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# Line 58 | Line 58 | Notre Dame, Indiana 46556}
58   Notre Dame, Indiana 46556}
59  
60   %Date
61 < \date{Mar 4, 2013}
61 > \date{Mar 5, 2013}
62  
63   %authors
64  
# Line 68 | Line 68 | We examine potential surface reconstructions of Pt and
68   \begin{doublespace}
69  
70   \begin{abstract}
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.
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  
86   \newpage
# Line 112 | Line 112 | This work is an attempt to understand the mechanism an
112   reversible restructuring under exposure to moderate pressures of
113   carbon monoxide.\cite{Tao:2010}
114  
115 < This work is an attempt to understand the mechanism and timescale for
115 > This work is an investigation into the mechanism and timescale for
116   surface restructuring 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 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
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.
123 > to undergo a large scale reconstruction under certain conditions.\cite{Tao:2010}
124 > The Au(557) surface, because of a weaker interaction with CO, is seen as less
125 > likely to undergo this kind of reconstruction. However, Peters et al.\cite{Peters:2000}
126 > and Piccolo et al.\cite{Piccolo:2004} have both observed CO-induced
127 > reconstruction of a Au(111) surface. Peters et al. saw a relaxation to the
128 > 22 x $\sqrt{3}$ cell. They argued that only a few Au atoms
129 > become adatoms, limiting the stress of this reconstruction while
130 > allowing the rest to relax and approach the ideal (111)
131 > configuration. They did not see the usual herringbone pattern being greatly
132 > affected by this relaxation. Piccolo et al. on the other hand, did see a
133 > disruption of the herringbone pattern as CO was adsorbed to the
134 > surface. Both groups suggested that the preference CO shows for
135 > low-coordinated Au atoms was the primary driving force for the reconstruction.
136  
137 +
138 +
139   %Platinum molecular dynamics
140   %gold molecular dynamics
141  
142   \section{Simulation Methods}
143 < The challenge in modeling any solid/gas interface problem is the
143 > The challenge in modeling any solid/gas interface is the
144   development of a sufficiently general yet computationally tractable
145   model of the chemical interactions between the surface atoms and
146   adsorbates.  Since the interfaces involved are quite large (10$^3$ -
# Line 144 | Line 156 | Au-Au and Pt-Pt interactions\cite{EAM}, while modeling
156   Coulomb potential.  For this work, we have used classical molecular
157   dynamics with potential energy surfaces that are specifically tuned
158   for transition metals.  In particular, we used the EAM potential for
159 < Au-Au and Pt-Pt interactions\cite{EAM}, while modeling the CO using a rigid
159 > Au-Au and Pt-Pt interactions\cite{EAM}. The CO was modeled using a rigid
160   three-site model developed by Straub and Karplus for studying
161   photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
162   Pt-CO cross interactions were parameterized as part of this work.
# Line 194 | Line 206 | dynamics.\cite{Shibata:2002hh} All of these potentials
206   melting,\cite{Belonoshko00,sankaranarayanan:155441,Sankaranarayanan:2005lr}
207   fracture,\cite{Shastry:1996qg,Shastry:1998dx} crack
208   propagation,\cite{BECQUART:1993rg} and alloying
209 < dynamics.\cite{Shibata:2002hh} All of these potentials have their
210 < strengths and weaknesses.  One of the strengths common to all of the
211 < methods is the relatively large library of metals for which these
212 < potentials have been
213 < parameterized.\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
209 > dynamics.\cite{Shibata:2002hh} One of EAM's strengths
210 > is its sensitivity to small changes in structure. This arises
211 > from the original parameterization, where the interactions
212 > up to the third nearest neighbor were taken into account.\cite{Voter95a}
213 > Comparing that to the glue model of Ercolessi et al.\cite{Ercolessi88}
214 > which is only parameterized up to the nearest-neighbor
215 > interactions, EAM is a suitable choice for systems where
216 > the bulk properties are of secondary importance to low-index
217 > surface structures. Additionally, the similarity of EAMs functional
218 > treatment of the embedding energy to standard density functional
219 > theory (DFT) makes fitting DFT-derived cross potentials with adsorbates somewhat easier.
220 > \cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
221  
222 +
223 +
224 +
225   \subsection{Carbon Monoxide model}
226   Previous explanations for the surface rearrangements center on
227 < the large linear quadrupole moment of carbon monoxide.  
