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# Line 45 | Line 45 | We have developed a Non-Isotropic Velocity Scaling alg
45  
46   \begin{abstract}
47  
48 < We have developed a Non-Isotropic Velocity Scaling algorithm for
49 < setting up and maintaining stable thermal gradients in non-equilibrium
50 < molecular dynamics simulations. This approach effectively imposes
51 < unphysical thermal flux even between particles of different
52 < identities, conserves linear momentum and kinetic energy, and
53 < minimally perturbs the velocity profile of a system when compared with
54 < previous RNEMD methods. We have used this method to simulate thermal
55 < conductance at metal / organic solvent interfaces both with and
56 < without the presence of thiol-based capping agents.  We obtained
57 < values comparable with experimental values, and observed significant
58 < conductance enhancement with the presence of capping agents. Computed
59 < power spectra indicate the acoustic impedance mismatch between metal
60 < and liquid phase is greatly reduced by the capping agents and thus
61 < leads to higher interfacial thermal transfer efficiency.
48 > With the Non-Isotropic Velocity Scaling algorithm (NIVS) we have
49 > developed, an unphysical thermal flux can be effectively set up even
50 > for non-homogeneous systems like interfaces in non-equilibrium
51 > molecular dynamics simulations. In this work, this algorithm is
52 > applied for simulating thermal conductance at metal / organic solvent
53 > interfaces with various coverages of butanethiol capping
54 > agents. Different solvents and force field models were tested. Our
55 > results suggest that the United-Atom models are able to provide an
56 > estimate of the interfacial thermal conductivity comparable to
57 > experiments in our simulations with satisfactory computational
58 > efficiency. From our results, the acoustic impedance mismatch between
59 > metal and liquid phase is effectively reduced by the capping
60 > agents, and thus leads to interfacial thermal conductance
61 > enhancement. Furthermore, this effect is closely related to the
62 > capping agent coverage on the metal surfaces and the type of solvent
63 > molecules, and is affected by the models used in the simulations.
64  
65   \end{abstract}
66  
# Line 211 | Line 213 | obtain the 1st and 2nd derivatives of the temperature
213   \label{gradT}
214   \end{figure}
215  
216 + [MAY INCLUDE POWER SPECTRUM PROTOCOL]
217 +
218   \section{Computational Details}
219 < \subsection{System Geometry}
219 > \subsection{Simulation Protocol}
220   In our simulations, Au is used to construct a metal slab with bare
221   (111) surface perpendicular to the $z$-axis. Different slab thickness
222   (layer numbers of Au) are simulated. This metal slab is first
# Line 240 | Line 244 | vibrational frequencies and chain-like shape ({\it n}-
244   interactions do not disrupt the simulations. Two solvents are
245   investigated, one which has little vibrational overlap with the
246   alkanethiol and plane-like shape (toluene), and one which has similar
247 < vibrational frequencies and chain-like shape ({\it n}-hexane). The
248 < spacing filled by solvent molecules, i.e. the gap between periodically
245 < repeated Au-butanethiol surfaces should be carefully chosen so that it
246 < would not be too short to affect the liquid phase structure, nor too
247 < long, leading to over cooling (freezing) or heating (boiling) when a
248 < thermal flux is applied. In our simulations, this spacing is usually
249 < $35 \sim 60$\AA.
247 > vibrational frequencies and chain-like shape ({\it n}-hexane). [MAY
248 > EXPLAIN WHY WE CHOOSE THEM]
249  
250 + The spacing filled by solvent molecules, i.e. the gap between
251 + periodically repeated Au-butanethiol surfaces should be carefully
252 + chosen. A very long length scale for the thermal gradient axis ($z$)
253 + may cause excessively hot or cold temperatures in the middle of the
254 + solvent region and lead to undesired phenomena such as solvent boiling
255 + or freezing when a thermal flux is applied. Conversely, too few
256 + solvent molecules would change the normal behavior of the liquid
257 + phase. Therefore, our $N_{solvent}$ values were chosen to ensure that
258 + these extreme cases did not happen to our simulations. And the
259 + corresponding spacing is usually $35 \sim 60$\AA.
260 +
261   The initial configurations generated by Packmol are further
262   equilibrated with the $x$ and $y$ dimensions fixed, only allowing
263   length scale change in $z$ dimension. This is to ensure that the
# Line 287 | Line 297 | For both solvent molecules, straight chain {\it n}-hex
297   reparametrized for accurate surface energies compared to the
298   Sutton-Chen potentials\cite{Chen90}.
299  
300 + Figure [REF] demonstrates how we name our pseudo-atoms of the
301 + molecules in our simulations.
