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# Line 58 | Line 58 | Notre Dame, Indiana 46556}
58   Notre Dame, Indiana 46556}
59  
60   %Date
61 < \date{Dec 15, 2012}
61 > \date{Mar 5, 2013}
62  
63   %authors
64  
# Line 68 | Line 68 | Notre Dame, Indiana 46556}
68   \begin{doublespace}
69  
70   \begin{abstract}
71 <
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 large difference in binding strengths of the metal-CO
77 > interactions was found to play a significant role with regards to
78 > step-edge stability and adatom diffusion. A small correlation
79 > between coverage and the magnitude 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
116 < surface restructuring using molecular simulations.  Since the dynamics
117 < of the process is of particular interest, we utilize classical force
115 > This work is an attempt to understand the mechanism and timescale for
116 > surface restructuring by using molecular simulations.  Since the dynamics
117 > of the process are of particular interest, we employ classical force
118   fields that represent a compromise between chemical accuracy and the
119 < computational efficiency necessary to observe the process of interest.
120 <
121 < Since restructuring occurs as a result of specific interactions of the
122 < catalyst with adsorbates, two metal systems exposed to carbon monoxide
111 < were examined in this work. The Pt(557) surface has already been shown
119 > computational efficiency necessary to simulate the process of interest.
120 > Since restructuring typically occurs as a result of specific interactions of the
121 > catalyst with adsorbates, in this work, two metal systems exposed
122 > to carbon monoxide were examined. The Pt(557) surface has already been shown
123   to reconstruct under certain conditions. The Au(557) surface, because
124   of a weaker interaction with CO, is less likely to undergo this kind
125 < of reconstruction.  MORE HERE ON PT AND AU PREVIOUS WORK.
125 > of reconstruction.  
126  
127 +
128 +
129   %Platinum molecular dynamics
130   %gold molecular dynamics
131  
# Line 133 | Line 146 | Au-Au and Pt-Pt interactions, while modeling the CO us
146   Coulomb potential.  For this work, we have used classical molecular
147   dynamics with potential energy surfaces that are specifically tuned
148   for transition metals.  In particular, we used the EAM potential for
149 < Au-Au and Pt-Pt interactions, while modeling the CO using a rigid
149 > Au-Au and Pt-Pt interactions\cite{EAM}, while modeling the CO using a rigid
150   three-site model developed by Straub and Karplus for studying
151   photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
152   Pt-CO cross interactions were parameterized as part of this work.
# Line 146 | Line 159 | parameter sets. The glue model of Ercolessi {\it et al
159   methods,\cite{Daw84,Foiles86,Johnson89,Daw89,Plimpton93,Voter95a,Lu97,Alemany98}
160   but other models like the Finnis-Sinclair\cite{Finnis84,Chen90} and
161   the quantum-corrected Sutton-Chen method\cite{QSC,Qi99} have simpler
162 < parameter sets. The glue model of Ercolessi {\it et al.} is among the
162 > parameter sets. The glue model of Ercolessi et al. is among the
163   fastest of these density functional approaches.\cite{Ercolessi88} In
164   all of these models, atoms are conceptualized as a positively charged
165   core with a radially-decaying valence electron distribution. To
# Line 164 | Line 177 | $\phi_{ij}(r_{ij})$ is an pairwise term that is meant
177   V_i =  F[ \bar{\rho}_i ]  + \sum_{j \neq i} \phi_{ij}(r_{ij})
178   \end{equation*}
179   where $F[ \bar{\rho}_i ]$ is an energy embedding functional, and
180 < $\phi_{ij}(r_{ij})$ is an pairwise term that is meant to represent the
181 < overlap of the two positively charged cores.  
180 > $\phi_{ij}(r_{ij})$ is a pairwise term that is meant to represent the
181 > repulsive overlap of the two positively charged cores.  
182  
183   % The {\it modified} embedded atom method (MEAM) adds angular terms to
184   % the electron density functions and an angular screening factor to the
# Line 176 | Line 189 | The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen
189   % metals,\cite{Lee:2001qf} and also interfaces.\cite{Beurden:2002ys})
190   % MEAM presents significant additional computational costs, however.
191  
192 < The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen potentials
192 > The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen (QSC) potentials
193   have all been widely used by the materials simulation community for
194   simulations of bulk and nanoparticle
195   properties,\cite{Chui:2003fk,Wang:2005qy,Medasani:2007uq}
# Line 190 | Line 203 | Since previous explanations for the surface rearrangem
203   parameterized.\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
204  
205   \subsection{Carbon Monoxide model}
206 < Since previous explanations for the surface rearrangements center on
207 < the large linear quadrupole moment of carbon monoxide, the model
208 < chosen for this molecule exhibits this property in an efficient
209 < manner.  We used a model first proposed by Karplus and Straub to study
210 < the photodissociation of CO from myoglobin.\cite{Straub} The Straub and
211 < Karplus model is a rigid three site model which places a massless M
212 < site at the center of mass along the CO bond.  The geometry used along
213 < with the interaction parameters are reproduced in Table~1. The effective
206 > Previous explanations for the surface rearrangements center on
207 > the large linear quadrupole moment of carbon monoxide.  
