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Revision 3743 by skuang, Fri Jul 15 19:36:02 2011 UTC

# 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 227 | Line 227 | illustrated in Figure \ref{demoPic}.
227   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.}
230 > \includegraphics[width=\linewidth]{method}
231 > \caption{Interfacial conductance can be calculated by applying an
232 >  (unphysical) kinetic energy flux between two slabs, one located
233 >  within the metal and another on the edge of the periodic box.  The
234 >  system responds by forming a thermal response or a gradient.  In
235 >  bulk liquids, this gradient typically has a single slope, but in
236 >  interfacial systems, there are distinct thermal conductivity
237 >  domains.  The interfacial conductance, $G$ is found by measuring the
238 >  temperature gap at the Gibbs dividing surface, or by using second
239 >  derivatives of the thermal profile.}
240   \label{demoPic}
241   \end{figure}
242  
# Line 332 | Line 339 | organic solvent molecules in our simulations.
339   organic solvent molecules in our simulations.
340  
341   \begin{figure}
342 < \includegraphics[width=\linewidth]{demoMol}
343 < \caption{Denomination of atoms or pseudo-atoms in our simulations: a)
344 <  UA-hexane; b) AA-hexane; c) UA-toluene; d) AA-toluene.}
342 > \includegraphics[width=\linewidth]{structures}
343 > \caption{Structures of the capping agent and solvents utilized in
344 >  these simulations. The chemically-distinct sites (a-e) are expanded
345 >  in terms of constituent atoms for both United Atom (UA) and All Atom
346 >  (AA) force fields.  Most parameters are from
347 >  Refs. \protect\cite{TraPPE-UA.alkanes,TraPPE-UA.alkylbenzenes} (UA) and
348 >  \protect\cite{OPLSAA} (AA).  Cross-interactions with the Au atoms are given
349 >  in Table \ref{MnM}.}
350   \label{demoMol}
351   \end{figure}
352  
# Line 375 | Line 387 | Lorentz-Berthelot Mixing Rule:[EQN'S]
387   (UA or AA) of capping agent can be different from the
388   solvent. Regardless of model choice, the force field parameters for
389   interactions between capping agent and solvent can be derived using
390 < Lorentz-Berthelot Mixing Rule:[EQN'S]
391 <
390 > Lorentz-Berthelot Mixing Rule:
391 > \begin{eqnarray}
392 > \sigma_{ij} & = & \frac{1}{2} \left(\sigma_{ii} + \sigma_{jj}\right) \\
393 > \epsilon_{ij} & = & \sqrt{\epsilon_{ii}\epsilon_{jj}}
394 > \end{eqnarray}
395  
396   To describe the interactions between metal Au and non-metal capping
397   agent and solvent particles, we refer to an adsorption study of alkyl
# Line 405 | Line 420 | parameters in our simulations.
420   \begin{table*}
421    \begin{minipage}{\linewidth}
422      \begin{center}
423 <      \caption{Lennard-Jones parameters for Au-non-Metal
424 <        interactions in our simulations.}
425 <      
426 <      \begin{tabular}{ccc}
423 >      \caption{Non-bonded interaction parameters (including cross
424 >        interactions with Au atoms) for both force fields used in this
425 >        work.}      
426 >      \begin{tabular}{lllllll}
427          \hline\hline
428 <        Non-metal atom   & $\sigma$ & $\epsilon$ \\
429 <        (or pseudo-atom) & \AA      & kcal/mol  \\
428 >        & Site  & $\sigma_{ii}$ & $\epsilon_{ii}$ & $q_i$ &
429 >        $\sigma_{Au-i}$ & $\epsilon_{Au-i}$ \\
430 >        & & (\AA) & (kcal/mol) & ($e$) & (\AA) & (kcal/mol) \\
431          \hline
432 <        S    & 2.40   & 8.465   \\
