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# Line 58 | Line 58 | Notre Dame, Indiana 46556}
58   Notre Dame, Indiana 46556}
59  
60   %Date
61 < \date{Dec 15, 2012}
61 > \date{Mar 5, 2013}
62  
63   %authors
64  
# Line 68 | Line 68 | Notre Dame, Indiana 46556}
68   \begin{doublespace}
69  
70   \begin{abstract}
71 + We examine surface reconstructions of Pt and Au(557) under
72 + various CO coverages using molecular dynamics in order to
73 + explore possible mechanisms for any observed reconstructions
74 + and their dynamics. The metal-CO interactions were parameterized
75 + as part of this work so that an efficient large-scale treatment of
76 + this system could be undertaken. The large difference in binding
77 + strengths of the metal-CO interactions was found to play a significant
78 + role with regards to step-edge stability and adatom diffusion. A
79 + small correlation between coverage and the diffusion constant
80 + was also determined. The energetics of CO adsorbed to the surface
81 + is sufficient to explain the reconstructions observed on the Pt
82 + systems and the lack  of reconstruction of the Au systems.
83  
84   \end{abstract}
85  
# Line 100 | Line 112 | This work an effort to understand the mechanism and ti
112   reversible restructuring under exposure to moderate pressures of
113   carbon monoxide.\cite{Tao:2010}
114  
115 < This work an effort to understand the mechanism and timescale for
116 < surface restructuring using molecular simulations.  Since the dynamics
117 < of the process is of particular interest, we utilize classical force
115 > This work is an attempt to understand the mechanism and timescale for
116 > surface restructuring by using molecular simulations.  Since the dynamics
117 > of the process are of particular interest, we employ classical force
118   fields that represent a compromise between chemical accuracy and the
119 < computational efficiency necessary to observe the process of interest.
120 <
121 < Since restructuring occurs as a result of specific interactions of the
122 < catalyst with adsorbates, two metal systems exposed to carbon monoxide
111 < were examined in this work. The Pt(557) surface has already been shown
119 > computational efficiency necessary to simulate the process of interest.
120 > Since restructuring typically occurs as a result of specific interactions of the
121 > catalyst with adsorbates, in this work, two metal systems exposed
122 > to carbon monoxide were examined. The Pt(557) surface has already been shown
123   to reconstruct under certain conditions. The Au(557) surface, because
124   of a weaker interaction with CO, is less likely to undergo this kind
125 < of reconstruction.  MORE HERE ON PT AND AU PREVIOUS WORK.
125 > of reconstruction.  
126  
127 +
128 +
129   %Platinum molecular dynamics
130   %gold molecular dynamics
131  
132   \section{Simulation Methods}
133 < The challenge in modeling any solid/gas interface problem is the
133 > The challenge in modeling any solid/gas interface is the
134   development of a sufficiently general yet computationally tractable
135   model of the chemical interactions between the surface atoms and
136   adsorbates.  Since the interfaces involved are quite large (10$^3$ -
# Line 133 | Line 146 | Au-Au and Pt-Pt interactions, while modeling the CO us
146   Coulomb potential.  For this work, we have used classical molecular
147   dynamics with potential energy surfaces that are specifically tuned
148   for transition metals.  In particular, we used the EAM potential for
149 < Au-Au and Pt-Pt interactions, while modeling the CO using a rigid
149 > Au-Au and Pt-Pt interactions\cite{EAM}. The CO was modeled using a rigid
150   three-site model developed by Straub and Karplus for studying
151   photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
152   Pt-CO cross interactions were parameterized as part of this work.
# Line 146 | Line 159 | parameter sets. The glue model of Ercolessi {\it et al
159   methods,\cite{Daw84,Foiles86,Johnson89,Daw89,Plimpton93,Voter95a,Lu97,Alemany98}
160   but other models like the Finnis-Sinclair\cite{Finnis84,Chen90} and
161   the quantum-corrected Sutton-Chen method\cite{QSC,Qi99} have simpler
162 < parameter sets. The glue model of Ercolessi {\it et al.} is among the
162 > parameter sets. The glue model of Ercolessi et al. is among the
163   fastest of these density functional approaches.\cite{Ercolessi88} In
164   all of these models, atoms are conceptualized as a positively charged
165   core with a radially-decaying valence electron distribution. To
# Line 164 | Line 177 | $\phi_{ij}(r_{ij})$ is an pairwise term that is meant
177   V_i =  F[ \bar{\rho}_i ]  + \sum_{j \neq i} \phi_{ij}(r_{ij})
178   \end{equation*}
179   where $F[ \bar{\rho}_i ]$ is an energy embedding functional, and
180 < $\phi_{ij}(r_{ij})$ is an pairwise term that is meant to represent the
181 < overlap of the two positively charged cores.  
180 > $\phi_{ij}(r_{ij})$ is a pairwise term that is meant to represent the
181 > repulsive overlap of the two positively charged cores.  