302 + [FIGURE FOR MOLECULE NOMENCLATURE]
303 +
304   For both solvent molecules, straight chain {\it n}-hexane and aromatic
305   toluene, United-Atom (UA) and All-Atom (AA) models are used
306   respectively. The TraPPE-UA
# Line 300 | Line 314 | simulations should be much lower than the liquid boili
314   to a system, the temperature of ``hot'' area in the liquid phase would be
315   significantly higher than the average, to prevent over heating and
316   boiling of the liquid phase, the average temperature in our
317 < simulations should be much lower than the liquid boiling point. [NEED MORE DISCUSSION]
317 > simulations should be much lower than the liquid boiling point. [MORE DISCUSSION]
318   For UA-toluene model, rigid body constraints are applied, so that the
319 < benzene ring and the methyl-C(aromatic) bond are kept rigid. This
320 < would save computational time.[MORE DETAILS NEEDED]
319 > benzene ring and the methyl-CRar bond are kept rigid. This would save
320 > computational time.[MORE DETAILS]
321  
322   Besides the TraPPE-UA models, AA models for both organic solvents are
323 < included in our studies as well. For hexane, the OPLS
324 < all-atom\cite{OPLSAA} force field is used. [MORE DETAILS]
323 > included in our studies as well. For hexane, the OPLS-AA\cite{OPLSAA}
324 > force field is used. [MORE DETAILS]
325   For toluene, the United Force Field developed by Rapp\'{e} {\it et
326    al.}\cite{doi:10.1021/ja00051a040} is adopted.[MORE DETAILS]
327  
328   The capping agent in our simulations, the butanethiol molecules can
329   either use UA or AA model. The TraPPE-UA force fields includes
330 < parameters for thiol molecules\cite{TraPPE-UA.thiols} and are used in
331 < our simulations corresponding to our TraPPE-UA models for solvent.
332 < and All-Atom models [NEED CITATIONS]
333 < However, the model choice (UA or AA) of capping agent can be different
334 < from the solvent. Regardless of model choice, the force field
335 < parameters for interactions between capping agent and solvent can be
336 < derived using Lorentz-Berthelot Mixing Rule.
337 <
338 < To describe the interactions between metal Au and non-metal capping
339 < agent and solvent, we refer to Vlugt\cite{vlugt:cpc2007154} and derive
340 < other interactions which are not yet finely parametrized. [can add
327 < hautman and klein's paper here and more discussion; need to put
328 < aromatic-metal interaction approximation here]\cite{doi:10.1021/jp034405s}
329 <
330 < [TABULATED FORCE FIELD PARAMETERS NEEDED]
331 <
332 <
333 < [SURFACE RECONSTRUCTION PREVENTS SIMULATION TEMP TO GO HIGHER]
330 > parameters for thiol molecules\cite{TraPPE-UA.thiols} and are used for
331 > UA butanethiol model in our simulations. The OPLS-AA also provides
332 > parameters for alkyl thiols. However, alkyl thiols adsorbed on Au(111)
333 > surfaces do not have the hydrogen atom bonded to sulfur. To adapt this
334 > change and derive suitable parameters for butanethiol adsorbed on
335 > Au(111) surfaces, we adopt the S parameters from [CITATION CF VLUGT]
336 > and modify parameters for its neighbor C atom for charge balance in
337 > the molecule. Note that the model choice (UA or AA) of capping agent
338 > can be different from the solvent. Regardless of model choice, the
339 > force field parameters for interactions between capping agent and
340 > solvent can be derived using Lorentz-Berthelot Mixing Rule:
341  
342  
343 < \section{Results}
344 < [REARRANGEMENT NEEDED]
345 < \subsection{Toluene Solvent}
343 > To describe the interactions between metal Au and non-metal capping
344 > agent and solvent particles, we refer to an adsorption study of alkyl
345 > thiols on gold surfaces by Vlugt {\it et
346 >  al.}\cite{vlugt:cpc2007154} They fitted an effective Lennard-Jones
347 > form of potential parameters for the interaction between Au and
348 > pseudo-atoms CH$_x$ and S based on a well-established and widely-used
349 > effective potential of Hautman and Klein[CITATION] for the Au(111)
350 > surface. As our simulations require the gold lattice slab to be
351 > non-rigid so that it could accommodate kinetic energy for thermal
352 > transport study purpose, the pair-wise form of potentials is
353 > preferred.
354  
355 < The results (Table \ref{AuThiolToluene}) show a
356 < significant conductance enhancement compared to the gold/water
357 < interface without capping agent and agree with available experimental
343 < data. This indicates that the metal-metal potential, though not
344 < predicting an accurate bulk metal thermal conductivity, does not
345 < greatly interfere with the simulation of the thermal conductance
346 < behavior across a non-metal interface. The solvent model is not
347 < particularly volatile, so the simulation cell does not expand
348 < significantly under higher temperature. We did not observe a
349 < significant conductance decrease when the temperature was increased to
350 < 300K. The results show that the two definitions used for $G$ yield
351 < comparable values, though $G^\prime$ tends to be smaller.
355 > Besides, the potentials developed from {\it ab initio} calculations by
356 > Leng {\it et al.}\cite{doi:10.1021/jp034405s} are adopted for the
357 > interactions between Au and aromatic C/H atoms in toluene.[MORE DETAILS]
358  
359 + However, the Lennard-Jones parameters between Au and other types of
360 + particles in our simulations are not yet well-established. For these
361 + interactions, we attempt to derive their parameters using the Mixing
362 + Rule. To do this, the ``Metal-non-Metal'' (MnM) interaction parameters
363 + for Au is first extracted from the Au-CH$_x$ parameters by applying
364 + the Mixing Rule reversely. Table \ref{MnM} summarizes these ``MnM''
365 + parameters in our simulations.
