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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 4, 2013}
62  
63   %authors
64  
# Line 68 | Line 68 | Notre Dame, Indiana 46556}
68   \begin{doublespace}
69  
70   \begin{abstract}
71 <
71 > We examine potential surface reconstructions of Pt and Au(557)
72 > under various CO coverages using molecular dynamics in order
73 > to explore possible mechanisms for any observed reconstructions and their dynamics.
74 > The metal-CO interactions were parameterized as part of this
75 > work so that an efficient large-scale treatment of this system could be
76 > undertaken. The relative binding strengths of the metal-CO
77 > interactions were found to play a large role with regards to
78 > step-edge stability and adatom diffusion. A small correlation
79 > between coverage and the size of the diffusion constant was
80 > also determined. An in-depth examination of the energetics of CO
81 > adsorbed to the surface provides results that appear sufficient to explain the
82 > reconstructions observed on the Pt systems and the corresponding lack  
83 > on the Au systems.
84   \end{abstract}
85  
86   \newpage
# 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
115 > This work is an attempt 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
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 > Restructuring can occur 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.
# Line 133 | Line 144 | Au-Au and Pt-Pt interactions, while modeling the CO us
144   Coulomb potential.  For this work, we have used classical molecular
145   dynamics with potential energy surfaces that are specifically tuned
146   for transition metals.  In particular, we used the EAM potential for
147 < Au-Au and Pt-Pt interactions, while modeling the CO using a rigid
147 > Au-Au and Pt-Pt interactions\cite{EAM}, while modeling the CO using a rigid
148   three-site model developed by Straub and Karplus for studying
149   photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
150   Pt-CO cross interactions were parameterized as part of this work.
# Line 146 | Line 157 | parameter sets. The glue model of Ercolessi {\it et al
157   methods,\cite{Daw84,Foiles86,Johnson89,Daw89,Plimpton93,Voter95a,Lu97,Alemany98}
158   but other models like the Finnis-Sinclair\cite{Finnis84,Chen90} and
159   the quantum-corrected Sutton-Chen method\cite{QSC,Qi99} have simpler
160 < parameter sets. The glue model of Ercolessi {\it et al.} is among the
160 > parameter sets. The glue model of Ercolessi et al. is among the
161   fastest of these density functional approaches.\cite{Ercolessi88} In
162   all of these models, atoms are conceptualized as a positively charged
163   core with a radially-decaying valence electron distribution. To
# Line 164 | Line 175 | $\phi_{ij}(r_{ij})$ is an pairwise term that is meant
175   V_i =  F[ \bar{\rho}_i ]  + \sum_{j \neq i} \phi_{ij}(r_{ij})
176   \end{equation*}
177   where $F[ \bar{\rho}_i ]$ is an energy embedding functional, and
178 < $\phi_{ij}(r_{ij})$ is an pairwise term that is meant to represent the
179 < overlap of the two positively charged cores.  
178 > $\phi_{ij}(r_{ij})$ is a pairwise term that is meant to represent the
179 > repulsive overlap of the two positively charged cores.  
180  
181   % The {\it modified} embedded atom method (MEAM) adds angular terms to
182   % the electron density functions and an angular screening factor to the
# Line 176 | Line 187 | The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen
187   % metals,\cite{Lee:2001qf} and also interfaces.\cite{Beurden:2002ys})
188   % MEAM presents significant additional computational costs, however.
189  
190 < The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen potentials
190 > The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen (QSC) potentials
191   have all been widely used by the materials simulation community for
192   simulations of bulk and nanoparticle
193   properties,\cite{Chui:2003fk,Wang:2005qy,Medasani:2007uq}
# Line 190 | Line 201 | Since previous explanations for the surface rearrangem
201   parameterized.\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
202  
203   \subsection{Carbon Monoxide model}
204 < Since previous explanations for the surface rearrangements center on
205 < the large linear quadrupole moment of carbon monoxide, the model
206 < chosen for this molecule exhibits this property in an efficient
207 < manner.  We used a model first proposed by Karplus and Straub to study
208 < the photodissociation of CO from myoglobin.\cite{Straub} The Straub and
209 < Karplus model is a rigid three site model which places a massless M
210 < site at the center of mass along the CO bond.  The geometry used along
211 < with the interaction parameters are reproduced in Table~1. The effective
204 > Previous explanations for the surface rearrangements center on
205 > the large linear quadrupole moment of carbon monoxide.  
