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# Line 23 | Line 23
23   \setlength{\belowcaptionskip}{30 pt}
24  
25   %\renewcommand\citemid{\ } % no comma in optional reference note
26 < \bibpunct{[}{]}{,}{s}{}{;}
27 < \bibliographystyle{aip}
26 > \bibpunct{[}{]}{,}{n}{}{;}
27 > \bibliographystyle{achemso}
28  
29   \begin{document}
30  
# Line 104 | Line 104 | monolayer of alkylthiolate with relatively long chain
104   this phenomena at the molecular level. Recently, Hase and coworkers
105   employed Non-Equilibrium Molecular Dynamics (NEMD) simulations to
106   study thermal transport from hot Au(111) substrate to a self-assembled
107 < monolayer of alkylthiolate with relatively long chain (8-20 carbon
107 > monolayer of alkylthiol with relatively long chain (8-20 carbon
108   atoms)\cite{hase:2010,hase:2011}. However, ensemble averaged
109   measurements for heat conductance of interfaces between the capping
110   monolayer on Au and a solvent phase has yet to be studied.
111 < The relatively low thermal flux through interfaces is
111 > The comparatively low thermal flux through interfaces is
112   difficult to measure with Equilibrium MD or forward NEMD simulation
113   methods. Therefore, the Reverse NEMD (RNEMD) methods would have the
114   advantage of having this difficult to measure flux known when studying
# Line 193 | Line 193 | gradient max($\Delta T$), which occurs at the Gibbs de
193   One way is to assume the temperature is discrete on the two sides of
194   the interface. $G$ can be calculated using the applied thermal flux
195   $J$ and the maximum temperature difference measured along the thermal
196 < gradient max($\Delta T$), which occurs at the Gibbs deviding surface,
197 < as:
196 > gradient max($\Delta T$), which occurs at the Gibbs deviding surface
197 > (Figure \ref{demoPic}):
198   \begin{equation}
199   G=\frac{J}{\Delta T}
200   \label{discreteG}
201   \end{equation}
202  
203 + \begin{figure}
204 + \includegraphics[width=\linewidth]{method}
205 + \caption{Interfacial conductance can be calculated by applying an
206 +  (unphysical) kinetic energy flux between two slabs, one located
207 +  within the metal and another on the edge of the periodic box.  The
208 +  system responds by forming a thermal response or a gradient.  In
209 +  bulk liquids, this gradient typically has a single slope, but in
210 +  interfacial systems, there are distinct thermal conductivity
211 +  domains.  The interfacial conductance, $G$ is found by measuring the
212 +  temperature gap at the Gibbs dividing surface, or by using second
213 +  derivatives of the thermal profile.}
214 + \label{demoPic}
215 + \end{figure}
216 +
217   The other approach is to assume a continuous temperature profile along
218   the thermal gradient axis (e.g. $z$) and define $G$ at the point where
219   the magnitude of thermal conductivity $\lambda$ change reach its
# Line 222 | Line 236 | our simulation cells. Both with and withour capping ag
236  
237   To compare the above definitions ($G$ and $G^\prime$), we have modeled
238   a metal slab with its (111) surfaces perpendicular to the $z$-axis of
239 < our simulation cells. Both with and withour capping agents on the
239 > our simulation cells. Both with and without capping agents on the
240   surfaces, the metal slab is solvated with simple organic solvents, as
241   illustrated in Figure \ref{demoPic}.
228
229 \begin{figure}
230 \includegraphics[width=\linewidth]{demoPic}
231 \caption{A sample showing how a metal slab has its (111) surface
232  covered by capping agent molecules and solvated by hexane.}
233 \label{demoPic}
234 \end{figure}
242  
243   With the simulation cell described above, we are able to equilibrate
244   the system and impose an unphysical thermal flux between the liquid
# Line 244 | Line 251 | and 2nd derivatives of the temperature profile.
251  
252   \begin{figure}
253   \includegraphics[width=\linewidth]{gradT}
254 < \caption{The 1st and 2nd derivatives of temperature profile can be
255 <  obtained with finite difference approximation.}
254 > \caption{A sample of Au-butanethiol/hexane interfacial system and the
255 >  temperature profile after a kinetic energy flux is imposed to
256 >  it. The 1st and 2nd derivatives of the temperature profile can be
257 >  obtained with finite difference approximation (lower panel).}
258   \label{gradT}
259   \end{figure}
260  
# Line 287 | Line 296 | corresponding spacing is usually $35 \sim 60$\AA.
296   solvent molecules would change the normal behavior of the liquid
297   phase. Therefore, our $N_{solvent}$ values were chosen to ensure that
298   these extreme cases did not happen to our simulations. And the
299 < corresponding spacing is usually $35 \sim 60$\AA.
299 > corresponding spacing is usually $35 \sim 75$\AA.
300  
301   The initial configurations generated by Packmol are further
302   equilibrated with the $x$ and $y$ dimensions fixed, only allowing
# Line 318 | Line 327 | Our simulations include various components. Therefore,
327   \end{equation}
328  
329   \subsection{Force Field Parameters}
330 < Our simulations include various components. Therefore, force field
331 < parameter descriptions are needed for interactions both between the
332 < same type of particles and between particles of different species.
