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Comparing trunk/COonPt/firstTry.tex (file contents):
Revision 3839 by jmichalk, Thu Dec 20 21:36:33 2012 UTC vs.
Revision 3860 by jmichalk, Fri Feb 15 19:15:17 2013 UTC

# Line 343 | Line 343 | source molecular dynamics package, OpenMD.\cite{Ewald,
343   source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,OpenMD}
344  
345   % Just results, leave discussion for discussion section
346 + % structure
347 + %       Pt: step wandering, double layers, no triangular motifs
348 + %       Au: step wandering, no double layers
349 + % dynamics
350 + %       diffusion
351 + %       time scale, formation, breakage
352   \section{Results}
353 < Tao {\it et al.} showed experimentally that the Pt(557) surface
354 < undergoes two separate reconstructions upon CO
355 < adsorption.\cite{Tao:2010} The first reconstruction involves a
356 < doubling of the step edge height which is accomplished by a doubling
357 < of the plateau length. The second reconstruction led to the formation
358 < of triangular clusters that arrange themselves along the lengthened
359 < plateaus.
360 <
361 < The primary observation and results of our simulation is that the
362 < presence of CO overlayer on Pt(557) causes the same kind of
363 < reconstruction observed experimentally. The 6-atom 111 facets
364 < initially become disordered, and after 20-40 ns, a double-layer (with
365 < a 2-atom step between terraces) forms.  However, we did not observe
366 < the triangular cluster formation that was observed at longer times in
367 < the experiments.  Without the CO present on the Pt(557) surface, there
368 < was some disorder at the step edges, but no significant restructuring
363 < was observed.
353 > \subsection{Structural remodeling}
354 > Tao {\it et al.} showed experimentally that the Pt(557) surface undergoes
355 > two separate reconstructions upon CO adsorption.\cite{Tao:2010} The first
356 > reconstruction involves a doubling of the step height and plateau length. Similar
357 > behavior has been seen to occur on numerous surfaces at varying conditions.\cite{}
358 > Of the two systems we examined, the Platinum system showed the most surface
359 > reconstruction. Additionally, the amount of reconstruction appears to be
360 > dependent on the amount of CO adsorbed upon the surface. This result is likely
361 > related to the effect that coverage has on surface diffusion. While both systems
362 > displayed step edge wandering, only the Pt surface underwent doubling within
363 > the time scales we were modeling. Specifically only the 50 \% coverage Pt system
364 > was observed to undergo doubling in the time scales we were able to monitor.
365 > Although, the other Platinum systems tended to show more cumulative lateral movement of
366 > the step edges when compared to the Gold systems. The 50 \% Pt system is highlighted
367 > in figure \ref{fig:reconstruct} at various times along the simulation showing
368 > the evolution of the system.
369  
370 < In these simulations, the Au(557) surface did not exhibit any
371 < significant restructuring either with or without the presence of a CO
372 < overlayer.
370 > The second reconstruction on the Pt(557) surface observed by Tao involved the
371 > formation of triangular clusters that stretched across the plateau between two step edges.
372 > Neither system, within our simulated time scales, experiences this reconstruction. A constructed
373 > system in which the triangular motifs were constructed on the surface will be explored in future
374 > work and is shown in the supporting information.
375  
376 < \subsection{Transport of surface metal atoms}
377 < An ideal metal surface displaying a low energy (111) face is unlikely
378 < to experience much surface diffusion because of the large vacancy
379 < formation energy for atoms at the surface.  This implies that
380 < significant energy must be expended to lift an atom out of the flat
381 < face so it can migrate on the surface.  Rougher surfaces and those
382 < that already contain numerous adatoms, step edges, and kinks, are
383 < expected to have higher surface diffusion rates.  Metal atoms that are
384 < mobile on the surface were observed to leave and then rejoin step
385 < edges or other formations. They may travel together or as isolated
386 < atoms.  The primary challenge of quantifying the overall surface
387 < mobility is in defining ``mobile'' vs. ``static'' atoms.