433 <        CH3  & 3.54   & 0.2146  \\
434 <        CH2  & 3.54   & 0.1749  \\
435 <        CT3  & 3.365  & 0.1373  \\
436 <        CT2  & 3.365  & 0.1373  \\
437 <        CTT  & 3.365  & 0.1373  \\
438 <        HC   & 2.865  & 0.09256 \\
439 <        CHar & 3.4625 & 0.1680  \\
440 <        CRar & 3.555  & 0.1604  \\
441 <        CA   & 3.173  & 0.0640  \\
442 <        HA   & 2.746  & 0.0414  \\
432 >        United Atom (UA)
433 >        &CH3  & 3.75  & 0.1947  & -      & 3.54   & 0.2146  \\
434 >        &CH2  & 3.95  & 0.0914  & -      & 3.54   & 0.1749  \\
435 >        &CHar & 3.695 & 0.1003  & -      & 3.4625 & 0.1680  \\
436 >        &CRar & 3.88  & 0.04173 & -      & 3.555  & 0.1604  \\
437 >        \hline
438 >        All Atom (AA)
439 >        &CT3  & 3.50  & 0.066   & -0.18  & 3.365  & 0.1373  \\
440 >        &CT2  & 3.50  & 0.066   & -0.12  & 3.365  & 0.1373  \\
441 >        &CTT  & 3.50  & 0.066   & -0.065 & 3.365  & 0.1373  \\
442 >        &HC   & 2.50  & 0.030   &  0.06  & 2.865  & 0.09256 \\
443 >        &CA   & 3.55  & 0.070   & -0.115 & 3.173  & 0.0640  \\
444 >        &HA   & 2.42  & 0.030   &  0.115 & 2.746  & 0.0414  \\
445 >        \hline
446 >        Both UA and AA & S    & 4.45  & 0.25    & -      & 2.40   & 8.465   \\
447          \hline\hline
448        \end{tabular}
449        \label{MnM}
# Line 484 | Line 504 | couple $J_z$'s and do not need to test a large series
504   investigations in that we can rely on $G$ measurement with only a
505   couple $J_z$'s and do not need to test a large series of fluxes.
506  
507 < %ADD MORE TO TABLE
507 > [LOW FLUX, LARGE ERROR]
508   \begin{table*}
509    \begin{minipage}{\linewidth}
510      \begin{center}
# Line 493 | Line 513 | couple $J_z$'s and do not need to test a large series
513          interfaces with UA model and different hexane molecule numbers
514          at different temperatures using a range of energy fluxes.}
515        
516 <      \begin{tabular}{cccccccc}
516 >      \begin{tabular}{ccccccc}
517          \hline\hline
518 <        $\langle T\rangle$ & & $L_x$ & $L_y$ & $L_z$ & $J_z$ &
519 <        $G$ & $G^\prime$ \\
520 <        (K) & $N_{hexane}$ & \multicolumn{3}{c}{(\AA)} & (GW/m$^2$) &
518 >        $\langle T\rangle$ & $N_{hexane}$ & Fixed & $\rho_{hexane}$ &
519 >        $J_z$ & $G$ & $G^\prime$ \\
520 >        (K) & & $L_x$ \& $L_y$? & (g/cm$^3$) & (GW/m$^2$) &
521          \multicolumn{2}{c}{(MW/m$^2$/K)} \\
522          \hline
523 <        200 & 266 & 29.86 & 25.80 & 113.1 & -0.96 &
524 <        102()  & 80.0() \\
525 <            & 200 & 29.84 & 25.81 &  93.9 &  1.92 &
526 <        129()  & 87.3() \\
527 <            &     & 29.84 & 25.81 &  95.3 &  1.93 &
528 <        131()  & 77.5() \\
529 <            & 166 & 29.84 & 25.81 &  85.7 &  0.97 &
530 <        115()  & 69.3() \\
531 <            &     &       &       &       &  1.94 &
532 <        125()  & 87.1() \\
533 <        250 & 200 & 29.84 & 25.87 & 106.8 &  0.96 &
534 <        81.8() & 67.0() \\
535 <            & 166 & 29.87 & 25.84 &  94.8 &  0.98 &
536 <        79.0() & 62.9() \\
537 <            &     & 29.84 & 25.85 &  95.0 &  1.44 &
538 <        76.2() & 64.8() \\
523 >        200 & 266 & No  & 0.672 & -0.96 & 102()     & 80.0()    \\
524 >            & 200 & Yes & 0.694 &  1.92 & 129(11)   & 87.3(0.3) \\
525 >            &     & Yes & 0.672 &  1.93 & 131(16)   & 78(13)    \\
526 >            &     & No  & 0.688 &  0.96 & 125()     & 90.2()    \\