330 > Our simulations include various components. Figure \ref{demoMol}
331 > demonstrates the sites defined for both United-Atom and All-Atom
332 > models of the organic solvent and capping agent molecules in our
333 > simulations. Force field parameter descriptions are needed for
334 > interactions both between the same type of particles and between
335 > particles of different species.
336  
337 + \begin{figure}
338 + \includegraphics[width=\linewidth]{structures}
339 + \caption{Structures of the capping agent and solvents utilized in
340 +  these simulations. The chemically-distinct sites (a-e) are expanded
341 +  in terms of constituent atoms for both United Atom (UA) and All Atom
342 +  (AA) force fields.  Most parameters are from
343 +  Refs. \protect\cite{TraPPE-UA.alkanes,TraPPE-UA.alkylbenzenes} (UA) and
344 +  \protect\cite{OPLSAA} (AA).  Cross-interactions with the Au atoms are given
345 +  in Table \ref{MnM}.}
346 + \label{demoMol}
347 + \end{figure}
348 +
349   The Au-Au interactions in metal lattice slab is described by the
350   quantum Sutton-Chen (QSC) formulation\cite{PhysRevB.59.3527}. The QSC
351   potentials include zero-point quantum corrections and are
352   reparametrized for accurate surface energies compared to the
353   Sutton-Chen potentials\cite{Chen90}.
354  
331 Figure \ref{demoMol} demonstrates how we name our pseudo-atoms of the
332 organic solvent molecules in our simulations.
333
334 \begin{figure}
335 \includegraphics[width=\linewidth]{demoMol}
336 \caption{Denomination of atoms or pseudo-atoms in our simulations: a)
337  UA-hexane; b) AA-hexane; c) UA-toluene; d) AA-toluene.}
338 \label{demoMol}
339 \end{figure}
340
355   For both solvent molecules, straight chain {\it n}-hexane and aromatic
356   toluene, United-Atom (UA) and All-Atom (AA) models are used
357   respectively. The TraPPE-UA
358   parameters\cite{TraPPE-UA.alkanes,TraPPE-UA.alkylbenzenes} are used
359 < for our UA solvent molecules. In these models, pseudo-atoms are
360 < located at the carbon centers for alkyl groups. By eliminating
361 < explicit hydrogen atoms, these models are simple and computationally
362 < efficient, while maintains good accuracy. However, the TraPPE-UA for
363 < alkanes is known to predict a lower boiling point than experimental
350 < values. Considering that after an unphysical thermal flux is applied
351 < to a system, the temperature of ``hot'' area in the liquid phase would be
352 < significantly higher than the average, to prevent over heating and
353 < boiling of the liquid phase, the average temperature in our
354 < simulations should be much lower than the liquid boiling point. [MORE DISCUSSION]
355 < For UA-toluene model, rigid body constraints are applied, so that the
356 < benzene ring and the methyl-CRar bond are kept rigid. This would save
357 < computational time.[MORE DETAILS]
359 > for our UA solvent molecules. In these models, sites are located at
360 > the carbon centers for alkyl groups. Bonding interactions, including
361 > bond stretches and bends and torsions, were used for intra-molecular
362 > sites not separated by more than 3 bonds. Otherwise, for non-bonded
363 > interactions, Lennard-Jones potentials are used. [MORE CITATION?]
364  
365 + By eliminating explicit hydrogen atoms, these models are simple and
366 + computationally efficient, while maintains good accuracy. However, the
367 + TraPPE-UA for alkanes is known to predict a lower boiling point than
368 + experimental values. Considering that after an unphysical thermal flux
369 + is applied to a system, the temperature of ``hot'' area in the liquid
370 + phase would be significantly higher than the average, to prevent over
371 + heating and boiling of the liquid phase, the average temperature in
372 + our simulations should be much lower than the liquid boiling point.
373 +
374 + For UA-toluene model, the non-bonded potentials between
375 + inter-molecular sites have a similar Lennard-Jones formulation. For
376 + intra-molecular interactions, considering the stiffness of the benzene
377 + ring, rigid body constraints are applied for further computational
378 + efficiency. All bonds in the benzene ring and between the ring and the
379 + methyl group remain rigid during the progress of simulations.
380 +
381   Besides the TraPPE-UA models, AA models for both organic solvents are
382   included in our studies as well. For hexane, the OPLS-AA\cite{OPLSAA}
383 < force field is used. [MORE DETAILS]
384 < For toluene, the United Force Field developed by Rapp\'{e} {\it et
385 <  al.}\cite{doi:10.1021/ja00051a040} is adopted.[MORE DETAILS]
383 > force field is used. Additional explicit hydrogen sites were
384 > included. Besides bonding and non-bonded site-site interactions,
385 > partial charges and the electrostatic interactions were added to each
386 > CT and HC site. For toluene, the United Force Field developed by
387 > Rapp\'{e} {\it et al.}\cite{doi:10.1021/ja00051a040} is
388 > adopted. Without the rigid body constraints, bonding interactions were
389 > included. For the aromatic ring, improper torsions (inversions) were
390 > added as an extra potential for maintaining the planar shape.
391 > [MORE CITATION?]