206 > We used a model first proposed by Karplus and Straub to study
207 > the photodissociation of CO from myoglobin because it reproduces
208 > the quadrupole moment well.\cite{Straub} The Straub and
209 > Karplus model, treats CO as a rigid three site molecule which places a massless M
210 > site at the center of mass position along the CO bond.  The geometry used along
211 > with the interaction parameters are reproduced in Table~\ref{tab:CO}. The effective
212   dipole moment, calculated from the assigned charges, is still
213   small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is close
214   to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum
# Line 206 | Line 217 | mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCO
217   \begin{table}[H]
218    \caption{Positions, Lennard-Jones parameters ($\sigma$ and
219      $\epsilon$), and charges for the CO-CO
220 <    interactions borrowed from Ref. \bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA~, energies are
220 >    interactions borrowed from Ref.\bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA, energies are
221      in kcal/mol, and charges are in atomic units.}
222   \centering
223   \begin{tabular}{| c | c | ccc |}
# Line 218 | Line 229 | mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCO
229   \textbf{M} & 0.0 & -  &  -  &    1.6 \\
230   \hline
231   \end{tabular}
232 + \label{tab:CO}
233   \end{table}
234  
235   \subsection{Cross-Interactions between the metals and carbon monoxide}
236  
237 < Since the adsorption of CO onto a platinum surface has been the focus
237 > Since the adsorption of CO onto a Pt surface has been the focus
238   of much experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979}
239   and theoretical work
240   \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
# Line 230 | Line 242 | position on Pt(111). This resulting binding energies a
242   clean metal surfaces. Parameters reported by Korzeniewski {\it et
243    al.}\cite{Pons:1986} were a starting point for our fits, which were
244   modified to ensure that the Pt-CO interaction favored the atop binding
245 < position on Pt(111). This resulting binding energies are on the higher
246 < side of the experimentally-reported values. Following Korzeniewski
247 < {\it et al.},\cite{Pons:1986} the Pt-C interaction was fit to a deep
245 > position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}
246 > This resulted in binding energies that are slightly higher
247 > than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
248 > et al.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
249   Lennard-Jones interaction to mimic strong, but short-ranged partial
250   binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
251 < Pt-O interaction was parameterized to a Morse potential with a large
252 < range parameter ($r_o$).  In most cases, this contributes a weak
251 > Pt-O interaction was parameterized to a Morse potential at a larger
252 > minimum distance, ($r_o$).  This was chosen so that the C would be preferred
253 > over O as the binder to the surface. In most cases, this parameterization contributes a weak
254   repulsion which favors the atop site.  The resulting potential-energy
255   surface suitably recovers the calculated Pt-C separation length
256   (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
# Line 245 | Line 259 | The Au-C and Au-O cross-interactions were fit using Le
259   %where did you actually get the functionals for citation?
260   %scf calculations, so initial relaxation was of the four layers, but two layers weren't kept fixed, I don't think
261   %same cutoff for slab and slab + CO ? seems low, although feibelmen had values around there...
262 < The Au-C and Au-O cross-interactions were fit using Lennard-Jones and
262 > The Au-C and Au-O cross-interactions were also fit using Lennard-Jones and
263   Morse potentials, respectively, to reproduce Au-CO binding energies.
264 <
265 < The fits were refined against gas-surface DFT calculations with a
264 > The limited experimental data for CO adsorption on Au lead us to refine our fits against DFT.
265 > Adsorption energies were obtained from gas-surface DFT calculations with a
266   periodic supercell plane-wave basis approach, as implemented in the
267   {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores are
268   described with the projector augmented-wave (PAW)
# Line 257 | Line 271 | Ionic relaxations were performed until the energy diff
271   computed with the PBE implementation of the generalized gradient
272   approximation (GGA) for gold, carbon, and oxygen that was constructed
273   by Rappe, Rabe, Kaxiras, and Joannopoulos.\cite{Perdew_GGA,RRKJ_PP}
274 < 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
274 > In testing the Au-CO interaction, Au(111) supercells were constructed of four layers of 4
275   Au x 2 Au surface planes and separated from vertical images by six
276 < layers of vacuum space. The surface atoms were all allowed to relax.
