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# 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
116 < surface restructuring by using molecular simulations.  Since the dynamics
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.
# Line 123 | Line 123 | and Piccolo et al.\cite{Piccolo:2004} have both observ
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 relaxing of the
128 < 22 x $\sqrt{3}$ cell. They argued that a very small number of Au atoms
129 < would become adatoms, limiting the stress of this reconstruction while
130 < allowing the rest of the row to relax and approach the ideal (111)
131 < configuration. They did not see the ``herringbone'' pattern being greatly
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
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 particles was the primary driving force for these reconstructions.
135 > low-coordinated Au atoms was the primary driving force for the reconstruction.
136  
137  
138  
# Line 209 | Line 209 | up to the third nearest-neighbor were taken into accou
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}
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 only parameterized up to the nearest-neighbor
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) approaches gives EAM, and conclusions derived, a firm theoretical footing.
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  
# Line 228 | Line 228 | Karplus model, treats CO as a rigid three site molecul
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 with a massless M
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
# Line 311 | Line 311 | a future work.\cite{Deshlahra:2012,StreitzMintmire:199
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 addressed in
314 < a future work.\cite{Deshlahra:2012,StreitzMintmire:1994}
314 > future work.
315  
316   %Table  of Parameters
317   %Pt Parameter Set 9
# Line 353 | Line 353 | Our Pt system has dimensions of 18~x~24~x~9 in a box o
353   \end{table}
354  
355   \subsection{Pt(557) and Au(557) metal interfaces}
356 < Our Pt system has dimensions of 18~x~24~x~9 in a box of size
357 < 54.482~x~50.046~x~120.88~\AA while our Au system has
358 < dimensions of 18~x~24~x~8 in a box of size 57.4~x~51.9285~x~100~\AA.
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 observe the relative
364 > 1200~K were performed to confirm the relative
365   stability of the surfaces without a CO overlayer.  
366  
367   The different bulk melting temperatures (1337~K for Au
# Line 373 | Line 373 | coverage. Higher coverages resulted in CO double layer
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 concentrations correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
376 < coverage. Higher coverages resulted in CO double layer formation, which introduces artifacts that are not relevant to (557) reconstruction.
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 200~ns.  Simulations were run using the open
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
391 < %       diffusion
392 < %       time scale, formation, breakage
387 >
388 >
389 >
390 > % RESULTS
391 > %
392   \section{Results}
393   \subsection{Structural remodeling}
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 to which no CO was exposed
397 + did experience minor roughening of the step-edge, but the
398 + (557) lattice was well-maintained throughout the simulation
399 + time. The Au systems were limited to greater amounts of
400 + roughening, i.e. breakup of the step-edge, and some step
401 + wandering. The lower coverage Pt systems experienced
402 + similar restructuring but to a greater extent when
403 + compared to the Au systems. The 50\% coverage
404 + Pt system formed double layers at numerous spots upon its surface.
405 +
406 +
407   \subsubsection{Step wandering}
408 + The 0\% coverage surfaces for both metals showed
409 + minimal movement at their respective run temperatures.
410 + As the coverage increased, the mobility of the surface
411 + also increased. Additionally, at the higher coverages
412 + on both metals, there was a large increase in the amount
413 + of observed step-wandering. Previous work by
414 + Williams\cite{Williams:1993} highlighted the entropic
415 + contribution to the repulsion felt between step-edges,
416 + and situations were that repulsion could be negated, or
417 + overcome, to allow for step coalescence or facet formation.
418 +
419   \subsubsection{Double layers}
420   Tao et al. have shown experimentally that the Pt(557) surface
421   undergoes two separate reconstructions upon CO
# Line 400 | Line 423 | we examined, the Pt system showed a larger amount of
423   the step height and plateau length. Similar behavior has been
424   seen to occur on numerous surfaces at varying conditions: Ni(977), Si(111).
425   \cite{Williams:1994,Williams:1991,Pearl} Of the two systems
426 < we examined, the Pt system showed a larger amount of
426 > we examined, the Pt system showed a greater propensity for
427   reconstruction when compared to the Au system. The amount
428   of reconstruction is correlated to the amount of CO
429   adsorbed upon the surface.  This appears to be related to the
# Line 423 | Line 446 | Previous atomistic simulations of stepped surfaces wer
446   the 40~ns time scale, experienced this reconstruction.