392  
393   The capping agent in our simulations, the butanethiol molecules can
394   either use UA or AA model. The TraPPE-UA force fields includes
# Line 375 | Line 403 | Lorentz-Berthelot Mixing Rule:[EQN'S]
403   (UA or AA) of capping agent can be different from the
404   solvent. Regardless of model choice, the force field parameters for
405   interactions between capping agent and solvent can be derived using
406 < Lorentz-Berthelot Mixing Rule:[EQN'S]
406 > Lorentz-Berthelot Mixing Rule:
407 > \begin{eqnarray}
408 > \sigma_{ij} & = & \frac{1}{2} \left(\sigma_{ii} + \sigma_{jj}\right) \\
409 > \epsilon_{ij} & = & \sqrt{\epsilon_{ii}\epsilon_{jj}}
410 > \end{eqnarray}
411  
380
412   To describe the interactions between metal Au and non-metal capping
413   agent and solvent particles, we refer to an adsorption study of alkyl
414   thiols on gold surfaces by Vlugt {\it et
# Line 392 | Line 423 | interactions between Au and aromatic C/H atoms in tolu
423  
424   Besides, the potentials developed from {\it ab initio} calculations by
425   Leng {\it et al.}\cite{doi:10.1021/jp034405s} are adopted for the
426 < interactions between Au and aromatic C/H atoms in toluene.[MORE DETAILS]
426 > interactions between Au and aromatic C/H atoms in toluene. A set of
427 > pseudo Lennard-Jones parameters were provided for Au in their force
428 > fields. By using the Mixing Rule, this can be used to derive pair-wise
429 > potentials for non-bonded interactions between Au and non-metal sites.
430  
431   However, the Lennard-Jones parameters between Au and other types of
432 < particles in our simulations are not yet well-established. For these
433 < interactions, we attempt to derive their parameters using the Mixing
434 < Rule. To do this, the ``Metal-non-Metal'' (MnM) interaction parameters
435 < for Au is first extracted from the Au-CH$_x$ parameters by applying
436 < the Mixing Rule reversely. Table \ref{MnM} summarizes these ``MnM''
432 > particles, such as All-Atom normal alkanes in our simulations are not
433 > yet well-established. For these interactions, we attempt to derive
434 > their parameters using the Mixing Rule. To do this, Au pseudo
435 > Lennard-Jones parameters for ``Metal-non-Metal'' (MnM) interactions
436 > were first extracted from the Au-CH$_x$ parameters by applying the
437 > Mixing Rule reversely. Table \ref{MnM} summarizes these ``MnM''
438   parameters in our simulations.
439  
440   \begin{table*}
441    \begin{minipage}{\linewidth}
442      \begin{center}
443 <      \caption{Lennard-Jones parameters for Au-non-Metal
444 <        interactions in our simulations.}
445 <      
446 <      \begin{tabular}{ccc}
443 >      \caption{Non-bonded interaction parameters (including cross
444 >        interactions with Au atoms) for both force fields used in this
445 >        work.}      
446 >      \begin{tabular}{lllllll}
447          \hline\hline
448 <        Non-metal atom   & $\sigma$ & $\epsilon$ \\
449 <        (or pseudo-atom) & \AA      & kcal/mol  \\
448 >        & Site  & $\sigma_{ii}$ & $\epsilon_{ii}$ & $q_i$ &
449 >        $\sigma_{Au-i}$ & $\epsilon_{Au-i}$ \\
450 >        & & (\AA) & (kcal/mol) & ($e$) & (\AA) & (kcal/mol) \\
451          \hline
452 <        S    & 2.40   & 8.465   \\
453 <        CH3  & 3.54   & 0.2146  \\
454 <        CH2  & 3.54   & 0.1749  \\
455 <        CT3  & 3.365  & 0.1373  \\
456 <        CT2  & 3.365  & 0.1373  \\
457 <        CTT  & 3.365  & 0.1373  \\
458 <        HC   & 2.865  & 0.09256 \\
459 <        CHar & 3.4625 & 0.1680  \\
460 <        CRar & 3.555  & 0.1604  \\
461 <        CA   & 3.173  & 0.0640  \\
462 <        HA   & 2.746  & 0.0414  \\
452 >        United Atom (UA)
453 >        &CH3  & 3.75  & 0.1947  & -      & 3.54   & 0.2146  \\
454 >        &CH2  & 3.95  & 0.0914  & -      & 3.54   & 0.1749  \\
455 >        &CHar & 3.695 & 0.1003  & -      & 3.4625 & 0.1680  \\
456 >        &CRar & 3.88  & 0.04173 & -      & 3.555  & 0.1604  \\
457 >        \hline
458 >        All Atom (AA)
459 >        &CT3  & 3.50  & 0.066   & -0.18  & 3.365  & 0.1373  \\
460 >        &CT2  & 3.50  & 0.066   & -0.12  & 3.365  & 0.1373  \\
461 >        &CTT  & 3.50  & 0.066   & -0.065 & 3.365  & 0.1373  \\
462 >        &HC   & 2.50  & 0.030   &  0.06  & 2.865  & 0.09256 \\
463 >        &CA   & 3.55  & 0.070   & -0.115 & 3.173  & 0.0640  \\
464 >        &HA   & 2.42  & 0.030   &  0.115 & 2.746  & 0.0414  \\
465 >        \hline
466 >        Both UA and AA
467 >        & S   & 4.45  & 0.25    & -      & 2.40   & 8.465   \\
468          \hline\hline
469        \end{tabular}
470        \label{MnM}
# Line 444 | Line 485 | during equilibrating the liquid phase. Due to the stif
485   results.