277 < Supercell calculations were performed nonspin-polarized with a 4 x 4 x
278 < 4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
276 > layers of vacuum space. The surface atoms were all allowed to relax
277 > before CO was added to the system. Electronic relaxations were
278 > performed until the energy difference between subsequent steps
279 > was less than $10^{-8}$ Ry.   Nonspin-polarized supercell calculations
280 > were performed with a 4~x~4~x~4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
281   zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxed gold slab was
282   then used in numerous single point calculations with CO at various
283   heights (and angles relative to the surface) to allow fitting of the
284   empirical force field.
285  
286   %Hint at future work
287 < The parameters employed in this work are shown in Table 2 and the
288 < binding energies on the 111 surfaces are displayed in Table 3.  To
289 < speed up the computations, charge transfer and polarization are not
290 < being treated in this model, although these effects are likely to
291 < affect binding energies and binding site
292 < preferences.\cite{Deshlahra:2012}
287 > The parameters employed for the metal-CO cross-interactions in this work
288 > are shown in Table~\ref{co_parameters} and the binding energies on the
289 > (111) surfaces are displayed in Table~\ref{co_energies}.  Charge transfer
290 > and polarization are neglected in this model, although these effects are likely to
291 > affect binding energies and binding site preferences, and will be added in
292 > a future work.\cite{Deshlahra:2012,StreitzMintmire:1994}
293  
294   %Table  of Parameters
295   %Pt Parameter Set 9
296   %Au Parameter Set 35
297   \begin{table}[H]
298 <  \caption{Best fit parameters for metal-CO cross-interactions.   Metal-C
298 >  \caption{Best fit parameters for metal-CO cross-interactions. Metal-C
299      interactions are modeled with Lennard-Jones potential, while the
300 <    (mostly-repulsive) metal-O interactions were fit to Morse
300 >    metal-O interactions were fit to Morse
301      potentials.  Distances are given in \AA~and energies in kcal/mol. }
302   \centering
303   \begin{tabular}{| c | cc | c | ccc |}
# Line 295 | Line 309 | preferences.\cite{Deshlahra:2012}
309  
310   \hline
311   \end{tabular}
312 + \label{tab:co_parameters}
313   \end{table}
314  
315   %Table of energies
316   \begin{table}[H]
317 <  \caption{Adsorption energies for CO on M(111) using the potentials
318 <    described in this work.  All values are in eV}
317 >  \caption{Adsorption energies for CO on M(111) at the atop site using the potentials
318 >    described in this work.  All values are in eV.}
319   \centering
320   \begin{tabular}{| c | cc |}
321    \hline
# Line 312 | Line 327 | preferences.\cite{Deshlahra:2012}
327    \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPD_Gold}) \\
328    \hline
329   \end{tabular}
330 + \label{tab:co_energies}
331   \end{table}
332  
333   \subsection{Pt(557) and Au(557) metal interfaces}
334  
335   Our model systems are composed of 3888 Pt atoms and 3384 Au atoms in a
336 < FCC crystal that have been cut along the 557 plane so that they are
337 < periodic in the {\it x} and {\it y} directions, and have been rotated
338 < to expose two parallel 557 cuts along the positive and negative {\it
336 > FCC crystal that have been cut along the (557) plane so that they are
337 > periodic in the {\it x} and {\it y} directions, and have been oriented
338 > to expose two aligned (557) cuts along the extended {\it
339    z}-axis.  Simulations of the bare metal interfaces at temperatures
340 < ranging from 300~K to 1200~K were done to observe the relative
340 > ranging from 300~K to 1200~K were performed to observe the relative
341   stability of the surfaces without a CO overlayer.  