227 > the large linear quadrupole moment of carbon monoxide.\cite{Tao:2010}  
228   We used a model first proposed by Karplus and Straub to study
229   the photodissociation of CO from myoglobin because it reproduces
230   the quadrupole moment well.\cite{Straub} The Straub and
231 < Karplus model, treats CO as a rigid three site molecule which places a massless M
232 < site at the center of mass position along the CO bond.  The geometry used along
233 < with the interaction parameters are reproduced in Table~\ref{tab:CO}. The effective
231 > Karplus model treats CO as a rigid three site molecule with a massless M
232 > site at the molecular center of mass. The geometry and interaction
233 > parameters are reproduced in Table~\ref{tab:CO}. The effective
234   dipole moment, calculated from the assigned charges, is still
235   small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is close
236   to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum
# Line 217 | Line 239 | mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCO
239   \begin{table}[H]
240    \caption{Positions, Lennard-Jones parameters ($\sigma$ and
241      $\epsilon$), and charges for the CO-CO
242 <    interactions borrowed from Ref.\bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA, energies are
242 >    interactions in Ref.\bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA, energies are
243      in kcal/mol, and charges are in atomic units.}
244   \centering
245   \begin{tabular}{| c | c | ccc |}
246   \hline
247   &  {\it z} & $\sigma$ & $\epsilon$ & q\\
248   \hline
249 < \textbf{C} & -0.6457 &  0.0262  & 3.83   &   -0.75 \\
250 < \textbf{O} &  0.4843 &   0.1591 &   3.12 &   -0.85 \\
249 > \textbf{C} & -0.6457 &  3.83 & 0.0262   &   -0.75 \\
250 > \textbf{O} &  0.4843 &  3.12 &  0.1591  &   -0.85 \\
251   \textbf{M} & 0.0 & -  &  -  &    1.6 \\
252   \hline
253   \end{tabular}
# Line 239 | Line 261 | clean metal surfaces. Parameters reported by Korzeniew
261   and theoretical work
262   \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
263   there is a significant amount of data on adsorption energies for CO on
264 < clean metal surfaces. Parameters reported by Korzeniewski {\it et
265 <  al.}\cite{Pons:1986} were a starting point for our fits, which were
264 > clean metal surfaces. An earlier model by Korzeniewski {\it et
265 >  al.}\cite{Pons:1986} served as a starting point for our fits. The parameters were
266   modified to ensure that the Pt-CO interaction favored the atop binding
267 < position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}
268 < This resulted in binding energies that are slightly higher
267 > position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}.
268 > The modified parameters yield binding energies that are slightly higher
269   than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
270   et al.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
271   Lennard-Jones interaction to mimic strong, but short-ranged partial
272   binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
273 < Pt-O interaction was parameterized to a Morse potential at a larger
274 < minimum distance, ($r_o$).  This was chosen so that the C would be preferred
275 < over O as the binder to the surface. In most cases, this parameterization contributes a weak
273 > Pt-O interaction was modeled with a Morse potential with a large
274 > equilibrium distance, ($r_o$).  These choices ensure that the C is preferred
275 > over O as the surface-binding atom. In most cases, the Pt-O parameterization contributes a weak
276   repulsion which favors the atop site.  The resulting potential-energy
277   surface suitably recovers the calculated Pt-C separation length
278   (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
# Line 261 | Line 283 | The limited experimental data for CO adsorption on Au
283   %same cutoff for slab and slab + CO ? seems low, although feibelmen had values around there...
284   The Au-C and Au-O cross-interactions were also fit using Lennard-Jones and
285   Morse potentials, respectively, to reproduce Au-CO binding energies.
286 < The limited experimental data for CO adsorption on Au lead us to refine our fits against DFT.
286 > The limited experimental data for CO adsorption on Au required refining the fits against plane-wave DFT calculations.
287   Adsorption energies were obtained from gas-surface DFT calculations with a
288   periodic supercell plane-wave basis approach, as implemented in the
289 < {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores are
289 > {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores were
290   described with the projector augmented-wave (PAW)
291   method,\cite{PhysRevB.50.17953,PhysRevB.59.1758} with plane waves
292   included to an energy cutoff of 20 Ry. Electronic energies are
# Line 285 | Line 307 | are shown in Table~\ref{co_parameters} and the binding
307  
308   %Hint at future work
309   The parameters employed for the metal-CO cross-interactions in this work
310 < are shown in Table~\ref{co_parameters} and the binding energies on the
311 < (111) surfaces are displayed in Table~\ref{co_energies}.  Charge transfer
310 > are shown in Table~\ref{tab:co_parameters} and the binding energies on the
311 > (111) surfaces are displayed in Table~\ref{tab:co_energies}.  Charge transfer
312   and polarization are neglected in this model, although these effects are likely to
313 < affect binding energies and binding site preferences, and will be added in
314 < a future work.\cite{Deshlahra:2012,StreitzMintmire:1994}
313 > affect binding energies and binding site preferences, and will be addressed in
314 > future work.