486  
487   In some of our simulations, we allowed $L_x$ and $L_y$ to change
488 < during equilibrating the liquid phase. Due to the stiffness of the Au
489 < slab, $L_x$ and $L_y$ would not change noticeably after
490 < equilibration. Although $L_z$ could fluctuate $\sim$1\% after a system
491 < is fully equilibrated in the NPT ensemble, this fluctuation, as well
492 < as those comparably smaller to $L_x$ and $L_y$, would not be magnified
493 < on the calculated $G$'s, as shown in Table \ref{AuThiolHexaneUA}. This
494 < insensivity to $L_i$ fluctuations allows reliable measurement of $G$'s
495 < without the necessity of extremely cautious equilibration process.
488 > during equilibrating the liquid phase. Due to the stiffness of the
489 > crystalline Au structure, $L_x$ and $L_y$ would not change noticeably
490 > after equilibration. Although $L_z$ could fluctuate $\sim$1\% after a
491 > system is fully equilibrated in the NPT ensemble, this fluctuation, as
492 > well as those of $L_x$ and $L_y$ (which is significantly smaller),
493 > would not be magnified on the calculated $G$'s, as shown in Table
494 > \ref{AuThiolHexaneUA}. This insensivity to $L_i$ fluctuations allows
495 > reliable measurement of $G$'s without the necessity of extremely
496 > cautious equilibration process.
497  
498   As stated in our computational details, the spacing filled with
499   solvent molecules can be chosen within a range. This allows some
# Line 478 | Line 520 | $J_z$ is listed in Table \ref{AuThiolHexaneUA} and [RE
520   the thermal flux across the interface. For our simulations, we denote
521   $J_z$ to be positive when the physical thermal flux is from the liquid
522   to metal, and negative vice versa. The $G$'s measured under different
523 < $J_z$ is listed in Table \ref{AuThiolHexaneUA} and [REF]. These
524 < results do not suggest that $G$ is dependent on $J_z$ within this flux
525 < range. The linear response of flux to thermal gradient simplifies our
526 < investigations in that we can rely on $G$ measurement with only a
527 < couple $J_z$'s and do not need to test a large series of fluxes.
523 > $J_z$ is listed in Table \ref{AuThiolHexaneUA} and
524 > \ref{AuThiolToluene}. These results do not suggest that $G$ is
525 > dependent on $J_z$ within this flux range. The linear response of flux
526 > to thermal gradient simplifies our investigations in that we can rely
527 > on $G$ measurement with only a couple $J_z$'s and do not need to test
528 > a large series of fluxes.
529  
487 %ADD MORE TO TABLE
530   \begin{table*}
531    \begin{minipage}{\linewidth}
532      \begin{center}
533        \caption{Computed interfacial thermal conductivity ($G$ and
534          $G^\prime$) values for the 100\% covered Au-butanethiol/hexane
535          interfaces with UA model and different hexane molecule numbers
536 <        at different temperatures using a range of energy fluxes.}
536 >        at different temperatures using a range of energy
537 >        fluxes. Error estimates indicated in parenthesis.}
538        
539 <      \begin{tabular}{cccccccc}
539 >      \begin{tabular}{ccccccc}
540          \hline\hline
541 <        $\langle T\rangle$ & & $L_x$ & $L_y$ & $L_z$ & $J_z$ &
542 <        $G$ & $G^\prime$ \\
543 <        (K) & $N_{hexane}$ & \multicolumn{3}{c}{(\AA)} & (GW/m$^2$) &
541 >        $\langle T\rangle$ & $N_{hexane}$ & Fixed & $\rho_{hexane}$ &
542 >        $J_z$ & $G$ & $G^\prime$ \\
543 >        (K) & & $L_x$ \& $L_y$? & (g/cm$^3$) & (GW/m$^2$) &
544          \multicolumn{2}{c}{(MW/m$^2$/K)} \\
545          \hline
546 <        200 & 266 & 29.86 & 25.80 & 113.1 & -0.96 &
547 <        102()  & 80.0() \\
548 <            & 200 & 29.84 & 25.81 &  93.9 &  1.92 &
549 <        129()  & 87.3() \\
550 <            &     & 29.84 & 25.81 &  95.3 &  1.93 &
551 <        131()  & 77.5() \\
552 <            & 166 & 29.84 & 25.81 &  85.7 &  0.97 &
553 <        115()  & 69.3() \\
554 <            &     &       &       &       &  1.94 &
555 <        125()  & 87.1() \\
556 <        250 & 200 & 29.84 & 25.87 & 106.8 &  0.96 &
557 <        81.8() & 67.0() \\
558 <            & 166 & 29.87 & 25.84 &  94.8 &  0.98 &
559 <        79.0() & 62.9() \\
560 <            &     & 29.84 & 25.85 &  95.0 &  1.44 &
561 <        76.2() & 64.8() \\
546 >        200 & 266 & No  & 0.672 & -0.96 & 102(3)    & 80.0(0.8) \\
547 >            & 200 & Yes & 0.694 &  1.92 & 129(11)   & 87.3(0.3) \\
548 >            &     & Yes & 0.672 &  1.93 & 131(16)   & 78(13)    \\
549 >            &     & No  & 0.688 &  0.96 & 125(16)   & 90.2(15)  \\
550 >            &     &     &       &  1.91 & 139(10)   & 101(10)   \\
