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1 gezelter 3640 \documentclass[11pt]{article}
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15     % double space list of tables and figures
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21     \bibliographystyle{aip}
22    
23     \begin{document}
24    
25     \title{The Langevin Hull: Constant pressure and temperature dynamics for non-periodic systems}
26    
27 kstocke1 3644 \author{Charles F. Vardeman II, Kelsey M. Stocker, and J. Daniel
28 gezelter 3640 Gezelter\footnote{Corresponding author. \ Electronic mail: gezelter@nd.edu} \\
29     Department of Chemistry and Biochemistry,\\
30     University of Notre Dame\\
31     Notre Dame, Indiana 46556}
32    
33     \date{\today}
34    
35     \maketitle
36    
37     \begin{doublespace}
38    
39     \begin{abstract}
40     We have developed a new isobaric-isothermal (NPT) algorithm which
41     applies an external pressure to the facets comprising the convex
42     hull surrounding the objects in the system. Additionally, a Langevin
43     thermostat is applied to facets of the hull to mimic contact with an
44 gezelter 3652 external heat bath. This new method, the ``Langevin Hull'', performs
45     better than traditional affine transform methods for systems
46     containing heterogeneous mixtures of materials with different
47     compressibilities. It does not suffer from the edge effects of
48     boundary potential methods, and allows realistic treatment of both
49     external pressure and thermal conductivity to an implicit solvent.
50     We apply this method to several different systems including bare
51     nanoparticles, nanoparticles in an explicit solvent, as well as
52     clusters of liquid water and ice. The predicted mechanical and
53     thermal properties of these systems are in good agreement with
54     experimental data.
55 gezelter 3640 \end{abstract}
56    
57     \newpage
58    
59     %\narrowtext
60    
61     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
62     % BODY OF TEXT
63     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
64    
65    
66     \section{Introduction}
67    
68 gezelter 3641 The most common molecular dynamics methods for sampling configurations
69     of an isobaric-isothermal (NPT) ensemble attempt to maintain a target
70     pressure in a simulation by coupling the volume of the system to an
71     extra degree of freedom, the {\it barostat}. These methods require
72     periodic boundary conditions, because when the instantaneous pressure
73     in the system differs from the target pressure, the volume is
74     typically reduced or expanded using {\it affine transforms} of the
75     system geometry. An affine transform scales both the box lengths as
76     well as the scaled particle positions (but not the sizes of the
77     particles). The most common constant pressure methods, including the
78 gezelter 3651 Melchionna modification\cite{Melchionna1993} to the
79 gezelter 3652 Nos\'e-Hoover-Andersen equations of
80     motion,\cite{Hoover85,ANDERSEN:1980vn,Sturgeon:2000kx} the Berendsen
81     pressure bath,\cite{ISI:A1984TQ73500045} and the Langevin
82     Piston,\cite{FELLER:1995fk,Jakobsen:2005uq} all utilize coordinate
83 gezelter 3653 transformation to adjust the box volume. As long as the material in
84     the simulation box is essentially a bulk-like liquid which has a
85     relatively uniform compressibility, the standard affine transform
86 gezelter 3652 approach provides an excellent way of adjusting the volume of the
87     system and applying pressure directly via the interactions between
88 gezelter 3653 atomic sites.
89 gezelter 3652
90 gezelter 3653 The problem with this approach becomes apparent when the material
91 gezelter 3652 being simulated is an inhomogeneous mixture in which portions of the
92     simulation box are incompressible relative to other portions.
93     Examples include simulations of metallic nanoparticles in liquid
94     environments, proteins at interfaces, as well as other multi-phase or
95     interfacial environments. In these cases, the affine transform of
96     atomic coordinates will either cause numerical instability when the
97     sites in the incompressible medium collide with each other, or lead to
98     inefficient sampling of system volumes if the barostat is set slow
99 gezelter 3653 enough to avoid the instabilities in the incompressible region.
100 gezelter 3652
101 gezelter 3640 \begin{figure}
102 gezelter 3641 \includegraphics[width=\linewidth]{AffineScale2}
103     \caption{Affine Scaling constant pressure methods use box-length
104     scaling to adjust the volume to adjust to under- or over-pressure
105     conditions. In a system with a uniform compressibility (e.g. bulk
106     fluids) these methods can work well. In systems containing
107     heterogeneous mixtures, the affine scaling moves required to adjust
108     the pressure in the high-compressibility regions can cause molecules
109     in low compressibility regions to collide.}
110 gezelter 3640 \label{affineScale}
111     \end{figure}
112    
113 gezelter 3653 One may also wish to avoid affine transform periodic boundary methods
114     to simulate {\it explicitly non-periodic systems} under constant
115     pressure conditions. The use of periodic boxes to enforce a system
116     volume either requires effective solute concentrations that are much
117     higher than desirable, or unreasonable system sizes to avoid this
118     effect. For example, calculations using typical hydration shells
119     solvating a protein under periodic boundary conditions are quite
120     expensive. [CALCULATE EFFECTIVE PROTEIN CONCENTRATIONS IN TYPICAL
121     SIMULATIONS]
122 gezelter 3640
123 gezelter 3653 There have been a number of other approaches to explicit
124     non-periodicity that focus on constant or nearly-constant {\it volume}
125     conditions while maintaining bulk-like behavior. Berkowitz and
126     McCammon introduced a stochastic (Langevin) boundary layer inside a
127     region of fixed molecules which effectively enforces constant
128     temperature and volume (NVT) conditions.\cite{Berkowitz1982} In this
129     approach, the stochastic and fixed regions were defined relative to a
130     central atom. Brooks and Karplus extended this method to include
131     deformable stochastic boundaries.\cite{iii:6312} The stochastic
132     boundary approach has been used widely for protein
133     simulations. [CITATIONS NEEDED]
134 gezelter 3640
135 gezelter 3653 The electrostatic and dispersive behavior near the boundary has long
136     been a cause for concern. King and Warshel introduced a surface
137     constrained all-atom solvent (SCAAS) which included polarization
138     effects of a fixed spherical boundary to mimic bulk-like behavior
139     without periodic boundaries.\cite{king:3647} In the SCAAS model, a
140     layer of fixed solvent molecules surrounds the solute and any explicit
141     solvent, and this in turn is surrounded by a continuum dielectric.