447  
448   \subsection{Dynamics}
449 < Previous atomistic simulations of stepped surfaces were largely
450 < concerned with the energetics and structures at different conditions
449 > Previous atomistic simulations of stepped surfaces dealt largely
450 > with the energetics and structures at different conditions
451   \cite{Williams:1991,Williams:1994}. Consequently, the most common
452 < technique has been Monte Carlo. Monte Carlo gives an efficient
452 > technique utilized to date has been Monte Carlo sampling. Monte Carlo gives an efficient
453   sampling of the equilibrium thermodynamic landscape at the expense
454   of ignoring the dynamics of the system. Previous work by Pearl and
455   Sibener\cite{Pearl}, using STM, has been able to show the coalescing
# Line 440 | Line 463 | diffusion, of the atoms making up the steps An ideal m
463   %forcedSystems/stepSeparation
464   The movement or wandering of a step-edge is a cooperative effect
465   arising from the individual movements, primarily through surface
466 < diffusion, of the atoms making up the steps An ideal metal surface
467 < displaying a low index facet, (111) or (100) is unlikely to experience
466 > diffusion, of the atoms making up the steps. An ideal metal surface
467 > displaying a low index facet, (111) or (100), is unlikely to experience
468   much surface diffusion because of the large energetic barrier that must
469   be overcome to lift an atom out of the surface. The presence of step-edges
470   on higher-index surfaces provide a source for mobile metal atoms.
471   Breaking away from the step-edge on a clean surface still imposes an
472 < energetic penalty around $\sim$~40 kcal/mol, but is much less than lifting
472 > energetic penalty around $\sim$~40 kcal/mol, but this is significantly easier than lifting
473   the same metal atom vertically out of the surface,  \textgreater~60 kcal/mol.
474   The penalty lowers significantly when CO is present in sufficient quantities
475 < on the surface. For certain distributions of CO, the penalty can be as low as
475 > on the surface. For certain distributions of CO, the penalty can fall as low as
476   $\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for
477 < diffusion is negligible ( \textless~4 kcal/mol) and these adatoms are well
478 < able to explore the terrace before rejoining either the original step-edge or becoming a part
479 < of a different edge. Atoms traversing separate terraces is a more difficult
480 < process, but can be overcome through a joining and lifting stage which is
481 < examined in the discussion section. By tracking the mobility of individual
477 > diffusion is negligible ( \textless~4 kcal/mol) and these adatoms are
478 > able to explore the terrace before rejoining either the original step-edge or
479 > becoming a part of a different edge. It is a more difficult process for an atom
480 > to traverse to a separate terrace although the presence of CO can lower the
481 > energy barrier required to lift or lower the adatom. By tracking the mobility of individual
482   metal atoms on the Pt and Au surfaces we were able to determine the relative
483   diffusion constants, as well as how varying coverages of CO affect the diffusion. Close
484   observation of the mobile metal atoms showed that they were typically in
485   equilibrium with the step-edges, dynamically breaking apart and rejoining the edges.
486   At times, their motion was concerted and two or more adatoms would be
487 < observed moving together across the surfaces. The primary challenge in
465 < quantifying the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
487 > observed moving together across the surfaces.
488  
489 < A particle was considered mobile once it had traveled more than 2~\AA~
489 > A particle was considered ``mobile'' once it had traveled more than 2~\AA~
490   between saved configurations of the system (typically 10-100 ps). An atom that was
491 < truly mobile would typically travel much greater distances than this, but the 2~\AA~ cutoff
492 < was to prevent swamping the diffusion data with the in-place vibrational
491 > truly mobile would typically travel much greater distances than this, but the 2~\AA~cutoff
492 > was used to prevent swamping the diffusion data with the in-place vibrational
493   movement of buried atoms. Diffusion on  a surface is strongly affected by
494   local structures and in this work, the presence of single and double layer
495   step-edges causes the diffusion parallel to the step-edges to be different
# Line 475 | Line 497 | The increased amounts of diffusion on Pt at the higher
497   diffusion constants are shown in Figure \ref{fig:diff}.