182  
183   % The {\it modified} embedded atom method (MEAM) adds angular terms to
184   % the electron density functions and an angular screening factor to the
# Line 176 | Line 189 | The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen
189   % metals,\cite{Lee:2001qf} and also interfaces.\cite{Beurden:2002ys})
190   % MEAM presents significant additional computational costs, however.
191  
192 < The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen potentials
192 > The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen (QSC) potentials
193   have all been widely used by the materials simulation community for
194   simulations of bulk and nanoparticle
195   properties,\cite{Chui:2003fk,Wang:2005qy,Medasani:2007uq}
# Line 184 | Line 197 | strengths and weaknesses.  One of the strengths common
197   fracture,\cite{Shastry:1996qg,Shastry:1998dx} crack
198   propagation,\cite{BECQUART:1993rg} and alloying
199   dynamics.\cite{Shibata:2002hh} All of these potentials have their
200 < strengths and weaknesses.  One of the strengths common to all of the
188 < methods is the relatively large library of metals for which these
189 < potentials have been
190 < parameterized.\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
200 > strengths and weaknesses.  \cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
201  
202   \subsection{Carbon Monoxide model}
203 < Since previous explanations for the surface rearrangements center on
204 < the large linear quadrupole moment of carbon monoxide, the model
205 < chosen for this molecule exhibits this property in an efficient
206 < manner.  We used a model first proposed by Karplus and Straub to study
207 < the photodissociation of CO from myoglobin.\cite{Straub} The Straub and
208 < Karplus model is a rigid three site model which places a massless M
209 < site at the center of mass along the CO bond.  The geometry used along
210 < with the interaction parameters are reproduced in Table~1. The effective
203 > Previous explanations for the surface rearrangements center on
204 > the large linear quadrupole moment of carbon monoxide.\cite{Tao:2010}  
205 > We used a model first proposed by Karplus and Straub to study
206 > the photodissociation of CO from myoglobin because it reproduces
207 > the quadrupole moment well.\cite{Straub} The Straub and
208 > Karplus model, treats CO as a rigid three site molecule with a massless M
209 > site at the molecular center of mass. The geometry and interaction
210 > parameters are reproduced in Table~\ref{tab:CO}. The effective
211   dipole moment, calculated from the assigned charges, is still
212   small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is close
213   to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum
# Line 206 | Line 216 | mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCO
216   \begin{table}[H]
217    \caption{Positions, Lennard-Jones parameters ($\sigma$ and
218      $\epsilon$), and charges for the CO-CO
219 <    interactions borrowed from Ref. \bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA~, energies are
219 >    interactions in Ref.\bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA, energies are
220      in kcal/mol, and charges are in atomic units.}
221   \centering
222   \begin{tabular}{| c | c | ccc |}
223   \hline
224   &  {\it z} & $\sigma$ & $\epsilon$ & q\\
225   \hline
226 < \textbf{C} & -0.6457 &  0.0262  & 3.83   &   -0.75 \\
227 < \textbf{O} &  0.4843 &   0.1591 &   3.12 &   -0.85 \\
226 > \textbf{C} & -0.6457 &  3.83 & 0.0262   &   -0.75 \\
227 > \textbf{O} &  0.4843 &  3.12 &  0.1591  &   -0.85 \\
228   \textbf{M} & 0.0 & -  &  -  &    1.6 \\
229   \hline
230   \end{tabular}
231 + \label{tab:CO}
232   \end{table}
233  
234   \subsection{Cross-Interactions between the metals and carbon monoxide}
235  
236 < Since the adsorption of CO onto a platinum surface has been the focus
236 > Since the adsorption of CO onto a Pt surface has been the focus
237   of much experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979}
238   and theoretical work
239   \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
240   there is a significant amount of data on adsorption energies for CO on
241 < clean metal surfaces. Parameters reported by Korzeniewski {\it et
242 <  al.}\cite{Pons:1986} were a starting point for our fits, which were
241 > clean metal surfaces. An earlier model by Korzeniewski {\it et
242 >  al.}\cite{Pons:1986} served as a starting point for our fits. The parameters were
243   modified to ensure that the Pt-CO interaction favored the atop binding
244 < position on Pt(111). This resulting binding energies are on the higher
245 < side of the experimentally-reported values. Following Korzeniewski
246 < {\it et al.},\cite{Pons:1986} the Pt-C interaction was fit to a deep
244 > position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}.
245 > The modified parameters yield binding energies that are slightly higher
246 > than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
247 > et al.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
248   Lennard-Jones interaction to mimic strong, but short-ranged partial
249   binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
250 < Pt-O interaction was parameterized to a Morse potential with a large
251 < range parameter ($r_o$).  In most cases, this contributes a weak
250 > Pt-O interaction was modeled with a Morse potential with a large
251 > equilibrium distance, ($r_o$).  These choices ensure that the C is preferred
252 > over O as the surface-binding atom. In most cases, the Pt-O parameterization contributes a weak
253   repulsion which favors the atop site.  The resulting potential-energy
254   surface suitably recovers the calculated Pt-C separation length
255   (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
# Line 245 | Line 258 | The Au-C and Au-O cross-interactions were fit using Le
258   %where did you actually get the functionals for citation?