376 > \subsection{Dynamics}
377 > While atomistic simulations of stepped surfaces have been performed before \cite{}, they tend to be
378 > performed using Monte Carlo techniques\cite{}. This allows them to efficiently sample the thermodynamic
379 > landscape but at the expense of ignoring the dynamics of the system. Previous work, using STM (?)\cite{},
380 > has been able to visualize the coalescing of steps of (system). The time scale of the image acquisition
381 > provides an upper bounds for the time required for the doubling to actually occur. While statistical treatments
382 > of step edges are adept at analyzing such systems, it is important to remember that the edges are made
383 > up of individual atoms and thus can be examined in numerous ways.
384 >
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.
400  
401 < A particle was considered mobile once it had traveled more than 2~\AA~
402 < between saved configurations (10-100 ps). Restricting the transport
403 < calculations to only mobile atoms eliminates all of the bulk metal as
404 < well as any surface atoms that remain fixed for a significant length
405 < of time.  Since diffusion on a surface is strongly affected by local
406 < structures, the diffusion parallel to the step edges was determined
388 < separately from the diffusion perpendicular to these edges.  The
389 < parallel and perpendicular diffusion constants (determined using
390 < linear fits to the mean squared displacement) are shown in figure \ref{fig:diff}.
401 > A particle was considered mobile once it had traveled more than 2~\AA~ between saved configurations
402 > of the system (10-100 ps). An atom that was truly mobile would typically travel much greater than this, but
403 > the 2~\AA~ cutoff was to prevent the in place vibrational movement of atoms from being included in the analysis.
404 > Since diffusion on  a surface is strongly affected by local structures, in this case the presence of single and double
405 > layer step edges, the diffusion parallel to the step edges was determined separately from the diffusion perpendicular
406 > to these edges. The parallel and perpendicular diffusion constants are shown in figure \ref{fig:diff}.
407  
408 < %While an ideal metallic surface is unlikely to experience much surface diffusion, high-index surfaces have large numbers of low-coordinated atoms which have a much easier time overcoming the energetic barriers limiting diffusion, leading to easier surface reconstructions. Surface movement was divided between the parallel ($\parallel$) and perpendicular ($\perp$) directions relative to the step edge. We were then able to calculate diffusion constants as a function of CO coverage. As can be seen in Table 4, the presence and amount of CO directly affects the diffusion constants of surface platinum atoms. The presence of two 50\% coverage systems is to show how the diffusion process is affected by time. The majority of the systems were run for approximately 50 ns while the half monolayer system has been running continuously. The lowered diffusion constant at longer run times will be examined in-depth in the discussion section.
408 > \subsubsection{Double layer formation}
409 > The increased amounts of diffusion on Pt at the higher CO coverages appears to play a role in the
410 > formation of double layers. Seeing as how that was the only system within our observed simulation time
411 > that showed the formation. As mentioned earlier, previous experimental work has given some insight into
412 > the upper bounds of the time required for enough atoms to move around to allow two steps to coalesce\cite{}.
413 > As seen in figure \ref{fig:reconstruct}, the first appearance of a double layer, a nodal site, appears at 19 ns into
414 > the simulation. Within 10 ns, nearly half of the step has formed the double layer and by 86 ns, the complete
415 > layer has formed. From the appearance of the first node to the complete doubling of the layers, only ~65 ns
416 > have elapsed. The other two layers in this simulation form over a period of ---- and ---- ns respectively.
417  
418   \begin{figure}[H]
419   \includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade.pdf}
# Line 476 | Line 500 | As shown in the results section, the diffusion paralle
500    doubling of the layers appears only after two adjacent step edges
501    touch.  The circled spot in (b) nucleated the growth of the double
502    step observed in the later configurations.}
503 +  \label{fig:reconstruct}
504   \end{figure}
505  
506  

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