342  
343   The different bulk (and surface) melting temperatures (1337~K for Au
344 < and 2045~K for Pt) suggest that the reconstruction may happen at
345 < different temperatures for the two metals.  To copy experimental
330 < conditions for the CO-exposed surfaces, the bare surfaces were
344 > and 2045~K for Pt) suggest that any possible reconstruction may happen at
345 > different temperatures for the two metals.  The bare Au and Pt surfaces were
346   initially run in the canonical (NVT) ensemble at 800~K and 1000~K
347 < respectively for 100 ps.  Each surface was exposed to a range of CO
347 > respectively for 100 ps. These temperatures were chosen because the
348 > surfaces were relatively stable at these temperatures when no CO was
349 > present, but experienced additional instability upon addition of CO in the time
350 > frames we were examining. Each surface was exposed to a range of CO
351   that was initially placed in the vacuum region.  Upon full adsorption,
352   these amounts correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
353 < coverage.  Because of the difference in binding energies, the platinum
353 > coverage. Higher coverages were tried, but the CO-CO repulsion was preventing
354 > a higher amount of adsorption.  Because of the difference in binding energies, the Pt
355   systems very rarely had CO that was not bound to the surface, while
356 < the gold surfaces often had a significant CO population in the gas
356 > the Au surfaces often had a significant CO population in the gas
357   phase.  These systems were allowed to reach thermal equilibrium (over
358 < 5 ns) before being shifted to the microcanonical (NVE) ensemble for
358 > 5 ns) before being run in the microcanonical (NVE) ensemble for
359   data collection. All of the systems examined had at least 40 ns in the
360   data collection stage, although simulation times for some of the
361   systems exceeded 200ns.  All simulations were run using the open
362 < source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,OpenMD}
362 > source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE}
363  
364   % Just results, leave discussion for discussion section
365 + % structure
366 + %       Pt: step wandering, double layers, no triangular motifs
367 + %       Au: step wandering, no double layers
368 + % dynamics
369 + %       diffusion
370 + %       time scale, formation, breakage
371   \section{Results}
372 < Tao {\it et al.} showed experimentally that the Pt(557) surface
373 < undergoes two separate reconstructions upon CO
374 < adsorption.\cite{Tao:2010} The first reconstruction involves a
375 < doubling of the step edge height which is accomplished by a doubling
376 < of the plateau length. The second reconstruction led to the formation
377 < of triangular clusters that arrange themselves along the lengthened
378 < plateaus.
372 > \subsection{Structural remodeling}
373 > Tao et al. showed experimentally that the Pt(557) surface
374 > undergoes two separate reconstructions upon CO
375 > adsorption.\cite{Tao:2010} The first involves a doubling of
376 > the step height and plateau length. Similar behavior has been
377 > seen to occur on numerous surfaces at varying conditions (Ni 977, Si 111, etc).
378 > \cite{Williams:1994,Williams:1991,Pearl} Of the two systems
379 > we examined, the Pt system showed a larger amount of
380 > reconstruction when compared to the Au system. The amount
381 > of reconstruction appears to be correlated to the amount of CO
382 > adsorbed upon the surface.  We believe this is related to the
383 > effect that adsorbate coverage has on edge breakup and surface
384 > diffusion of adatoms. While both systems displayed step-edge
385 > wandering, only the Pt surface underwent the doubling seen by
386 > Tao et al., within the time scales we were modeling. Specifically,
387 > only the 50~\% coverage Pt system was observed to have a
388 > step-edge undergo a complete doubling in the time scales we
389 > were able to monitor. This event encouraged us to allow that
390 > specific system to run for much longer periods during which two
391 > more double layers were created. The other systems, not displaying
392 > any large scale changes of interest, were all stopped after running
393 > for 40 ns in the microcanonical ensemble. Despite no observation
394 > of double layer formation, the other Pt systems tended to show
395 > more cumulative lateral movement of the step-edges when
396 > compared to the Au systems. The 50\% Pt system is highlighted
397 > in Figure \ref{fig:reconstruct} at various times along the simulation
398 > showing the evolution of the system.
399  
400 < The primary observation and results of our simulation is that the
401 < presence of CO overlayer on Pt(557) causes the same kind of
402 < reconstruction observed experimentally. The 6-atom 111 facets
403 < initially become disordered, and after 20-40 ns, a double-layer (with
404 < a 2-atom step between terraces) forms.  However, we did not observe
405 < 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.