366 +
367   \begin{table*}
368    \begin{minipage}{\linewidth}
369      \begin{center}
370 <      \caption{Computed interfacial thermal conductivity ($G$ and
371 <        $G^\prime$) values for the Au/butanethiol/toluene interface at
358 <        different temperatures using a range of energy fluxes.}
370 >      \caption{Lennard-Jones parameters for Au-non-Metal
371 >        interactions in our simulations.}
372        
373 <      \begin{tabular}{cccc}
373 >      \begin{tabular}{ccc}
374          \hline\hline
375 <        $\langle T\rangle$ & $J_z$ & $G$ & $G^\prime$ \\
376 <        (K) & (GW/m$^2$) & \multicolumn{2}{c}{(MW/m$^2$/K)} \\
375 >        Non-metal atom   & $\sigma$ & $\epsilon$ \\
376 >        (or pseudo-atom) & \AA      & kcal/mol  \\
377          \hline
378 <        200 & 1.86 & 180 & 135 \\
379 <            & 2.15 & 204 & 113 \\
380 <            & 3.93 & 175 & 114 \\
381 <        300 & 1.91 & 143 & 125 \\
382 <            & 4.19 & 134 & 113 \\
378 >        S    & 2.40   & 8.465   \\
379 >        CH3  & 3.54   & 0.2146  \\
380 >        CH2  & 3.54   & 0.1749  \\
381 >        CT3  & 3.365  & 0.1373  \\
382 >        CT2  & 3.365  & 0.1373  \\
383 >        CTT  & 3.365  & 0.1373  \\
384 >        HC   & 2.865  & 0.09256 \\
385 >        CHar & 3.4625 & 0.1680  \\
386 >        CRar & 3.555  & 0.1604  \\
387 >        CA   & 3.173  & 0.0640  \\
388 >        HA   & 2.746  & 0.0414  \\
389          \hline\hline
390        \end{tabular}
391 <      \label{AuThiolToluene}
391 >      \label{MnM}
392      \end{center}
393    \end{minipage}
394   \end{table*}
395  
377 \subsection{Hexane Solvent}
396  
397 < Using the united-atom model, different coverages of capping agent,
398 < temperatures of simulations and numbers of solvent molecules were all
399 < investigated and Table \ref{AuThiolHexaneUA} shows the results of
400 < these computations. The number of hexane molecules in our simulations
401 < does not affect the calculations significantly. However, a very long
402 < length scale for the thermal gradient axis ($z$) may cause excessively
403 < hot or cold temperatures in the middle of the solvent region and lead
404 < to undesired phenomena such as solvent boiling or freezing, while too
405 < few solvent molecules would change the normal behavior of the liquid
406 < phase. Our $N_{hexane}$ values were chosen to ensure that these
389 < extreme cases did not happen to our simulations.
397 > \section{Results and Discussions}
398 > [MAY HAVE A BRIEF SUMMARY]
399 > \subsection{How Simulation Parameters Affects $G$}
400 > [MAY NOT PUT AT FIRST]
401 > We have varied our protocol or other parameters of the simulations in
402 > order to investigate how these factors would affect the measurement of
403 > $G$'s. It turned out that while some of these parameters would not
404 > affect the results substantially, some other changes to the
405 > simulations would have a significant impact on the measurement
406 > results.
407  
408 < Table \ref{AuThiolHexaneUA} enables direct comparison between
409 < different coverages of capping agent, when other system parameters are
410 < held constant. With high coverage of butanethiol on the gold surface,
411 < the interfacial thermal conductance is enhanced
412 < significantly. Interestingly, a slightly lower butanethiol coverage
413 < leads to a moderately higher conductivity. This is probably due to
414 < more solvent/capping agent contact when butanethiol molecules are
415 < not densely packed, which enhances the interactions between the two
416 < phases and lowers the thermal transfer barrier of this interface.
400 < % [COMPARE TO AU/WATER IN PAPER]
408 > In some of our simulations, we allowed $L_x$ and $L_y$ to change
409 > during equilibrating the liquid phase. Due to the stiffness of the Au
410 > slab, $L_x$ and $L_y$ would not change noticeably after
411 > equilibration. Although $L_z$ could fluctuate $\sim$1\% after a system
412 > is fully equilibrated in the NPT ensemble, this fluctuation, as well
413 > as those comparably smaller to $L_x$ and $L_y$, would not be magnified
414 > on the calculated $G$'s, as shown in Table \ref{AuThiolHexaneUA}. This
415 > insensivity to $L_i$ fluctuations allows reliable measurement of $G$'s
416 > without the necessity of extremely cautious equilibration process.
417  
418 < It is also noted that the overall simulation temperature is another
419 < factor that affects the interfacial thermal conductance. One
420 < possibility of this effect may be rooted in the decrease in density of
421 < the liquid phase. We observed that when the average temperature
422 < increases from 200K to 250K, the bulk hexane density becomes lower
423 < than experimental value, as the system is equilibrated under NPT
424 < ensemble. This leads to lower contact between solvent and capping
425 < agent, and thus lower conductivity.
418 > As stated in our computational details, the spacing filled with
419 > solvent molecules can be chosen within a range. This allows some
420 > change of solvent molecule numbers for the same Au-butanethiol
421 > surfaces. We did this study on our Au-butanethiol/hexane
422 > simulations. Nevertheless, the results obtained from systems of
423 > different $N_{hexane}$ did not indicate that the measurement of $G$ is
424 > susceptible to this parameter. For computational efficiency concern,
425 > smaller system size would be preferable, given that the liquid phase
426 > structure is not affected.
