for our fits. The parameters were
272   modified to ensure that the Pt-CO interaction favored the atop binding
273 < position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}
274 < This resulted in binding energies that are slightly higher
273 > position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}.
274 > The modified parameters yield binding energies that are slightly higher
275   than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
276 < {\it et al.},\cite{Pons:1986} the Pt-C interaction was fit to a deep
277 < Lennard-Jones interaction to mimic strong, but short-ranged partial
276 > {\it et al}.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
277 > Lennard-Jones interaction to mimic strong, but short-ranged, partial
278   binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
279 < Pt-O interaction was parameterized to a Morse potential at a larger
280 < minimum distance, ($r_o$).  This was chosen so that the C would be preferred
281 < over O as the binder to the surface. In most cases, this parameterization contributes a weak
279 > Pt-O interaction was modeled with a Morse potential with a large
280 > equilibrium distance, ($r_o$).  These choices ensure that the C is preferred
281 > over O as the surface-binding atom. In most geometries, the Pt-O parameterization contributes a weak
282   repulsion which favors the atop site.  The resulting potential-energy
283   surface suitably recovers the calculated Pt-C separation length
284   (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
# Line 250 | Line 289 | The limited experimental data for CO adsorption on Au
289   %same cutoff for slab and slab + CO ? seems low, although feibelmen had values around there...
290   The Au-C and Au-O cross-interactions were also fit using Lennard-Jones and
291   Morse potentials, respectively, to reproduce Au-CO binding energies.
292 < The limited experimental data for CO adsorption on Au lead us to refine our fits against DFT.
292 > The limited experimental data for CO adsorption on Au required refining the fits against plane-wave DFT calculations.
293   Adsorption energies were obtained from gas-surface DFT calculations with a
294   periodic supercell plane-wave basis approach, as implemented in the
295 < {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores are
295 > {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores were
296   described with the projector augmented-wave (PAW)
297   method,\cite{PhysRevB.50.17953,PhysRevB.59.1758} with plane waves
298   included to an energy cutoff of 20 Ry. Electronic energies are
# Line 267 | Line 306 | zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxe
306   performed until the energy difference between subsequent steps
307   was less than $10^{-8}$ Ry.   Nonspin-polarized supercell calculations
308   were performed with a 4~x~4~x~4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
309 < zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxed gold slab was
309 > zone.\cite{Monkhorst:1976} The relaxed gold slab was
310   then used in numerous single point calculations with CO at various
311   heights (and angles relative to the surface) to allow fitting of the
312   empirical force field.
313  
314   %Hint at future work
315   The parameters employed for the metal-CO cross-interactions in this work
316 < are shown in Table~\ref{co_parameters} and the binding energies on the
317 < (111) surfaces are displayed in Table~\ref{co_energies}.  Charge transfer
318 < and polarization are neglected in this model, although these effects are likely to
319 < affect binding energies and binding site preferences, and will be added in
281 < a future work.\cite{Deshlahra:2012,StreitzMintmire}
316 > are shown in Table~\ref{tab:co_parameters} and the binding energies on the
317 > (111) surfaces are displayed in Table~\ref{tab:co_energies}.  Charge transfer
318 > and polarization are neglected in this model, although these effects could have
319 > an effect on  binding energies and binding site preferences.
320  
321   %Table  of Parameters
322   %Pt Parameter Set 9
323   %Au Parameter Set 35
324   \begin{table}[H]
325 <  \caption{Best fit parameters for metal-CO cross-interactions.   Metal-C
326 <    interactions are modeled with Lennard-Jones potential, while the
327 <    (mostly-repulsive) metal-O interactions were fit to Morse
325 >  \caption{Best fit parameters for metal-CO cross-interactions. Metal-C
326 >    interactions are modeled with Lennard-Jones potentials. While the
327 >    metal-O interactions were fit to Morse
328      potentials.  Distances are given in \AA~and energies in kcal/mol. }
329   \centering
330   \begin{tabular}{| c | cc | c | ccc |}
# Line 303 | Line 341 | a future work.\cite{Deshlahra:2012,StreitzMintmire}
341  
342   %Table of energies
343   \begin{table}[H]
344 <  \caption{Adsorption energies for CO on M(111) using the potentials
345 <    described in this work.  All values are in eV}
344 >  \caption{Adsorption energies for a single CO at the atop site on M(111) at the atop site using the potentials
345 >    described in this work.  All values are in eV.}
346   \centering
347   \begin{tabular}{| c | cc |}
348    \hline
# Line 313 | Line 351 | a future work.\cite{Deshlahra:2012,StreitzMintmire}
351    \multirow{2}{*}{\textbf{Pt-CO}} & \multirow{2}{*}{-1.9} & -1.4 \bibpunct{}{}{,}{n}{}{,}
352    (Ref. \protect\cite{Kelemen:1979}) \\
353   & &  -1.9 \bibpunct{}{}{,}{n}{}{,} (Ref. \protect\cite{Yeo}) \\ \hline
354 <  \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPD_Gold}) \\
354 >  \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPDGold}) \\
355    \hline
356   \end{tabular}
357   \label{tab:co_energies}
358   \end{table}
359  
360   \subsection{Pt(557) and Au(557) metal interfaces}
361 <
362 < Our model systems are composed of 3888 Pt atoms and 3384 Au atoms in a
363 < FCC crystal that have been cut along the 557 plane so that they are
364 < periodic in the {\it x} and {\it y} directions, and have been rotated
365 < to expose two parallel 557 cuts along the positive and negative {\it
366 <  z}-axis.  Simulations of the bare metal interfaces at temperatures
367 < ranging from 300~K to 1200~K were done to observe the relative
361 > Our Pt system is an orthorhombic periodic box of dimensions
362 > 54.482~x~50.046~x~120.88~\AA~while our Au system has
363 > dimensions of 57.4~x~51.9285~x~100~\AA. The metal slabs
364 > are 9 and 8 atoms deep respectively, corresponding to a slab
365 > thickness of $\sim$21~\AA~ for Pt and $\sim$19~\AA~for Au.