208 > We used a model first proposed by Karplus and Straub to study
209 > the photodissociation of CO from myoglobin because it reproduces
210 > the quadrupole moment well.\cite{Straub} The Straub and
211 > Karplus model, treats CO as a rigid three site molecule which places a massless M
212 > site at the center of mass position along the CO bond.  The geometry used along
213 > with the interaction parameters are reproduced in Table~\ref{tab:CO}. The effective
214   dipole moment, calculated from the assigned charges, is still
215   small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is close
216   to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum
# Line 206 | Line 219 | mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCO
219   \begin{table}[H]
220    \caption{Positions, Lennard-Jones parameters ($\sigma$ and
221      $\epsilon$), and charges for the CO-CO
222 <    interactions borrowed from Ref. \bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA~, energies are
222 >    interactions borrowed from Ref.\bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA, energies are
223      in kcal/mol, and charges are in atomic units.}
224   \centering
225   \begin{tabular}{| c | c | ccc |}
# Line 218 | Line 231 | mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCO
231   \textbf{M} & 0.0 & -  &  -  &    1.6 \\
232   \hline
233   \end{tabular}
234 + \label{tab:CO}
235   \end{table}
236  
237   \subsection{Cross-Interactions between the metals and carbon monoxide}
238  
239 < Since the adsorption of CO onto a platinum surface has been the focus
239 > Since the adsorption of CO onto a Pt surface has been the focus
240   of much experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979}
241   and theoretical work
242   \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
# Line 230 | Line 244 | position on Pt(111). This resulting binding energies a
244   clean metal surfaces. Parameters reported by Korzeniewski {\it et
245    al.}\cite{Pons:1986} were a starting point for our fits, which were
246   modified to ensure that the Pt-CO interaction favored the atop binding
247 < position on Pt(111). This resulting binding energies are on the higher
248 < side of the experimentally-reported values. Following Korzeniewski
249 < {\it et al.},\cite{Pons:1986} the Pt-C interaction was fit to a deep
247 > position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}
248 > This resulted in binding energies that are slightly higher
249 > than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
250 > et al.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
251   Lennard-Jones interaction to mimic strong, but short-ranged partial
252   binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
253 < Pt-O interaction was parameterized to a Morse potential with a large
254 < range parameter ($r_o$).  In most cases, this contributes a weak
253 > Pt-O interaction was parameterized to a Morse potential at a larger
254 > minimum distance, ($r_o$).  This was chosen so that the C would be preferred
255 > over O as the binder to the surface. In most cases, this parameterization contributes a weak
256   repulsion which favors the atop site.  The resulting potential-energy
257   surface suitably recovers the calculated Pt-C separation length
258   (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
# Line 245 | Line 261 | The Au-C and Au-O cross-interactions were fit using Le
261   %where did you actually get the functionals for citation?
262   %scf calculations, so initial relaxation was of the four layers, but two layers weren't kept fixed, I don't think
263   %same cutoff for slab and slab + CO ? seems low, although feibelmen had values around there...
264 < The Au-C and Au-O cross-interactions were fit using Lennard-Jones and
264 > The Au-C and Au-O cross-interactions were also fit using Lennard-Jones and
265   Morse potentials, respectively, to reproduce Au-CO binding energies.
266 <
267 < The fits were refined against gas-surface DFT calculations with a
266 > The limited experimental data for CO adsorption on Au lead us to refine our fits against DFT.
267 > Adsorption energies were obtained from gas-surface DFT calculations with a
268   periodic supercell plane-wave basis approach, as implemented in the
269   {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores are
270   described with the projector augmented-wave (PAW)
# Line 257 | Line 273 | Ionic relaxations were performed until the energy diff
273   computed with the PBE implementation of the generalized gradient
274   approximation (GGA) for gold, carbon, and oxygen that was constructed
275   by Rappe, Rabe, Kaxiras, and Joannopoulos.\cite{Perdew_GGA,RRKJ_PP}
276 < 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
276 > In testing the Au-CO interaction, Au(111) supercells were constructed of four layers of 4
277   Au x 2 Au surface planes and separated from vertical images by six
278 < layers of vacuum space. The surface atoms were all allowed to relax.
279 < Supercell calculations were performed nonspin-polarized with a 4 x 4 x
280 < 4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
278 > layers of vacuum space. The surface atoms were all allowed to relax
279 > before CO was added to the system. Electronic relaxations were
280 > performed until the energy difference between subsequent steps
281 > was less than $10^{-8}$ Ry.   Nonspin-polarized supercell calculations
282 > were performed with a 4~x~4~x~4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
283   zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxed gold slab was
284   then used in numerous single point calculations with CO at various
285   heights (and angles relative to the surface) to allow fitting of the
286   empirical force field.