259   %scf calculations, so initial relaxation was of the four layers, but two layers weren't kept fixed, I don't think
260   %same cutoff for slab and slab + CO ? seems low, although feibelmen had values around there...
261 < The Au-C and Au-O cross-interactions were fit using Lennard-Jones and
261 > The Au-C and Au-O cross-interactions were also fit using Lennard-Jones and
262   Morse potentials, respectively, to reproduce Au-CO binding energies.
263 <
264 < The fits were refined against gas-surface DFT calculations with a
263 > The limited experimental data for CO adsorption on Au required refining the fits against plane-wave DFT calculations.
264 > Adsorption energies were obtained from gas-surface DFT calculations with a
265   periodic supercell plane-wave basis approach, as implemented in the
266 < {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores are
266 > {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores were
267   described with the projector augmented-wave (PAW)
268   method,\cite{PhysRevB.50.17953,PhysRevB.59.1758} with plane waves
269   included to an energy cutoff of 20 Ry. Electronic energies are
270   computed with the PBE implementation of the generalized gradient
271   approximation (GGA) for gold, carbon, and oxygen that was constructed
272   by Rappe, Rabe, Kaxiras, and Joannopoulos.\cite{Perdew_GGA,RRKJ_PP}
273 < Ionic relaxations were performed until the energy difference between
261 < subsequent steps was less than $10^{-8}$ Ry.  In testing the CO-Au
262 < interaction, Au(111) supercells were constructed of four layers of 4
273 > In testing the Au-CO interaction, Au(111) supercells were constructed of four layers of 4
274   Au x 2 Au surface planes and separated from vertical images by six
275 < layers of vacuum space. The surface atoms were all allowed to relax.
276 < Supercell calculations were performed nonspin-polarized with a 4 x 4 x
277 < 4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
275 > layers of vacuum space. The surface atoms were all allowed to relax
276 > before CO was added to the system. Electronic relaxations were
277 > performed until the energy difference between subsequent steps
278 > was less than $10^{-8}$ Ry.   Nonspin-polarized supercell calculations
279 > were performed with a 4~x~4~x~4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
280   zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxed gold slab was
281   then used in numerous single point calculations with CO at various
282   heights (and angles relative to the surface) to allow fitting of the
283   empirical force field.
284  
285   %Hint at future work
286 < The parameters employed in this work are shown in Table 2 and the
287 < binding energies on the 111 surfaces are displayed in Table 3.  To
288 < speed up the computations, charge transfer and polarization are not
289 < being treated in this model, although these effects are likely to
290 < affect binding energies and binding site
291 < preferences.\cite{Deshlahra:2012}
286 > The parameters employed for the metal-CO cross-interactions in this work
287 > are shown in Table~\ref{tab:co_parameters} and the binding energies on the
288 > (111) surfaces are displayed in Table~\ref{tab:co_energies}.  Charge transfer
289 > and polarization are neglected in this model, although these effects are likely to
290 > affect binding energies and binding site preferences, and will be addressed in
291 > a future work.\cite{Deshlahra:2012,StreitzMintmire:1994}
292  
293   %Table  of Parameters
294   %Pt Parameter Set 9
295   %Au Parameter Set 35
296   \begin{table}[H]
297 <  \caption{Best fit parameters for metal-CO cross-interactions.   Metal-C
298 <    interactions are modeled with Lennard-Jones potential, while the
299 <    (mostly-repulsive) metal-O interactions were fit to Morse
297 >  \caption{Best fit parameters for metal-CO cross-interactions. Metal-C
298 >    interactions are modeled with Lennard-Jones potentials. While the
299 >    metal-O interactions were fit to Morse
300      potentials.  Distances are given in \AA~and energies in kcal/mol. }
301   \centering
302   \begin{tabular}{| c | cc | c | ccc |}
# Line 295 | Line 308 | preferences.\cite{Deshlahra:2012}
308  
309   \hline
310   \end{tabular}
311 + \label{tab:co_parameters}
312   \end{table}
313  
314   %Table of energies
315   \begin{table}[H]
316 <  \caption{Adsorption energies for CO on M(111) using the potentials
317 <    described in this work.  All values are in eV}
316 >  \caption{Adsorption energies for a single CO at the atop site on M(111) at the atop site using the potentials
317 >    described in this work.  All values are in eV.}
318   \centering
319   \begin{tabular}{| c | cc |}
320    \hline
# Line 312 | Line 326 | preferences.\cite{Deshlahra:2012}
326    \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPD_Gold}) \\
327    \hline
328   \end{tabular}
329 + \label{tab:co_energies}
330   \end{table}
331  
332   \subsection{Pt(557) and Au(557) metal interfaces}
333  
334   Our model systems are composed of 3888 Pt atoms and 3384 Au atoms in a
335 < FCC crystal that have been cut along the 557 plane so that they are
336 < periodic in the {\it x} and {\it y} directions, and have been rotated
337 < to expose two parallel 557 cuts along the positive and negative {\it
335 > FCC crystal that have been cut along the (557) plane so that they are
336 > periodic in the {\it x} and {\it y} directions, and have been oriented
337 > to expose two aligned (557) cuts along the extended {\it
338    z}-axis.  Simulations of the bare metal interfaces at temperatures
339 < ranging from 300~K to 1200~K were done to observe the relative
339 > ranging from 300~K to 1200~K were performed to observe the relative
340   stability of the surfaces without a CO overlayer.  