366 > The systems are arranged in a FCC crystal that have been cut
367 > along the (557) plane so that they are periodic in the {\it x} and
368 > {\it y} directions, and have been oriented to expose two aligned
369 > (557) cuts along the extended {\it z}-axis.  Simulations of the
370 > bare metal interfaces at temperatures ranging from 300~K to
371 > 1200~K were performed to confirm the relative
372   stability of the surfaces without a CO overlayer.  
373  
374 < The different bulk (and surface) melting temperatures (1337~K for Au
375 < and 2045~K for Pt) suggest that the reconstruction may happen at
376 < different temperatures for the two metals.  To copy experimental
335 < conditions for the CO-exposed surfaces, the bare surfaces were
374 > The different bulk melting temperatures predicted by EAM (1345~$\pm$~10~K for Au\cite{Au:melting}
375 > and $\sim$~2045~K for Pt\cite{Pt:melting}) suggest that any possible reconstruction should happen at
376 > different temperatures for the two metals.  The bare Au and Pt surfaces were
377   initially run in the canonical (NVT) ensemble at 800~K and 1000~K
378 < respectively for 100 ps.  Each surface was exposed to a range of CO
378 > respectively for 100 ps. The two surfaces were relatively stable at these
379 > temperatures when no CO was present, but experienced increased surface
380 > mobility on addition of CO. Each surface was then dosed with different concentrations of CO
381   that was initially placed in the vacuum region.  Upon full adsorption,
382 < these amounts correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
383 < coverage.  Because of the difference in binding energies, the platinum
384 < systems very rarely had CO that was not bound to the surface, while
385 < the gold surfaces often had a significant CO population in the gas
382 > these concentrations correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
383 > coverage. Higher coverages resulted in the formation of a double layer of CO,
384 > which introduces artifacts that are not relevant to (557) reconstruction.
385 > Because of the difference in binding energies, nearly all of the CO was bound to the Pt surface, while
386 > the Au surfaces often had a significant CO population in the gas
387   phase.  These systems were allowed to reach thermal equilibrium (over
388 < 5 ns) before being shifted to the microcanonical (NVE) ensemble for
389 < data collection. All of the systems examined had at least 40 ns in the
390 < data collection stage, although simulation times for some of the
391 < systems exceeded 200ns.  All simulations were run using the open
392 < source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,OpenMD}
388 > 5~ns) before being run in the microcanonical (NVE) ensemble for
389 > data collection. All of the systems examined had at least 40~ns in the
390 > data collection stage, although simulation times for some Pt of the
391 > systems exceeded 200~ns.  Simulations were carried out using the open
392 > source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,openmd}
393  
394 < % Just results, leave discussion for discussion section
395 < % structure
396 < %       Pt: step wandering, double layers, no triangular motifs
397 < %       Au: step wandering, no double layers
398 < % dynamics
355 < %       diffusion
356 < %       time scale, formation, breakage
394 >
395 >
396 >
397 > % RESULTS
398 > %
399   \section{Results}
400   \subsection{Structural remodeling}
401 < Tao {\it et al.} showed experimentally that the Pt(557) surface undergoes
402 < two separate reconstructions upon CO adsorption.\cite{Tao:2010} The first
403 < reconstruction involves a doubling of the step height and plateau length. Similar
404 < behavior has been seen to occur on numerous surfaces at varying conditions.\cite{Williams:1994,Williams:1991,Pearl}
405 < Of the two systems we examined, the Platinum system showed the most surface
406 < reconstruction. Additionally, the amount of reconstruction appears to be
407 < dependent on the amount of CO adsorbed upon the surface. This result is likely
408 < related to the effect that coverage has on surface diffusion. While both systems
409 < displayed step edge wandering, only the Pt surface underwent doubling within
410 < the time scales we were modeling. Specifically only the 50 \% coverage Pt system
411 < was observed to undergo a complete doubling in the time scales we were able to monitor.
370 < This event encouraged us to allow that specific system to run continuously during which two
371 < more double layers were created. The other systems, not displaying any large scale changes
372 < of interest, were all stopped after 40 ns of simulation. Neverthless, the other Platinum systems tended to show
373 < more cumulative lateral movement of the step edges when compared to the Gold systems.
374 < The 50 \% Pt system is highlighted in figure \ref{fig:reconstruct} at various times along the
375 < simulation showing the evolution of the system.
401 > The bare metal surfaces experienced minor roughening of the
402 > step-edge because of the elevated temperatures, but the (557)
403 > face was stable throughout the simulations. The surface of both
404 > systems, upon dosage of CO, began to undergo extensive remodeling
405 > that was not observed in the bare systems. Reconstructions of
406 > the Au systems were limited to breakup of the step-edges and
407 > some step wandering. The lower coverage Pt systems experienced
408 > similar restructuring but to a greater extent. The 50\% coverage
409 > Pt system was unique among our simulations in that it formed
410 > well-defined and stable double layers through step coalescence,
411 > similar to results reported by Tao {\it et al}.\cite{Tao:2010}
412  
377 The second reconstruction on the Pt(557) surface observed by Tao involved the
378 formation of triangular clusters that stretched across the plateau between two step edges.
