--- interfacial/interfacial.tex	2011/07/14 19:49:12	3739
+++ interfacial/interfacial.tex	2011/07/15 17:55:16	3742
@@ -23,8 +23,8 @@
 \setlength{\belowcaptionskip}{30 pt}
 
 %\renewcommand\citemid{\ } % no comma in optional reference note
-\bibpunct{[}{]}{,}{s}{}{;}
-\bibliographystyle{aip}
+\bibpunct{[}{]}{,}{n}{}{;}
+\bibliographystyle{achemso}
 
 \begin{document}
 
@@ -227,9 +227,16 @@ illustrated in Figure \ref{demoPic}.
 illustrated in Figure \ref{demoPic}.
 
 \begin{figure}
-\includegraphics[width=\linewidth]{demoPic}
-\caption{A sample showing how a metal slab has its (111) surface
-  covered by capping agent molecules and solvated by hexane.}
+\includegraphics[width=\linewidth]{method}
+\caption{Interfacial conductance can be calculated by applying an
+  (unphysical) kinetic energy flux between two slabs, one located
+  within the metal and another on the edge of the periodic box.  The
+  system responds by forming a thermal response or a gradient.  In
+  bulk liquids, this gradient typically has a single slope, but in
+  interfacial systems, there are distinct thermal conductivity
+  domains.  The interfacial conductance, $G$ is found by measuring the
+  temperature gap at the Gibbs dividing surface, or by using second
+  derivatives of the thermal profile.}
 \label{demoPic}
 \end{figure}
 
@@ -332,9 +339,14 @@ organic solvent molecules in our simulations.
 organic solvent molecules in our simulations.
 
 \begin{figure}
-\includegraphics[width=\linewidth]{demoMol}
-\caption{Denomination of atoms or pseudo-atoms in our simulations: a)
-  UA-hexane; b) AA-hexane; c) UA-toluene; d) AA-toluene.}
+\includegraphics[width=\linewidth]{structures}
+\caption{Structures of the capping agent and solvents utilized in
+  these simulations. The chemically-distinct sites (a-e) are expanded
+  in terms of constituent atoms for both United Atom (UA) and All Atom
+  (AA) force fields.  Most parameters are from
+  Refs. \protect\cite{TraPPE-UA.alkanes,TraPPE-UA.alkylbenzenes} (UA) and
+  \protect\cite{OPLSAA} (AA).  Cross-interactions with the Au atoms are given
+  in Table \ref{MnM}.}
 \label{demoMol}
 \end{figure}
 
@@ -377,8 +389,8 @@ Lorentz-Berthelot Mixing Rule:
 interactions between capping agent and solvent can be derived using
 Lorentz-Berthelot Mixing Rule:
 \begin{eqnarray}
-\sigma_{IJ} & = & \frac{1}{2} \left(\sigma_{II} + \sigma_{JJ}\right) \\
-\epsilon_{IJ} & = & \sqrt{\epsilon_{II}\epsilon_{JJ}}
+\sigma_{ij} & = & \frac{1}{2} \left(\sigma_{ii} + \sigma_{jj}\right) \\
+\epsilon_{ij} & = & \sqrt{\epsilon_{ii}\epsilon_{jj}}
 \end{eqnarray}
 
 To describe the interactions between metal Au and non-metal capping
@@ -408,27 +420,30 @@ parameters in our simulations.
 \begin{table*}
   \begin{minipage}{\linewidth}
     \begin{center}
-      \caption{Non-bonded interaction paramters for non-metal
-        particles and metal-non-metal interactions in our
-        simulations.}
-      
-      \begin{tabular}{cccccc}
+      \caption{Non-bonded interaction parameters (including cross
+        interactions with Au atoms) for both force fields used in this
+        work.}      
+      \begin{tabular}{lllllll}
         \hline\hline
-        Non-metal atom $I$ & $\sigma_{II}$ & $\epsilon_{II}$ & $q_I$ &
-        $\sigma_{AuI}$ & $\epsilon_{AuI}$ \\
-        (or pseudo-atom) & \AA & kcal/mol & & \AA & kcal/mol \\
+        & Site  & $\sigma_{ii}$ & $\epsilon_{ii}$ & $q_i$ &
+        $\sigma_{Au-i}$ & $\epsilon_{Au-i}$ \\
+        & & (\AA) & (kcal/mol) & ($e$) & (\AA) & (kcal/mol) \\
         \hline
-        CH3  & 3.75  & 0.1947  & -      & 3.54   & 0.2146  \\
-        CH2  & 3.95  & 0.0914  & -      & 3.54   & 0.1749  \\
-        CHar & 3.695 & 0.1003  & -      & 3.4625 & 0.1680  \\
-        CRar & 3.88  & 0.04173 & -      & 3.555  & 0.1604  \\
-        S    & 4.45  & 0.25    & -      & 2.40   & 8.465   \\
-        CT3  & 3.50  & 0.066   & -0.18  & 3.365  & 0.1373  \\
-        CT2  & 3.50  & 0.066   & -0.12  & 3.365  & 0.1373  \\
-        CTT  & 3.50  & 0.066   & -0.065 & 3.365  & 0.1373  \\
-        HC   & 2.50  & 0.030   &  0.06  & 2.865  & 0.09256 \\
-        CA   & 3.55  & 0.070   & -0.115 & 3.173  & 0.0640  \\
-        HA   & 2.42  & 0.030   &  0.115 & 2.746  & 0.0414  \\
+        United Atom (UA)
+        &CH3  & 3.75  & 0.1947  & -      & 3.54   & 0.2146  \\
+        &CH2  & 3.95  & 0.0914  & -      & 3.54   & 0.1749  \\
+        &CHar & 3.695 & 0.1003  & -      & 3.4625 & 0.1680  \\
+        &CRar & 3.88  & 0.04173 & -      & 3.555  & 0.1604  \\
+        \hline
+        All Atom (AA) 
+        &CT3  & 3.50  & 0.066   & -0.18  & 3.365  & 0.1373  \\
+        &CT2  & 3.50  & 0.066   & -0.12  & 3.365  & 0.1373  \\
+        &CTT  & 3.50  & 0.066   & -0.065 & 3.365  & 0.1373  \\
+        &HC   & 2.50  & 0.030   &  0.06  & 2.865  & 0.09256 \\
+        &CA   & 3.55  & 0.070   & -0.115 & 3.173  & 0.0640  \\
+        &HA   & 2.42  & 0.030   &  0.115 & 2.746  & 0.0414  \\
+        \hline
+        Both UA and AA & S    & 4.45  & 0.25    & -      & 2.40   & 8.465   \\
         \hline\hline
       \end{tabular}
       \label{MnM}
@@ -688,7 +703,6 @@ can see a plateau of $G$ vs. butanethiol coverage in o
 its effect to the process of interfacial thermal transport. Thus, one
 can see a plateau of $G$ vs. butanethiol coverage in our results.
 