341  
342 < The different bulk (and surface) melting temperatures (1337~K for Au
343 < and 2045~K for Pt) suggest that the reconstruction may happen at
344 < different temperatures for the two metals.  To copy experimental
330 < conditions for the CO-exposed surfaces, the bare surfaces were
342 > The different bulk melting temperatures (1337~K for Au
343 > and 2045~K for Pt) suggest that any possible reconstruction should happen at
344 > different temperatures for the two metals.  The bare Au and Pt surfaces were
345   initially run in the canonical (NVT) ensemble at 800~K and 1000~K
346 < respectively for 100 ps.  Each surface was exposed to a range of CO
346 > respectively for 100 ps. The two surfaces were relatively stable at these
347 > temperatures when no CO was present, but experienced increased surface
348 > mobility on addition of CO. Each surface was then dosed with different concentrations of CO
349   that was initially placed in the vacuum region.  Upon full adsorption,
350 < these amounts correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
351 < coverage.  Because of the difference in binding energies, the platinum
352 < systems very rarely had CO that was not bound to the surface, while
353 < the gold surfaces often had a significant CO population in the gas
350 > these concentrations correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
351 > coverage. Higher coverages resulted in CO double layer formation, which introduces artifacts that are not relevant to (557) reconstruction.
352 > Because of the difference in binding energies, nearly all of the CO was bound to the Pt surface, while
353 > the Au surfaces often had a significant CO population in the gas
354   phase.  These systems were allowed to reach thermal equilibrium (over
355 < 5 ns) before being shifted to the microcanonical (NVE) ensemble for
355 > 5 ns) before being run in the microcanonical (NVE) ensemble for
356   data collection. All of the systems examined had at least 40 ns in the
357   data collection stage, although simulation times for some of the
358 < systems exceeded 200ns.  All simulations were run using the open
359 < source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,OpenMD}
358 > systems exceeded 200~ns.  Simulations were run using the open
359 > source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE}
360  
361   % Just results, leave discussion for discussion section
362 + % structure
363 + %       Pt: step wandering, double layers, no triangular motifs
364 + %       Au: step wandering, no double layers
365 + % dynamics
366 + %       diffusion
367 + %       time scale, formation, breakage
368   \section{Results}
369 < Tao {\it et al.} showed experimentally that the Pt(557) surface
370 < undergoes two separate reconstructions upon CO
371 < adsorption.\cite{Tao:2010} The first reconstruction involves a
372 < doubling of the step edge height which is accomplished by a doubling
373 < of the plateau length. The second reconstruction led to the formation
374 < of triangular clusters that arrange themselves along the lengthened
375 < plateaus.
369 > \subsection{Structural remodeling}
370 > Tao et al. have shown experimentally that the Pt(557) surface
371 > undergoes two separate reconstructions upon CO
372 > adsorption.\cite{Tao:2010} The first involves a doubling of
373 > the step height and plateau length. Similar behavior has been
374 > seen to occur on numerous surfaces at varying conditions: Ni(977), Si(111).
375 > \cite{Williams:1994,Williams:1991,Pearl} Of the two systems
376 > we examined, the Pt system showed a larger amount of
377 > reconstruction when compared to the Au system. The amount
378 > of reconstruction is correlated to the amount of CO
379 > adsorbed upon the surface.  This appears to be related to the
380 > effect that adsorbate coverage has on edge breakup and on the surface
381 > diffusion of metal adatoms. While both systems displayed step-edge
382 > wandering, only the Pt surface underwent the doubling seen by
383 > Tao et al. within the time scales studied here.  
384 > Only the 50~\% coverage Pt system exhibited
385 > a complete doubling in the time scales we
386 > were able to monitor. Over longer periods (150~ns) two more double layers formed on this interface.
387 > Although double layer formation did not occur in the other Pt systems, they show
388 > more lateral movement of the step-edges
389 > compared to the Au systems. The 50\% Pt system is highlighted
390 > in Figure \ref{fig:reconstruct} at various times along the simulation
391 > showing the evolution of a step-edge.