379 Neither system, within our simulated time scales, experiences this reconstruction. A constructed
380 system in which the triangular motifs were constructed on the surface will be explored in future
381 work and is shown in the supporting information.
413  
414 < \subsection{Dynamics}
415 < While atomistic-like simulations of stepped surfaces have been performed before \cite{}, they tend to be
416 < performed using Monte Carlo techniques\cite{Williams:1991,Williams:1994}. This allows them to efficiently sample the thermodynamic
417 < landscape but at the expense of ignoring the dynamics of the system. Previous work, using STM \cite{Pearl},
418 < has been able to visualize the coalescing of steps of (system). The time scale of the image acquisition, ~ 70 s/image
419 < provides an upper bounds for the time required for the doubling to actually occur. While statistical treatments
420 < of step edges are adept at analyzing such systems, it is important to remember that the edges are made
421 < up of individual atoms and thus can be examined in numerous ways.
414 > \subsubsection{Step wandering}
415 > The 0\% coverage surfaces for both metals showed minimal
416 > step-wandering at their respective temperatures. As the CO
417 > coverage increased however, the mobility of the surface atoms,
418 > described through adatom diffusion and step-edge wandering,
419 > also increased.  Except for the 50\% Pt system where step
420 > coalescence occurred, the step-edges in the other simulations
421 > preferred to keep nearly the same distance between steps as in
422 > the original (557) lattice, $\sim$13\AA~for Pt and $\sim$14\AA~for Au.
423 > Previous work by Williams {\it et al}.\cite{Williams:1991, Williams:1994}
424 > highlights the repulsion that exists between step-edges even
425 > when no direct interactions are present in the system. This
426 > repulsion is caused by an entropic barrier that arises from
427 > the fact that steps cannot cross over one another. This entropic
428 > repulsion does not completely define the interactions between
429 > steps, however, so it is possible to observe step coalescence
430 > on some surfaces.\cite{Williams:1991} The presence and
431 > concentration of adsorbates, as shown in this work, can
432 > affect step-step interactions, potentially leading to a new
433 > surface structure as the thermodynamic equilibrium.
434  
435 < \subsubsection{Transport of surface metal atoms}
436 < %forcedSystems/stepSeparation
437 < The movement of a step edge is a cooperative effect arising from the individual movements of the atoms
438 < making up the step. An ideal metal surface displaying a low index facet (111, 100, 110) is unlikely to
439 < experience much surface diffusion because of the large energetic barrier to lift an atom out of the surface.
440 < For our surfaces however, the presence of step edges provide a source for mobile metal atoms. Breaking away
441 < from the step edge still imposes an energetic penalty around 40 kcal/mole, but is much less than lifting the same metal
442 < atom out from the surface,  > 60 kcal/mole, and the penalty lowers even further when CO is present in sufficient quantities
443 < on the surface, ~20 kcal/mole. Once an adatom exists on the surface, its barrier for diffusion is negligible ( < 4 kcal/mole)
444 < and is well able to explore its terrace. Atoms traversing terraces is more difficult, but can be overcome through a joining and lifting stage.
445 < By tracking the mobility of individual metal atoms on the Platinum and Gold surfaces we were able to determine
446 < the relative diffusion rates and how varying coverages of CO affected the rates. Close
447 < observation of the mobile metal atoms showed that they were typically in equilibrium with the
448 < step edges, constantly breaking apart and rejoining. Additionally, at times their motion was concerted and
449 < two or more atoms would be observed moving together across the surfaces. The primary challenge in quantifying
450 < the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
435 > \subsubsection{Double layers}
436 > Tao {\it et al}.\cite{Tao:2010} have shown experimentally that the Pt(557) surface
437 > undergoes two separate reconstructions upon CO adsorption.
438 > The first involves a doubling of the step height and plateau length.
439 > Similar behavior has been seen on a number of surfaces
440 > at varying conditions, including Ni(977) and Si(111).\cite{Williams:1994,Williams:1991,Pearl}
441 > Of the two systems we examined, the Pt system showed a greater
442 > propensity for reconstruction  
443 > because of the larger surface mobility and the greater extent of step wandering.
444 > The amount of reconstruction was strongly correlated to the amount of CO
445 > adsorbed upon the surface.  This appears to be related to the
446 > effect that adsorbate coverage has on edge breakup and on the
447 > surface diffusion of metal adatoms. Only the 50\% Pt surface underwent the
448 > doubling seen by Tao {\it et al}.\cite{Tao:2010} within the time scales studied here.
449 > Over a longer time scale (150~ns) two more double layers formed
450 > on this surface. Although double layer formation did not occur
451 > in the other Pt systems, they exhibited more step-wandering and
452 > roughening compared to their Au counterparts. The
453 > 50\% Pt system is highlighted in Figure \ref{fig:reconstruct} at
454 > various times along the simulation showing the evolution of a double layer step-edge.
455  
456 < A particle was considered mobile once it had traveled more than 2~\AA~ between saved configurations
457 < of the system (10-100 ps). An atom that was truly mobile would typically travel much greater than this, but
458 < the 2~\AA~ cutoff was to prevent the in-place vibrational movement of atoms from being included in the analysis.
459 < Since diffusion on  a surface is strongly affected by local structures, in this case the presence of single and double
460 < layer step edges, the diffusion parallel to the step edges was determined separately from the diffusion perpendicular
414 < to these edges. The parallel and perpendicular diffusion constants are shown in figure \ref{fig:diff}.
