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1 \documentclass[journal = jctcce, manuscript = article]{achemso}
2 \setkeys{acs}{usetitle = true}
3
4 \usepackage{caption}
5 \usepackage{endfloat}
6 \usepackage{geometry}
7 \usepackage{natbib}
8 \usepackage{setspace}
9 \usepackage{xkeyval}
10 %%%%%%%%%%%%%%%%%%%%%%%
11 \usepackage{amsmath}
12 \usepackage{amssymb}
13 \usepackage{times}
14 \usepackage{mathptm}
15 \usepackage{setspace}
16 \usepackage{endfloat}
17 \usepackage{caption}
18 \usepackage{tabularx}
19 \usepackage{longtable}
20 \usepackage{graphicx}
21 \usepackage{multirow}
22 \usepackage{multicol}
23 \usepackage{achemso}
24 \usepackage[version=3]{mhchem} % this is a great package for formatting chemical reactions
25 % \usepackage[square, comma, sort&compress]{natbib}
26 \usepackage{url}
27 \pagestyle{plain} \pagenumbering{arabic} \oddsidemargin 0.0cm
28 \evensidemargin 0.0cm \topmargin -21pt \headsep 10pt \textheight
29 9.0in \textwidth 6.5in \brokenpenalty=10000
30
31 % double space list of tables and figures
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36 % \bibpunct{}{}{,}{s}{}{;}
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38 % \citestyle{nature}
39 % \bibliographystyle{achemso}
40
41 \title{A Method for Creating Thermal and Angular Momentum Fluxes in Non-Periodic Systems}
42
43 \author{Kelsey M. Stocker}
44 \author{J. Daniel Gezelter}
45 \email{gezelter@nd.edu}
46 \affiliation[University of Notre Dame]{251 Nieuwland Science Hall\\ Department of Chemistry and Biochemistry\\ University of Notre Dame\\ Notre Dame, Indiana 46556}
47
48 \begin{document}
49
50 \newcolumntype{A}{p{1.5in}}
51 \newcolumntype{B}{p{0.75in}}
52
53 % \author{Kelsey M. Stocker and J. Daniel
54 % Gezelter\footnote{Corresponding author. \ Electronic mail:
55 % gezelter@nd.edu} \\
56 % 251 Nieuwland Science Hall, \\
57 % Department of Chemistry and Biochemistry,\\
58 % University of Notre Dame\\
59 % Notre Dame, Indiana 46556}
60
61 \date{\today}
62
63 \maketitle
64
65 \begin{doublespace}
66
67 \begin{abstract}
68
69 We have adapted the Velocity Shearing and Scaling Reverse Non-Equilibium Molecular Dynamics (VSS-RNEMD) method for use with aperiodic system geometries. This new method is capable of creating stable temperature and angular velocity gradients in heterogeneous non-periodic systems while conserving total energy and angular momentum. To demonstrate the method, we have computed the thermal conductivities of a gold nanoparticle and water cluster, the shear viscosity of a water cluster, the interfacial thermal conductivity of a solvated gold nanoparticle and the interfacial friction of solvated gold nanostructures.
70
71 \end{abstract}
72
73 \newpage
74
75 %\narrowtext
76
77 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
78 % **INTRODUCTION**
79 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
80 \section{Introduction}
81
82
83 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
84 % **METHODOLOGY**
85 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
86 \section{Methodology}
87
88 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
89 % FORCE FIELD PARAMETERS
90 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
91 \subsection{Force field parameters}
92
93 We have chosen the SPC/E water model for these simulations. There are many values for physical properties from previous simulations available for direct comparison.
94
95 Gold-gold interactions are described by the quantum Sutton-Chen (QSC) model. The QSC parameters are tuned to experimental properties such as density, cohesive energy, and elastic moduli and include zero-point quantum corrections.
96
97 Hexane molecules are described by the TraPPE united atom model. This model provides good computational efficiency and reasonable accuracy for bulk thermal conductivity values.
98
99 Metal-nonmetal interactions are governed by parameters derived from Luedtke and Landman.
100
101
102 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
103 % NON-PERIODIC DYNAMICS
104 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
105 \subsection{Dynamics for non-periodic systems}
106
107 We have run all tests using the Langevin Hull nonperiodic simulation methodology. The Langevin Hull uses a Delaunay tesselation to create a dynamic convex hull composed of triangular facets with vertices at atomic sites. Atomic sites included in the hull are coupled to an external bath defined by a temperature, pressure and viscosity. Atoms not included in the hull are subject to standard Newtonian dynamics. Thermal coupling to the bath was turned off to avoid interference with any imposed kinetic flux. Systems containing liquids were run under moderate pressure ($\sim$ 5 atm) to avoid the formation of a substantial vapor phase, which would have a hull created out of a relatively small number of molecules.