527 >            &     &     &       &  1.91 & 139(10)   & 101(10)   \\
528 >            &     &     &       &  2.83 & 141(6)    & 89.9(9.8) \\
529 >            & 166 & Yes & 0.679 &  0.97 & 115(19)   & 69(18)    \\
530 >            &     &     &       &  1.94 & 125(9)    & 87.1(0.2) \\
531 >            &     & No  & 0.681 &  0.97 & 141(30)   & 78(22)    \\
532 >            &     &     &       &  1.92 & 138(4)    & 98.9(9.5) \\
533 >        \hline
534 >        250 & 200 & No  & 0.560 &  0.96 & 75(10)    & 61.8(7.3) \\
535 >            &     &     &       & -0.95 & 49.4(0.3) & 45.7(2.1) \\
536 >            & 166 & Yes & 0.570 &  0.98 & 79.0(3.5) & 62.9(3.0) \\
537 >            &     & No  & 0.569 &  0.97 & 80.3(0.6) & 67(11)    \\
538 >            &     &     &       &  1.44 & 76.2(5.0) & 64.8(3.8) \\
539 >            &     &     &       & -0.95 & 56.4(2.5) & 54.4(1.1) \\
540 >            &     &     &       & -1.85 & 47.8(1.1) & 53.5(1.5) \\
541          \hline\hline
542        \end{tabular}
543        \label{AuThiolHexaneUA}
# Line 546 | Line 568 | in that higher degree of contact could yield increased
568   important role in the thermal transport process across the interface
569   in that higher degree of contact could yield increased conductance.
570  
571 < [ADD Lxyz AND ERROR ESTIMATE TO TABLE]
571 > [ADD ERROR ESTIMATE TO TABLE]
572   \begin{table*}
573    \begin{minipage}{\linewidth}
574      \begin{center}
# Line 555 | Line 577 | in that higher degree of contact could yield increased
577          interface at different temperatures using a range of energy
578          fluxes.}
579        
580 <      \begin{tabular}{cccc}
580 >      \begin{tabular}{ccccc}
581          \hline\hline
582 <        $\langle T\rangle$ & $J_z$ & $G$ & $G^\prime$ \\
583 <        (K) & (GW/m$^2$) & \multicolumn{2}{c}{(MW/m$^2$/K)} \\
582 >        $\langle T\rangle$ & $\rho_{toluene}$ & $J_z$ & $G$ & $G^\prime$ \\
583 >        (K) & (g/cm$^3$) & (GW/m$^2$) & \multicolumn{2}{c}{(MW/m$^2$/K)} \\
584          \hline
585 <        200 & -1.86 & 180() & 135() \\
586 <            &  2.15 & 204() & 113() \\
587 <            & -3.93 & 175() & 114() \\
588 <        300 & -1.91 & 143() & 125() \\
589 <            & -4.19 & 134() & 113() \\
585 >        200 & 0.933 & -1.86 & 180() & 135() \\
586 >            &       &  2.15 & 204() & 113() \\
587 >            &       & -3.93 & 175() & 114() \\
588 >        \hline
589 >        300 & 0.855 & -1.91 & 143() & 125() \\
590 >            &       & -4.19 & 134() & 113() \\
591          \hline\hline
592        \end{tabular}
593        \label{AuThiolToluene}
# Line 597 | Line 620 | even at $\langle T\rangle\sim$300K. The Au(111) surfac
620   However, when the surface is not completely covered by butanethiols,
621   the simulated system is more resistent to the reconstruction
622   above. Our Au-butanethiol/toluene system did not see this phenomena
623 < even at $\langle T\rangle\sim$300K. The Au(111) surfaces have a 90\% coverage of
624 < butanethiols and have empty three-fold sites. These empty sites could
625 < help prevent surface reconstruction in that they provide other means
626 < of capping agent relaxation. It is observed that butanethiols can
627 < migrate to their neighbor empty sites during a simulation. Therefore,
628 < we were able to obtain $G$'s for these interfaces even at a relatively
629 < high temperature without being affected by surface reconstructions.