456 > The second reconstruction observed by
457 > Tao {\it et al}.\cite{Tao:2010} involved the formation of triangular clusters that stretched
458 > across the plateau between two step-edges. Neither metal, within
459 > the 40~ns time scale or the extended simulation time of 150~ns for
460 > the 50\% Pt system, experienced this reconstruction.
461  
416 \subsubsection{Double layer formation}
417 The increased amounts of diffusion on Pt at the higher CO coverages appears to play a role in the
418 formation of double layers, seeing as how that was the only system within our observed simulation time
419 that showed the formation. Despite this being the only system where this reconstruction occurs, three separate layers
420 were formed over the extended run time of this system. As mentioned earlier, previous experimental work has given some insight into
421 the upper bounds of the time required for enough atoms to move around to allow two steps to coalesce\cite{Williams:1991,Pearl}.
422 As seen in figure \ref{fig:reconstruct}, the first appearance of a double layer, a nodal site, appears at 19 ns into
423 the simulation. Within 12 ns, nearly half of the step has formed the double layer and by 86 ns, a smooth complete
424 layer has formed. The double layer is complete by 37 ns but is a bit rough.
425 From the appearance of the first node to the initial doubling of the layers ignoring their roughness took ~20 ns.
426 Another ~40 ns was necessary for the layer to completely straighten. The other two layers in this simulation form
427 over a period of 22 ns and 42 ns respectively.
428
462   %Evolution of surface
463   \begin{figure}[H]
464 < \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
464 > \includegraphics[width=\linewidth]{EPS_ProgressionOfDoubleLayerFormation}
465   \caption{The Pt(557) / 50\% CO system at a sequence of times after
466 <  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
467 <  (d) 86.1 ns. Disruption of the 557 step edges occurs quickly.  The
468 <  doubling of the layers appears only after two adjacent step edges
466 >  initial exposure to the CO: (a) 258~ps, (b) 19~ns, (c) 31.2~ns, and
467 >  (d) 86.1~ns. Disruption of the (557) step-edges occurs quickly.  The
468 >  doubling of the layers appears only after two adjacent step-edges
469    touch.  The circled spot in (b) nucleated the growth of the double
470    step observed in the later configurations.}
471    \label{fig:reconstruct}
472   \end{figure}
473 +
474 + \subsection{Dynamics}
475 + Previous experimental work by Pearl and Sibener\cite{Pearl},
476 + using STM, has been able to capture the coalescence of steps
477 + on Ni(977). The time scale of the image acquisition, $\sim$70~s/image,
478 + provides an upper bound for the time required for the doubling
479 + to occur. By utilizing Molecular Dynamics we are able to probe
480 + the dynamics of these reconstructions at elevated temperatures
481 + and in this section we provide data on the timescales for transport
482 + properties, e.g. diffusion and layer formation time.
483 +
484 +
485 + \subsubsection{Transport of surface metal atoms}
486 + %forcedSystems/stepSeparation
487 + The wandering of a step-edge is a cooperative effect
488 + arising from the individual movements of the atoms making up the steps. An ideal metal surface
489 + displaying a low index facet, (111) or (100), is unlikely to experience
490 + much surface diffusion because of the large energetic barrier that must
491 + be overcome to lift an atom out of the surface. The presence of step-edges and other surface features
492 + on higher-index facets provides a lower energy source for mobile metal atoms.
493 + Single-atom break-away from a step-edge on a clean surface still imposes an
494 + energetic penalty around $\sim$~45 kcal/mol, but this is easier than lifting
495 + the same metal atom vertically out of the surface,  \textgreater~60 kcal/mol.
496 + The penalty lowers significantly when CO is present in sufficient quantities
497 + on the surface. For certain distributions of CO, see Discussion, the penalty can fall to as low as
498 + $\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for
499 + diffusion is negligible (\textless~4 kcal/mol for a Pt adatom). These adatoms are then
500 + able to explore the terrace before rejoining either their original step-edge or
501 + becoming a part of a different edge. It is an energetically unfavorable process with a high barrier for an atom
502 + to traverse to a separate terrace although the presence of CO can lower the
503 + energy barrier required to lift or lower an adatom. By tracking the mobility of individual
504 + metal atoms on the Pt and Au surfaces we were able to determine the relative
505 + diffusion constants, as well as how varying coverages of CO affect the diffusion. Close
506 + observation of the mobile metal atoms showed that they were typically in
507 + equilibrium with the step-edges.
508 + At times, their motion was concerted and two or more adatoms would be
509 + observed moving together across the surfaces.
510  
511 + A particle was considered ``mobile'' once it had traveled more than 2~\AA~
512 + between saved configurations of the system (typically 10-100 ps). A mobile atom
513 + would typically travel much greater distances than this, but the 2~\AA~cutoff
514 + was used to prevent swamping the diffusion data with the in-place vibrational
515 + movement of buried atoms. Diffusion on a surface is strongly affected by
516 + local structures and in this work, the presence of single and double layer
517 + step-edges causes the diffusion parallel to the step-edges to be larger than
518 + the diffusion perpendicular to these edges. Parallel and perpendicular
519 + diffusion constants are shown in Figure \ref{fig:diff}.