427  
428 < Conductivity values are more difficult to obtain under higher
429 < temperatures. This is because the Au surface tends to undergo
430 < reconstructions in relatively high temperatures. Surface Au atoms can
431 < migrate outward to reach higher Au-S contact; and capping agent
432 < molecules can be embedded into the surface Au layer due to the same
433 < driving force. This phenomenon agrees with experimental
434 < results\cite{doi:10.1021/j100035a033,doi:10.1021/la026493y}. A surface
435 < fully covered in capping agent is more susceptible to reconstruction,
436 < possibly because fully coverage prevents other means of capping agent
437 < relaxation, such as migration to an empty neighbor three-fold site.
428 > Our NIVS algorithm allows change of unphysical thermal flux both in
429 > direction and in quantity. This feature extends our investigation of
430 > interfacial thermal conductance. However, the magnitude of this
431 > thermal flux is not arbitary if one aims to obtain a stable and
432 > reliable thermal gradient. A temperature profile would be
433 > substantially affected by noise when $|J_z|$ has a much too low
434 > magnitude; while an excessively large $|J_z|$ that overwhelms the
435 > conductance capacity of the interface would prevent a thermal gradient
436 > to reach a stablized steady state. NIVS has the advantage of allowing
437 > $J$ to vary in a wide range such that the optimal flux range for $G$
438 > measurement can generally be simulated by the algorithm. Within the
439 > optimal range, we were able to study how $G$ would change according to
440 > the thermal flux across the interface. For our simulations, we denote
441 > $J_z$ to be positive when the physical thermal flux is from the liquid
442 > to metal, and negative vice versa. The $G$'s measured under different
443 > $J_z$ is listed in Table \ref{AuThiolHexaneUA} and [REF]. These
444 > results do not suggest that $G$ is dependent on $J_z$ within this flux
445 > range. The linear response of flux to thermal gradient simplifies our
446 > investigations in that we can rely on $G$ measurement with only a
447 > couple $J_z$'s and do not need to test a large series of fluxes.
448  
449 < %MAY ADD MORE DATA TO TABLE
449 > %ADD MORE TO TABLE
450   \begin{table*}
451    \begin{minipage}{\linewidth}
452      \begin{center}
453        \caption{Computed interfacial thermal conductivity ($G$ and
454 <        $G^\prime$) values for the Au/butanethiol/hexane interface
455 <        with united-atom model and different capping agent coverage
456 <        and solvent molecule numbers at different temperatures using a
430 <        range of energy fluxes.}
454 >        $G^\prime$) values for the 100\% covered Au-butanethiol/hexane
455 >        interfaces with UA model and different hexane molecule numbers
456 >        at different temperatures using a range of energy fluxes.}
457        
458 <      \begin{tabular}{cccccc}
458 >      \begin{tabular}{cccccccc}
459          \hline\hline
460 <        Thiol & $\langle T\rangle$ & & $J_z$ & $G$ & $G^\prime$ \\
461 <        coverage (\%) & (K) & $N_{hexane}$ & (GW/m$^2$) &
460 >        $\langle T\rangle$ & & $L_x$ & $L_y$ & $L_z$ & $J_z$ &
461 >        $G$ & $G^\prime$ \\
462 >        (K) & $N_{hexane}$ & \multicolumn{3}{c}{(\AA)} & (GW/m$^2$) &
463          \multicolumn{2}{c}{(MW/m$^2$/K)} \\
464          \hline
465 <        0.0   & 200 & 200 & 0.96 & 43.3 & 42.7 \\
466 <              &     &     & 1.91 & 45.7 & 42.9 \\
467 <              &     & 166 & 0.96 & 43.1 & 53.4 \\
468 <        88.9  & 200 & 166 & 1.94 & 172  & 108  \\
469 <        100.0 & 250 & 200 & 0.96 & 81.8 & 67.0 \\
470 <              &     & 166 & 0.98 & 79.0 & 62.9 \\
471 <              &     &     & 1.44 & 76.2 & 64.8 \\
472 <              & 200 & 200 & 1.92 & 129  & 87.3 \\
473 <              &     &     & 1.93 & 131  & 77.5 \\
474 <              &     & 166 & 0.97 & 115  & 69.3 \\
475 <              &     &     & 1.94 & 125  & 87.1 \\
465 >        200 & 266 & 29.86 & 25.80 & 113.1 & -0.96 &
466 >        102()  & 80.0() \\
467 >            & 200 & 29.84 & 25.81 &  93.9 &  1.92 &
468 >        129()  & 87.3() \\
469 >            &     & 29.84 & 25.81 &  95.3 &  1.93 &
470 >        131()  & 77.5() \\
471 >            & 166 & 29.84 & 25.81 &  85.7 &  0.97 &
472 >        115()  & 69.3() \\
473 >            &     &       &       &       &  1.94 &
474 >        125()  & 87.1() \\
475 >        250 & 200 & 29.84 & 25.87 & 106.8 &  0.96 &
476 >        81.8() & 67.0() \\
477 >            & 166 & 29.87 & 25.84 &  94.8 &  0.98 &
478 >        79.0() & 62.9() \\
479 >            &     & 29.84 & 25.85 &  95.0 &  1.44 &
480 >        76.2() & 64.8() \\
481          \hline\hline
482        \end{tabular}
483        \label{AuThiolHexaneUA}
# Line 453 | Line 485 | For the all-atom model, the liquid hexane phase was no
485    \end{minipage}
486   \end{table*}
487  
488 < For the all-atom model, the liquid hexane phase was not stable under NPT
489 < conditions. Therefore, the simulation length scale parameters are
490 < adopted from previous equilibration results of the united-atom model
491 < at 200K. Table \ref{AuThiolHexaneAA} shows the results of these
492 < simulations. The conductivity values calculated with full capping
493 < agent coverage are substantially larger than observed in the
494 < united-atom model, and is even higher than predicted by
495 < experiments. It is possible that our parameters for metal-non-metal
496 < particle interactions lead to an overestimate of the interfacial
497 < thermal conductivity, although the active C-H vibrations in the
498 < all-atom model (which should not be appreciably populated at normal
467 < temperatures) could also account for this high conductivity. The major
468 < thermal transfer barrier of Au/butanethiol/hexane interface is between
469 < the liquid phase and the capping agent, so extra degrees of freedom
470 < such as the C-H vibrations could enhance heat exchange between these
471 < two phases and result in a much higher conductivity.
