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# Line 161 | Line 161 | Au-Au and Pt-Pt interactions\cite{EAM}. The CO was mod
161   Coulomb potential.  For this work, we have used classical molecular
162   dynamics with potential energy surfaces that are specifically tuned
163   for transition metals.  In particular, we used the EAM potential for
164 < Au-Au and Pt-Pt interactions\cite{EAM}. The CO was modeled using a rigid
164 > Au-Au and Pt-Pt interactions.\cite{EAM} The CO was modeled using a rigid
165   three-site model developed by Straub and Karplus for studying
166   photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
167   Pt-CO cross interactions were parameterized as part of this work.
# Line 475 | Line 475 | with the energetics and structures at different condit
475  
476   \subsection{Dynamics}
477   Previous atomistic simulations of stepped surfaces dealt largely
478 < with the energetics and structures at different conditions
479 < \cite{Williams:1991,Williams:1994}. Consequently, the most common
478 > with the energetics and structures at different conditions.
479 > \cite{Williams:1991,Williams:1994} Consequently, the most common
480   technique utilized to date has been Monte Carlo sampling. Monte Carlo approaches give an efficient
481   sampling of the equilibrium thermodynamic landscape at the expense
482   of ignoring the dynamics of the system. Previous experimental work by Pearl and
# Line 499 | Line 499 | on the surface. For certain distributions of CO, see F
499   energetic penalty around $\sim$~45 kcal/mol, but this is easier than lifting
500   the same metal atom vertically out of the surface,  \textgreater~60 kcal/mol.
501   The penalty lowers significantly when CO is present in sufficient quantities
502 < on the surface. For certain distributions of CO, see Figures \ref{fig:sketchGraphic} and \ref{fig:sketchEnergies}, the penalty can fall to as low as
502 > on the surface. For certain distributions of CO, see Figures \ref{fig:SketchGraphic} and \ref{fig:SketchEnergies}, the penalty can fall to as low as
503   $\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for
504   diffusion is negligible ( \textless~4 kcal/mol for a Pt adatom). These adatoms are then
505   able to explore the terrace before rejoining either their original step-edge or
# Line 547 | Line 547 | stability strongly and is no longer a good source for
547   definite trend marred by the highest coverage surface. Two
548   explanations arise for this drop. First, upon a visual inspection of
549   the system, after a double layer has been formed, it maintains its
550 < stability strongly and is no longer a good source for adatoms and so
551 < atoms that had been tracked for mobility data have now been buried. By
552 < performing the same diffusion calculation but on a shorter run time
553 < (20~ns), only including data before the formation of the double layer, we obtain
554 < the larger values for both $\mathbf{D}_{\parallel}$ and $\mathbf{D}_{\perp}$ at the 50\% coverage.
550 > stability strongly and many atoms that had been tracked for mobility
551 > data have now been buried. By performing the same diffusion
552 > calculation but on a shorter run time (20~ns), only including data
553 > before the formation of the first double layer, we obtain the larger
554 > values for both $\mathbf{D}_{\parallel}$ and $\mathbf{D}_{\perp}$
555 > at the 50\% coverage as seen in Figure \ref{fig:diff}.
556   This places the parallel diffusion constant more closely in line with the
557   expected trend, while the perpendicular diffusion constant does not
558   drop as far. A secondary explanation arising from our analysis of the
# Line 559 | Line 560 | arrangements of CO on the surface allowing the formati
560   surface has with respect to overcoming surface diffusion of Pt. If the
561   coverage is too sparse, the Pt engages in minimal interactions and
562   thus minimal diffusion. As coverage increases, there are more favorable
563 < arrangements of CO on the surface allowing the formation of a path,
563 > arrangements of CO on the surface allowing for the formation of a path,
564   a minimum energy trajectory, for the adatom to explore the surface.
565   As the CO is constantly moving on the surface, this path is constantly
566   changing. If the coverage becomes too great, the paths could
# Line 569 | Line 570 | The increased diffusion on Pt at the higher
570  
571  
572   \subsubsection{Dynamics of double layer formation}
573 < The increased diffusion on Pt at the higher
574 < CO coverages plays a primary role in double layer formation. However, this is not
575 < a complete explanation -- the 33\%~Pt system
576 < has higher diffusion constants but did not show
577 < any signs of edge doubling in the observed run time. On the
578 < 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
579 < 110~ns (150~ns total). Previous experimental
580 < work gives insight into the upper bounds of the
581 < time required for step coalescence.\cite{Williams:1991,Pearl}
573 > The increased diffusion on Pt at the higher CO coverages
574 > plays a primary role in double layer formation. However,
575 > this is not a complete explanation -- the 33\%~Pt system
576 > has higher diffusion constants but did not show any signs
577 > of edge doubling in the observed run time. On the
578 > 50\%~Pt system, one layer formed within the first 40~ns
579 > of simulation time, while two more were formed as the
580 > system was allowed to run for an additional
581 > 110~ns (150~ns total). This suggests that this reconstruction is
582 > a rapid process and that the previously mentioned upper bound
583 > will be lowered as experimental techniques continue to improve.\cite{Williams:1991,Pearl}
584   In this system, as seen in Figure \ref{fig:reconstruct}, the first
585   appearance of a double layer, appears at 19~ns
586   into the simulation. Within 12~ns of this nucleation event, nearly half of the step has
# Line 587 | Line 590 | The other two layers in this simulation formed over pe
590   appearance of the first nucleation event to the first observed double layer, the process took $\sim$20~ns. Another
591   $\sim$40~ns was necessary for the layer to completely straighten.
592   The other two layers in this simulation formed over periods of
593 < 22~ns and 42~ns respectively. Comparing this to the upper
591 < bounds of the image scan, it is likely that most aspects of this
592 < reconstruction occur very rapidly. A possible explanation
593 > 22~ns and 42~ns respectively. A possible explanation
594   for this rapid reconstruction is the elevated temperatures
595   under which our systems were simulated. It is probable that the process would
596 < take longer at lower temperatures.
596 > take longer at lower temperatures. Additionally, our measured times for completion
597 > of the doubling after the appearance of a nucleation site are likely affected by our
598 > constrained axes. A longer step-edge will likely take longer to ``zipper''. However,
599 > the first appearance of a nucleation site will likely occur more quickly due to its stochastic nature.
600  
601  
602  
# Line 696 | Line 700 | configurations are displayed in Figure \ref{fig:lambda
700   Pt atoms. To test this hypothesis, numerous configurations of
701   CO in varying quantities were arranged on the higher and lower plateaus
702   around a step on a otherwise clean Pt(557) surface. A few sample
703 < configurations are displayed in Figure \ref{fig:lambdaTable}, with
703 > configurations are displayed in Figure \ref{fig:SketchGraphic}, with
704   energies at various positions along the path displayed in Table
705 < \ref{tab:rxcoord}. Certain configurations of CO, cases B and D for
705 > NO TABLE. Certain configurations of CO, cases B and D for
706   example, can have quite strong energetic reasons for breaking
707   away from the step-edge. Although the packing of these configurations
708   is unlikely until CO coverage has reached a high enough value.

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