108
109 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
110 % NON-PERIODIC RNEMD
111 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
112 \subsection{VSS-RNEMD for non-periodic systems}
113
114 The adaptation of VSS-RNEMD for non-periodic systems is relatively
115 straightforward. The major modifications to the method are the addition of a rotational shearing term and the use of more versatile hot / cold regions instead
116 of rectangular slabs. A temperature profile along the $r$ coordinate is created by recording the average temperature of concentric spherical shells.
117
118 \begin{figure}
119 \center{\includegraphics[width=7in]{figures/VSS}}
120 \caption{Schematics of periodic (left) and nonperiodic (right) Velocity Shearing and Scaling RNEMD. A kinetic energy or momentum flux is applied from region B to region A. Thermal gradients are depicted by a color gradient. Linear or angular velocity gradients are shown as arrows.}
121 \label{fig:VSS}
122 \end{figure}
123
124 At each time interval, the particle velocities ($\mathbf{v}_i$ and
125 $\mathbf{v}_j$) in the cold and hot shells ($C$ and $H$) are modified by a
126 velocity scaling coefficient ($c$ and $h$), an additive linear velocity shearing
127 term ($\mathbf{a}_c$ and $\mathbf{a}_h$), and an additive angular velocity
128 shearing term ($\mathbf{b}_c$ and $\mathbf{b}_h$). Here, $\langle
129 \mathbf{v}_{i,j} \rangle$ and $\langle \mathbf{\omega}_{i,j} \rangle$ are the
130 average linear and angular velocities for each shell.
131
132 \begin{displaymath}
133 \begin{array}{rclcl}
134 & \underline{~~~~~~~~~~\mathrm{scaling}~~~~~~~~~~} & &
135 \underline{\mathrm{rotational \; shearing}} \\ \\
136 \mathbf{v}_i $~~~$\leftarrow &
137 c \, \left(\mathbf{v}_i - \langle \omega_c
138 \rangle \times r_i\right) & + & \mathbf{b}_c \times r_i \\
139 \mathbf{v}_j $~~~$\leftarrow &
140 h \, \left(\mathbf{v}_j - \langle \omega_h
141 \rangle \times r_j\right) & + & \mathbf{b}_h \times r_j
142 \end{array}
143 \end{displaymath}
144
145 \begin{eqnarray}
146 \mathbf{b}_c & = & - \mathbf{j}_r(\mathbf{L}) \; \Delta \, t \; I_c^{-1} + \langle \omega_c \rangle \label{eq:bc}\\
147 \mathbf{b}_h & = & + \mathbf{j}_r(\mathbf{L}) \; \Delta \, t \; I_h^{-1} + \langle \omega_h \rangle \label{eq:bh}
148 \end{eqnarray}
149
150 The total energy is constrained via two quadratic formulae,
151
152 \begin{eqnarray}
153 K_c - J_r \; \Delta \, t & = & c^2 \, (K_c - \frac{1}{2}\langle \omega_c \rangle \cdot I_c\langle \omega_c \rangle) + \frac{1}{2} \mathbf{b}_c \cdot I_c \, \mathbf{b}_c \label{eq:Kc}\\
154 K_h + J_r \; \Delta \, t & = & h^2 \, (K_h - \frac{1}{2}\langle \omega_h \rangle \cdot I_h\langle \omega_h \rangle) + \frac{1}{2} \mathbf{b}_h \cdot I_h \, \mathbf{b}_h \label{eq:Kh}
155 \end{eqnarray}
156
157 the simultaneous
158 solution of which provide the velocity scaling coefficients $c$ and $h$. Given an
159 imposed angular momentum flux, $\mathbf{j}_{r} \left( \mathbf{L} \right)$, and/or
160 thermal flux, $J_r$, equations \ref{eq:bc} - \ref{eq:Kh} are sufficient to obtain
161 the velocity scaling ($c$ and $h$) and shearing ($\mathbf{b}_c,\,$ and $\mathbf{b}_h$) at each time interval.