488 > Furthermore, we also attempted to increase system average temperatures
489 > to above 200K. These simulations are first equilibrated in the NPT
490 > ensemble under normal pressure. As stated above, the TraPPE-UA model
491 > for hexane tends to predict a lower boiling point. In our simulations,
492 > hexane had diffculty to remain in liquid phase when NPT equilibration
493 > temperature is higher than 250K. Additionally, the equilibrated liquid
494 > hexane density under 250K becomes lower than experimental value. This
495 > expanded liquid phase leads to lower contact between hexane and
496 > butanethiol as well.[MAY NEED FIGURE] And this reduced contact would
497 > probably be accountable for a lower interfacial thermal conductance,
498 > as shown in Table \ref{AuThiolHexaneUA}.
499  
500 + A similar study for TraPPE-UA toluene agrees with the above result as
501 + well. Having a higher boiling point, toluene tends to remain liquid in
502 + our simulations even equilibrated under 300K in NPT
503 + ensembles. Furthermore, the expansion of the toluene liquid phase is
504 + not as significant as that of the hexane. This prevents severe
505 + decrease of liquid-capping agent contact and the results (Table
506 + \ref{AuThiolToluene}) show only a slightly decreased interface
507 + conductance. Therefore, solvent-capping agent contact should play an
508 + important role in the thermal transport process across the interface
509 + in that higher degree of contact could yield increased conductance.
510 +
511 + [ADD Lxyz AND ERROR ESTIMATE TO TABLE]
512   \begin{table*}
513    \begin{minipage}{\linewidth}
514      \begin{center}
476      
515        \caption{Computed interfacial thermal conductivity ($G$ and
516 <        $G^\prime$) values for the Au/butanethiol/hexane interface
517 <        with all-atom model and different capping agent coverage at
518 <        200K using a range of energy fluxes.}
516 >        $G^\prime$) values for a 90\% coverage Au-butanethiol/toluene
517 >        interface at different temperatures using a range of energy
518 >        fluxes.}
519        
520        \begin{tabular}{cccc}
521          \hline\hline
522 <        Thiol & $J_z$ & $G$ & $G^\prime$ \\
523 <        coverage (\%) & (GW/m$^2$) & \multicolumn{2}{c}{(MW/m$^2$/K)} \\
522 >        $\langle T\rangle$ & $J_z$ & $G$ & $G^\prime$ \\
523 >        (K) & (GW/m$^2$) & \multicolumn{2}{c}{(MW/m$^2$/K)} \\
524          \hline
525 <        0.0   & 0.95 & 28.5 & 27.2 \\
526 <              & 1.88 & 30.3 & 28.9 \\
527 <        100.0 & 2.87 & 551  & 294  \\
528 <              & 3.81 & 494  & 193  \\
525 >        200 & -1.86 & 180() & 135() \\
526 >            &  2.15 & 204() & 113() \\
527 >            & -3.93 & 175() & 114() \\
528 >        300 & -1.91 & 143() & 125() \\
529 >            & -4.19 & 134() & 113() \\
530          \hline\hline
531        \end{tabular}
532 <      \label{AuThiolHexaneAA}
532 >      \label{AuThiolToluene}
533      \end{center}
534    \end{minipage}
535   \end{table*}
536  
537 < %subsubsection{Vibrational spectrum study on conductance mechanism}
537 > Besides lower interfacial thermal conductance, surfaces in relatively
538 > high temperatures are susceptible to reconstructions, when
539 > butanethiols have a full coverage on the Au(111) surface. These
540 > reconstructions include surface Au atoms migrated outward to the S
541 > atom layer, and butanethiol molecules embedded into the original
542 > surface Au layer. The driving force for this behavior is the strong
543 > Au-S interactions in our simulations. And these reconstructions lead
544 > to higher ratio of Au-S attraction and thus is energetically
545 > favorable. Furthermore, this phenomenon agrees with experimental
546 > results\cite{doi:10.1021/j100035a033,doi:10.1021/la026493y}. Vlugt
547 > {\it et al.} had kept their Au(111) slab rigid so that their
548 > simulations can reach 300K without surface reconstructions. Without
549 > this practice, simulating 100\% thiol covered interfaces under higher
550 > temperatures could hardly avoid surface reconstructions. However, our
551 > measurement is based on assuming homogeneity on $x$ and $y$ dimensions
552 > so that measurement of $T$ at particular $z$ would be an effective
553 > average of the particles of the same type. Since surface
554 > reconstructions could eliminate the original $x$ and $y$ dimensional
555 > homogeneity, measurement of $G$ is more difficult to conduct under
556 > higher temperatures. Therefore, most of our measurements are
557 > undertaken at $\langle T\rangle\sim$200K.