520 +
521 + %Diffusion graph
522   \begin{figure}[H]
523 < \includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade.pdf}
523 > \includegraphics[width=\linewidth]{Portrait_DiffusionComparison_1}
524   \caption{Diffusion constants for mobile surface atoms along directions
525    parallel ($\mathbf{D}_{\parallel}$) and perpendicular
526 <  ($\mathbf{D}_{\perp}$) to the 557 step edges as a function of CO
527 <  surface coverage.  Diffusion parallel to the step edge is higher
526 >  ($\mathbf{D}_{\perp}$) to the (557) step-edges as a function of CO
527 >  surface coverage.  Diffusion parallel to the step-edge is higher
528    than that perpendicular to the edge because of the lower energy
529 <  barrier associated with going from approximately 7 nearest neighbors
530 <  to 5, as compared to the 3 of an adatom. Additionally, the observed
531 <  maximum and subsequent decrease for the Pt system suggests that the
532 <  CO self-interactions are playing a significant role with regards to
533 <  movement of the platinum atoms around and more importantly across
453 <  the surface. }
529 >  barrier associated with traversing along the edge as compared to
530 >  completely breaking away. The two reported diffusion constants for
531 >  the 50\% Pt system arise from different sample sets. The lower values
532 >  correspond to the same 40~ns amount that all of the other systems were
533 >  examined at, while the larger values correspond to a 20~ns period }
534   \label{fig:diff}
535   \end{figure}
536  
537 + The weaker Au-CO interaction is evident in the weak CO-coverage
538 + dependance of Au diffusion. This weak interaction leads to lower
539 + observed coverages when compared to dosage amounts. This further
540 + limits the effect the CO can have on surface diffusion. The correlation
541 + between coverage and Pt diffusion rates shows a near linear relationship
542 + at the earliest times in the simulations. Following double layer formation,
543 + however, there is a precipitous drop in adatom diffusion. As the double
544 + layer forms, many atoms that had been tracked for mobility data have
545 + now been buried resulting in a smaller reported diffusion constant. A
546 + secondary effect of higher coverages is CO-CO cross interactions that
547 + lower the effective mobility of the Pt adatoms that are bound to each CO.
548 + This effect would become evident only at higher coverages. A detailed
549 + account of Pt adatom energetics follows in the Discussion.
550 +
551  
552 + \subsubsection{Dynamics of double layer formation}
553 + The increased diffusion on Pt at the higher CO coverages is the primary
554 + contributor to double layer formation. However, this is not a complete
555 + explanation -- the 33\%~Pt system has higher diffusion constants, but
556 + did not show any signs of edge doubling in 40~ns. On the 50\%~Pt
557 + system, one double layer formed within the first 40~ns of simulation time,
558 + while two more were formed as the system was allowed to run for an
559 + additional 110~ns (150~ns total). This suggests that this reconstruction
560 + is a rapid process and that the previously mentioned upper bound is a
561 + very large overestimate.\cite{Williams:1991,Pearl} In this system the first
562 + appearance of a double layer appears at 19~ns into the simulation.
563 + Within 12~ns of this nucleation event, nearly half of the step has formed
564 + the double layer and by 86~ns the complete layer has flattened out.
565 + From the appearance of the first nucleation event to the first observed
566 + double layer, the process took $\sim$20~ns. Another $\sim$40~ns was
567 + necessary for the layer to completely straighten. The other two layers in
568 + this simulation formed over periods of 22~ns and 42~ns respectively.
569 + A possible explanation for this rapid reconstruction is the elevated
570 + temperatures under which our systems were simulated. The process
571 + would almost certainly take longer at lower temperatures. Additionally,
572 + our measured times for completion of the doubling after the appearance
573 + of a nucleation site are likely affected by our periodic boxes. A longer
574 + step-edge will likely take longer to ``zipper''.
575  
576  
577   %Discussion
578   \section{Discussion}
579 < In this paper we have shown that we were able to accurately model the initial reconstruction of the
580 < Pt (557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
581 < were able to capture the dynamic processes inherent within this reconstruction.
579 > We have shown that a classical potential is able to model the initial
580 > reconstruction of the Pt(557) surface upon CO adsorption, and have
581 > reproduced the double layer structure observed by Tao {\it et
582 >  al}.\cite{Tao:2010}. Additionally, this reconstruction appears to be
583 > rapid -- occurring within 100 ns of the initial exposure to CO.  Here
584 > we discuss the features of the classical potential that are
585 > contributing to the stability and speed of the Pt(557) reconstruction.
586  
587 < \subsection{Mechanism for restructuring}
588 < The increased computational cost to examine this system using molecular dynamics rather than
589 < a Monte Carlo based approach was necessary so that our predictions on possible mechanisms
590 < and driving forces would have support not only from thermodynamic arguments but also from the
591 < actual dynamics of the system.
587 > \subsection{Diffusion}
588 > The perpendicular diffusion constant appears to be the most important
589 > indicator of double layer formation. As highlighted in Figure
590 > \ref{fig:reconstruct}, the formation of the double layer did not begin
591 > until a nucleation site appeared.  Williams {\it et
592 >  al}.\cite{Williams:1991,Williams:1994} cite an effective edge-edge
593 > repulsion arising from the inability of edge crossing.  This repulsion
594 > must be overcome to allow step coalescence.  A larger
595 > $\textbf{D}_\perp$ value implies more step-wandering and a larger
596 > chance for the stochastic meeting of two edges to create a nucleation
597 > point.  Diffusion parallel to the step-edge can help ``zipper'' up a
598 > nascent double layer. This helps explain the rapid time scale for
599 > double layer completion after the appearance of a nucleation site, while
600 > the initial appearance of the nucleation site was unpredictable.