498  
499   \subsubsection{Dynamics of double layer formation}
500 < The increased amounts of diffusion on Pt at the higher CO coverages plays a primary role in the formation of the double layers observed on Pt. However, this is not a complete explanation as seen by the 33\% Pt system which has higher diffusion constants but did not show any signs of undergoing the doubling. This difference will be explored more fully in the discussion. On the 50\% Pt system, three separate layers were formed over the extended run time of this system. Previous experimental work has given some insight into the upper bounds of the time required for step coalescing.\cite{Williams:1991,Pearl} In this system, as seen in Figure \ref{fig:reconstruct}, the first appearance of a double layer, a nodal site, appears at 19 ns into the simulation. Within 12 ns, nearly half of the step has formed the double layer and by 86 ns, the complete layer has been smoothed. The double layer could be considered ``complete" by 37 ns but is a bit rough or wavy. From the appearance of the first node to the first observed double layer, ignoring roughening, the process took $\sim$20 ns. Another $\sim$40 ns was necessary for the layer to completely straighten. The other two layers in this simulation form over a period of 22 ns and 42 ns respectively. Comparing this to the upper bounds of the image scan, it is likely that aspects of this reconstruction occur very quickly. A possible explanation for this rapid reconstruction is the elevated temperatures our systems were run at. It is likely that the process would take longer at lower temperatures and is an area of exploration for future work.
500 > The increased diffusion on Pt at the higher
501 > CO coverages plays a primary role in double layer formation. However, this is not
502 > a complete explanation -- the 33\%~Pt system
503 > has higher diffusion constants but did not show
504 > any signs of edge doubling. On the
505 > 50\%~Pt system, three separate layers were formed over
506 > 150~ns of simulation time. Previous experimental
507 > work gives insight into the upper bounds of the
508 > time required for step coalescence.\cite{Williams:1991,Pearl}
509 > In this system, as seen in Figure \ref{fig:reconstruct}, the first
510 > appearance of a double layer, appears at 19~ns
511 > into the simulation. Within 12~ns of this nucleation event, nearly half of the step has
512 > formed the double layer and by 86 ns, the complete layer
513 > has been flattened out. The double layer could be considered
514 > ``complete" by 37~ns but remains a bit rough. From the
515 > appearance of the first nucleation event to the first observed double layer, the process took $\sim$20~ns. Another
516 > $\sim$40~ns was necessary for the layer to completely straighten.
517 > The other two layers in this simulation formed over periods of
518 > 22~ns and 42~ns respectively. Comparing this to the upper
519 > bounds of the image scan, it is likely that most aspects of this
520 > reconstruction occur very rapidly. A possible explanation
521 > for this rapid reconstruction is the elevated temperatures
522 > under which our systems were simulated. It is probable that the process would
523 > take longer at lower temperatures.
524  
525   %Evolution of surface
526   \begin{figure}[H]
# Line 509 | Line 554 | In this paper we have shown that we were able to accur
554  
555   %Discussion
556   \section{Discussion}
557 < In this paper we have shown that we were able to accurately model the initial reconstruction of the
557 > We have shown that the classical potential models are able to model the initial reconstruction of the
558   Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
559 < were able to observe the dynamic processes necessary for this reconstruction.
559 > were able to observe features of the dynamic processes necessary for this reconstruction.
560  
561   \subsection{Mechanism for restructuring}
562   Since the Au surface showed no large scale restructuring throughout
563   our simulation time our discussion will focus on the 50\% Pt-CO system
564   which did undergo the doubling featured in Figure \ref{fig:reconstruct}.
565 < Comparing the results from this simulation to those reported previously by
566 < Tao et al.\cite{Tao:2010} the similarities in the Pt-CO system are quite
567 < strong. As shown in Figure \ref{fig:reconstruct}, the simulated Pt
568 < system exposed to a large dosage of CO will restructure by doubling the terrace
569 < widths and step heights. The restructuring occurs in a piecemeal fashion, one to two Pt atoms at a time and as such is a fairly stochastic event.