558 >
559 > However, when the surface is not completely covered by butanethiols,
560 > the simulated system is more resistent to the reconstruction
561 > above. Our Au-butanethiol/toluene system did not see this phenomena
562 > even at $<T>\sim$300K. The Au(111) surfaces have a 90\% coverage of
563 > butanethiols and have empty three-fold sites. These empty sites could
564 > help prevent surface reconstruction in that they provide other means
565 > of capping agent relaxation. It is observed that butanethiols can
566 > migrate to their neighbor empty sites during a simulation. Therefore,
567 > we were able to obtain $G$'s for these interfaces even at a relatively
568 > high temperature without being affected by surface reconstructions.
569 >
570 > \subsection{Influence of Capping Agent Coverage on $G$}
571 > To investigate the influence of butanethiol coverage on interfacial
572 > thermal conductance, a series of different coverage Au-butanethiol
573 > surfaces is prepared and solvated with various organic
574 > molecules. These systems are then equilibrated and their interfacial
575 > thermal conductivity are measured with our NIVS algorithm. Table
576 > \ref{tlnUhxnUhxnD} lists these results for direct comparison between
577 > different coverages of butanethiol. To study the isotope effect in
578 > interfacial thermal conductance, deuterated UA-hexane is included as
579 > well.
580 >
581 > It turned out that with partial covered butanethiol on the Au(111)
582 > surface, the derivative definition for $G$ (Eq. \ref{derivativeG}) has
583 > difficulty to apply, due to the difficulty in locating the maximum of
584 > change of $\lambda$. Instead, the discrete definition
585 > (Eq. \ref{discreteG}) is easier to apply, as max($\Delta T$) can still
586 > be well-defined. Therefore, $G$'s (not $G^\prime$) are used for this
587 > section.
588 >
589 > From Table \ref{tlnUhxnUhxnD}, one can see the significance of the
590 > presence of capping agents. Even when a fraction of the Au(111)
591 > surface sites are covered with butanethiols, the conductivity would
592 > see an enhancement by at least a factor of 3. This indicates the
593 > important role cappping agent is playing for thermal transport
594 > phenomena on metal/organic solvent surfaces.
595 >
596 > Interestingly, as one could observe from our results, the maximum
597 > conductance enhancement (largest $G$) happens while the surfaces are
598 > about 75\% covered with butanethiols. This again indicates that
599 > solvent-capping agent contact has an important role of the thermal
600 > transport process. Slightly lower butanethiol coverage allows small
601 > gaps between butanethiols to form. And these gaps could be filled with
602 > solvent molecules, which acts like ``heat conductors'' on the
603 > surface. The higher degree of interaction between these solvent
604 > molecules and capping agents increases the enhancement effect and thus
605 > produces a higher $G$ than densely packed butanethiol arrays. However,
606 > once this maximum conductance enhancement is reached, $G$ decreases
607 > when butanethiol coverage continues to decrease. Each capping agent
608 > molecule reaches its maximum capacity for thermal
609 > conductance. Therefore, even higher solvent-capping agent contact
610 > would not offset this effect. Eventually, when butanethiol coverage
611 > continues to decrease, solvent-capping agent contact actually
612 > decreases with the disappearing of butanethiol molecules. In this
613 > case, $G$ decrease could not be offset but instead accelerated.
614 >
615 > A comparison of the results obtained from differenet organic solvents
616 > can also provide useful information of the interfacial thermal
617 > transport process. The deuterated hexane (UA) results do not appear to
618 > be much different from those of normal hexane (UA), given that
619 > butanethiol (UA) is non-deuterated for both solvents. These UA model
620 > studies, even though eliminating C-H vibration samplings, still have
621 > C-C vibrational frequencies different from each other. However, these
622 > differences in the infrared range do not seem to produce an observable
623 > difference for the results of $G$. [MAY NEED FIGURE]
624 >
625 > Furthermore, results for rigid body toluene solvent, as well as other
626 > UA-hexane solvents, are reasonable within the general experimental
627 > ranges[CITATIONS]. This suggests that explicit hydrogen might not be a
628 > required factor for modeling thermal transport phenomena of systems
629 > such as Au-thiol/organic solvent.
630 >
631 > However, results for Au-butanethiol/toluene do not show an identical
632 > trend with those for Au-butanethiol/hexane in that $G$'s remain at
633 > approximately the same magnitue when butanethiol coverage differs from
634 > 25\% to 75\%. This might be rooted in the molecule shape difference
635 > for plane-like toluene and chain-like {\it n}-hexane. Due to this
636 > difference, toluene molecules have more difficulty in occupying
637 > relatively small gaps among capping agents when their coverage is not
638 > too low. Therefore, the solvent-capping agent contact may keep
639 > increasing until the capping agent coverage reaches a relatively low
640 > level. This becomes an offset for decreasing butanethiol molecules on
641 > its effect to the process of interfacial thermal transport. Thus, one
642 > can see a plateau of $G$ vs. butanethiol coverage in our results.