551 >            &     &     &       &  2.83 & 141(6)    & 89.9(9.8) \\
552 >            & 166 & Yes & 0.679 &  0.97 & 115(19)   & 69(18)    \\
553 >            &     &     &       &  1.94 & 125(9)    & 87.1(0.2) \\
554 >            &     & No  & 0.681 &  0.97 & 141(30)   & 78(22)    \\
555 >            &     &     &       &  1.92 & 138(4)    & 98.9(9.5) \\
556 >        \hline
557 >        250 & 200 & No  & 0.560 &  0.96 & 75(10)    & 61.8(7.3) \\
558 >            &     &     &       & -0.95 & 49.4(0.3) & 45.7(2.1) \\
559 >            & 166 & Yes & 0.570 &  0.98 & 79.0(3.5) & 62.9(3.0) \\
560 >            &     & No  & 0.569 &  0.97 & 80.3(0.6) & 67(11)    \\
561 >            &     &     &       &  1.44 & 76.2(5.0) & 64.8(3.8) \\
562 >            &     &     &       & -0.95 & 56.4(2.5) & 54.4(1.1) \\
563 >            &     &     &       & -1.85 & 47.8(1.1) & 53.5(1.5) \\
564          \hline\hline
565        \end{tabular}
566        \label{AuThiolHexaneUA}
# Line 531 | Line 576 | butanethiol as well.[MAY NEED FIGURE] And this reduced
576   temperature is higher than 250K. Additionally, the equilibrated liquid
577   hexane density under 250K becomes lower than experimental value. This
578   expanded liquid phase leads to lower contact between hexane and
579 < butanethiol as well.[MAY NEED FIGURE] And this reduced contact would
579 > butanethiol as well.[MAY NEED SLAB DENSITY FIGURE]
580 > And this reduced contact would
581   probably be accountable for a lower interfacial thermal conductance,
582   as shown in Table \ref{AuThiolHexaneUA}.
583  
# Line 546 | Line 592 | in that higher degree of contact could yield increased
592   important role in the thermal transport process across the interface
593   in that higher degree of contact could yield increased conductance.
594  
549 [ADD Lxyz AND ERROR ESTIMATE TO TABLE]
595   \begin{table*}
596    \begin{minipage}{\linewidth}
597      \begin{center}
598        \caption{Computed interfacial thermal conductivity ($G$ and
599          $G^\prime$) values for a 90\% coverage Au-butanethiol/toluene
600          interface at different temperatures using a range of energy
601 <        fluxes.}
601 >        fluxes. Error estimates indicated in parenthesis.}
602        
603 <      \begin{tabular}{cccc}
603 >      \begin{tabular}{ccccc}
604          \hline\hline
605 <        $\langle T\rangle$ & $J_z$ & $G$ & $G^\prime$ \\
606 <        (K) & (GW/m$^2$) & \multicolumn{2}{c}{(MW/m$^2$/K)} \\
605 >        $\langle T\rangle$ & $\rho_{toluene}$ & $J_z$ & $G$ & $G^\prime$ \\
606 >        (K) & (g/cm$^3$) & (GW/m$^2$) & \multicolumn{2}{c}{(MW/m$^2$/K)} \\
607          \hline
608 <        200 & -1.86 & 180() & 135() \\
609 <            &  2.15 & 204() & 113() \\
610 <            & -3.93 & 175() & 114() \\
611 <        300 & -1.91 & 143() & 125() \\
612 <            & -4.19 & 134() & 113() \\
608 >        200 & 0.933 &  2.15 & 204(12) & 113(12) \\
609 >            &       & -1.86 & 180(3)  & 135(21) \\
610 >            &       & -3.93 & 176(5)  & 113(12) \\
611 >        \hline
612 >        300 & 0.855 & -1.91 & 143(5)  & 125(2)  \\
613 >            &       & -4.19 & 135(9)  & 113(12) \\
614          \hline\hline
615        \end{tabular}
616        \label{AuThiolToluene}
# Line 596 | Line 642 | above. Our Au-butanethiol/toluene system did not see t
642  
643   However, when the surface is not completely covered by butanethiols,
644   the simulated system is more resistent to the reconstruction
645 < above. Our Au-butanethiol/toluene system did not see this phenomena
646 < even at $\langle T\rangle\sim$300K. The Au(111) surfaces have a 90\% coverage of
647 < butanethiols and have empty three-fold sites. These empty sites could
648 < help prevent surface reconstruction in that they provide other means
649 < of capping agent relaxation. It is observed that butanethiols can
650 < migrate to their neighbor empty sites during a simulation. Therefore,
651 < we were able to obtain $G$'s for these interfaces even at a relatively
652 < high temperature without being affected by surface reconstructions.
645 > above. Our Au-butanethiol/toluene system had the Au(111) surfaces 90\%
646 > covered by butanethiols, but did not see this above phenomena even at
647 > $\langle T\rangle\sim$300K. The empty three-fold sites not occupied by
648 > capping agents could help prevent surface reconstruction in that they
649 > provide other means of capping agent relaxation. It is observed that
650 > butanethiols can migrate to their neighbor empty sites during a
651 > simulation. Therefore, we were able to obtain $G$'s for these
652 > interfaces even at a relatively high temperature without being
653 > affected by surface reconstructions.