-[NEED ERROR ESTIMATE]
 \begin{figure}
 \includegraphics[width=\linewidth]{coverage}
 \caption{Comparison of interfacial thermal conductivity ($G$) values
@@ -709,7 +723,6 @@ these studies.
 the previous section. Table \ref{modelTest} summarizes the results of
 these studies.
 
-[MORE DATA; ERROR ESTIMATE]
 \begin{table*}
   \begin{minipage}{\linewidth}
     \begin{center}
@@ -719,35 +732,35 @@ these studies.
         solvent and capping agent (or without capping agent) at
         $\langle T\rangle\sim$200K. (D stands for deuterated solvent
         or capping agent molecules; ``Avg.'' denotes results that are
-        averages of several simulations.)}
+        averages of simulations under different $J_z$'s. Error
+        estimates indicated in parenthesis.)}
       
-      \begin{tabular}{ccccc}
+      \begin{tabular}{llccc}
         \hline\hline
         Butanethiol model & Solvent & $J_z$ & $G$ & $G^\prime$ \\
         (or bare surface) & model & (GW/m$^2$) &
         \multicolumn{2}{c}{(MW/m$^2$/K)} \\
         \hline
-        UA    & UA hexane    & Avg. & 131()  & 86.5() \\
-              & UA hexane(D) & 1.95 & 153()  & 136()  \\
-              & AA hexane    & 1.94 & 135()  & 129()  \\
-              &              & 2.86 & 126()  & 115()  \\
-              & UA toluene   & 1.96 & 187()  & 151()  \\
-              & AA toluene   & 1.89 & 200()  & 149()  \\
+        UA    & UA hexane    & Avg. & 131(9)    & 87(10)    \\
+              & UA hexane(D) & 1.95 & 153(5)    & 136(13)   \\
+              & AA hexane    & Avg. & 131(6)    & 122(10)   \\
+              & UA toluene   & 1.96 & 187(16)   & 151(11)   \\
+              & AA toluene   & 1.89 & 200(36)   & 149(53)   \\
         \hline
-        AA    & UA hexane    & 1.94 & 116()  & 129()  \\
-              & AA hexane    & Avg. & 442()  & 356()  \\
-              & AA hexane(D) & 1.93 & 222()  & 234()  \\
-              & UA toluene   & 1.98 & 125()  & 96.5() \\
-              & AA toluene   & 3.79 & 487()  & 290()  \\
+        AA    & UA hexane    & 1.94 & 116(9)    & 129(8)    \\
+              & AA hexane    & Avg. & 442(14)   & 356(31)   \\
+              & AA hexane(D) & 1.93 & 222(12)   & 234(54)   \\
+              & UA toluene   & 1.98 & 125(25)   & 97(60)    \\
+              & AA toluene   & 3.79 & 487(56)   & 290(42)   \\
         \hline
-        AA(D) & UA hexane    & 1.94 & 158()  & 172()  \\
-              & AA hexane    & 1.92 & 243()  & 191()  \\
-              & AA toluene   & 1.93 & 364()  & 322()  \\
+        AA(D) & UA hexane    & 1.94 & 158(25)   & 172(4)    \\
+              & AA hexane    & 1.92 & 243(29)   & 191(11)   \\
+              & AA toluene   & 1.93 & 364(36)   & 322(67)   \\
         \hline
-        bare  & UA hexane    & Avg. & 46.5() & 49.4() \\
-              & UA hexane(D) & 0.98 & 43.9() & 43.0() \\
-              & AA hexane    & 0.96 & 31.0() & 29.4() \\
-              & UA toluene   & 1.99 & 70.1() & 65.8() \\
+        bare  & UA hexane    & Avg. & 46.5(3.2) & 49.4(4.5) \\
+              & UA hexane(D) & 0.98 & 43.9(4.6) & 43.0(2.0) \\
+              & AA hexane    & 0.96 & 31.0(1.4) & 29.4(1.3) \\
+              & UA toluene   & 1.99 & 70.1(1.3) & 65.8(0.5) \\
         \hline\hline
       \end{tabular}
       \label{modelTest}