643 >
644 > [NEED ERROR ESTIMATE, MAY ALSO PUT J HERE]
645 > \begin{table*}
646 >  \begin{minipage}{\linewidth}
647 >    \begin{center}
648 >      \caption{Computed interfacial thermal conductivity ($G$) values
649 >        for the Au-butanethiol/solvent interface with various UA
650 >        models and different capping agent coverages at $\langle
651 >        T\rangle\sim$200K using certain energy flux respectively.}
652 >      
653 >      \begin{tabular}{cccc}
654 >        \hline\hline
655 >        Thiol & \multicolumn{3}{c}{$G$(MW/m$^2$/K)} \\
656 >        coverage (\%) & hexane & hexane(D) & toluene \\
657 >        \hline
658 >        0.0   & 46.5() & 43.9() & 70.1() \\
659 >        25.0  & 151()  & 153()  & 249()  \\
660 >        50.0  & 172()  & 182()  & 214()  \\
661 >        75.0  & 242()  & 229()  & 244()  \\
662 >        88.9  & 178()  & -      & -      \\
663 >        100.0 & 137()  & 153()  & 187()  \\
664 >        \hline\hline
665 >      \end{tabular}
666 >      \label{tlnUhxnUhxnD}
667 >    \end{center}
668 >  \end{minipage}
669 > \end{table*}
670 >
671 > \subsection{Influence of Chosen Molecule Model on $G$}
672 > [MAY COMBINE W MECHANISM STUDY]
673 >
674 > In addition to UA solvent/capping agent models, AA models are included
675 > in our simulations as well. Besides simulations of the same (UA or AA)
676 > model for solvent and capping agent, different models can be applied
677 > to different components. Furthermore, regardless of models chosen,
678 > either the solvent or the capping agent can be deuterated, similar to
679 > the previous section. Table \ref{modelTest} summarizes the results of
680 > these studies.
681 >
682 > [MORE DATA; ERROR ESTIMATE]
683 > \begin{table*}
684 >  \begin{minipage}{\linewidth}
685 >    \begin{center}
686 >      
687 >      \caption{Computed interfacial thermal conductivity ($G$ and
688 >        $G^\prime$) values for interfaces using various models for
689 >        solvent and capping agent (or without capping agent) at
690 >        $\langle T\rangle\sim$200K.}
691 >      
692 >      \begin{tabular}{ccccc}
693 >        \hline\hline
694 >        Butanethiol model & Solvent & $J_z$ & $G$ & $G^\prime$ \\
695 >        (or bare surface) & model & (GW/m$^2$) &
696 >        \multicolumn{2}{c}{(MW/m$^2$/K)} \\
697 >        \hline
698 >        UA    & AA hexane  & 1.94 & 135()  & 129()  \\
699 >              &            & 2.86 & 126()  & 115()  \\
700 >              & AA toluene & 1.89 & 200()  & 149()  \\
701 >        AA    & UA hexane  & 1.94 & 116()  & 129()  \\
702 >              & AA hexane  & 3.76 & 451()  & 378()  \\
703 >              &            & 4.71 & 432()  & 334()  \\
704 >              & AA toluene & 3.79 & 487()  & 290()  \\
705 >        AA(D) & UA hexane  & 1.94 & 158()  & 172()  \\
706 >        bare  & AA hexane  & 0.96 & 31.0() & 29.4() \\
707 >        \hline\hline
708 >      \end{tabular}
709 >      \label{modelTest}
710 >    \end{center}
711 >  \end{minipage}
712 > \end{table*}
713 >
714 > To facilitate direct comparison, the same system with differnt models
715 > for different components uses the same length scale for their
716 > simulation cells. Without the presence of capping agent, using
717 > different models for hexane yields similar results for both $G$ and
718 > $G^\prime$, and these two definitions agree with eath other very
719 > well. This indicates very weak interaction between the metal and the
720 > solvent, and is a typical case for acoustic impedance mismatch between
721 > these two phases.
722 >
723 > As for Au(111) surfaces completely covered by butanethiols, the choice
724 > of models for capping agent and solvent could impact the measurement
725 > of $G$ and $G^\prime$ quite significantly. For Au-butanethiol/hexane
726 > interfaces, using AA model for both butanethiol and hexane yields
727 > substantially higher conductivity values than using UA model for at
728 > least one component of the solvent and capping agent, which exceeds
729 > the upper bond of experimental value range. This is probably due to
730 > the classically treated C-H vibrations in the AA model, which should
731 > not be appreciably populated at normal temperatures. In comparison,
732 > once either the hexanes or the butanethiols are deuterated, one can
733 > see a significantly lower $G$ and $G^\prime$. In either of these
734 > cases, the C-H(D) vibrational overlap between the solvent and the
735 > capping agent is removed. [MAY NEED FIGURE] Conclusively, the
736 > improperly treated C-H vibration in the AA model produced
737 > over-predicted results accordingly. Compared to the AA model, the UA
738 > model yields more reasonable results with higher computational
739 > efficiency.
740 >
741 > However, for Au-butanethiol/toluene interfaces, having the AA
742 > butanethiol deuterated did not yield a significant change in the
743 > measurement results.