287  
288   %Hint at future work
289 < The parameters employed in this work are shown in Table 2 and the
290 < binding energies on the 111 surfaces are displayed in Table 3.  To
291 < speed up the computations, charge transfer and polarization are not
292 < being treated in this model, although these effects are likely to
293 < affect binding energies and binding site
294 < preferences.\cite{Deshlahra:2012}
289 > The parameters employed for the metal-CO cross-interactions in this work
290 > are shown in Table~\ref{co_parameters} and the binding energies on the
291 > (111) surfaces are displayed in Table~\ref{co_energies}.  Charge transfer
292 > and polarization are neglected in this model, although these effects are likely to
293 > affect binding energies and binding site preferences, and will be added in
294 > a future work.\cite{Deshlahra:2012,StreitzMintmire:1994}
295  
296   %Table  of Parameters
297   %Pt Parameter Set 9
298   %Au Parameter Set 35
299   \begin{table}[H]
300 <  \caption{Best fit parameters for metal-CO cross-interactions.   Metal-C
300 >  \caption{Best fit parameters for metal-CO cross-interactions. Metal-C
301      interactions are modeled with Lennard-Jones potential, while the
302 <    (mostly-repulsive) metal-O interactions were fit to Morse
302 >    metal-O interactions were fit to Morse
303      potentials.  Distances are given in \AA~and energies in kcal/mol. }
304   \centering
305   \begin{tabular}{| c | cc | c | ccc |}
# Line 295 | Line 311 | preferences.\cite{Deshlahra:2012}
311  
312   \hline
313   \end{tabular}
314 + \label{tab:co_parameters}
315   \end{table}
316  
317   %Table of energies
318   \begin{table}[H]
319 <  \caption{Adsorption energies for CO on M(111) using the potentials
320 <    described in this work.  All values are in eV}
319 >  \caption{Adsorption energies for CO on M(111) at the atop site using the potentials
320 >    described in this work.  All values are in eV.}
321   \centering
322   \begin{tabular}{| c | cc |}
323    \hline
# Line 312 | Line 329 | preferences.\cite{Deshlahra:2012}
329    \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPD_Gold}) \\
330    \hline
331   \end{tabular}
332 + \label{tab:co_energies}
333   \end{table}
334  
335   \subsection{Pt(557) and Au(557) metal interfaces}
336  
337   Our model systems are composed of 3888 Pt atoms and 3384 Au atoms in a
338 < FCC crystal that have been cut along the 557 plane so that they are
339 < periodic in the {\it x} and {\it y} directions, and have been rotated
340 < to expose two parallel 557 cuts along the positive and negative {\it
338 > FCC crystal that have been cut along the (557) plane so that they are
339 > periodic in the {\it x} and {\it y} directions, and have been oriented
340 > to expose two aligned (557) cuts along the extended {\it
341    z}-axis.  Simulations of the bare metal interfaces at temperatures
342 < ranging from 300~K to 1200~K were done to observe the relative
342 > ranging from 300~K to 1200~K were performed to observe the relative
343   stability of the surfaces without a CO overlayer.  
344  
345   The different bulk (and surface) melting temperatures (1337~K for Au
346 < and 2045~K for Pt) suggest that the reconstruction may happen at
347 < different temperatures for the two metals.  To copy experimental
330 < conditions for the CO-exposed surfaces, the bare surfaces were
346 > and 2045~K for Pt) suggest that any possible reconstruction may happen at
347 > different temperatures for the two metals.  The bare Au and Pt surfaces were
348   initially run in the canonical (NVT) ensemble at 800~K and 1000~K
349 < respectively for 100 ps.  Each surface was exposed to a range of CO
349 > respectively for 100 ps. These temperatures were chosen because the
350 > surfaces were relatively stable at these temperatures when no CO was
351 > present, but experienced additional instability upon addition of CO in the time
352 > frames we were examining. Each surface was exposed to a range of CO
353   that was initially placed in the vacuum region.  Upon full adsorption,
354   these amounts correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
355 < coverage.  Because of the difference in binding energies, the platinum
355 > coverage. Higher coverages were tried, but the CO-CO repulsion was preventing
356 > a higher amount of adsorption.  Because of the difference in binding energies, the Pt
357   systems very rarely had CO that was not bound to the surface, while
358 < the gold surfaces often had a significant CO population in the gas
358 > the Au surfaces often had a significant CO population in the gas
359   phase.  These systems were allowed to reach thermal equilibrium (over
360 < 5 ns) before being shifted to the microcanonical (NVE) ensemble for
360 > 5 ns) before being run in the microcanonical (NVE) ensemble for
361   data collection. All of the systems examined had at least 40 ns in the
362   data collection stage, although simulation times for some of the
363   systems exceeded 200ns.  All simulations were run using the open
364 < source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,OpenMD}
364 > source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE}
365  
366   % Just results, leave discussion for discussion section
367   % structure
# Line 351 | Line 372 | Tao {\it et al.} showed experimentally that the Pt(557
372   %       time scale, formation, breakage
373   \section{Results}
374   \subsection{Structural remodeling}
375 < Tao {\it et al.} showed experimentally that the Pt(557) surface undergoes
376 < two separate reconstructions upon CO adsorption.\cite{Tao:2010} The first
377 < reconstruction involves a doubling of the step height and plateau length. Similar
378 < behavior has been seen to occur on numerous surfaces at varying conditions.\cite{}
379 < Of the two systems we examined, the Platinum system showed the most surface
380 < reconstruction. Additionally, the amount of reconstruction appears to be
381 < dependent on the amount of CO adsorbed upon the surface. This result is likely
382 < related to the effect that coverage has on surface diffusion. While both systems
383 < displayed step edge wandering, only the Pt surface underwent doubling within
384 < the time scales we were modeling. Specifically only the 50 \% coverage Pt system
385 < was observed to undergo doubling in the time scales we were able to monitor.