654  
655   \subsection{Influence of Capping Agent Coverage on $G$}
656   To investigate the influence of butanethiol coverage on interfacial
657   thermal conductance, a series of different coverage Au-butanethiol
658   surfaces is prepared and solvated with various organic
659   molecules. These systems are then equilibrated and their interfacial
660 < thermal conductivity are measured with our NIVS algorithm. Table
661 < \ref{tlnUhxnUhxnD} lists these results for direct comparison between
662 < different coverages of butanethiol. To study the isotope effect in
663 < interfacial thermal conductance, deuterated UA-hexane is included as
664 < well.
660 > thermal conductivity are measured with our NIVS algorithm. Figure
661 > \ref{coverage} demonstrates the trend of conductance change with
662 > respect to different coverages of butanethiol. To study the isotope
663 > effect in interfacial thermal conductance, deuterated UA-hexane is
664 > included as well.
665  
666   It turned out that with partial covered butanethiol on the Au(111)
667 < surface, the derivative definition for $G$ (Eq. \ref{derivativeG}) has
668 < difficulty to apply, due to the difficulty in locating the maximum of
669 < change of $\lambda$. Instead, the discrete definition
670 < (Eq. \ref{discreteG}) is easier to apply, as max($\Delta T$) can still
671 < be well-defined. Therefore, $G$'s (not $G^\prime$) are used for this
672 < section.
667 > surface, the derivative definition for $G^\prime$
668 > (Eq. \ref{derivativeG}) was difficult to apply, due to the difficulty
669 > in locating the maximum of change of $\lambda$. Instead, the discrete
670 > definition (Eq. \ref{discreteG}) is easier to apply, as the Gibbs
671 > deviding surface can still be well-defined. Therefore, $G$ (not
672 > $G^\prime$) was used for this section.
673  
674 < From Table \ref{tlnUhxnUhxnD}, one can see the significance of the
674 > From Figure \ref{coverage}, one can see the significance of the
675   presence of capping agents. Even when a fraction of the Au(111)
676   surface sites are covered with butanethiols, the conductivity would
677   see an enhancement by at least a factor of 3. This indicates the
678   important role cappping agent is playing for thermal transport
679 < phenomena on metal/organic solvent surfaces.
679 > phenomena on metal / organic solvent surfaces.
680  
681   Interestingly, as one could observe from our results, the maximum
682   conductance enhancement (largest $G$) happens while the surfaces are
# Line 648 | Line 695 | case, $G$ decrease could not be offset but instead acc
695   would not offset this effect. Eventually, when butanethiol coverage
696   continues to decrease, solvent-capping agent contact actually
697   decreases with the disappearing of butanethiol molecules. In this
698 < case, $G$ decrease could not be offset but instead accelerated.
698 > case, $G$ decrease could not be offset but instead accelerated. [NEED
699 > SNAPSHOT SHOWING THE PHENOMENA]
700  
701   A comparison of the results obtained from differenet organic solvents
702   can also provide useful information of the interfacial thermal
# Line 658 | Line 706 | difference for the results of $G$. [MAY NEED FIGURE]
706   studies, even though eliminating C-H vibration samplings, still have
707   C-C vibrational frequencies different from each other. However, these
708   differences in the infrared range do not seem to produce an observable
709 < difference for the results of $G$. [MAY NEED FIGURE]
709 > difference for the results of $G$. [MAY NEED SPECTRA FIGURE]
710  
711   Furthermore, results for rigid body toluene solvent, as well as other
712   UA-hexane solvents, are reasonable within the general experimental
# Line 667 | Line 715 | trend with those for Au-butanethiol/hexane in that $G$
715   such as Au-thiol/organic solvent.
716  
717   However, results for Au-butanethiol/toluene do not show an identical
718 < trend with those for Au-butanethiol/hexane in that $G$'s remain at
718 > trend with those for Au-butanethiol/hexane in that $G$ remains at
719   approximately the same magnitue when butanethiol coverage differs from
720   25\% to 75\%. This might be rooted in the molecule shape difference
721 < for plane-like toluene and chain-like {\it n}-hexane. Due to this
721 > for planar toluene and chain-like {\it n}-hexane. Due to this
722   difference, toluene molecules have more difficulty in occupying
723   relatively small gaps among capping agents when their coverage is not
724   too low. Therefore, the solvent-capping agent contact may keep
# Line 679 | Line 727 | can see a plateau of $G$ vs. butanethiol coverage in o
727   its effect to the process of interfacial thermal transport. Thus, one
728   can see a plateau of $G$ vs. butanethiol coverage in our results.
729  
730 < [NEED ERROR ESTIMATE, MAY ALSO PUT J HERE]
731 < \begin{table*}
732 <  \begin{minipage}{\linewidth}
733 <    \begin{center}
734 <      \caption{Computed interfacial thermal conductivity ($G$) values
735 <        for the Au-butanethiol/solvent interface with various UA
736 <        models and different capping agent coverages at $\langle
737 <        T\rangle\sim$200K using certain energy flux respectively.}
690 <      
691 <      \begin{tabular}{cccc}
692 <        \hline\hline
693 <        Thiol & \multicolumn{3}{c}{$G$(MW/m$^2$/K)} \\
694 <        coverage (\%) & hexane & hexane(D) & toluene \\
695 <        \hline
696 <        0.0   & 46.5() & 43.9() & 70.1() \\
697 <        25.0  & 151()  & 153()  & 249()  \\
698 <        50.0  & 172()  & 182()  & 214()  \\
699 <        75.0  & 242()  & 229()  & 244()  \\
700 <        88.9  & 178()  & -      & -      \\
701 <        100.0 & 137()  & 153()  & 187()  \\
702 <        \hline\hline
703 <      \end{tabular}
704 <      \label{tlnUhxnUhxnD}
705 <    \end{center}
706 <  \end{minipage}
707 < \end{table*}
730 > \begin{figure}
731 > \includegraphics[width=\linewidth]{coverage}
732 > \caption{Comparison of interfacial thermal conductivity ($G$) values
733 >  for the Au-butanethiol/solvent interface with various UA models and
734 >  different capping agent coverages at $\langle T\rangle\sim$200K
735 >  using certain energy flux respectively.}
736 > \label{coverage}
737 > \end{figure}
738  
739   \subsection{Influence of Chosen Molecule Model on $G$}
740   [MAY COMBINE W MECHANISM STUDY]