744 > . , so extra degrees of freedom
745 > such as the C-H vibrations could enhance heat exchange between these
746 > two phases and result in a much higher conductivity.
747 >
748 >
749 > Although the QSC model for Au is known to predict an overly low value
750 > for bulk metal gold conductivity[CITE NIVSRNEMD], our computational
751 > results for $G$ and $G^\prime$ do not seem to be affected by this
752 > drawback of the model for metal. Instead, the modeling of interfacial
753 > thermal transport behavior relies mainly on an accurate description of
754 > the interactions between components occupying the interfaces.
755 >
756 > \subsection{Mechanism of Interfacial Thermal Conductance Enhancement
757 >  by Capping Agent}
758 > %OR\subsection{Vibrational spectrum study on conductance mechanism}
759 >
760 > [MAY INTRODUCE PROTOCOL IN METHODOLOGY/COMPUTATIONAL DETAIL, EQN'S]
761 >
762   To investigate the mechanism of this interfacial thermal conductance,
763   the vibrational spectra of various gold systems were obtained and are
764   shown as in the upper panel of Fig. \ref{vibration}. To obtain these
765   spectra, one first runs a simulation in the NVE ensemble and collects
766   snapshots of configurations; these configurations are used to compute
767   the velocity auto-correlation functions, which is used to construct a
768 < power spectrum via a Fourier transform. The gold surfaces covered by
506 < butanethiol molecules exhibit an additional peak observed at a
507 < frequency of $\sim$170cm$^{-1}$, which is attributed to the vibration
508 < of the S-Au bond. This vibration enables efficient thermal transport
509 < from surface Au atoms to the capping agents. Simultaneously, as shown
510 < in the lower panel of Fig. \ref{vibration}, the large overlap of the
511 < vibration spectra of butanethiol and hexane in the all-atom model,
512 < including the C-H vibration, also suggests high thermal exchange
513 < efficiency. The combination of these two effects produces the drastic
514 < interfacial thermal conductance enhancement in the all-atom model.
768 > power spectrum via a Fourier transform.
769  
770 + The gold surfaces covered by
771 + butanethiol molecules, compared to bare gold surfaces, exhibit an
772 + additional peak observed at a frequency of $\sim$170cm$^{-1}$, which
773 + is attributed to the vibration of the S-Au bond. This vibration
774 + enables efficient thermal transport from surface Au atoms to the
775 + capping agents. Simultaneously, as shown in the lower panel of
776 + Fig. \ref{vibration}, the large overlap of the vibration spectra of
777 + butanethiol and hexane in the all-atom model, including the C-H
778 + vibration, also suggests high thermal exchange efficiency. The
779 + combination of these two effects produces the drastic interfacial
780 + thermal conductance enhancement in the all-atom model.
781 +
782 + [MAY NEED TO CONVERT TO JPEG]
783   \begin{figure}
784   \includegraphics[width=\linewidth]{vibration}
785   \caption{Vibrational spectra obtained for gold in different
# Line 520 | Line 787 | interfacial thermal conductance enhancement in the all
787    all-atom model (lower panel).}
788   \label{vibration}
789   \end{figure}
523 % 600dpi, letter size. too large?
790  
791 + [COMPARISON OF TWO G'S; AU SLAB WIDTHS; ETC]
792 + % The results show that the two definitions used for $G$ yield
793 + % comparable values, though $G^\prime$ tends to be smaller.
794  
795 + \section{Conclusions}
796 + The NIVS algorithm we developed has been applied to simulations of
797 + Au-butanethiol surfaces with organic solvents. This algorithm allows
798 + effective unphysical thermal flux transferred between the metal and
799 + the liquid phase. With the flux applied, we were able to measure the
800 + corresponding thermal gradient and to obtain interfacial thermal
801 + conductivities. Our simulations have seen significant conductance
802 + enhancement with the presence of capping agent, compared to the bare
803 + gold/liquid interfaces. The acoustic impedance mismatch between the
804 + metal and the liquid phase is effectively eliminated by proper capping
805 + agent. Furthermore, the coverage precentage of the capping agent plays
806 + an important role in the interfacial thermal transport process.
807 +
808 + Our measurement results, particularly of the UA models, agree with
809 + available experimental data. This indicates that our force field
810 + parameters have a nice description of the interactions between the
811 + particles at the interfaces. AA models tend to overestimate the
812 + interfacial thermal conductance in that the classically treated C-H
813 + vibration would be overly sampled. Compared to the AA models, the UA
814 + models have higher computational efficiency with satisfactory
815 + accuracy, and thus are preferable in interfacial thermal transport
816 + modelings.
817 +
818 + Vlugt {\it et al.} has investigated the surface thiol structures for
819 + nanocrystal gold and pointed out that they differs from those of the
820 + Au(111) surface\cite{vlugt:cpc2007154}. This difference might lead to
821 + change of interfacial thermal transport behavior as well. To
822 + investigate this problem, an effective means to introduce thermal flux
823 + and measure the corresponding thermal gradient is desirable for
824 + simulating structures with spherical symmetry.
825 +
826 +
827   \section{Acknowledgments}
828   Support for this project was provided by the National Science
829   Foundation under grant CHE-0848243. Computational time was provided by
830   the Center for Research Computing (CRC) at the University of Notre
831 < Dame.  \newpage
831 > Dame. \newpage
832  
833   \bibliography{interfacial}
834  

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