386 < Although, the other Platinum systems tended to show more cumulative lateral movement of
387 < the step edges when compared to the Gold systems. The 50 \% Pt system is highlighted
388 < in figure \ref{fig:reconstruct} at various times along the simulation showing
389 < the evolution of the system.
375 > Tao et al. showed experimentally that the Pt(557) surface
376 > undergoes two separate reconstructions upon CO
377 > adsorption.\cite{Tao:2010} The first involves a doubling of
378 > the step height and plateau length. Similar behavior has been
379 > seen to occur on numerous surfaces at varying conditions (Ni 977, Si 111, etc).
380 > \cite{Williams:1994,Williams:1991,Pearl} Of the two systems
381 > we examined, the Pt system showed a larger amount of
382 > reconstruction when compared to the Au system. The amount
383 > of reconstruction appears to be correlated to the amount of CO
384 > adsorbed upon the surface.  We believe this is related to the
385 > effect that adsorbate coverage has on edge breakup and surface
386 > diffusion of adatoms. While both systems displayed step-edge
387 > wandering, only the Pt surface underwent the doubling seen by
388 > Tao et al., within the time scales we were modeling. Specifically,
389 > only the 50~\% coverage Pt system was observed to have a
390 > step-edge undergo a complete doubling in the time scales we
391 > were able to monitor. This event encouraged us to allow that
392 > specific system to run for much longer periods during which two
393 > more double layers were created. The other systems, not displaying
394 > any large scale changes of interest, were all stopped after running
395 > for 40 ns in the microcanonical ensemble. Despite no observation
396 > of double layer formation, the other Pt systems tended to show
397 > more cumulative lateral movement of the step-edges when
398 > compared to the Au systems. The 50\% Pt system is highlighted
399 > in Figure \ref{fig:reconstruct} at various times along the simulation
400 > showing the evolution of the system.
401  
402 < The second reconstruction on the Pt(557) surface observed by Tao involved the
403 < formation of triangular clusters that stretched across the plateau between two step edges.
404 < Neither system, within our simulated time scales, experiences this reconstruction. A constructed
405 < system in which the triangular motifs were constructed on the surface will be explored in future
406 < work and is shown in the supporting information.
402 > The second reconstruction on the Pt(557) surface observed by
403 > Tao involved the formation of triangular clusters that stretched
404 > across the plateau between two step-edges. Neither system, within
405 > our simulated time scales, experiences this reconstruction. A constructed
406 > system in which the triangular motifs were constructed on the surface
407 > will be explored in future work and is shown in the supporting information.
408  
409   \subsection{Dynamics}
410 < While atomistic simulations of stepped surfaces have been performed before \cite{}, they tend to be
411 < performed using Monte Carlo techniques\cite{}. This allows them to efficiently sample the thermodynamic
412 < landscape but at the expense of ignoring the dynamics of the system. Previous work, using STM (?)\cite{},
413 < has been able to visualize the coalescing of steps of (system). The time scale of the image acquisition
414 < provides an upper bounds for the time required for the doubling to actually occur. While statistical treatments
415 < of step edges are adept at analyzing such systems, it is important to remember that the edges are made
416 < up of individual atoms and thus can be examined in numerous ways.