400 > The second reconstruction on the Pt(557) surface observed by
401 > Tao involved the formation of triangular clusters that stretched
402 > across the plateau between two step-edges. Neither system, within
403 > our simulated time scales, experiences this reconstruction. A constructed
404 > system in which the triangular motifs were constructed on the surface
405 > will be explored in future work and is shown in the supporting information.
406  
407 < In these simulations, the Au(557) surface did not exhibit any
408 < significant restructuring either with or without the presence of a CO
409 < overlayer.
407 > \subsection{Dynamics}
408 > While atomistic-like simulations of stepped surfaces have been
409 > performed before, they tend to be performed using Monte Carlo
410 > techniques\cite{Williams:1991,Williams:1994}. This allows them
411 > to efficiently sample the equilibrium thermodynamic landscape
412 > but at the expense of ignoring the dynamics of the system. Previous
413 > work by Pearl and Sibener\cite{Pearl}, using STM, has been able to
414 > visualize the coalescing of steps of Ni(977). The time scale of the image
415 > acquisition, $\sim$70 s/image provides an upper bounds for the time
416 > required for the doubling to actually occur. Statistical treatments of step-edges
417 > are adept at analyzing such systems. However, in a system where
418 > the number of steps is limited, examining the individual atoms that make
419 > up the steps can provide useful information as well.
420  
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.
421  
422 < A particle was considered mobile once it had traveled more than 2~\AA~
423 < between saved configurations (10-100 ps). Restricting the transport
424 < calculations to only mobile atoms eliminates all of the bulk metal as
425 < well as any surface atoms that remain fixed for a significant length
426 < of time.  Since diffusion on a surface is strongly affected by local
427 < structures, the diffusion parallel to the step edges was determined
428 < separately from the diffusion perpendicular to these edges.  The
429 < parallel and perpendicular diffusion constants (determined using
430 < linear fits to the mean squared displacement) are shown in figure \ref{fig:diff}.
422 > \subsubsection{Transport of surface metal atoms}
423 > %forcedSystems/stepSeparation
424 > The movement or wandering of a step-edge is a cooperative effect
425 > arising from the individual movements, primarily through surface
426 > diffusion, of the atoms making up the step. An ideal metal surface
427 > displaying a low index facet, (111) or (100) is unlikely to experience
428 > much surface diffusion because of the large energetic barrier that must
429 > be overcome to lift an atom out of the surface. The presence of step-edges
430 > on higher-index surfaces provide a source for mobile metal atoms.
431 > Breaking away from the step-edge on a clean surface still imposes an
432 > energetic penalty around $\sim$~40 kcal/mole, but is much less than lifting
433 > the same metal atom out from the surface,  \textgreater~60 kcal/mole, and
434 > the penalty lowers even further when CO is present in sufficient quantities
435 > on the surface. For certain tested distributions of CO, the penalty was lowered
436 > to $\sim$~20 kcal/mole. Once an adatom exists on the surface, its barrier for
437 > diffusion is negligible ( \textless~4 kcal/mole) and is well able to explore the
438 > terrace before potentially rejoining its original step-edge or becoming a part
439 > of a different edge. Atoms traversing separate terraces is a more difficult
440 > process, but can be overcome through a joining and lifting stage which is
441 > examined in the discussion section. By tracking the mobility of individual
442 > metal atoms on the Pt and Au surfaces we were able to determine the relative
443 > diffusion rates and how varying coverages of CO affected the rates. Close
444 > observation of the mobile metal atoms showed that they were typically in
445 > equilibrium with the step-edges, constantly breaking apart and rejoining.
446 > At times their motion was concerted and two or more adatoms would be
447 > observed moving together across the surfaces. The primary challenge in
448 > quantifying the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
449  
450 < %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.
450 > A particle was considered mobile once it had traveled more than 2~\AA~
451 > between saved configurations of the system (10-100 ps). An atom that was
452 > truly mobile would typically travel much greater than this, but the 2~\AA~ cutoff
453 > was to prevent the in-place vibrational movement of non-surface atoms from
454 > being included in the analysis. Diffusion on  a surface is strongly affected by
455 > local structures and in this work the presence of single and double layer
456 > step-edges causes the diffusion parallel to the step-edges to be different
457 > from the diffusion perpendicular to these edges. This led us to compute
458 > those diffusions separately as seen in Figure \ref{fig:diff}.