392  
393 < The primary observation and results of our simulation is that the
394 < presence of CO overlayer on Pt(557) causes the same kind of
395 < reconstruction observed experimentally. The 6-atom 111 facets
396 < initially become disordered, and after 20-40 ns, a double-layer (with
359 < a 2-atom step between terraces) forms.  However, we did not observe
360 < the triangular cluster formation that was observed at longer times in
361 < the experiments.  Without the CO present on the Pt(557) surface, there
362 < was some disorder at the step edges, but no significant restructuring
363 < was observed.
393 > The second reconstruction on the Pt(557) surface observed by
394 > Tao involved the formation of triangular clusters that stretched
395 > across the plateau between two step-edges. Neither system, within
396 > the 40~ns time scale, experienced this reconstruction.
397  
398 < In these simulations, the Au(557) surface did not exhibit any
399 < significant restructuring either with or without the presence of a CO
400 < overlayer.
398 > \subsection{Dynamics}
399 > While atomistic-like simulations of stepped surfaces have been
400 > performed before, they tend to be performed using Monte Carlo
401 > techniques\cite{Williams:1991,Williams:1994}. This allows them
402 > to efficiently sample the equilibrium thermodynamic landscape
403 > but at the expense of ignoring the dynamics of the system. Previous
404 > work by Pearl and Sibener\cite{Pearl}, using STM, has been able to
405 > visualize the coalescing of steps of Ni(977). The time scale of the image
406 > acquisition, $\sim$70 s/image provides an upper bounds for the time
407 > required for the doubling to actually occur. Statistical treatments of step-edges
408 > are adept at analyzing such systems. However, in a system where
409 > the number of steps is limited, examining the individual atoms that make
410 > up the steps can provide useful information as well.
411  
369 \subsection{Transport of surface metal atoms}
370 An ideal metal surface displaying a low energy (111) face is unlikely
371 to experience much surface diffusion because of the large vacancy
372 formation energy for atoms at the surface.  This implies that
373 significant energy must be expended to lift an atom out of the flat
374 face so it can migrate on the surface.  Rougher surfaces and those
375 that already contain numerous adatoms, step edges, and kinks, are
376 expected to have higher surface diffusion rates.  Metal atoms that are
377 mobile on the surface were observed to leave and then rejoin step
378 edges or other formations. They may travel together or as isolated
379 atoms.  The primary challenge of quantifying the overall surface
380 mobility is in defining ``mobile'' vs. ``static'' atoms.
412  
413 < A particle was considered mobile once it had traveled more than 2~\AA~
414 < between saved configurations (10-100 ps). Restricting the transport
415 < calculations to only mobile atoms eliminates all of the bulk metal as
416 < well as any surface atoms that remain fixed for a significant length
417 < of time.  Since diffusion on a surface is strongly affected by local
418 < structures, the diffusion parallel to the step edges was determined
419 < separately from the diffusion perpendicular to these edges.  The
420 < parallel and perpendicular diffusion constants (determined using
421 < linear fits to the mean squared displacement) are shown in figure \ref{fig:diff}.
413 > \subsubsection{Transport of surface metal atoms}
414 > %forcedSystems/stepSeparation
415 > The movement or wandering of a step-edge is a cooperative effect
416 > arising from the individual movements, primarily through surface
417 > diffusion, of the atoms making up the step. An ideal metal surface
418 > displaying a low index facet, (111) or (100) is unlikely to experience
419 > much surface diffusion because of the large energetic barrier that must
420 > be overcome to lift an atom out of the surface. The presence of step-edges
421 > on higher-index surfaces provide a source for mobile metal atoms.
422 > Breaking away from the step-edge on a clean surface still imposes an
423 > energetic penalty around $\sim$~40 kcal/mole, but is much less than lifting
424 > the same metal atom out from the surface,  \textgreater~60 kcal/mole, and
425 > the penalty lowers even further when CO is present in sufficient quantities
426 > on the surface. For certain tested distributions of CO, the penalty was lowered
427 > to $\sim$~20 kcal/mole. Once an adatom exists on the surface, its barrier for
428 > diffusion is negligible ( \textless~4 kcal/mole) and is well able to explore the
429 > terrace before potentially rejoining its original step-edge or becoming a part
430 > of a different edge. Atoms traversing separate terraces is a more difficult
431 > process, but can be overcome through a joining and lifting stage which is
432 > examined in the discussion section. By tracking the mobility of individual
433 > metal atoms on the Pt and Au surfaces we were able to determine the relative
434 > diffusion rates and how varying coverages of CO affected the rates. Close
435 > observation of the mobile metal atoms showed that they were typically in
436 > equilibrium with the step-edges, constantly breaking apart and rejoining.
437 > At times their motion was concerted and two or more adatoms would be
438 > observed moving together across the surfaces. The primary challenge in
439 > quantifying the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
440  
441 < %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.