410 > While atomistic-like simulations of stepped surfaces have been
411 > performed before, they tend to be performed using Monte Carlo
412 > techniques\cite{Williams:1991,Williams:1994}. This allows them
413 > to efficiently sample the equilibrium thermodynamic landscape
414 > but at the expense of ignoring the dynamics of the system. Previous
415 > work by Pearl and Sibener\cite{Pearl}, using STM, has been able to
416 > visualize the coalescing of steps of Ni(977). The time scale of the image
417 > acquisition, $\sim$70 s/image provides an upper bounds for the time
418 > required for the doubling to actually occur. Statistical treatments of step-edges
419 > are adept at analyzing such systems. However, in a system where
420 > the number of steps is limited, examining the individual atoms that make
421 > up the steps can provide useful information as well.
422  
385 \subsubsection{Transport of surface metal atoms}
386 The movement of a step edge is a cooperative effect arising from the individual movements of the atoms
387 making up the step. An ideal metal surface displaying a low index facet (111, 100, 110) is unlikely to
388 experience much surface diffusion because of the large energetic barrier to lift an atom out of the surface.
389 For our surfaces, the presence of step edges provide a source for mobile metal atoms. Breaking away
390 from the step edge is still an energetic penalty around (value) but is much less than lifting the same metal
391 atom out from the surface and the penalty lowers even further when CO is present in sufficient quantities
392 on the surface. Once an adatom exists on the surface, its barrier for diffusion is negligible ( < 4 kcal/mole)
393 and is well able to explore its terrace because both steps act as barriers constraining the area in which
394 diffusion is allowed. By tracking the mobility of individual metal atoms on the surface we were able to determine
395 the relative diffusion rates and how varying coverages of CO affected the diffusion constants. Close
396 observation of the mobile metal atoms showed that they were typically in equilibrium with the
397 step edges, constantly breaking apart and rejoining. Additionally, at times their motion was concerted and
398 two or more atoms would be observed moving together across the surfaces. The primary challenge in quantifying
399 the overall surface mobility is in defining ``mobile" vs. ``static" atoms.
423  
424 < A particle was considered mobile once it had traveled more than 2~\AA~ between saved configurations
425 < of the system (10-100 ps). An atom that was truly mobile would typically travel much greater than this, but
426 < the 2~\AA~ cutoff was to prevent the in place vibrational movement of atoms from being included in the analysis.
427 < Since diffusion on  a surface is strongly affected by local structures, in this case the presence of single and double
428 < layer step edges, the diffusion parallel to the step edges was determined separately from the diffusion perpendicular
429 < to these edges. The parallel and perpendicular diffusion constants are shown in figure \ref{fig:diff}.
424 > \subsubsection{Transport of surface metal atoms}
425 > %forcedSystems/stepSeparation
426 > The movement or wandering of a step-edge is a cooperative effect
427 > arising from the individual movements, primarily through surface
428 > diffusion, of the atoms making up the step. An ideal metal surface
429 > displaying a low index facet, (111) or (100) is unlikely to experience
430 > much surface diffusion because of the large energetic barrier that must
431 > be overcome to lift an atom out of the surface. The presence of step-edges
432 > on higher-index surfaces provide a source for mobile metal atoms.
433 > Breaking away from the step-edge on a clean surface still imposes an
434 > energetic penalty around $\sim$~40 kcal/mole, but is much less than lifting
435 > the same metal atom out from the surface,  \textgreater~60 kcal/mole, and
436 > the penalty lowers even further when CO is present in sufficient quantities
437 > on the surface. For certain tested distributions of CO, the penalty was lowered
438 > to $\sim$~20 kcal/mole. Once an adatom exists on the surface, its barrier for
439 > diffusion is negligible ( \textless~4 kcal/mole) and is well able to explore the
440 > terrace before potentially rejoining its original step-edge or becoming a part
441 > of a different edge. Atoms traversing separate terraces is a more difficult
442 > process, but can be overcome through a joining and lifting stage which is
443 > examined in the discussion section. By tracking the mobility of individual
444 > metal atoms on the Pt and Au surfaces we were able to determine the relative
445 > diffusion rates and how varying coverages of CO affected the rates. Close
446 > observation of the mobile metal atoms showed that they were typically in
447 > equilibrium with the step-edges, constantly breaking apart and rejoining.
448 > At times their motion was concerted and two or more adatoms would be
449 > observed moving together across the surfaces. The primary challenge in
450 > quantifying the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
451  
452 + A particle was considered mobile once it had traveled more than 2~\AA~
453 + between saved configurations of the system (10-100 ps). An atom that was
454 + truly mobile would typically travel much greater than this, but the 2~\AA~ cutoff
455 + was to prevent the in-place vibrational movement of non-surface atoms from
456 + being included in the analysis. Diffusion on  a surface is strongly affected by
457 + local structures and in this work the presence of single and double layer
458 + step-edges causes the diffusion parallel to the step-edges to be different
459 + from the diffusion perpendicular to these edges. This led us to compute
460 + those diffusions separately as seen in Figure \ref{fig:diff}.