459  
460 + \subsubsection{Double layer formation}
461 + The increased amounts of diffusion on Pt at the higher CO coverages appears
462 + to play a primary role in the formation of double layers, although this conclusion
463 + does not explain the 33\% coverage Pt system. On the 50\% system, three
464 + separate layers were formed over the extended run time of this system. As
465 + mentioned earlier, previous experimental work has given some insight into the
466 + upper bounds of the time required for enough atoms to move around to allow two
467 + steps to coalesce\cite{Williams:1991,Pearl}. As seen in Figure \ref{fig:reconstruct},
468 + the first appearance of a double layer, a nodal site, appears at 19 ns into the
469 + simulation. Within 12 ns, nearly half of the step has formed the double layer and
470 + by 86 ns, a smooth complete layer has formed. The double layer is ``complete" by
471 + 37 ns but is a bit rough. From the appearance of the first node to the initial doubling
472 + of the layers ignoring their roughness took $\sim$~20 ns. Another ~40 ns was
473 + necessary for the layer to completely straighten. The other two layers in this
474 + simulation form over a period of 22 ns and 42 ns respectively. Comparing this to
475 + the upper bounds of the image scan, it is likely that aspects of this reconstruction
476 + occur very quickly.
477 +
478 + %Evolution of surface
479   \begin{figure}[H]
480 + \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
481 + \caption{The Pt(557) / 50\% CO system at a sequence of times after
482 +  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
483 +  (d) 86.1 ns. Disruption of the (557) step-edges occurs quickly.  The
484 +  doubling of the layers appears only after two adjacent step-edges
485 +  touch.  The circled spot in (b) nucleated the growth of the double
486 +  step observed in the later configurations.}
487 +  \label{fig:reconstruct}
488 + \end{figure}
489 +
490 + \begin{figure}[H]
491   \includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade.pdf}
492   \caption{Diffusion constants for mobile surface atoms along directions
493    parallel ($\mathbf{D}_{\parallel}$) and perpendicular
494 <  ($\mathbf{D}_{\perp}$) to the 557 step edges as a function of CO
495 <  surface coverage.  Diffusion parallel to the step edge is higher
494 >  ($\mathbf{D}_{\perp}$) to the (557) step-edges as a function of CO
495 >  surface coverage.  Diffusion parallel to the step-edge is higher
496    than that perpendicular to the edge because of the lower energy
497 <  barrier associated with going from approximately 7 nearest neighbors
498 <  to 5, as compared to the 3 of an adatom. Additionally, the observed
497 >  barrier associated with traversing along the edge as compared to
498 >  completely breaking away. Additionally, the observed
499    maximum and subsequent decrease for the Pt system suggests that the
500    CO self-interactions are playing a significant role with regards to
501 <  movement of the platinum atoms around and more importantly across
406 <  the surface. }
501 >  movement of the Pt atoms around and across the surface. }
502   \label{fig:diff}
503   \end{figure}
504  
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}
505  
506 +
507 +
508   %Discussion
509   \section{Discussion}
510 + In this paper we have shown that we were able to accurately model the initial reconstruction of the
511 + Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
512 + were able to observe the dynamic processes necessary for this reconstruction.
513  
514 < Mechanism for restructuring
514 > \subsection{Mechanism for restructuring}
515 > Comparing the results from simulation to those reported previously by
516 > Tao et al.\cite{Tao:2010} the similarities in the Pt-CO system are quite
517 > strong. As shown in Figure \ref{fig:reconstruct}, the simulated Pt
518 > system under a CO atmosphere will restructure by doubling the terrace
519 > heights. The restructuring occurs slowly, one to two Pt atoms at a time.
520 > Looking at individual configurations of the system, the adatoms either
521 > break away from the step-edge and stay on the lower terrace or they lift
522 > up onto the higher terrace. Once ``free'' they will diffuse on the terrace
523 > until reaching another step-edge or coming back to their original edge.  
524 > This combination of growth and decay of the step-edges is in a state of
525 > dynamic equilibrium. However, once two previously separated edges
526 > meet as shown in Figure 1.B, this meeting point tends to act as a focus
527 > or growth point for the rest of the edge to meet up, akin to that of a zipper.