570 < Looking at individual configurations of the system, the adatoms either
565 > Similarities of our results to those reported previously by
566 > Tao et al.\cite{Tao:2010} are quite
567 > strong. The simulated Pt
568 > system exposed to a large dosage of CO readily restructures by doubling the terrace
569 > 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.
570 > The adatoms either
571   break away from the step-edge and stay on the lower terrace or they lift
572 < up onto the higher terrace. Once ``free'', they will diffuse on the terrace
572 > up onto a higher terrace. Once ``free'', they diffuse on the terrace
573   until reaching another step-edge or rejoining their original edge.  
574   This combination of growth and decay of the step-edges is in a state of
575   dynamic equilibrium. However, once two previously separated edges
576 < meet as shown in Figure 1.B, this meeting point tends to act as a focus
577 < or growth point for the rest of the edge to meet up, akin to that of a zipper.
533 < From the handful of cases where a double layer was formed during the
534 < simulation, measuring from the initial appearance of a growth point, the
535 < double layer tends to be fully formed within $\sim$35 ns.
576 > meet as shown in Figure 1.B, this nucleates the rest of the edge to meet up, forming a double layer.
577 > 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.
578  
579   A number of possible mechanisms exist to explain the role of adsorbed
580   CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent
581 < CO molecules adsorbed on the surface is one likely possibility.  However,
581 > CO molecules adsorbed on the surface is one possibility.  However,
582   the quadrupole-quadrupole interaction is short-ranged and is attractive for
583   some orientations.  If the CO molecules are ``locked'' in a specific orientation
584   relative to each other, through atop adsorption for example, this explanation
585 < gains some weight.  The energetic repulsion between two CO located a
586 < distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in
587 < a  vertical orientation is 8.62 kcal/mol. Moving the CO apart to the second
585 > gains some credence.  The energetic repulsion between two CO located a
586 > distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) and both in
587 > a  vertical orientation, is 8.62 kcal/mol. Moving the CO apart to the second
588   nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to
589   nearly 0 kcal/mol. Allowing the CO's to leave a purely vertical orientation
590   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.
591   As mentioned above, the energy barrier for surface diffusion
592 < of a Pt adatom is only 4 kcal/mol. So this repulsion between CO can help
592 > of a Pt adatom is only 4 kcal/mol. So this repulsion between neighboring CO molecules can
593   increase the surface diffusion. However, the residence time of CO on Pt was
594   examined and while the majority of the CO is on or near the surface throughout
595 < the run, it is extremely mobile. This mobility suggests that the CO are more
596 < likely to shift their positions without necessarily dragging the Pt along with them.
595 > the run, most molecules are mobile. This mobility suggests that the CO are more
596 > likely to shift their positions without necessarily the Pt along with them.
597  
598   Another possible and more likely mechanism for the restructuring is in the
599   destabilization of strong Pt-Pt interactions by CO adsorbed on surface
# Line 585 | Line 627 | As shown in the results section, the diffusion paralle
627  
628  
629   \subsection{Diffusion}
630 < As shown in the results section, the diffusion parallel to the step-edge tends to be
631 < much larger than that perpendicular to the step-edge, likely because of the dynamic
630 > The diffusion parallel to the step-edge tends to be
631 > much larger than that perpendicular to the step-edge. The dynamic
632   equilibrium that is established between the step-edge and adatom interface. The coverage
633   of CO also appears to play a slight role in relative rates of diffusion, as shown in Figure \ref{fig:diff}.
634   The
# Line 614 | Line 656 | more likely a growth point is to be formed.
656  
657  
658   %Peaks!
659 < \begin{figure}[H]
660 < \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
661 < \caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
662 < of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
663 < aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
664 < \label{fig:peaks}
665 < \end{figure}
659 > %\begin{figure}[H]
660 > %\includegraphics[width=\linewidth]{doublePeaks_noCO.png}
661 > %\caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
662 > %of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
663 > %aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
664 > %\label{fig:peaks}
665 > %\end{figure}
666  
667  
668   %Don't think I need this

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