601  
602 < Comparing the results from simulation to those reported previously by
603 < Tao et al. the similarities in the platinum and CO system are quite
604 < strong. As shown in figure \ref{fig:reconstruct}, the simulated platinum system under a CO
605 < atmosphere will restructure slightly by doubling the terrace
606 < heights. The restructuring appears to occur slowly, one to two
607 < platinum atoms at a time. Looking at individual snapshots, these
478 < adatoms tend to either rise on top of the plateau or break away from
479 < the step edge and then diffuse perpendicularly to the step direction
480 < until reaching another step edge. This combination of growth and decay
481 < of the step edges appears to be in somewhat of a state of dynamic
482 < equilibrium. However, once two previously separated edges meet as
483 < shown in figure 1.B, this point tends to act as a focus or growth
484 < point for the rest of the edge to meet up, akin to that of a
485 < zipper. From the handful of cases where a double layer was formed
486 < during the simulation, measuring from the initial appearance of a
487 < growth point, the double layer tends to be fully formed within
488 < $\sim$~35 ns.
489 <
490 < There are a number of possible mechanisms to explain the role of
491 < adsorbed CO in restructuring the Pt surface. Quadrupolar repulsion
492 < between adjacent CO molecules adsorbed on the surface is one
602 > \subsection{Mechanism for restructuring}
603 > Since the Au surface showed no large scale restructuring in any of our
604 > simulations, our discussion will focus on the 50\% Pt-CO system which
605 > did exhibit doubling. A number of possible mechanisms exist to explain
606 > the role of adsorbed CO in restructuring the Pt surface. Quadrupolar
607 > repulsion between adjacent CO molecules adsorbed on the surface is one
608   possibility.  However, the quadrupole-quadrupole interaction is
609   short-ranged and is attractive for some orientations.  If the CO
610 < molecules are ``locked'' in a specific orientation relative to each other however,
611 < this explanation gains some weight.  The energetic repulsion between two CO
612 < located a distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in a
613 < vertical orientation is 8.62 kcal/mole. Moving the CO apart to the second nearest-neighbor
614 < distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to nearly 0 kcal/mole. SHOW A NUMBER FOR ROTATION.
615 < As mentioned above, the energy barrier for surface diffusion of a platinum adatom is only 4 kcal/mole. So this
616 < repulsion between CO can help increase the surface diffusion. However, the residence time of CO was examined
617 < and while the majority of the CO is on or near the surface throughout the run, it is extremely mobile. This mobility
618 < suggests that the CO are more likely to shift their positions without necessarily dragging the platinum along
619 < with them.
610 > molecules are ``locked'' in a vertical orientation, through atop
611 > adsorption for example, this explanation would gain credence. The
612 > calculated energetic repulsion between two CO molecules located a
613 > distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) and both
614 > in a vertical orientation, is 8.62 kcal/mol. Moving the CO to the
615 > second nearest-neighbor distance of 4.8~\AA~drops the repulsion to
616 > nearly 0. Allowing the CO to rotate away from a purely vertical
617 > orientation also lowers the repulsion. When the carbons are locked at
618 > a distance of 2.77~\AA, a minimum of 6.2 kcal/mol is reached when the
619 > angle between the 2 CO is $\sim$24\textsuperscript{o}.  The calculated
620 > barrier for surface diffusion of a Pt adatom is only 4 kcal/mol, so
621 > repulsion between adjacent CO molecules bound to Pt could increase the
622 > surface diffusion. However, the residence time of CO on Pt suggests
623 > that the CO molecules are extremely mobile, with diffusion constants 40
624 > to 2500 times larger than surface Pt atoms. This mobility suggests
625 > that the CO molecules jump between different Pt atoms throughout the
626 > simulation, but can stay bound for significant periods of time.
627  
628 < Another possible and more likely mechanism for the restructuring is in the
629 < destabilization of strong Pt-Pt interactions by CO adsorbed on surface
630 < Pt atoms.  This could have the effect of increasing surface mobility
631 < of these atoms.  To test this hypothesis, numerous configurations of
632 < CO in varying quantities were arranged on the higher and lower plateaus
633 < around a step on a otherwise clean Pt (557) surface. One representative
634 < configuration is displayed in figure \ref{fig:lambda}. Single or concerted movement
635 < of platinum atoms was then examined to determine possible barriers. Because
636 < of the forced movement along a pre-defined reaction coordinate that may differ
637 < from the true minimum of this path, only the beginning and ending energies
638 < are displayed in table \ref{tab:energies}. The presence of CO at suitable
639 < sites can lead to lowered barriers for platinum breaking apart from the step edge.
640 < Additionally, as highlighted in figure \ref{fig:lambda}, the presence of CO makes the
641 < burrowing and lifting nature favorable, whereas without CO, the process is neutral
642 < in terms of energetics.
628 > A different interpretation of the above mechanism which takes the
629 > large mobility of the CO into account, would be in the destabilization
630 > of Pt-Pt interactions due to bound CO.  Destabilizing Pt-Pt bonds at
631 > the edges could lead to increased step-edge breakup and diffusion. On
632 > the bare Pt(557) surface the barrier to completely detach an edge atom
633 > is $\sim$43~kcal/mol, as is shown in configuration (a) in Figures
634 > \ref{fig:SketchGraphic} \& \ref{fig:SketchEnergies}. For certain
635 > configurations, cases (e), (g), and (h), the barrier can be lowered to
636 > $\sim$23~kcal/mol by the presence of bound CO molecules. In these
637 > instances, it becomes energetically favorable to roughen the edge by
638 > introducing a small separation of 0.5 to 1.0~\AA. This roughening
639 > becomes immediately obvious in simulations with significant CO
640 > populations. The roughening is present to a lesser extent on surfaces
641 > with lower CO coverage (and even on the bare surfaces), although in
642 > these cases it is likely due to random fluctuations that squeeze out
643 > step-edge atoms. Step-edge breakup by continuous single-atom
644 > translations (as suggested by these energy curves) is probably a
645 > worst-case scenario.  Multistep mechanisms in which an adatom moves
646 > laterally on the surface after being ejected would be more
647 > energetically favorable.  This would leave the adatom alongside the
648 > ledge, providing it with 5 nearest neighbors.  While fewer than the 7
649 > neighbors it had as part of the step-edge, it keeps more Pt neighbors
650 > than the 3 an isolated adatom would have on the terrace. In this
651 > proposed mechanism, the CO quadrupolar repulsion still plays a role in
652 > the initial roughening of the step-edge, but not in any long-term
653 > bonds with individual Pt atoms.  Higher CO coverages create more
654 > opportunities for the crowded CO configurations shown in Figure
655 > \ref{fig:SketchGraphic}, and this is likely to cause an increased
656 > propensity for step-edge breakup.