315  
316   %Table  of Parameters
317   %Pt Parameter Set 9
318   %Au Parameter Set 35
319   \begin{table}[H]
320    \caption{Best fit parameters for metal-CO cross-interactions. Metal-C
321 <    interactions are modeled with Lennard-Jones potential, while the
321 >    interactions are modeled with Lennard-Jones potentials. While the
322      metal-O interactions were fit to Morse
323      potentials.  Distances are given in \AA~and energies in kcal/mol. }
324   \centering
# Line 314 | Line 336 | a future work.\cite{Deshlahra:2012,StreitzMintmire:199
336  
337   %Table of energies
338   \begin{table}[H]
339 <  \caption{Adsorption energies for CO on M(111) at the atop site using the potentials
339 >  \caption{Adsorption energies for a single CO at the atop site on M(111) at the atop site using the potentials
340      described in this work.  All values are in eV.}
341   \centering
342   \begin{tabular}{| c | cc |}
# Line 331 | Line 353 | a future work.\cite{Deshlahra:2012,StreitzMintmire:199
353   \end{table}
354  
355   \subsection{Pt(557) and Au(557) metal interfaces}
356 <
357 < Our model systems are composed of 3888 Pt atoms and 3384 Au atoms in a
358 < FCC crystal that have been cut along the (557) plane so that they are
359 < periodic in the {\it x} and {\it y} directions, and have been oriented
360 < to expose two aligned (557) cuts along the extended {\it
361 <  z}-axis.  Simulations of the bare metal interfaces at temperatures
362 < ranging from 300~K to 1200~K were performed to observe the relative
356 > Our Pt system is an orthorhombic periodic box of dimensions
357 > 54.482~x~50.046~x~120.88~\AA~while our Au system has
358 > dimensions of 57.4~x~51.9285~x~100~\AA.
359 > The systems are arranged in a FCC crystal that have been cut
360 > along the (557) plane so that they are periodic in the {\it x} and
361 > {\it y} directions, and have been oriented to expose two aligned
362 > (557) cuts along the extended {\it z}-axis.  Simulations of the
363 > bare metal interfaces at temperatures ranging from 300~K to
364 > 1200~K were performed to confirm the relative
365   stability of the surfaces without a CO overlayer.  
366  
367 < The different bulk (and surface) melting temperatures (1337~K for Au
368 < and 2045~K for Pt) suggest that any possible reconstruction may happen at
367 > The different bulk melting temperatures (1337~K for Au
368 > and 2045~K for Pt) suggest that any possible reconstruction should happen at
369   different temperatures for the two metals.  The bare Au and Pt surfaces were
370   initially run in the canonical (NVT) ensemble at 800~K and 1000~K
371 < respectively for 100 ps. These temperatures were chosen because the
372 < surfaces were relatively stable at these temperatures when no CO was
373 < 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
371 > respectively for 100 ps. The two surfaces were relatively stable at these
372 > temperatures when no CO was present, but experienced increased surface
373 > mobility on addition of CO. Each surface was then dosed with different concentrations of CO
374   that was initially placed in the vacuum region.  Upon full adsorption,
375 < these amounts correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
376 < coverage. Higher coverages were tried, but the CO-CO repulsion was preventing
377 < a higher amount of adsorption.  Because of the difference in binding energies, the Pt
378 < systems very rarely had CO that was not bound to the surface, while
375 > these concentrations correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
376 > coverage. Higher coverages resulted in the formation of a double layer of CO,
377 > which introduces artifacts that are not relevant to (557) reconstruction.
378 > Because of the difference in binding energies, nearly all of the CO was bound to the Pt surface, while
379   the Au surfaces often had a significant CO population in the gas
380   phase.  These systems were allowed to reach thermal equilibrium (over
381 < 5 ns) before being run in the microcanonical (NVE) ensemble for
382 < data collection. All of the systems examined had at least 40 ns in the
383 < data collection stage, although simulation times for some of the
384 < systems exceeded 200ns.  All simulations were run using the open
381 > 5~ns) before being run in the microcanonical (NVE) ensemble for
382 > data collection. All of the systems examined had at least 40~ns in the
383 > data collection stage, although simulation times for some Pt of the
384 > systems exceeded 200~ns.  Simulations were carried out using the open
385   source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE}
386  
387 < % Just results, leave discussion for discussion section
388 < % structure
389 < %       Pt: step wandering, double layers, no triangular motifs
390 < %       Au: step wandering, no double layers
391 < % dynamics
369 < %       diffusion
370 < %       time scale, formation, breakage
387 >
388 >
389 >
390 > % RESULTS
391 > %
392   \section{Results}
393   \subsection{Structural remodeling}
394 < Tao et al. showed experimentally that the Pt(557) surface
395 < undergoes two separate reconstructions upon CO
396 < adsorption.\cite{Tao:2010} The first involves a doubling of
397 < the step height and plateau length. Similar behavior has been
398 < seen to occur on numerous surfaces at varying conditions (Ni 977, Si 111, etc).