461 +
462   \subsubsection{Double layer formation}
463 < The increased amounts of diffusion on Pt at the higher CO coverages appears to play a role in the
464 < formation of double layers. Seeing as how that was the only system within our observed simulation time
465 < that showed the formation. As mentioned earlier, previous experimental work has given some insight into
466 < the upper bounds of the time required for enough atoms to move around to allow two steps to coalesce\cite{}.
467 < As seen in figure \ref{fig:reconstruct}, the first appearance of a double layer, a nodal site, appears at 19 ns into
468 < the simulation. Within 10 ns, nearly half of the step has formed the double layer and by 86 ns, the complete
469 < layer has formed. From the appearance of the first node to the complete doubling of the layers, only ~65 ns
470 < have elapsed. The other two layers in this simulation form over a period of ---- and ---- ns respectively.
463 > The increased amounts of diffusion on Pt at the higher CO coverages appears
464 > to play a primary role in the formation of double layers, although this conclusion
465 > does not explain the 33\% coverage Pt system. On the 50\% system, three
466 > separate layers were formed over the extended run time of this system. As
467 > mentioned earlier, previous experimental work has given some insight into the
468 > upper bounds of the time required for enough atoms to move around to allow two
469 > steps to coalesce\cite{Williams:1991,Pearl}. As seen in Figure \ref{fig:reconstruct},
470 > the first appearance of a double layer, a nodal site, appears at 19 ns into the
471 > simulation. Within 12 ns, nearly half of the step has formed the double layer and
472 > by 86 ns, a smooth complete layer has formed. The double layer is ``complete" by
473 > 37 ns but is a bit rough. From the appearance of the first node to the initial doubling
474 > of the layers ignoring their roughness took $\sim$~20 ns. Another ~40 ns was
475 > necessary for the layer to completely straighten. The other two layers in this
476 > simulation form over a period of 22 ns and 42 ns respectively. Comparing this to
477 > the upper bounds of the image scan, it is likely that aspects of this reconstruction
478 > occur very quickly.
479  
480 + %Evolution of surface
481   \begin{figure}[H]
482 + \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
483 + \caption{The Pt(557) / 50\% CO system at a sequence of times after
484 +  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
485 +  (d) 86.1 ns. Disruption of the (557) step-edges occurs quickly.  The
486 +  doubling of the layers appears only after two adjacent step-edges
487 +  touch.  The circled spot in (b) nucleated the growth of the double
488 +  step observed in the later configurations.}
489 +  \label{fig:reconstruct}
490 + \end{figure}
491 +
492 + \begin{figure}[H]
493   \includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade.pdf}
494   \caption{Diffusion constants for mobile surface atoms along directions
495    parallel ($\mathbf{D}_{\parallel}$) and perpendicular
496 <  ($\mathbf{D}_{\perp}$) to the 557 step edges as a function of CO
497 <  surface coverage.  Diffusion parallel to the step edge is higher
496 >  ($\mathbf{D}_{\perp}$) to the (557) step-edges as a function of CO
497 >  surface coverage.  Diffusion parallel to the step-edge is higher
498    than that perpendicular to the edge because of the lower energy
499 <  barrier associated with going from approximately 7 nearest neighbors
500 <  to 5, as compared to the 3 of an adatom. Additionally, the observed
499 >  barrier associated with traversing along the edge as compared to
500 >  completely breaking away. Additionally, the observed
501    maximum and subsequent decrease for the Pt system suggests that the
502    CO self-interactions are playing a significant role with regards to
503 <  movement of the platinum atoms around and more importantly across
430 <  the surface. }
503 >  movement of the Pt atoms around and across the surface. }
504   \label{fig:diff}
505   \end{figure}
506  
434 %Table of Diffusion Constants
435 %Add gold?M
436 % \begin{table}[H]
437 %   \caption{}
438 %   \centering
439 % \begin{tabular}{| c | cc | cc | }
440 %   \hline
441 %   &\multicolumn{2}{c|}{\textbf{Platinum}}&\multicolumn{2}{c|}{\textbf{Gold}} \\
442 %   \hline
443 %   \textbf{Surface Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  \\
444 %   \hline
445 %   50\% & 4.32(2) & 1.185(8)  & 1.72(2) & 0.455(6) \\
446 %   33\% & 5.18(3)  & 1.999(5)  & 1.95(2) & 0.337(4)   \\
447 %   25\% & 5.01(2)  & 1.574(4)  & 1.26(3) & 0.377(6) \\
448 %   5\%   & 3.61(2)  & 0.355(2)  & 1.84(3)  & 0.169(4)  \\
449 %   0\%   & 3.27(2)  & 0.147(4)  & 1.50(2)  & 0.194(2)   \\
450 %   \hline
451 % \end{tabular}
452 % \end{table}
507  
508 +
509 +
510   %Discussion
511   \section{Discussion}
512 + In this paper we have shown that we were able to accurately model the initial reconstruction of the
513 + Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
514 + were able to observe the dynamic processes necessary for this reconstruction.