528 > From the handful of cases where a double layer was formed during the
529 > simulation, measuring from the initial appearance of a growth point, the
530 > double layer tends to be fully formed within $\sim$~35 ns.
531  
532 < There are a number of possible mechanisms to explain the role of
533 < adsorbed CO in restructuring the Pt surface. Quadrupolar repulsion
534 < between adjacent CO molecules adsorbed on the surface is one
535 < possibility.  However, the quadrupole-quadrupole interaction is
536 < short-ranged and is attractive for some orientations.  If the CO
537 < molecules are locked in a specific orientation relative to each other,
538 < this explanation gains some weight.  
532 > A number of possible mechanisms exist to explain the role of adsorbed
533 > CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent
534 > CO molecules adsorbed on the surface is one likely possibility.  However,
535 > the quadrupole-quadrupole interaction is short-ranged and is attractive for
536 > some orientations.  If the CO molecules are ``locked'' in a specific orientation
537 > relative to each other, through atop adsorption perhaps, this explanation
538 > gains some weight.  The energetic repulsion between two CO located a
539 > distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in
540 > a  vertical orientation is 8.62 kcal/mole. Moving the CO apart to the second
541 > nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to
542 > nearly 0 kcal/mole. Allowing the CO's to leave a purely vertical orientation
543 > also quickly drops the repulsion, a minimum is reached at $\sim$24 degrees
544 > of 6.2 kcal/mole. As mentioned above, the energy barrier for surface diffusion
545 > of a Pt adatom is only 4 kcal/mole. So this repulsion between CO can help
546 > increase the surface diffusion. However, the residence time of CO was
547 > examined and while the majority of the CO is on or near the surface throughout
548 > the run, it is extremely mobile. This mobility suggests that the CO are more
549 > likely to shift their positions without necessarily dragging the Pt along with them.
550  
551 < Another possible mechanism for the restructuring is in the
551 > Another possible and more likely mechanism for the restructuring is in the
552   destabilization of strong Pt-Pt interactions by CO adsorbed on surface
553 < Pt atoms.  This could have the effect of increasing surface mobility
554 < of these atoms.  
553 > Pt atoms.  This would then have the effect of increasing surface mobility
554 > of these atoms.  To test this hypothesis, numerous configurations of
555 > CO in varying quantities were arranged on the higher and lower plateaus
556 > around a step on a otherwise clean Pt(557) surface. One representative
557 > configuration is displayed in Figure \ref{fig:lambda}. Single or concerted movement
558 > of Pt atoms was then examined to determine possible barriers. Because
559 > the movement was forced along a pre-defined reaction coordinate that may differ
560 > from the true minimum of this path, only the beginning and ending energies
561 > are displayed in Table \ref{tab:energies}. These values suggest that the presence of CO at suitable
562 > locations can lead to lowered barriers for Pt breaking apart from the step-edge.
563 > Additionally, as highlighted in Figure \ref{fig:lambda}, the presence of CO makes the
564 > burrowing and lifting of adatoms favorable, whereas without CO, the process is neutral
565 > in terms of energetics.
566  
567 < Comparing the results from simulation to those reported previously by
568 < Tao et al. the similarities in the platinum and CO system are quite
569 < strong. As shown in figure, the simulated platinum system under a CO
570 < atmosphere will restructure slightly by doubling the terrace
571 < heights. The restructuring appears to occur slowly, one to two
572 < platinum atoms at a time. Looking at individual snapshots, these
573 < adatoms tend to either rise on top of the plateau or break away from
574 < the step edge and then diffuse perpendicularly to the step direction
575 < until reaching another step edge. This combination of growth and decay
576 < of the step edges appears to be in somewhat of a state of dynamic
577 < equilibrium. However, once two previously separated edges meet as
578 < 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.
567 > %lambda progression of Pt -> shoving its way into the step
568 > \begin{figure}[H]
569 > \includegraphics[width=\linewidth]{lambdaProgression_atopCO.png}
570 > \caption{A model system of the Pt(557) surface was used as the framework
571 > for exploring energy barriers along a reaction coordinate. Various numbers,
572 > placements, and rotations of CO were examined as they affect Pt movement.