399 < \cite{Williams:1994,Williams:1991,Pearl} Of the two systems
400 < we examined, the Pt system showed a larger amount of
401 < reconstruction when compared to the Au system. The amount
402 < of reconstruction appears to be correlated to the amount of CO
403 < adsorbed upon the surface.  We believe this is related to the
404 < effect that adsorbate coverage has on edge breakup and surface
405 < diffusion of adatoms. While both systems displayed step-edge
406 < wandering, only the Pt surface underwent the doubling seen by
407 < 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.
394 > The surfaces of both systems, upon dosage of CO, began
395 > to undergo remodeling that was not observed in the bare
396 > metal system. The surfaces which were not exposed to CO
397 > did experience minor roughening of the step-edge because
398 > of the elevated temperatures, but the
399 > (557) lattice was well-maintained throughout the simulation
400 > time. The Au systems were limited to greater amounts of
401 > roughening, i.e. breakup of the step-edge, and some step
402 > wandering. The lower coverage Pt systems experienced
403 > similar restructuring but to a greater extent when
404 > compared to the Au systems. The 50\% coverage
405 > Pt system was unique among our simulations in that it
406 > formed numerous double layers through step coalescence,
407 > similar to results reported by Tao et al.\cite{Tao:2010}
408  
409 +
410 + \subsubsection{Step wandering}
411 + The 0\% coverage surfaces for both metals showed minimal
412 + movement at their respective run temperatures. As the CO
413 + coverage increased however, the mobility of the surface,
414 + adatoms and step-edges alike, also increased. Additionally,
415 + at the higher coverages on both metals, there was more
416 + step-wandering. Except for the 50\% Pt system, the step-edges
417 + did not coalesce in any of the other simulations, instead preferring
418 + to keep nearly the same distance between steps as in the
419 + original (557) lattice. Previous work by Williams et al.\cite{Williams:1991, Williams:1994}
420 + highlights the repulsion that exists between step-edges even
421 + when no direct interactions are present in the system. This
422 + repulsion exists because the entropy of the step-edges is constrained
423 + since step-edge crossing is not allowed. This entropic repulsion
424 + does not completely define the interactions between steps,
425 + which is why some surfaces will undergo step coalescence,
426 + where additional attractive interactions can overcome the
427 + repulsion\cite{Williams:1991} and others will not. The presence
428 + of adsorbates can affect these step interactions, potentially
429 + leading to a new surface structure as the thermodynamic minimum.
430 +
431 + \subsubsection{Double layers}
432 + Tao et al. have shown experimentally that the Pt(557) surface
433 + undergoes two separate reconstructions upon CO adsorption.\cite{Tao:2010}
434 + The first involves a doubling of the step height and plateau length.
435 + Similar behavior has been seen to occur on numerous surfaces
436 + at varying conditions: Ni(977), Si(111).\cite{Williams:1994,Williams:1991,Pearl}
437 + Of the two systems we examined, the Pt system showed a greater
438 + propensity for reconstruction when compared to the Au system
439 + because of the larger surface mobility and extent of step wandering.
440 + The amount of reconstruction is correlated to the amount of CO
441 + adsorbed upon the surface.  This appears to be related to the
442 + effect that adsorbate coverage has on edge breakup and on the
443 + surface diffusion of metal adatoms. While both systems displayed
444 + step-edge wandering, only the 50\% Pt surface underwent the
445 + doubling seen by Tao et al. within the time scales studied here.
446 + Over longer periods (150~ns) two more double layers formed
447 + on this interface. Although double layer formation did not occur
448 + in the other Pt systems, they show more step-wandering and
449 + general roughening compared to their Au counterparts. The
450 + 50\% Pt system is highlighted in Figure \ref{fig:reconstruct} at
451 + various times along the simulation showing the evolution of a step-edge.
452 +
453   The second reconstruction on the Pt(557) surface observed by
454   Tao involved the formation of triangular clusters that stretched
455   across the plateau between two step-edges. Neither system, within
456 < our simulated time scales, experiences this reconstruction. A constructed
457 < 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.
456 > the 40~ns time scale or the extended simulation time of 150~ns for
457 > the 50\% Pt system, experienced this reconstruction.
458  
459   \subsection{Dynamics}
460 < While atomistic-like simulations of stepped surfaces have been
461 < performed before, they tend to be performed using Monte Carlo
462 < techniques\cite{Williams:1991,Williams:1994}. This allows them
463 < to efficiently sample the equilibrium thermodynamic landscape
464 < but at the expense of ignoring the dynamics of the system. Previous
465 < work by Pearl and Sibener\cite{Pearl}, using STM, has been able to
466 < visualize the coalescing of steps of Ni(977). The time scale of the image
467 < acquisition, $\sim$70 s/image provides an upper bounds for the time
468 < required for the doubling to actually occur. Statistical treatments of step-edges
469 < are adept at analyzing such systems. However, in a system where
470 < the number of steps is limited, examining the individual atoms that make
419 < up the steps can provide useful information as well.