515  
516 < Mechanism for restructuring
516 > \subsection{Mechanism for restructuring}
517 > Comparing the results from simulation to those reported previously by
518 > Tao et al.\cite{Tao:2010} the similarities in the Pt-CO system are quite
519 > strong. As shown in Figure \ref{fig:reconstruct}, the simulated Pt
520 > system under a CO atmosphere will restructure by doubling the terrace
521 > heights. The restructuring occurs slowly, one to two Pt atoms at a time.
522 > Looking at individual configurations of the system, the adatoms either
523 > break away from the step-edge and stay on the lower terrace or they lift
524 > up onto the higher terrace. Once ``free'' they will diffuse on the terrace
525 > until reaching another step-edge or coming back to their original edge.  
526 > This combination of growth and decay of the step-edges is in a state of
527 > dynamic equilibrium. However, once two previously separated edges
528 > meet as shown in Figure 1.B, this meeting point tends to act as a focus
529 > or growth point for the rest of the edge to meet up, akin to that of a zipper.
530 > From the handful of cases where a double layer was formed during the
531 > simulation, measuring from the initial appearance of a growth point, the
532 > double layer tends to be fully formed within $\sim$~35 ns.
533  
534 < There are a number of possible mechanisms to explain the role of
535 < adsorbed CO in restructuring the Pt surface. Quadrupolar repulsion
536 < between adjacent CO molecules adsorbed on the surface is one
537 < possibility.  However, the quadrupole-quadrupole interaction is
538 < short-ranged and is attractive for some orientations.  If the CO
539 < molecules are locked in a specific orientation relative to each other,
540 < this explanation gains some weight.  
534 > A number of possible mechanisms exist to explain the role of adsorbed
535 > CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent
536 > CO molecules adsorbed on the surface is one likely possibility.  However,
537 > the quadrupole-quadrupole interaction is short-ranged and is attractive for
538 > some orientations.  If the CO molecules are ``locked'' in a specific orientation
539 > relative to each other, through atop adsorption perhaps, this explanation
540 > gains some weight.  The energetic repulsion between two CO located a
541 > distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in
542 > a  vertical orientation is 8.62 kcal/mole. Moving the CO apart to the second
543 > nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to
544 > nearly 0 kcal/mole. Allowing the CO's to leave a purely vertical orientation
545 > also quickly drops the repulsion, a minimum is reached at $\sim$24 degrees
546 > of 6.2 kcal/mole. As mentioned above, the energy barrier for surface diffusion
547 > of a Pt adatom is only 4 kcal/mole. So this repulsion between CO can help
548 > increase the surface diffusion. However, the residence time of CO was
549 > examined and while the majority of the CO is on or near the surface throughout
550 > the run, it is extremely mobile. This mobility suggests that the CO are more
551 > likely to shift their positions without necessarily dragging the Pt along with them.
552  
553 < Another possible mechanism for the restructuring is in the
553 > Another possible and more likely mechanism for the restructuring is in the
554   destabilization of strong Pt-Pt interactions by CO adsorbed on surface
555 < Pt atoms.  This could have the effect of increasing surface mobility
556 < of these atoms.  
555 > Pt atoms.  This would then have the effect of increasing surface mobility
556 > of these atoms.  To test this hypothesis, numerous configurations of
557 > CO in varying quantities were arranged on the higher and lower plateaus
558 > around a step on a otherwise clean Pt(557) surface. One representative
559 > configuration is displayed in Figure \ref{fig:lambda}. Single or concerted movement
560 > of Pt atoms was then examined to determine possible barriers. Because
561 > the movement was forced along a pre-defined reaction coordinate that may differ
562 > from the true minimum of this path, only the beginning and ending energies
563 > are displayed in Table \ref{tab:energies}. These values suggest that the presence of CO at suitable
564 > locations can lead to lowered barriers for Pt breaking apart from the step-edge.
565 > Additionally, as highlighted in Figure \ref{fig:lambda}, the presence of CO makes the
566 > burrowing and lifting of adatoms favorable, whereas without CO, the process is neutral
567 > in terms of energetics.
568  
569 < Comparing the results from simulation to those reported previously by
570 < Tao et al. the similarities in the platinum and CO system are quite
571 < strong. As shown in figure, the simulated platinum system under a CO
572 < atmosphere will restructure slightly by doubling the terrace
573 < heights. The restructuring appears to occur slowly, one to two
574 < platinum atoms at a time. Looking at individual snapshots, these
575 < adatoms tend to either rise on top of the plateau or break away from
576 < the step edge and then diffuse perpendicularly to the step direction
577 < until reaching another step edge. This combination of growth and decay
578 < of the step edges appears to be in somewhat of a state of dynamic
579 < equilibrium. However, once two previously separated edges meet as
580 < shown in figure 1.B, this point tends to act as a focus or growth
484 < point for the rest of the edge to meet up, akin to that of a
485 < zipper. From the handful of cases where a double layer was formed
486 < during the simulation, measuring from the initial appearance of a
487 < growth point, the double layer tends to be fully formed within
488 < $\sim$~35 ns.