441 > A particle was considered mobile once it had traveled more than 2~\AA~
442 > between saved configurations of the system (10-100 ps). An atom that was
443 > truly mobile would typically travel much greater than this, but the 2~\AA~ cutoff
444 > was to prevent the in-place vibrational movement of non-surface atoms from
445 > being included in the analysis. Diffusion on  a surface is strongly affected by
446 > local structures and in this work the presence of single and double layer
447 > step-edges causes the diffusion parallel to the step-edges to be different
448 > from the diffusion perpendicular to these edges. This led us to compute
449 > those diffusions separately as seen in Figure \ref{fig:diff}.
450  
451 + \subsubsection{Double layer formation}
452 + The increased amounts of diffusion on Pt at the higher CO coverages appears
453 + to play a primary role in the formation of double layers, although this conclusion
454 + does not explain the 33\% coverage Pt system. On the 50\% system, three
455 + separate layers were formed over the extended run time of this system. As
456 + mentioned earlier, previous experimental work has given some insight into the
457 + upper bounds of the time required for enough atoms to move around to allow two
458 + steps to coalesce\cite{Williams:1991,Pearl}. As seen in Figure \ref{fig:reconstruct},
459 + the first appearance of a double layer, a nodal site, appears at 19 ns into the
460 + simulation. Within 12 ns, nearly half of the step has formed the double layer and
461 + by 86 ns, a smooth complete layer has formed. The double layer is ``complete" by
462 + 37 ns but is a bit rough. From the appearance of the first node to the initial doubling
463 + of the layers ignoring their roughness took $\sim$~20 ns. Another ~40 ns was
464 + necessary for the layer to completely straighten. The other two layers in this
465 + simulation form over a period of 22 ns and 42 ns respectively. Comparing this to
466 + the upper bounds of the image scan, it is likely that aspects of this reconstruction
467 + occur very quickly.
468 +
469 + %Evolution of surface
470   \begin{figure}[H]
471 + \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
472 + \caption{The Pt(557) / 50\% CO system at a sequence of times after
473 +  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
474 +  (d) 86.1 ns. Disruption of the (557) step-edges occurs quickly.  The
475 +  doubling of the layers appears only after two adjacent step-edges
476 +  touch.  The circled spot in (b) nucleated the growth of the double
477 +  step observed in the later configurations.}
478 +  \label{fig:reconstruct}
479 + \end{figure}
480 +
481 + \begin{figure}[H]
482   \includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade.pdf}
483   \caption{Diffusion constants for mobile surface atoms along directions
484    parallel ($\mathbf{D}_{\parallel}$) and perpendicular
485 <  ($\mathbf{D}_{\perp}$) to the 557 step edges as a function of CO
486 <  surface coverage.  Diffusion parallel to the step edge is higher
485 >  ($\mathbf{D}_{\perp}$) to the (557) step-edges as a function of CO
486 >  surface coverage.  Diffusion parallel to the step-edge is higher
487    than that perpendicular to the edge because of the lower energy
488 <  barrier associated with going from approximately 7 nearest neighbors
489 <  to 5, as compared to the 3 of an adatom. Additionally, the observed
488 >  barrier associated with traversing along the edge as compared to
489 >  completely breaking away. Additionally, the observed
490    maximum and subsequent decrease for the Pt system suggests that the
491    CO self-interactions are playing a significant role with regards to
492 <  movement of the platinum atoms around and more importantly across
406 <  the surface. }
492 >  movement of the Pt atoms around and across the surface. }
493   \label{fig:diff}
494   \end{figure}
495  
410 %Table of Diffusion Constants
411 %Add gold?M
412 % \begin{table}[H]
413 %   \caption{}
414 %   \centering
415 % \begin{tabular}{| c | cc | cc | }
416 %   \hline
417 %   &\multicolumn{2}{c|}{\textbf{Platinum}}&\multicolumn{2}{c|}{\textbf{Gold}} \\
418 %   \hline
419 %   \textbf{Surface Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  \\
420 %   \hline
421 %   50\% & 4.32(2) & 1.185(8)  & 1.72(2) & 0.455(6) \\
422 %   33\% & 5.18(3)  & 1.999(5)  & 1.95(2) & 0.337(4)   \\
423 %   25\% & 5.01(2)  & 1.574(4)  & 1.26(3) & 0.377(6) \\
424 %   5\%   & 3.61(2)  & 0.355(2)  & 1.84(3)  & 0.169(4)  \\
425 %   0\%   & 3.27(2)  & 0.147(4)  & 1.50(2)  & 0.194(2)   \\
426 %   \hline
427 % \end{tabular}
428 % \end{table}
496  
497 +
498 +
499   %Discussion
500   \section{Discussion}
501 + In this paper we have shown that we were able to accurately model the initial reconstruction of the
502 + Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
503 + were able to observe the dynamic processes necessary for this reconstruction.