460 > Previous atomistic simulations of stepped surfaces dealt largely
461 > with the energetics and structures at different conditions
462 > \cite{Williams:1991,Williams:1994}. Consequently, the most common
463 > technique utilized to date has been Monte Carlo sampling. Monte Carlo gives an efficient
464 > sampling of the equilibrium thermodynamic landscape at the expense
465 > of ignoring the dynamics of the system. Previous experimental work by Pearl and
466 > Sibener\cite{Pearl}, using STM, has been able to capture the coalescing
467 > of steps on Ni(977). The time scale of the image acquisition,
468 > $\sim$70 s/image provides an upper bound for the time required for
469 > the doubling to occur. In this section we give data on dynamic and
470 > transport properties, e.g. diffusion, layer formation time, etc.
471  
472  
473   \subsubsection{Transport of surface metal atoms}
474   %forcedSystems/stepSeparation
475   The movement or wandering of a step-edge is a cooperative effect
476 < arising from the individual movements, primarily through surface
477 < 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
476 > arising from the individual movements of the atoms making up the steps. An ideal metal surface
477 > displaying a low index facet, (111) or (100), is unlikely to experience
478   much surface diffusion because of the large energetic barrier that must
479 < be overcome to lift an atom out of the surface. The presence of step-edges
480 < on higher-index surfaces provide a source for mobile metal atoms.
479 > be overcome to lift an atom out of the surface. The presence of step-edges and other surface features
480 > on higher-index facets provide a lower energy source for mobile metal atoms.
481   Breaking away from the step-edge on a clean surface still imposes an
482 < energetic penalty around $\sim$~40 kcal/mole, but is much less than lifting
483 < the same metal atom out from the surface,  \textgreater~60 kcal/mole, and
484 < the penalty lowers even further when CO is present in sufficient quantities
485 < on the surface. For certain tested distributions of CO, the penalty was lowered
486 < to $\sim$~20 kcal/mole. Once an adatom exists on the surface, its barrier for
487 < diffusion is negligible ( \textless~4 kcal/mole) and is well able to explore the
488 < terrace before potentially rejoining its original step-edge or becoming a part
489 < of a different edge. Atoms traversing separate terraces is a more difficult
490 < process, but can be overcome through a joining and lifting stage which is
491 < examined in the discussion section. By tracking the mobility of individual
482 > energetic penalty around $\sim$~40 kcal/mol, but this is significantly easier than lifting
483 > the same metal atom vertically out of the surface,  \textgreater~60 kcal/mol.
484 > The penalty lowers significantly when CO is present in sufficient quantities
485 > on the surface. For certain distributions of CO, the penalty can fall as low as
486 > $\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for
487 > diffusion is negligible ( \textless~4 kcal/mol for a Pt adatom). These adatoms are
488 > able to explore the terrace before rejoining either the original step-edge or
489 > becoming a part of a different edge. It is a more difficult process for an atom
490 > to traverse to a separate terrace although the presence of CO can lower the
491 > energy barrier required to lift or lower the adatom. By tracking the mobility of individual
492   metal atoms on the Pt and Au surfaces we were able to determine the relative
493 < diffusion rates and how varying coverages of CO affected the rates. Close
493 > diffusion constants, as well as how varying coverages of CO affect the diffusion. Close
494   observation of the mobile metal atoms showed that they were typically in
495 < equilibrium with the step-edges, constantly breaking apart and rejoining.
496 < At times their motion was concerted and two or more adatoms would be
497 < observed moving together across the surfaces. The primary challenge in
448 < quantifying the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
495 > equilibrium with the step-edges, dynamically breaking apart and rejoining the edges.
496 > At times, their motion was concerted and two or more adatoms would be
497 > observed moving together across the surfaces.
498  
499 < A particle was considered mobile once it had traveled more than 2~\AA~
500 < between saved configurations of the system (10-100 ps). An atom that was
501 < truly mobile would typically travel much greater than this, but the 2~\AA~ cutoff
502 < was to prevent the in-place vibrational movement of non-surface atoms from
503 < being included in the analysis. Diffusion on  a surface is strongly affected by
504 < local structures and in this work the presence of single and double layer
499 > A particle was considered ``mobile'' once it had traveled more than 2~\AA~
500 > between saved configurations of the system (typically 10-100 ps). An atom that was
501 > truly mobile would typically travel much greater distances than this, but the 2~\AA~cutoff
502 > was used to prevent swamping the diffusion data with the in-place vibrational
503 > movement of buried atoms. Diffusion on a surface is strongly affected by
504 > local structures and in this work, the presence of single and double layer
505   step-edges causes the diffusion parallel to the step-edges to be different
506 < from the diffusion perpendicular to these edges. This led us to compute
507 < those diffusions separately as seen in Figure \ref{fig:diff}.