# Line 717 | Line 747 | these studies.
747   the previous section. Table \ref{modelTest} summarizes the results of
748   these studies.
749  
720 [MORE DATA; ERROR ESTIMATE]
750   \begin{table*}
751    \begin{minipage}{\linewidth}
752      \begin{center}
# Line 725 | Line 754 | these studies.
754        \caption{Computed interfacial thermal conductivity ($G$ and
755          $G^\prime$) values for interfaces using various models for
756          solvent and capping agent (or without capping agent) at
757 <        $\langle T\rangle\sim$200K.}
757 >        $\langle T\rangle\sim$200K. (D stands for deuterated solvent
758 >        or capping agent molecules; ``Avg.'' denotes results that are
759 >        averages of simulations under different $J_z$'s. Error
760 >        estimates indicated in parenthesis.)}
761        
762 <      \begin{tabular}{ccccc}
762 >      \begin{tabular}{llccc}
763          \hline\hline
764          Butanethiol model & Solvent & $J_z$ & $G$ & $G^\prime$ \\
765          (or bare surface) & model & (GW/m$^2$) &
766          \multicolumn{2}{c}{(MW/m$^2$/K)} \\
767          \hline
768 <        UA    & AA hexane  & 1.94 & 135()  & 129()  \\
769 <              &            & 2.86 & 126()  & 115()  \\
770 <              & AA toluene & 1.89 & 200()  & 149()  \\
771 <        AA    & UA hexane  & 1.94 & 116()  & 129()  \\
772 <              & AA hexane  & 3.76 & 451()  & 378()  \\
773 <              &            & 4.71 & 432()  & 334()  \\
774 <              & AA toluene & 3.79 & 487()  & 290()  \\
775 <        AA(D) & UA hexane  & 1.94 & 158()  & 172()  \\
776 <        bare  & AA hexane  & 0.96 & 31.0() & 29.4() \\
768 >        UA    & UA hexane    & Avg. & 131(9)    & 87(10)    \\
769 >              & UA hexane(D) & 1.95 & 153(5)    & 136(13)   \\
770 >              & AA hexane    & Avg. & 131(6)    & 122(10)   \\
771 >              & UA toluene   & 1.96 & 187(16)   & 151(11)   \\
772 >              & AA toluene   & 1.89 & 200(36)   & 149(53)   \\
773 >        \hline
774 >        AA    & UA hexane    & 1.94 & 116(9)    & 129(8)    \\
775 >              & AA hexane    & Avg. & 442(14)   & 356(31)   \\
776 >              & AA hexane(D) & 1.93 & 222(12)   & 234(54)   \\
777 >              & UA toluene   & 1.98 & 125(25)   & 97(60)    \\
778 >              & AA toluene   & 3.79 & 487(56)   & 290(42)   \\
779 >        \hline
780 >        AA(D) & UA hexane    & 1.94 & 158(25)   & 172(4)    \\
781 >              & AA hexane    & 1.92 & 243(29)   & 191(11)   \\
782 >              & AA toluene   & 1.93 & 364(36)   & 322(67)   \\
783 >        \hline
784 >        bare  & UA hexane    & Avg. & 46.5(3.2) & 49.4(4.5) \\
785 >              & UA hexane(D) & 0.98 & 43.9(4.6) & 43.0(2.0) \\
786 >              & AA hexane    & 0.96 & 31.0(1.4) & 29.4(1.3) \\
787 >              & UA toluene   & 1.99 & 70.1(1.3) & 65.8(0.5) \\
788          \hline\hline
789        \end{tabular}
790        \label{modelTest}
# Line 764 | Line 807 | the upper bond of experimental value range. This is pr
807   interfaces, using AA model for both butanethiol and hexane yields
808   substantially higher conductivity values than using UA model for at
809   least one component of the solvent and capping agent, which exceeds
810 < the upper bond of experimental value range. This is probably due to
811 < the classically treated C-H vibrations in the AA model, which should
812 < not be appreciably populated at normal temperatures. In comparison,
813 < once either the hexanes or the butanethiols are deuterated, one can
814 < see a significantly lower $G$ and $G^\prime$. In either of these
815 < cases, the C-H(D) vibrational overlap between the solvent and the
816 < capping agent is removed. [MAY NEED FIGURE] Conclusively, the
810 > the general range of experimental measurement results. This is
811 > probably due to the classically treated C-H vibrations in the AA
812 > model, which should not be appreciably populated at normal
813 > temperatures. In comparison, once either the hexanes or the
814 > butanethiols are deuterated, one can see a significantly lower $G$ and
815 > $G^\prime$. In either of these cases, the C-H(D) vibrational overlap
816 > between the solvent and the capping agent is removed.