504  
505 < Mechanism for restructuring
505 > \subsection{Mechanism for restructuring}
506 > Comparing the results from simulation to those reported previously by
507 > Tao et al.\cite{Tao:2010} the similarities in the Pt-CO system are quite
508 > strong. As shown in Figure \ref{fig:reconstruct}, the simulated Pt
509 > system under a CO atmosphere will restructure by doubling the terrace
510 > heights. The restructuring occurs slowly, one to two Pt atoms at a time.
511 > Looking at individual configurations of the system, the adatoms either
512 > break away from the step-edge and stay on the lower terrace or they lift
513 > up onto the higher terrace. Once ``free'' they will diffuse on the terrace
514 > until reaching another step-edge or coming back to their original edge.  
515 > This combination of growth and decay of the step-edges is in a state of
516 > dynamic equilibrium. However, once two previously separated edges
517 > meet as shown in Figure 1.B, this meeting point tends to act as a focus
518 > or growth point for the rest of the edge to meet up, akin to that of a zipper.
519 > From the handful of cases where a double layer was formed during the
520 > simulation, measuring from the initial appearance of a growth point, the
521 > double layer tends to be fully formed within $\sim$~35 ns.
522  
523 < There are a number of possible mechanisms to explain the role of
524 < adsorbed CO in restructuring the Pt surface. Quadrupolar repulsion
525 < between adjacent CO molecules adsorbed on the surface is one
526 < possibility.  However, the quadrupole-quadrupole interaction is
527 < short-ranged and is attractive for some orientations.  If the CO
528 < molecules are locked in a specific orientation relative to each other,
529 < this explanation gains some weight.  
523 > A number of possible mechanisms exist to explain the role of adsorbed
524 > CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent
525 > CO molecules adsorbed on the surface is one likely possibility.  However,
526 > the quadrupole-quadrupole interaction is short-ranged and is attractive for
527 > some orientations.  If the CO molecules are ``locked'' in a specific orientation
528 > relative to each other, through atop adsorption perhaps, this explanation
529 > gains some weight.  The energetic repulsion between two CO located a
530 > distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in
531 > a  vertical orientation is 8.62 kcal/mole. Moving the CO apart to the second
532 > nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to
533 > nearly 0 kcal/mole. Allowing the CO's to leave a purely vertical orientation
534 > also quickly drops the repulsion, a minimum is reached at $\sim$24 degrees
535 > of 6.2 kcal/mole. As mentioned above, the energy barrier for surface diffusion
536 > of a Pt adatom is only 4 kcal/mole. So this repulsion between CO can help
537 > increase the surface diffusion. However, the residence time of CO was
538 > examined and while the majority of the CO is on or near the surface throughout
539 > the run, it is extremely mobile. This mobility suggests that the CO are more
540 > likely to shift their positions without necessarily dragging the Pt along with them.
541  
542 < Another possible mechanism for the restructuring is in the
542 > Another possible and more likely mechanism for the restructuring is in the
543   destabilization of strong Pt-Pt interactions by CO adsorbed on surface
544 < Pt atoms.  This could have the effect of increasing surface mobility
545 < of these atoms.  
544 > Pt atoms.  This would then have the effect of increasing surface mobility
545 > of these atoms.  To test this hypothesis, numerous configurations of
546 > CO in varying quantities were arranged on the higher and lower plateaus
547 > around a step on a otherwise clean Pt(557) surface. One representative
548 > configuration is displayed in Figure \ref{fig:lambda}. Single or concerted movement
549 > of Pt atoms was then examined to determine possible barriers. Because
550 > the movement was forced along a pre-defined reaction coordinate that may differ
551 > from the true minimum of this path, only the beginning and ending energies
552 > are displayed in Table \ref{tab:energies}. These values suggest that the presence of CO at suitable
553 > locations can lead to lowered barriers for Pt breaking apart from the step-edge.
554 > Additionally, as highlighted in Figure \ref{fig:lambda}, the presence of CO makes the
555 > burrowing and lifting of adatoms favorable, whereas without CO, the process is neutral
556 > in terms of energetics.
557  
558 < Comparing the results from simulation to those reported previously by
559 < Tao et al. the similarities in the platinum and CO system are quite
560 < strong. As shown in figure, the simulated platinum system under a CO
561 < atmosphere will restructure slightly by doubling the terrace
562 < heights. The restructuring appears to occur slowly, one to two
563 < platinum atoms at a time. Looking at individual snapshots, these
564 < adatoms tend to either rise on top of the plateau or break away from
565 < the step edge and then diffuse perpendicularly to the step direction
566 < until reaching another step edge. This combination of growth and decay
567 < of the step edges appears to be in somewhat of a state of dynamic
568 < equilibrium. However, once two previously separated edges meet as
569 < shown in figure 1.B, this point tends to act as a focus or growth
460 < point for the rest of the edge to meet up, akin to that of a
461 < zipper. From the handful of cases where a double layer was formed
462 < during the simulation, measuring from the initial appearance of a
463 < growth point, the double layer tends to be fully formed within
464 < $\sim$~35 ns.