506 > from the diffusion perpendicular to these edges. Parallel and perpendicular
507 > diffusion constants are shown in Figure \ref{fig:diff}.
508  
509 < \subsubsection{Double layer formation}
510 < The increased amounts of diffusion on Pt at the higher CO coverages appears
511 < to play a primary role in the formation of double layers, although this conclusion
512 < does not explain the 33\% coverage Pt system. On the 50\% system, three
513 < separate layers were formed over the extended run time of this system. As
514 < mentioned earlier, previous experimental work has given some insight into the
515 < upper bounds of the time required for enough atoms to move around to allow two
516 < steps to coalesce\cite{Williams:1991,Pearl}. As seen in Figure \ref{fig:reconstruct},
517 < the first appearance of a double layer, a nodal site, appears at 19 ns into the
518 < simulation. Within 12 ns, nearly half of the step has formed the double layer and
519 < by 86 ns, a smooth complete layer has formed. The double layer is ``complete" by
520 < 37 ns but is a bit rough. From the appearance of the first node to the initial doubling
521 < of the layers ignoring their roughness took $\sim$~20 ns. Another ~40 ns was
522 < necessary for the layer to completely straighten. The other two layers in this
523 < simulation form over a period of 22 ns and 42 ns respectively. Comparing this to
524 < the upper bounds of the image scan, it is likely that aspects of this reconstruction
525 < occur very quickly.
509 > The lack of a definite trend in the Au diffusion data is likely due
510 > to the weaker bonding between Au and CO. This leads to a lower
511 > coverage ({\it x}-axis) when compared to dosage amount, which
512 > then further limits the affects of the surface diffusion. The correlation
513 > between coverage and Pt diffusion rates conversely shows a
514 > definite trend marred by the highest coverage surface. Two
515 > explanations arise for this drop. First, upon a visual inspection of
516 > the system, after a double layer has been formed, it maintains its
517 > stability strongly and is no longer a good source for adatoms. By
518 > performing the same diffusion calculation but on a shorter run time
519 > (20~ns), only including data before the formation of the double layer,
520 > provides a $\mathbf{D}_{\perp}$ diffusion constant of $1.69~\pm~0.08$
521 > and a $\mathbf{D}_{\parallel}$ diffusion constant of $6.30~\pm~0.08$.
522 > This places the parallel diffusion constant more closely in line with the
523 > expected trend, while the perpendicular diffusion constant does not
524 > drop as far. A secondary explanation arising from our analysis of the
525 > mechanism of double layer formation show the affect that CO on the
526 > surface has with respect to overcoming surface diffusion of Pt. If the
527 > coverage is too sparse, the Pt engages in minimal interactions and
528 > thus minimal diffusion. As coverage increases, there are more favorable
529 > arrangements of CO on the surface allowing the formation of a path,
530 > a minimum energy trajectory, for the adatom to explore the surface.
531 > As the CO is constantly moving on the surface, this path is constantly
532 > changing. If the coverage becomes too great, the paths could
533 > potentially be clogged leading to a decrease in diffusion despite
534 > their being more adatoms and step-wandering.
535 >
536 > \subsubsection{Dynamics of double layer formation}
537 > The increased diffusion on Pt at the higher
538 > CO coverages plays a primary role in double layer formation. However, this is not
539 > a complete explanation -- the 33\%~Pt system
540 > has higher diffusion constants but did not show
541 > any signs of edge doubling in the observed run time. On the
542 > 50\%~Pt system, one layer formed within the first 40~ns of simulation time, while two more were formed as the system was run for an additional
543 > 110~ns (150~ns total). Previous experimental
544 > work gives insight into the upper bounds of the
545 > time required for step coalescence.\cite{Williams:1991,Pearl}
546 > In this system, as seen in Figure \ref{fig:reconstruct}, the first
547 > appearance of a double layer, appears at 19~ns
548 > into the simulation. Within 12~ns of this nucleation event, nearly half of the step has
549 > formed the double layer and by 86~ns, the complete layer
550 > has been flattened out. The double layer could be considered
551 > ``complete" by 37~ns but remains a bit rough. From the
552 > appearance of the first nucleation event to the first observed double layer, the process took $\sim$20~ns. Another
553 > $\sim$40~ns was necessary for the layer to completely straighten.
