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1 kstocke1 3927 \documentclass[journal = jctcce, manuscript = article]{achemso}
2     \setkeys{acs}{usetitle = true}
3    
4     \usepackage{caption}
5     \usepackage{float}
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
32     % \AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
33     \setlength{\abovecaptionskip}{20 pt}
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35    
36     % \bibpunct{}{}{,}{s}{}{;}
37    
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     At each time interval, the particle velocities ($\mathbf{v}_i$ and
119     $\mathbf{v}_j$) in the cold and hot shells ($C$ and $H$) are modified by a
120     velocity scaling coefficient ($c$ and $h$), an additive linear velocity shearing
121     term ($\mathbf{a}_c$ and $\mathbf{a}_h$), and an additive angular velocity
122     shearing term ($\mathbf{b}_c$ and $\mathbf{b}_h$). Here, $\langle
123     \mathbf{v}_{i,j} \rangle$ and $\langle \mathbf{\omega}_{i,j} \rangle$ are the
124     average linear and angular velocities for each shell.
125    
126     \begin{displaymath}
127     \begin{array}{rclcl}
128     & \underline{~~~~~~~~~~\mathrm{scaling}~~~~~~~~~~} & &
129     \underline{\mathrm{rotational \; shearing}} \\ \\
130     \mathbf{v}_i $~~~$\leftarrow &
131     c \, \left(\mathbf{v}_i - \langle \omega_c
132     \rangle \times r_i\right) & + & \mathbf{b}_c \times r_i \\
133     \mathbf{v}_j $~~~$\leftarrow &
134     h \, \left(\mathbf{v}_j - \langle \omega_h
135     \rangle \times r_j\right) & + & \mathbf{b}_h \times r_j
136     \end{array}
137     \end{displaymath}
138    
139     \begin{eqnarray}
140     \mathbf{b}_c & = & - \mathbf{j}_r(\mathbf{L}) \; \Delta \, t \; I_c^{-1} + \langle \omega_c \rangle \label{eq:bc}\\
141     \mathbf{b}_h & = & + \mathbf{j}_r(\mathbf{L}) \; \Delta \, t \; I_h^{-1} + \langle \omega_h \rangle \label{eq:bh}
142     \end{eqnarray}
143    
144     The total energy is constrained via two quadratic formulae,
145    
146     \begin{eqnarray}
147     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}\\
148     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}
149     \end{eqnarray}
150    
151     the simultaneous
152     solution of which provide the velocity scaling coefficients $c$ and $h$. Given an
153     imposed angular momentum flux, $\mathbf{j}_{r} \left( \mathbf{L} \right)$, and/or
154     thermal flux, $J_r$, equations \ref{eq:bc} - \ref{eq:Kh} are sufficient to obtain
155     the velocity scaling ($c$ and $h$) and shearing ($\mathbf{b}_c,\,$ and $\mathbf{b}_h$) at each time interval.
156    
157     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
158     % **TESTS AND APPLICATIONS**
159     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
160     \section{Tests and Applications}
161    
162     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
163     % THERMAL CONDUCTIVITIES
164     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
165     \subsection{Thermal conductivities}
166    
167 kstocke1 3932 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.