162
163 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
164 % **TESTS AND APPLICATIONS**
165 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
166 \section{Tests and Applications}
167
168 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
169 % THERMAL CONDUCTIVITIES
170 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
171 \subsection{Thermal conductivities}
172
173 Calculated values for the thermal conductivity of a 40 \AA$~$ radius gold nanoparticle (15707 atoms) at different kinetic energy flux values are shown in Table \ref{table:goldconductivity}. For these calculations, the hot and cold slabs were excluded from the linear regression of the thermal gradient. The measured linear slope $\langle dT / dr \rangle$ is linearly dependent on the applied kinetic energy flux $J_r$. Calculated thermal conductivity values compare well with previous bulk QSC values of 1.08 - 1.26 W m$^{-1}$ K$^{-1}$ [cite NIVS paper], though still significantly lower than the experimental value of 320 W m$^{-1}$ K$^{-1}$, as the QSC force field neglects significant electronic contributions to heat conduction. The small increase relative to previous simulated bulk values is due to a slight increase in gold density -- as expected, an increase in density results in higher thermal conductivity values. The increased density is a result of nanoparticle curvature relative to an infinite bulk slab, which introduces surface tension that increases ambient density.
174
175 \begin{longtable}{ccc}
176 \caption{Calculated thermal conductivity of a crystalline gold nanoparticle of radius 40 \AA. Calculations were performed at 300 K and ambient density. Gold-gold interactions are described by the Quantum Sutton-Chen potential.}
177 \\ \hline \hline
178 {$J_r$} & {$\langle dT / dr \rangle$} & {$\boldsymbol \lambda$}\\
179 {\small(kcal fs$^{-1}$ \AA$^{-2}$)} & {\small(K \AA$^{-1}$)} & {\small(W m$^{-1}$ K$^{-1}$)}\\ \hline
180 3.25$\times 10^{-6}$ & 0.11435 & 1.9753 \\
181 6.50$\times 10^{-6}$ & 0.2324 & 1.9438 \\
182 1.30$\times 10^{-5}$ & 0.44922 & 2.0113 \\
183 3.25$\times 10^{-5}$ & 1.1802 & 1.9139 \\
184 6.50$\times 10^{-5}$ & 2.339 & 1.9314
185 \\ \hline \hline
186 \label{table:goldconductivity}
187 \end{longtable}
188
189 SPC/E Water Cluster:
190
191 \begin{longtable}{ccc}
192 \caption{Calculated thermal conductivity of a cluster of 6912 SPC/E water molecules. Calculations were performed at 300 K and ambient density.}
193 \\ \hline \hline
194 {$J_r$} & {$\langle dT / dr \rangle$} & {$\boldsymbol \lambda$}\\
195 {\small(kcal fs$^{-1}$ \AA$^{-2}$)} & {\small(K \AA$^{-1}$)} & {\small(W m$^{-1}$ K$^{-1}$)}\\ \hline
196 \\ \hline \hline
197 \label{table:waterconductivity}
198 \end{longtable}
199
200 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
201 % SHEAR VISCOSITY
202 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
203 \subsection{Shear viscosity}
204
205 SPC/E Water Cluster:
206
207 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
208 % INTERFACIAL THERMAL CONDUCTANCE
209 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
210 \subsection{Interfacial thermal conductance}
211
212 The interfacial thermal conductance, $G$, is calculated by defining a temperature difference $\Delta T$ across a given interface.
213
214 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
215 % INTERFACIAL FRICTION
216 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
217 \subsection{Interfacial friction}
218
219 The interfacial friction coefficient, $\kappa$, can be calculated from the solvent dynamic viscosity, $\eta$, and the slip length, $\delta$. The slip length is measured from a radial angular momentum profile generated from a nonperiodic VSS-RNEMD simulation, as shown in Figure X.
220
221 Table \ref{table:interfacialfriction} shows the calculated interfacial friction coefficients $\kappa$ for a spherical gold nanoparticle and prolate ellipsoidal gold nanorod in TraPPE-UA hexane. An angular momentum flux was applied between the A and B regions defined as the gold structure and hexane molecules included in the convex hull, respectively. The resulting angular velocity gradient resulted in the gold structure rotating about the prescribed axis within the solvent.
222
223 Analytical solutions for the rotational friction coefficients for a solvated spherical body of radius $r$ under ``stick'' boundary conditions can be estimated using Stokes' law
224
225 \begin{equation}
226 \Xi = 8 \pi \eta r^3 \label{eq:Xi}.
227 \end{equation}
228
229 where $\eta$ is the dynamic viscosity of the surrounding solvent and was determined for TraPPE-UA hexane under these condition by applying a traditional VSS-RNEMD linear momentum flux to a periodic box of solvent.