554 > The other two layers in this simulation formed over periods of
555 > 22~ns and 42~ns respectively. Comparing this to the upper
556 > bounds of the image scan, it is likely that most aspects of this
557 > reconstruction occur very rapidly. A possible explanation
558 > for this rapid reconstruction is the elevated temperatures
559 > under which our systems were simulated. It is probable that the process would
560 > take longer at lower temperatures.
561  
562   %Evolution of surface
563   \begin{figure}[H]
564   \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
565   \caption{The Pt(557) / 50\% CO system at a sequence of times after
566 <  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
567 <  (d) 86.1 ns. Disruption of the (557) step-edges occurs quickly.  The
566 >  initial exposure to the CO: (a) 258~ps, (b) 19~ns, (c) 31.2~ns, and
567 >  (d) 86.1~ns. Disruption of the (557) step-edges occurs quickly.  The
568    doubling of the layers appears only after two adjacent step-edges
569    touch.  The circled spot in (b) nucleated the growth of the double
570    step observed in the later configurations.}
# Line 507 | Line 591 | In this paper we have shown that we were able to accur
591  
592   %Discussion
593   \section{Discussion}
594 < In this paper we have shown that we were able to accurately model the initial reconstruction of the
594 > We have shown that the classical potential models are able to model the initial reconstruction of the
595   Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
596 < were able to observe the dynamic processes necessary for this reconstruction.
596 > were able to observe features of the dynamic processes necessary for this reconstruction.
597  
598   \subsection{Mechanism for restructuring}
599 < Comparing the results from simulation to those reported previously by
600 < Tao et al.\cite{Tao:2010} the similarities in the Pt-CO system are quite
601 < strong. As shown in Figure \ref{fig:reconstruct}, the simulated Pt
602 < system under a CO atmosphere will restructure by doubling the terrace
603 < heights. The restructuring occurs slowly, one to two Pt atoms at a time.
604 < Looking at individual configurations of the system, the adatoms either
599 > Since the Au surface showed no large scale restructuring throughout
600 > our simulation time our discussion will focus on the 50\% Pt-CO system
601 > which did undergo the doubling featured in Figure \ref{fig:reconstruct}.
602 > Similarities of our results to those reported previously by
603 > Tao et al.\cite{Tao:2010} are quite
604 > strong. The simulated Pt
605 > system exposed to a large dosage of CO readily restructures by doubling the terrace
606 > widths and step heights. The restructuring occurs in a piecemeal fashion, one to two Pt atoms at a time, but is rapid on experimental timescales.
607 > The adatoms either
608   break away from the step-edge and stay on the lower terrace or they lift
609 < up onto the higher terrace. Once ``free'' they will diffuse on the terrace
610 < until reaching another step-edge or coming back to their original edge.  
609 > up onto a higher terrace. Once ``free'', they diffuse on the terrace
610 > until reaching another step-edge or rejoining their original edge.  
611   This combination of growth and decay of the step-edges is in a state of
612   dynamic equilibrium. However, once two previously separated edges
613 < meet as shown in Figure 1.B, this meeting point tends to act as a focus
614 < 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.
613 > meet as shown in Figure 1.B, this nucleates the rest of the edge to meet up, forming a double layer.
614 > From simulations which exhibit a double layer, the time delay from the initial appearance of a nucleation point to a fully formed double layer is $\sim$35~ns.
615  
616   A number of possible mechanisms exist to explain the role of adsorbed
617   CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent
618 < CO molecules adsorbed on the surface is one likely possibility.  However,
618 > CO molecules adsorbed on the surface is one possibility.  However,
619   the quadrupole-quadrupole interaction is short-ranged and is attractive for
620   some orientations.  If the CO molecules are ``locked'' in a specific orientation
621 < relative to each other, through atop adsorption perhaps, this explanation
622 < gains some weight.  The energetic repulsion between two CO located a
623 < distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in
624 < a  vertical orientation is 8.62 kcal/mole. Moving the CO apart to the second
621 > relative to each other, through atop adsorption for example, this explanation
622 > gains some credence.  The energetic repulsion between two CO located a
623 > distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) and both in
624 > a  vertical orientation, is 8.62 kcal/mol. Moving the CO apart to the second
625   nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to
626 < nearly 0 kcal/mole. Allowing the CO's to leave a purely vertical orientation
627 < also quickly drops the repulsion, a minimum is reached at $\sim$24 degrees
628 < of 6.2 kcal/mole. As mentioned above, the energy barrier for surface diffusion
629 < of a Pt adatom is only 4 kcal/mole. So this repulsion between CO can help
630 < increase the surface diffusion. However, the residence time of CO was
626 > nearly 0 kcal/mol. Allowing the CO's to leave a purely vertical orientation
627 > also quickly drops the repulsion, a minimum of 6.2 kcal/mol is reached at $\sim$24 degrees between the 2 CO when the carbons are locked at a distance of 2.77 \AA apart.