558 > %lambda progression of Pt -> shoving its way into the step
559 > \begin{figure}[H]
560 > \includegraphics[width=\linewidth]{lambdaProgression_atopCO.png}
561 > \caption{A model system of the Pt(557) surface was used as the framework
562 > for exploring energy barriers along a reaction coordinate. Various numbers,
563 > placements, and rotations of CO were examined as they affect Pt movement.
564 > The coordinate displayed in this Figure was a representative run. As shown
565 > in Table \ref{tab:rxcoord}, relative to the energy of the system at 0\%, there
566 > is a slight decrease upon insertion of the Pt atom into the step-edge along
567 > with the resultant lifting of the other Pt atom when CO is present at certain positions.}
568 > \label{fig:lambda}
569 > \end{figure}
570  
571 +
572 +
573   \subsection{Diffusion}
574 < 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?)
574 > As shown in the results section, the diffusion parallel to the step-edge tends to be
575 > much larger than that perpendicular to the step-edge, likely because of the dynamic
576 > equilibrium that is established between the step-edge and adatom interface. The coverage
577 > of CO also appears to play a slight role in relative rates of diffusion, as shown in Figure \ref{fig:diff}.
578 > The
579 > Thus, the bottleneck of the double layer formation appears to be the initial formation
580 > of this growth point, which seems to be somewhat of a stochastic event. Once it
581 > appears, parallel diffusion, along the now slightly angled step-edge, will allow for
582 > a faster formation of the double layer than if the entire process were dependent on
583 > only perpendicular diffusion across the plateaus. Thus, the larger $D_{\perp}$, the
584 > more likely a growth point is to be formed.
585   \\
586 < \\
587 < %Evolution of surface
586 >
587 >
588 > %breaking of the double layer upon removal of CO
589   \begin{figure}[H]
590 < \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
591 < \caption{The Pt(557) / 50\% CO system at a sequence of times after
592 <  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
593 <  (d) 86.1 ns. Disruption of the 557 step edges occurs quickly.  The
594 <  doubling of the layers appears only after two adjacent step edges
595 <  touch.  The circled spot in (b) nucleated the growth of the double
596 <  step observed in the later configurations.}
590 > \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
591 > %:
592 > \caption{(A)  0 ps, (B) 100 ps, (C) 1 ns, after the removal of CO. The presence of the CO
593 > helped maintain the stability of the double layer and upon removal the two layers break
594 > and begin separating. The separation is not a simple pulling apart however, rather
595 > there is a mixing of the lower and upper atoms at the edge.}
596 > \label{fig:breaking}
597   \end{figure}
598  
599  
600 +
601 +
602   %Peaks!
603   \begin{figure}[H]
604   \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
605 < \caption{}
605 > \caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
606 > of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
607 > aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
608 > \label{fig:peaks}
609   \end{figure}
610 < \begin{figure}[H]
611 < \includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
612 < \caption{}
613 < \end{figure}
610 >
611 >
612 > %Don't think I need this
613 > %clean surface...
614 > %\begin{figure}[H]
615 > %\includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
616 > %\caption{}
617 >
618 > %\end{figure}
619 > %\label{fig:clean}
620 >
621 >
622   \section{Conclusion}
623 + In this work we have shown the reconstruction of the Pt(557) crystalline surface upon adsorption of CO in < $\mu s$. Only the highest coverage Pt system showed this initial reconstruction similar to that seen previously. The strong interaction between Pt and CO and the limited interaction between Au and CO helps explain the differences between the two systems.
624  
625 + %Things I am not ready to remove yet
626  
627 + %Table of Diffusion Constants
628 + %Add gold?M
629 + % \begin{table}[H]
630 + %   \caption{}
631 + %   \centering
632 + % \begin{tabular}{| c | cc | cc | }
633 + %   \hline
634 + %   &\multicolumn{2}{c|}{\textbf{Platinum}}&\multicolumn{2}{c|}{\textbf{Gold}} \\
635 + %   \hline
636 + %   \textbf{Surface Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  \\
637 + %   \hline
638 + %   50\% & 4.32(2) & 1.185(8)  & 1.72(2) & 0.455(6) \\
639 + %   33\% & 5.18(3)  & 1.999(5)  & 1.95(2) & 0.337(4)   \\
640 + %   25\% & 5.01(2)  & 1.574(4)  & 1.26(3) & 0.377(6) \\
641 + %   5\%   & 3.61(2)  & 0.355(2)  & 1.84(3)  & 0.169(4)  \\
642 + %   0\%   & 3.27(2)  & 0.147(4)  & 1.50(2)  & 0.194(2)   \\
643 + %   \hline
644 + % \end{tabular}
645 + % \end{table}
646 +
647   \section{Acknowledgments}
648   Support for this project was provided by the National Science
649   Foundation under grant CHE-0848243 and by the Center for Sustainable

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