623 > even at $\langle T\rangle\sim$300K. The Au(111) surfaces have a 90\%
624 > coverage of butanethiols and have empty three-fold sites. These empty
625 > sites could help prevent surface reconstruction in that they provide
626 > other means of capping agent relaxation. It is observed that
627 > butanethiols can migrate to their neighbor empty sites during a
628 > simulation. Therefore, we were able to obtain $G$'s for these
629 > interfaces even at a relatively high temperature without being
630 > affected by surface reconstructions.
631  
632   \subsection{Influence of Capping Agent Coverage on $G$}
633   To investigate the influence of butanethiol coverage on interfacial
# Line 679 | Line 703 | can see a plateau of $G$ vs. butanethiol coverage in o
703   its effect to the process of interfacial thermal transport. Thus, one
704   can see a plateau of $G$ vs. butanethiol coverage in our results.
705  
706 < [NEED ERROR ESTIMATE, MAY ALSO PUT J HERE]
707 < \begin{table*}
708 <  \begin{minipage}{\linewidth}
709 <    \begin{center}
710 <      \caption{Computed interfacial thermal conductivity ($G$) values
711 <        for the Au-butanethiol/solvent interface with various UA
712 <        models and different capping agent coverages at $\langle
713 <        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$/K)} \\
694 <        coverage (\%) & hexane & hexane(D) & toluene \\
695 <        \hline
696 <        0.0   & 46.5() & 43.9() & 70.1() \\
697 <        25.0  & 151()  & 153()  & 249()  \\
698 <        50.0  & 172()  & 182()  & 214()  \\
699 <        75.0  & 242()  & 229()  & 244()  \\
700 <        88.9  & 178()  & -      & -      \\
701 <        100.0 & 137()  & 153()  & 187()  \\
702 <        \hline\hline
703 <      \end{tabular}
704 <      \label{tlnUhxnUhxnD}
705 <    \end{center}
706 <  \end{minipage}
707 < \end{table*}
706 > \begin{figure}
707 > \includegraphics[width=\linewidth]{coverage}
708 > \caption{Comparison of interfacial thermal conductivity ($G$) values
709 >  for the Au-butanethiol/solvent interface with various UA models and
710 >  different capping agent coverages at $\langle T\rangle\sim$200K
711 >  using certain energy flux respectively.}
712 > \label{coverage}
713 > \end{figure}
714  
715   \subsection{Influence of Chosen Molecule Model on $G$}
716   [MAY COMBINE W MECHANISM STUDY]
# Line 717 | Line 723 | these studies.
723   the previous section. Table \ref{modelTest} summarizes the results of
724   these studies.
725  
720 [MORE DATA; ERROR ESTIMATE]
726   \begin{table*}
727    \begin{minipage}{\linewidth}
728      \begin{center}
# Line 725 | Line 730 | these studies.
730        \caption{Computed interfacial thermal conductivity ($G$ and
731          $G^\prime$) values for interfaces using various models for
732          solvent and capping agent (or without capping agent) at
733 <        $\langle T\rangle\sim$200K.}
733 >        $\langle T\rangle\sim$200K. (D stands for deuterated solvent
734 >        or capping agent molecules; ``Avg.'' denotes results that are
735 >        averages of simulations under different $J_z$'s. Error
736 >        estimates indicated in parenthesis.)}
737        
738 <      \begin{tabular}{ccccc}
738 >      \begin{tabular}{llccc}
739          \hline\hline
740          Butanethiol model & Solvent & $J_z$ & $G$ & $G^\prime$ \\
741          (or bare surface) & model & (GW/m$^2$) &
742          \multicolumn{2}{c}{(MW/m$^2$/K)} \\
743          \hline
744 <        UA    & AA hexane  & 1.94 & 135()  & 129()  \\
745 <              &            & 2.86 & 126()  & 115()  \\
746 <              & AA toluene & 1.89 & 200()  & 149()  \\
747 <        AA    & UA hexane  & 1.94 & 116()  & 129()  \\
748 <              & AA hexane  & 3.76 & 451()  & 378()  \\
749 <              &            & 4.71 & 432()  & 334()  \\
750 <              & AA toluene & 3.79 & 487()  & 290()  \\
751 <        AA(D) & UA hexane  & 1.94 & 158()  & 172()  \\
752 <        bare  & AA hexane  & 0.96 & 31.0() & 29.4() \\