168 kstocke1 3927
169 kstocke1 3934 \begin{longtable}{ccc}
170     \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.}
171 kstocke1 3927 \\ \hline \hline
172 kstocke1 3934 {$J_r$} & {$\langle dT / dr \rangle$} & {$\boldsymbol \lambda$}\\
173     {\small(kcal fs$^{-1}$ \AA$^{-2}$)} & {\small(K \AA$^{-1}$)} & {\small(W m$^{-1}$ K$^{-1}$)}\\ \hline
174     3.25$\times 10^{-6}$ & 0.11435 & 1.9753 \\
175     6.50$\times 10^{-6}$ & 0.2324 & 1.9438 \\
176     1.30$\times 10^{-5}$ & 0.44922 & 2.0113 \\
177     3.25$\times 10^{-5}$ & 1.1802 & 1.9139 \\
178     6.50$\times 10^{-5}$ & 2.339 & 1.9314
179     \\ \hline \hline
180 kstocke1 3927 \label{table:goldconductivity}
181     \end{longtable}
182    
183     SPC/E Water Cluster:
184    
185 kstocke1 3934 \begin{longtable}{ccc}
186     \caption{Calculated thermal conductivity of a cluster of 6912 SPC/E water molecules. Calculations were performed at 300 K and ambient density.}
187 kstocke1 3927 \\ \hline \hline
188 kstocke1 3934 {$J_r$} & {$\langle dT / dr \rangle$} & {$\boldsymbol \lambda$}\\
189     {\small(kcal fs$^{-1}$ \AA$^{-2}$)} & {\small(K \AA$^{-1}$)} & {\small(W m$^{-1}$ K$^{-1}$)}\\ \hline
190     \\ \hline \hline
191 kstocke1 3927 \label{table:waterconductivity}
192     \end{longtable}
193    
194     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
195     % SHEAR VISCOSITY
196     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
197     \subsection{Shear viscosity}
198    
199     SPC/E Water Cluster:
200    
201     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
202     % INTERFACIAL THERMAL CONDUCTANCE
203     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
204     \subsection{Interfacial thermal conductance}
205    
206     Gold Nanoparticle in Hexane:
207    
208     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
209     % INTERFACIAL FRICTION
210     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
211     \subsection{Interfacial friction}
212    
213 kstocke1 3932 Table \ref{table:interfacialfriction} gives 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.
214 kstocke1 3927
215 kstocke1 3932 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
216    
217     \begin{equation}
218 kstocke1 3934 \Xi = 8 \pi \eta r^3 \label{eq:Xi}.
219 kstocke1 3932 \end{equation}
220    
221 kstocke1 3934 where $\eta$ is the dynamic viscosity of the surrounding solvent.
222 kstocke1 3932
223 kstocke1 3934 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, $S$,
224    
225     \begin{equation}
226     S = \frac{2}{\sqrt{a^2 - b^2}} ln \left[ \frac{a + \sqrt{a^2 - b^2}}{b} \right]. \label{eq:S}
227     \end{equation}
228    
229     For a prolate ellipsoidal rod, demonstrated here, the rotational resistance tensor $\Xi$ is a $3 \times 3$ diagonal matrix with elements
230    
231 kstocke1 3932 \begin{eqnarray}
232 kstocke1 3934 \Xi^{rr}_a = \frac{32 \Pi}{2} \eta \frac{ \left( a^2 - b^2 \right) b^2}{2a - b^2 S} \label{eq:Xia}\\
233     \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}
234 kstocke1 3932 \end{eqnarray}
235    
236 kstocke1 3934 The dynamic viscosity of the solvent, $\eta$, was determined by applying a traditional VSS-RNEMD linear momentum flux to a periodic box of TraPPE-UA hexane.
237 kstocke1 3932
238 kstocke1 3934 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.
239    
240     \begin{longtable}{lccccc}
241     \caption{Calculated 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.}
242 kstocke1 3927 \\ \hline \hline
243 kstocke1 3934 {Structure} & {Axis of rotation} & {$\kappa_{VSS}$} & {$\kappa_{Stokes-Perrin}$} & {$f_{VSS}$} & {$f_{Stokes-Perrin}$}\\
244     {} & {} & {\small($10^4$ Pa s m$^{-1}$)} & {\small($10^4$ Pa s m$^{-1}$)} & {} & {}\\ \hline
245     {Sphere} & {$x = y = z$} & {} & {} & {1} & {1}\\
246     {Prolate Ellipsoid} & {$x = y$} & {} & {} & {} & {}\\
247     {Prolate Ellipsoid} & {$z$} & {} & {} & {} & {}\\ \hline \hline
248 kstocke1 3927 \label{table:interfacialfriction}
249     \end{longtable}
250    
251     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
252     % **DISCUSSION**
253     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
254     \section{Discussion}
255    
256    
257     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
258     % **ACKNOWLEDGMENTS**
259     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
260     \section*{Acknowledgments}
261    
262     We gratefully acknowledge conversations with Dr. Shenyu Kuang. Support for
263     this project was provided by the National Science Foundation under grant
264     CHE-0848243. Computational time was provided by the Center for Research
265     Computing (CRC) at the University of Notre Dame.
266    
267     \newpage
268    
269     \bibliography{nonperiodicVSS}
270    
271     \end{doublespace}
272 kstocke1 3934 \end{document}

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