628 > As mentioned above, the energy barrier for surface diffusion
629 > of a Pt adatom is only 4 kcal/mol. So this repulsion between neighboring CO molecules can
630 > increase the surface diffusion. However, the residence time of CO on Pt was
631   examined and while the majority of the CO is on or near the surface throughout
632 < the run, it is extremely mobile. This mobility suggests that the CO are more
633 < likely to shift their positions without necessarily dragging the Pt along with them.
632 > the run, most molecules are mobile. This mobility suggests that the CO are more
633 > likely to shift their positions without necessarily the Pt along with them.
634  
635   Another possible and more likely mechanism for the restructuring is in the
636   destabilization of strong Pt-Pt interactions by CO adsorbed on surface
# Line 558 | Line 642 | are displayed in Table \ref{tab:energies}. These value
642   of Pt atoms was then examined to determine possible barriers. Because
643   the movement was forced along a pre-defined reaction coordinate that may differ
644   from the true minimum of this path, only the beginning and ending energies
645 < are displayed in Table \ref{tab:energies}. These values suggest that the presence of CO at suitable
645 > are displayed in Table \ref{tab:energies} with the corresponding beginning and ending reaction coordinates in Figure \ref{fig:lambdaTable}. These values suggest that the presence of CO at suitable
646   locations can lead to lowered barriers for Pt breaking apart from the step-edge.
647   Additionally, as highlighted in Figure \ref{fig:lambda}, the presence of CO makes the
648   burrowing and lifting of adatoms favorable, whereas without CO, the process is neutral
# Line 566 | Line 650 | in terms of energetics.
650  
651   %lambda progression of Pt -> shoving its way into the step
652   \begin{figure}[H]
653 < \includegraphics[width=\linewidth]{lambdaProgression_atopCO.png}
653 > \includegraphics[width=\linewidth]{lambdaProgression_atopCO_withLambda.png}
654   \caption{A model system of the Pt(557) surface was used as the framework
655   for exploring energy barriers along a reaction coordinate. Various numbers,
656   placements, and rotations of CO were examined as they affect Pt movement.
# Line 577 | Line 661 | in terms of energetics.
661   \label{fig:lambda}
662   \end{figure}
663  
664 + \begin{figure}[H]
665 + \includegraphics[totalheight=0.9\textheight]{lambdaTable.png}
666 + \caption{}
667 + \label{fig:lambdaTable}
668 + \end{figure}
669  
670  
671   \subsection{Diffusion}
672 < As shown in the results section, the diffusion parallel to the step-edge tends to be
673 < much larger than that perpendicular to the step-edge, likely because of the dynamic
672 > The diffusion parallel to the step-edge tends to be
673 > much larger than that perpendicular to the step-edge. The dynamic
674   equilibrium that is established between the step-edge and adatom interface. The coverage
675   of CO also appears to play a slight role in relative rates of diffusion, as shown in Figure \ref{fig:diff}.
676   The
# Line 597 | Line 686 | more likely a growth point is to be formed.
686   %breaking of the double layer upon removal of CO
687   \begin{figure}[H]
688   \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
689 < %:
601 < \caption{(A)  0 ps, (B) 100 ps, (C) 1 ns, after the removal of CO. The presence of the CO
689 > \caption{(A)  0~ps, (B) 100~ps, (C) 1~ns, after the removal of CO. The presence of the CO
690   helped maintain the stability of the double layer and upon removal the two layers break
691   and begin separating. The separation is not a simple pulling apart however, rather
692   there is a mixing of the lower and upper atoms at the edge.}
# Line 609 | Line 697 | more likely a growth point is to be formed.
697  
698  
699   %Peaks!
700 < \begin{figure}[H]
701 < \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
702 < \caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
703 < of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
704 < aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
705 < \label{fig:peaks}
706 < \end{figure}
700 > %\begin{figure}[H]
701 > %\includegraphics[width=\linewidth]{doublePeaks_noCO.png}
702 > %\caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
703 > %of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
704 > %aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
705 > %\label{fig:peaks}
706 > %\end{figure}
707  
708  
709   %Don't think I need this
# Line 629 | Line 717 | In this work we have shown the reconstruction of the P
717  
718  
719   \section{Conclusion}
720 < 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.
720 > In this work we have shown the reconstruction of the Pt(557) crystalline surface upon adsorption of CO in less than a $\mu s$. Only the highest coverage Pt system showed this initial reconstruction similar to that seen previously. The strong interaction between Pt and CO and the limited interaction between Au and CO helps explain the differences between the two systems.
721  
722   %Things I am not ready to remove yet
723  

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