569 > %lambda progression of Pt -> shoving its way into the step
570 > \begin{figure}[H]
571 > \includegraphics[width=\linewidth]{lambdaProgression_atopCO.png}
572 > \caption{A model system of the Pt(557) surface was used as the framework
573 > for exploring energy barriers along a reaction coordinate. Various numbers,
574 > placements, and rotations of CO were examined as they affect Pt movement.
575 > The coordinate displayed in this Figure was a representative run. As shown
576 > in Table \ref{tab:rxcoord}, relative to the energy of the system at 0\%, there
577 > is a slight decrease upon insertion of the Pt atom into the step-edge along
578 > with the resultant lifting of the other Pt atom when CO is present at certain positions.}
579 > \label{fig:lambda}
580 > \end{figure}
581  
582 +
583 +
584   \subsection{Diffusion}
585 < 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?)
585 > As shown in the results section, the diffusion parallel to the step-edge tends to be
586 > much larger than that perpendicular to the step-edge, likely because of the dynamic
587 > equilibrium that is established between the step-edge and adatom interface. The coverage
588 > of CO also appears to play a slight role in relative rates of diffusion, as shown in Figure \ref{fig:diff}.
589 > The
590 > Thus, the bottleneck of the double layer formation appears to be the initial formation
591 > of this growth point, which seems to be somewhat of a stochastic event. Once it
592 > appears, parallel diffusion, along the now slightly angled step-edge, will allow for
593 > a faster formation of the double layer than if the entire process were dependent on
594 > only perpendicular diffusion across the plateaus. Thus, the larger $D_{\perp}$, the
595 > more likely a growth point is to be formed.
596   \\
597 < \\
598 < %Evolution of surface
597 >
598 >
599 > %breaking of the double layer upon removal of CO
600   \begin{figure}[H]
601 < \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
602 < \caption{The Pt(557) / 50\% CO system at a sequence of times after
603 <  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
604 <  (d) 86.1 ns. Disruption of the 557 step edges occurs quickly.  The
605 <  doubling of the layers appears only after two adjacent step edges
606 <  touch.  The circled spot in (b) nucleated the growth of the double
607 <  step observed in the later configurations.}
503 <  \label{fig:reconstruct}
601 > \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
602 > %:
603 > \caption{(A)  0 ps, (B) 100 ps, (C) 1 ns, after the removal of CO. The presence of the CO
604 > helped maintain the stability of the double layer and upon removal the two layers break
605 > and begin separating. The separation is not a simple pulling apart however, rather
606 > there is a mixing of the lower and upper atoms at the edge.}
607 > \label{fig:breaking}
608   \end{figure}
609  
610  
611 +
612 +
613   %Peaks!
614   \begin{figure}[H]
615   \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
616 < \caption{}
616 > \caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
617 > of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
618 > aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
619 > \label{fig:peaks}
620   \end{figure}
621 < \begin{figure}[H]
622 < \includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
623 < \caption{}
624 < \end{figure}
621 >
622 >
623 > %Don't think I need this
624 > %clean surface...
625 > %\begin{figure}[H]
626 > %\includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
627 > %\caption{}
628 >
629 > %\end{figure}
630 > %\label{fig:clean}
631 >
632 >
633   \section{Conclusion}
634 + 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.
635  
636 + %Things I am not ready to remove yet
637  
638 + %Table of Diffusion Constants
639 + %Add gold?M
640 + % \begin{table}[H]
641 + %   \caption{}
642 + %   \centering
643 + % \begin{tabular}{| c | cc | cc | }
644 + %   \hline
645 + %   &\multicolumn{2}{c|}{\textbf{Platinum}}&\multicolumn{2}{c|}{\textbf{Gold}} \\
646 + %   \hline
647 + %   \textbf{Surface Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  \\
648 + %   \hline
649 + %   50\% & 4.32(2) & 1.185(8)  & 1.72(2) & 0.455(6) \\
650 + %   33\% & 5.18(3)  & 1.999(5)  & 1.95(2) & 0.337(4)   \\
651 + %   25\% & 5.01(2)  & 1.574(4)  & 1.26(3) & 0.377(6) \\
652 + %   5\%   & 3.61(2)  & 0.355(2)  & 1.84(3)  & 0.169(4)  \\
653 + %   0\%   & 3.27(2)  & 0.147(4)  & 1.50(2)  & 0.194(2)   \\
654 + %   \hline
655 + % \end{tabular}
656 + % \end{table}
657 +
658   \section{Acknowledgments}
659   Support for this project was provided by the National Science
660   Foundation under grant CHE-0848243 and by the Center for Sustainable

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