657  
658 + %Sketch graphic of different configurations
659 + \begin{figure}[H]
660 + \includegraphics[width=\linewidth]{COpaths}
661 + \caption{Configurations used to investigate the mechanism of step-edge
662 +  breakup on Pt(557). In each case, the central (starred) atom is
663 +  pulled directly across the surface away from the step edge.  The Pt
664 +  atoms on the upper terrace are colored dark grey, while those on the
665 +  lower terrace are in white.  In each of these configurations, some
666 +  number of the atoms (highlighted in blue) had a CO molecule bound in
667 +  a vertical atop position.  The energies of these configurations as a
668 +  function of central atom displacement are displayed in Figure
669 +  \ref{fig:SketchEnergies}.}
670 + \label{fig:SketchGraphic}
671 + \end{figure}
672 +
673 + %energy graph corresponding to sketch graphic
674 + \begin{figure}[H]
675 + \includegraphics[width=\linewidth]{Portrait_SeparationComparison}
676 + \caption{Energies for displacing a single edge atom perpendicular to
677 +  the step edge as a function of atomic displacement. Each of the
678 +  energy curves corresponds to one of the labeled configurations in
679 +  Figure \ref{fig:SketchGraphic}, and are referenced to the
680 +  unperturbed step-edge.  Certain arrangements of bound CO (notably
681 +  configurations g and h) can lower the energetic barrier for creating
682 +  an adatom relative to the bare surface (configuration a).}
683 + \label{fig:SketchEnergies}
684 + \end{figure}
685 +
686 + While configurations of CO on the surface are able to increase
687 + diffusion and the likelihood of edge wandering, this does not provide
688 + a complete explanation for the formation of double layers. If adatoms
689 + were constrained to their original terraces then doubling could not
690 + occur.  A mechanism for vertical displacement of adatoms at the
691 + step-edge is required to explain the doubling.
692 +
693 + We have discovered one possible mechanism for a CO-mediated vertical
694 + displacement of Pt atoms at the step edge. Figure \ref{fig:lambda}
695 + shows four points along a reaction coordinate in which a CO-bound
696 + adatom along the step-edge ``burrows'' into the edge and displaces the
697 + original edge atom onto the higher terrace. A number of events similar
698 + to this mechanism were observed during the simulations.  We predict an
699 + energetic barrier of 20~kcal/mol for this process (in which the
700 + displaced edge atom follows a curvilinear path into an adjacent 3-fold
701 + hollow site).  The barrier heights we obtain for this reaction
702 + coordinate are approximate because the exact path is unknown, but the
703 + calculated energy barriers would be easily accessible at operating
704 + conditions.  Additionally, this mechanism is exothermic, with a final
705 + energy 15~kcal/mol below the original $\lambda = 0$ configuration.
706 + When CO is not present and this reaction coordinate is followed, the
707 + process is endothermic by 3~kcal/mol.  The difference in the relative
708 + energies for the $\lambda=0$ and $\lambda=1$ case when CO is present
709 + provides strong support for CO-mediated Pt-Pt interactions giving rise
710 + to the doubling reconstruction.
711 +
712   %lambda progression of Pt -> shoving its way into the step
713   \begin{figure}[H]
714 < \includegraphics[width=\linewidth]{lambdaProgression_atopCO.png}
715 < \caption{A model system of the Pt 557 surface was used as the framework for a reaction coordinate.
716 < Various numbers, placements, and rotations of CO were examined. The one displayed was a
717 < representative sample. As shown in Table , relative to the energy at 0\% there is a slight decrease
718 < upon insertion of the platinum atom into the step edge along with the resultant lifting of the other
719 < platinum atom.}
714 > \includegraphics[width=\linewidth]{EPS_rxnCoord}
715 > \caption{Points along a possible reaction coordinate for CO-mediated
716 >  edge doubling. Here, a CO-bound adatom burrows into an established
717 >  step edge and displaces an edge atom onto the upper terrace along a
718 >  curvilinear path.  The approximate barrier for the process is
719 >  20~kcal/mol, and the complete process is exothermic by 15~kcal/mol
720 >  in the presence of CO, but is endothermic by 3~kcal/mol without.}
721   \label{fig:lambda}
722   \end{figure}
723  
724 + The mechanism for doubling on the Pt(557) surface appears to require
725 + the cooperation of at least two distinct processes. For complete
726 + doubling of a layer to occur there must be a breakup of one
727 + terrace. These atoms must then ``disappear'' from that terrace, either
728 + by travelling to the terraces above of below their original levels.
729 + The presence of CO helps explain mechanisms for both of these
730 + situations. There must be sufficient breakage of the step-edge to
731 + increase the concentration of adatoms on the surface and these adatoms
732 + must then undergo the burrowing highlighted above (or a comparable
733 + mechanism) to create the double layer.  With sufficient time, these
734 + mechanisms working in concert lead to the formation of a double layer.