744 >        UA    & UA hexane    & Avg. & 131(9)    & 87(10)    \\
745 >              & UA hexane(D) & 1.95 & 153(5)    & 136(13)   \\
746 >              & AA hexane    & Avg. & 131(6)    & 122(10)   \\
747 >              & UA toluene   & 1.96 & 187(16)   & 151(11)   \\
748 >              & AA toluene   & 1.89 & 200(36)   & 149(53)   \\
749 >        \hline
750 >        AA    & UA hexane    & 1.94 & 116(9)    & 129(8)    \\
751 >              & AA hexane    & Avg. & 442(14)   & 356(31)   \\
752 >              & AA hexane(D) & 1.93 & 222(12)   & 234(54)   \\
753 >              & UA toluene   & 1.98 & 125(25)   & 97(60)    \\
754 >              & AA toluene   & 3.79 & 487(56)   & 290(42)   \\
755 >        \hline
756 >        AA(D) & UA hexane    & 1.94 & 158(25)   & 172(4)    \\
757 >              & AA hexane    & 1.92 & 243(29)   & 191(11)   \\
758 >              & AA toluene   & 1.93 & 364(36)   & 322(67)   \\
759 >        \hline
760 >        bare  & UA hexane    & Avg. & 46.5(3.2) & 49.4(4.5) \\
761 >              & UA hexane(D) & 0.98 & 43.9(4.6) & 43.0(2.0) \\
762 >              & AA hexane    & 0.96 & 31.0(1.4) & 29.4(1.3) \\
763 >              & UA toluene   & 1.99 & 70.1(1.3) & 65.8(0.5) \\
764          \hline\hline
765        \end{tabular}
766        \label{modelTest}
# Line 778 | Line 797 | measurement results.
797  
798   However, for Au-butanethiol/toluene interfaces, having the AA
799   butanethiol deuterated did not yield a significant change in the
800 < measurement results.
801 < . , so extra degrees of freedom
802 < such as the C-H vibrations could enhance heat exchange between these
803 < two phases and result in a much higher conductivity.
800 > measurement results. Compared to the C-H vibrational overlap between
801 > hexane and butanethiol, both of which have alkyl chains, that overlap
802 > between toluene and butanethiol is not so significant and thus does
803 > not have as much contribution to the ``Intramolecular Vibration
804 > Redistribution''[CITE HASE]. Conversely, extra degrees of freedom such
805 > as the C-H vibrations could yield higher heat exchange rate between
806 > these two phases and result in a much higher conductivity.
807  
786
808   Although the QSC model for Au is known to predict an overly low value
809 < for bulk metal gold conductivity[CITE NIVSRNEMD], our computational
809 > for bulk metal gold conductivity\cite{kuang:164101}, our computational
810   results for $G$ and $G^\prime$ do not seem to be affected by this
811 < drawback of the model for metal. Instead, the modeling of interfacial
812 < thermal transport behavior relies mainly on an accurate description of
813 < the interactions between components occupying the interfaces.
811 > drawback of the model for metal. Instead, our results suggest that the
812 > modeling of interfacial thermal transport behavior relies mainly on
813 > the accuracy of the interaction descriptions between components
814 > occupying the interfaces.
815  
816   \subsection{Mechanism of Interfacial Thermal Conductance Enhancement
817    by Capping Agent}
# Line 805 | Line 827 | power spectrum via a Fourier transform.
827   the velocity auto-correlation functions, which is used to construct a
828   power spectrum via a Fourier transform.
829  
830 + [MAY RELATE TO HASE'S]
831   The gold surfaces covered by
832   butanethiol molecules, compared to bare gold surfaces, exhibit an
833   additional peak observed at a frequency of $\sim$170cm$^{-1}$, which
# Line 817 | Line 840 | thermal conductance enhancement in the all-atom model.
840   combination of these two effects produces the drastic interfacial
841   thermal conductance enhancement in the all-atom model.
842  
843 < [MAY NEED TO CONVERT TO JPEG]
843 > [REDO. MAY NEED TO CONVERT TO JPEG]
844   \begin{figure}
845   \includegraphics[width=\linewidth]{vibration}
846   \caption{Vibrational spectra obtained for gold in different

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