230
231 For general ellipsoids with semiaxes $a$, $b$, and $c$, Perrin's extension of Stokes' law provides exact solutions for symmetric prolate $(a \geq b = c)$ and oblate $(a < b = c)$ ellipsoids. For simplicity, we define a Perrin Factor, $S$,
232
233 \begin{equation}
234 S = \frac{2}{\sqrt{a^2 - b^2}} ln \left[ \frac{a + \sqrt{a^2 - b^2}}{b} \right]. \label{eq:S}
235 \end{equation}
236
237 For a prolate ellipsoidal rod, demonstrated here, the rotational resistance tensor $\Xi$ is a $3 \times 3$ diagonal matrix with elements
238
239 \begin{eqnarray}
240 \Xi^{rr}_a = \frac{32 \pi}{2} \eta \frac{ \left( a^2 - b^2 \right) b^2}{2a - b^2 S} \label{eq:Xia}\\
241 \Xi^{rr}_{b,c} = \frac{32 \pi}{2} \eta \frac{ \left( a^4 - b^4 \right)}{ \left( 2a^2 - b^2 \right)S - 2a}. \label{eq:Xibc}
242 \end{eqnarray}
243
244 However, the friction between hexane solvent and gold more likely falls within ``slip'' boundary conditions. Hu and Zwanzig investigated the rotational friction coefficients for spheroids under slip boundary conditions and obtained numerial results for a scaling factor as a function of $\tau$, the ratio of the shorter semiaxes and the longer semiaxis of the spheroid. For the sphere and prolate ellipsoid shown here, the values of $\tau$ are $1$ and $0.3939$, respectively. According to the values tabulated by Hu and Zwanzig, the sphere friction coefficient approaches $0$, while the ellipsoidal friction coefficient must be scaled by a factor of $0.880$ to account for the reduced interfacial friction under ``slip'' boundary conditions.
245
246 Another useful quantity is the friction factor $f$, or the friction coefficient of a non-spherical shape divided by the friction coefficient of a sphere of equivalent volume. The nanoparticle and ellipsoidal nanorod dimensions used here were specifically chosen to create structures with equal volumes.
247
248 \begin{longtable}{lccccc}
249 \caption{Calculated ``stick'' interfacial friction coefficients ($\kappa$) and friction factors ($f$) of gold nanostructures solvated in TraPPE-UA hexane. The ellipsoid is oriented with the long axis along the $z$ direction.}
250 \\ \hline \hline
251 {Structure} & {Axis of rotation} & {$\kappa_{VSS}$} & {$\kappa_{calc}$} & {$f_{VSS}$} & {$f_{calc}$}\\
252 {} & {} & {\small($10^{-29}$ Pa s m$^{3}$)} & {\small($10^{-29}$ Pa s m$^{3}$)} & {} & {}\\ \hline
253 {Sphere} & {$x = y = z$} & {} & {5.37237} & {1} & {1}\\
254 {Prolate Ellipsoid} & {$x = y$} & {} & {3.59881} & {} & {0.768726}\\
255 {Prolate Ellipsoid} & {$z$} & {} & {9.01084} & {} & {1.92477}\\ \hline \hline
256 \label{table:interfacialfriction}
257 \end{longtable}
258
259 \begin{longtable}{lccc}
260 \caption{Calculated ``slip'' interfacial friction coefficients ($\kappa$) and friction factors ($f$) of gold nanostructures solvated in TraPPE-UA hexane. The ellipsoid is oriented with the long axis along the $z$ direction.}
261 \\ \hline \hline
262 {Structure} & {Axis of rotation} & {$\kappa_{VSS}$} & {$\kappa_{calc}$}\\
263 {} & {} & {\small($10^{-29}$ Pa s m$^{3}$)} & {\small($10^{-29}$ Pa s m$^{3}$)}\\ \hline
264 {Sphere} & {$x = y = z$} & {} & {0}\\
265 {Prolate Ellipsoid} & {$x = y$} & {} & {0}\\
266 {Prolate Ellipsoid} & {$z$} & {} & {7.9295392}\\ \hline \hline
267 \label{table:interfacialfriction}
268 \end{longtable}
269
270 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
271 % **DISCUSSION**
272 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
273 \section{Discussion}
274
275
276 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
277 % **ACKNOWLEDGMENTS**
278 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
279 \section*{Acknowledgments}
280
281 We gratefully acknowledge conversations with Dr. Shenyu Kuang. Support for
282 this project was provided by the National Science Foundation under grant
283 CHE-0848243. Computational time was provided by the Center for Research
284 Computing (CRC) at the University of Notre Dame.
285
286 \newpage
287
288 \bibliography{nonperiodicVSS}
289
290 \end{doublespace}
291 \end{document}

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