735  
736 + \subsection{CO Removal and double layer stability}
737 + Once a double layer had formed on the 50\%~Pt system, it remained for
738 + the rest of the simulation time with minimal movement.  Random
739 + fluctuations that involved small clusters or divots were observed, but
740 + these features typically healed within a few nanoseconds.  Within our
741 + simulations, the formation of the double layer appeared to be
742 + irreversible and a double layer was never observed to split back into
743 + two single layer step-edges while CO was present.
744  
745 < \subsection{Diffusion}
746 < As shown in the results section, the diffusion parallel to the step edge tends to be
747 < much faster than that perpendicular to the step edge. Additionally, the coverage
748 < of CO appears to play a slight role in relative rates of diffusion, as shown in figure \ref{fig:diff}
749 < Thus, the bottleneck of the double layer formation appears to be the initial formation
750 < of this growth point, which seems to be somewhat of a stochastic event. Once it
751 < appears, parallel diffusion, along the now slightly angled step edge, will allow for
752 < a faster formation of the double layer than if the entire process were dependent on
753 < only perpendicular diffusion across the plateaus. Thus, the larger $D_{\perp}$, the
754 < more likely a growth point is to be formed.
755 < \\
745 > To further gauge the effect CO has on this surface, additional
746 > simulations were run starting from a late configuration of the 50\%~Pt
747 > system that had already formed double layers. These simulations then
748 > had their CO forcibly removed.  The double layer broke apart rapidly
749 > in these simulations, showing a well-defined edge-splitting after
750 > 100~ps. Configurations of this system are shown in Figure
751 > \ref{fig:breaking}. The coloring of the top and bottom layers helps to
752 > exhibit how much mixing the edges experience as they split. These
753 > systems were only examined for 10~ns, and within that time despite the
754 > initial rapid splitting, the edges only moved another few
755 > \AA~apart. It is possible that with longer simulation times, the (557)
756 > surface recovery observed by Tao {\it et al}.\cite{Tao:2010} could
757 > also be recovered.
758  
547
759   %breaking of the double layer upon removal of CO
760   \begin{figure}[H]
761 < \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
762 < \caption{Hi}
761 > \includegraphics[width=\linewidth]{EPS_doubleLayerBreaking}
762 > \caption{Dynamics of an established (111) double step after removal of
763 >  the adsorbed CO: (A) 0~ps, (B) 100~ps, and (C) 1~ns after the removal
764 >  of CO. The presence of the CO helped maintain the stability of the
765 >  double step.  Nearly immediately after the CO is removed, the step
766 >  edge reforms in a (100) configuration, which is also the step type
767 >  seen on clean (557) surfaces. The step separation involves
768 >  significant mixing of the lower and upper atoms at the edge.}
769   \label{fig:breaking}
770   \end{figure}
771  
772  
556
557
773   %Peaks!
774 < \begin{figure}[H]
775 < \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
776 < \caption{}
777 < \label{fig:peaks}
778 < \end{figure}
774 > %\begin{figure}[H]
775 > %\includegraphics[width=\linewidth]{doublePeaks_noCO.png}
776 > %\caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
777 > %of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
778 > %aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
779 > %\label{fig:peaks}
780 > %\end{figure}
781  
782 +
783 + %Don't think I need this
784   %clean surface...
785 < \begin{figure}[H]
786 < \includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
787 < \caption{}
785 > %\begin{figure}[H]
786 > %\includegraphics[width=\linewidth]{557_300K_cleanPDF}
787 > %\caption{}
788  
789 < \end{figure}
790 < \label{fig:clean}
789 > %\end{figure}
790 > %\label{fig:clean}
791 >
792 >
793   \section{Conclusion}
794 + The strength and directionality of the Pt-CO binding interaction, as
795 + well as the large quadrupolar repulsion between atop-bound CO
796 + molecules, help to explain the observed increase in surface mobility
797 + of Pt(557) and the resultant reconstruction into a double-layer
798 + configuration at the highest simulated CO-coverages.  The weaker Au-CO
799 + interaction results in significantly lower adataom diffusion
800 + constants, less step-wandering, and a lack of the double layer
801 + reconstruction on the Au(557) surface.
802  
803 + An in-depth examination of the energetics shows the important role CO
804 + plays in increasing step-breakup and in facilitating edge traversal
805 + which are both necessary for double layer formation.
806  
807   %Things I am not ready to remove yet
808  
# Line 594 | Line 826 | more likely a growth point is to be formed.
826   % \end{tabular}
827   % \end{table}
828  
829 < \section{Acknowledgments}
830 < Support for this project was provided by the National Science
831 < Foundation under grant CHE-0848243 and by the Center for Sustainable
832 < Energy at Notre Dame (cSEND). Computational time was provided by the
833 < Center for Research Computing (CRC) at the University of Notre Dame.
834 <
829 > \begin{acknowledgement}
830 >  We gratefully acknowledge conversations with Dr. William
831 >  F. Schneider and Dr. Feng Tao.  Support for this project was
832 >  provided by the National Science Foundation under grant CHE-0848243
833 >  and by the Center for Sustainable Energy at Notre Dame
834 >  (cSEND). Computational time was provided by the Center for Research
835 >  Computing (CRC) at the University of Notre Dame.
836 > \end{acknowledgement}
837   \newpage
838   \bibliography{firstTryBibliography}
839 < \end{doublespace}
839 > %\end{doublespace}
840 >
841 > \begin{tocentry}
842 > %\includegraphics[height=3.5cm]{timelapse}
843 > \includegraphics[height=3.5cm]{TOC_doubleLayer.pdf}
844 > \end{tocentry}
845 >
846   \end{document}

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