573 > The coordinate displayed in this Figure was a representative run. As shown
574 > in Table \ref{tab:rxcoord}, relative to the energy of the system at 0\%, there
575 > is a slight decrease upon insertion of the Pt atom into the step-edge along
576 > with the resultant lifting of the other Pt atom when CO is present at certain positions.}
577 > \label{fig:lambda}
578 > \end{figure}
579  
580 +
581 +
582   \subsection{Diffusion}
583 < 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?)
583 > As shown in the results section, the diffusion parallel to the step-edge tends to be
584 > much larger than that perpendicular to the step-edge, likely because of the dynamic
585 > equilibrium that is established between the step-edge and adatom interface. The coverage
586 > of CO also appears to play a slight role in relative rates of diffusion, as shown in Figure \ref{fig:diff}.
587 > The
588 > Thus, the bottleneck of the double layer formation appears to be the initial formation
589 > of this growth point, which seems to be somewhat of a stochastic event. Once it
590 > appears, parallel diffusion, along the now slightly angled step-edge, will allow for
591 > a faster formation of the double layer than if the entire process were dependent on
592 > only perpendicular diffusion across the plateaus. Thus, the larger $D_{\perp}$, the
593 > more likely a growth point is to be formed.
594   \\
595 < \\
596 < %Evolution of surface
595 >
596 >
597 > %breaking of the double layer upon removal of CO
598   \begin{figure}[H]
599 < \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
600 < \caption{The Pt(557) / 50\% CO system at a sequence of times after
601 <  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
602 <  (d) 86.1 ns. Disruption of the 557 step edges occurs quickly.  The
603 <  doubling of the layers appears only after two adjacent step edges
604 <  touch.  The circled spot in (b) nucleated the growth of the double
605 <  step observed in the later configurations.}
599 > \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
600 > %:
601 > \caption{(A)  0 ps, (B) 100 ps, (C) 1 ns, after the removal of CO. The presence of the CO
602 > helped maintain the stability of the double layer and upon removal the two layers break
603 > and begin separating. The separation is not a simple pulling apart however, rather
604 > there is a mixing of the lower and upper atoms at the edge.}
605 > \label{fig:breaking}
606   \end{figure}
607  
608  
609 +
610 +
611   %Peaks!
612   \begin{figure}[H]
613   \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
614 < \caption{}
614 > \caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
615 > of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
616 > aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
617 > \label{fig:peaks}
618   \end{figure}
619 < \begin{figure}[H]
620 < \includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
621 < \caption{}
622 < \end{figure}
619 >
620 >
621 > %Don't think I need this
622 > %clean surface...
623 > %\begin{figure}[H]
624 > %\includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
625 > %\caption{}
626 >
627 > %\end{figure}
628 > %\label{fig:clean}
629 >
630 >
631   \section{Conclusion}
632 + 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.
633  
634 + %Things I am not ready to remove yet
635  
636 + %Table of Diffusion Constants
637 + %Add gold?M
638 + % \begin{table}[H]
639 + %   \caption{}
640 + %   \centering
641 + % \begin{tabular}{| c | cc | cc | }
642 + %   \hline
643 + %   &\multicolumn{2}{c|}{\textbf{Platinum}}&\multicolumn{2}{c|}{\textbf{Gold}} \\
644 + %   \hline
645 + %   \textbf{Surface Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  \\
646 + %   \hline
647 + %   50\% & 4.32(2) & 1.185(8)  & 1.72(2) & 0.455(6) \\
648 + %   33\% & 5.18(3)  & 1.999(5)  & 1.95(2) & 0.337(4)   \\
649 + %   25\% & 5.01(2)  & 1.574(4)  & 1.26(3) & 0.377(6) \\
650 + %   5\%   & 3.61(2)  & 0.355(2)  & 1.84(3)  & 0.169(4)  \\
651 + %   0\%   & 3.27(2)  & 0.147(4)  & 1.50(2)  & 0.194(2)   \\
652 + %   \hline
653 + % \end{tabular}
654 + % \end{table}
655 +
656   \section{Acknowledgments}
657   Support for this project was provided by the National Science
658   Foundation under grant CHE-0848243 and by the Center for Sustainable

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