817 > [MAY NEED SPECTRA FIGURE] Conclusively, the
818   improperly treated C-H vibration in the AA model produced
819   over-predicted results accordingly. Compared to the AA model, the UA
820   model yields more reasonable results with higher computational
# Line 778 | Line 822 | measurement results.
822  
823   However, for Au-butanethiol/toluene interfaces, having the AA
824   butanethiol deuterated did not yield a significant change in the
825 < measurement results.
826 < . , so extra degrees of freedom
827 < such as the C-H vibrations could enhance heat exchange between these
828 < two phases and result in a much higher conductivity.
825 > measurement results. Compared to the C-H vibrational overlap between
826 > hexane and butanethiol, both of which have alkyl chains, that overlap
827 > between toluene and butanethiol is not so significant and thus does
828 > not have as much contribution to the ``Intramolecular Vibration
829 > Redistribution''[CITE HASE]. Conversely, extra degrees of freedom such
830 > as the C-H vibrations could yield higher heat exchange rate between
831 > these two phases and result in a much higher conductivity.
832  
786
833   Although the QSC model for Au is known to predict an overly low value
834 < for bulk metal gold conductivity[CITE NIVSRNEMD], our computational
834 > for bulk metal gold conductivity\cite{kuang:164101}, our computational
835   results for $G$ and $G^\prime$ do not seem to be affected by this
836 < drawback of the model for metal. Instead, the modeling of interfacial
837 < thermal transport behavior relies mainly on an accurate description of
838 < the interactions between components occupying the interfaces.
836 > drawback of the model for metal. Instead, our results suggest that the
837 > modeling of interfacial thermal transport behavior relies mainly on
838 > the accuracy of the interaction descriptions between components
839 > occupying the interfaces.
840  
841   \subsection{Mechanism of Interfacial Thermal Conductance Enhancement
842    by Capping Agent}
843 < %OR\subsection{Vibrational spectrum study on conductance mechanism}
843 > [OR: Vibrational Spectrum Study on Conductance Mechanism]
844  
845   [MAY INTRODUCE PROTOCOL IN METHODOLOGY/COMPUTATIONAL DETAIL, EQN'S]
846  
# Line 805 | Line 852 | power spectrum via a Fourier transform.
852   the velocity auto-correlation functions, which is used to construct a
853   power spectrum via a Fourier transform.
854  
855 < The gold surfaces covered by
856 < butanethiol molecules, compared to bare gold surfaces, exhibit an
857 < additional peak observed at a frequency of $\sim$170cm$^{-1}$, which
858 < is attributed to the vibration of the S-Au bond. This vibration
859 < enables efficient thermal transport from surface Au atoms to the
860 < capping agents. Simultaneously, as shown in the lower panel of
861 < Fig. \ref{vibration}, the large overlap of the vibration spectra of
862 < butanethiol and hexane in the all-atom model, including the C-H
863 < vibration, also suggests high thermal exchange efficiency. The
864 < combination of these two effects produces the drastic interfacial
865 < thermal conductance enhancement in the all-atom model.
855 > [MAY RELATE TO HASE'S]
856 > The gold surfaces covered by butanethiol molecules, compared to bare
857 > gold surfaces, exhibit an additional peak observed at the frequency of
858 > $\sim$170cm$^{-1}$, which is attributed to the S-Au bonding
859 > vibration. This vibration enables efficient thermal transport from
860 > surface Au layer to the capping agents.
861 > [MAY PUT IN OTHER SECTION] Simultaneously, as shown in
862 > the lower panel of Fig. \ref{vibration}, the large overlap of the
863 > vibration spectra of butanethiol and hexane in the All-Atom model,
864 > including the C-H vibration, also suggests high thermal exchange
865 > efficiency. The combination of these two effects produces the drastic
866 > interfacial thermal conductance enhancement in the All-Atom model.
867  
868 < [MAY NEED TO CONVERT TO JPEG]
868 > [NEED SEPARATE FIGURE. MAY NEED TO CONVERT TO JPEG]
869   \begin{figure}
870   \includegraphics[width=\linewidth]{vibration}
871   \caption{Vibrational spectra obtained for gold in different
872 <  environments (upper panel) and for Au/thiol/hexane simulation in
825 <  all-atom model (lower panel).}
872 >  environments.}
873   \label{vibration}
874   \end{figure}
875  
876 < [COMPARISON OF TWO G'S; AU SLAB WIDTHS; ETC]
876 > [MAY ADD COMPARISON OF G AND G', AU SLAB WIDTHS, ETC]
877   % The results show that the two definitions used for $G$ yield
878   % comparable values, though $G^\prime$ tends to be smaller.
879  
# Line 838 | Line 885 | gold/liquid interfaces. The acoustic impedance mismatc
885   corresponding thermal gradient and to obtain interfacial thermal
886   conductivities. Our simulations have seen significant conductance
887   enhancement with the presence of capping agent, compared to the bare
888 < gold/liquid interfaces. The acoustic impedance mismatch between the
888 > gold / liquid interfaces. The acoustic impedance mismatch between the
889   metal and the liquid phase is effectively eliminated by proper capping
890   agent. Furthermore, the coverage precentage of the capping agent plays
891   an important role in the interfacial thermal transport process.

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