142     MORE HERE. WHAT DID THEY FIND?
143 gezelter 3640
144 gezelter 3653 Beglov and Roux developed a boundary model in which the hard sphere
145     boundary has a radius that varies with the instantaneous configuration
146     of the solute (and solvent) molecules.\cite{beglov:9050} This model
147     contains a clear pressure and surface tension contribution to the free
148     energy which XXX.
149 gezelter 3640
150 gezelter 3653 Restraining {\it potentials} introduce repulsive potentials at the
151     surface of a sphere or other geometry. The solute and any explicit
152     solvent are therefore restrained inside this potential. Often the
153     potentials include a weak short-range attraction to maintain the
154     correct density at the boundary. Beglov and Roux have also introduced
155     a restraining boundary potential which relaxes dynamically depending
156     on the solute geometry and the force the explicit system exerts on the
157     shell.\cite{Beglov:1995fk}
158    
159     Recently, Krilov {\it et al.} introduced a flexible boundary model
160     that uses a Lennard-Jones potential between the solvent molecules and
161     a boundary which is determined dynamically from the position of the
162     nearest solute atom.\cite{LiY._jp046852t,Zhu:xw} This approach allows
163     the confining potential to prevent solvent molecules from migrating
164     too far from the solute surface, while providing a weak attractive
165     force pulling the solvent molecules towards a fictitious bulk solvent.
166     Although this approach is appealing and has physical motivation,
167     nanoparticles do not deform far from their original geometries even at
168     temperatures which vaporize the nearby solvent. For the systems like
169     the one described, the flexible boundary model will be nearly
170     identical to a fixed-volume restraining potential.
171    
172     The approach of Kohanoff, Caro, and Finnis is the most promising of
173     the methods for introducing both constant pressure and temperature
174     into non-periodic simulations.\cite{Kohanoff:2005qm,Baltazar:2006ru}
175     This method is based on standard Langevin dynamics, but the Brownian
176     or random forces are allowed to act only on peripheral atoms and exert
177     force in a direction that is inward-facing relative to the facets of a
178     closed bounding surface. The statistical distribution of the random
179     forces are uniquely tied to the pressure in the external reservoir, so
180     the method can be shown to sample the isobaric-isothermal ensemble.
181     Kohanoff {\it et al.} used a Delaunay tessellation to generate a
182     bounding surface surrounding the outermost atoms in the simulated
183     system. This is not the only possible triangulated outer surface, but
184     guarantees that all of the random forces point inward towards the
185     cluster.
186    
187     In the following sections, we extend and generalize the approach of
188     Kohanoff, Caro, and Finnis. The new method, which we are calling the
189     ``Langevin Hull'' applies the external pressure, Langevin drag, and
190     random forces on the facets of the {\it hull itself} instead of the
191     atomic sites comprising the vertices of the hull. This allows us to
192     decouple the external pressure contribution from the drag and random
193     force. Section \ref{sec:meth}
194    
195 gezelter 3640 \section{Methodology}
196 gezelter 3653 \label{sec:meth}
197 gezelter 3640
198 gezelter 3652 We have developed a new method which uses a constant pressure and
199     temperature bath. This bath interacts only with the objects that are
200     currently at the edge of the system. Since the edge is determined
201     dynamically as the simulation progresses, no {\it a priori} geometry
202     is defined. The pressure and temperature bath interacts {\it
203     directly} with the atoms on the edge and not with atoms interior to
204     the simulation. This means that there are no affine transforms
205     required. There are also no fictitious particles or bounding
206     potentials used in this approach.
207 gezelter 3640
208 gezelter 3652 The basics of the method are as follows. The simulation starts as a
209     collection of atomic locations in three dimensions (a point cloud).
210     Delaunay triangulation is used to find all facets between coplanar
211     neighbors. In highly symmetric point clouds, facets can contain many
212     atoms, but in all but the most symmetric of cases one might experience
213     in a molecular dynamics simulation, the facets are simple triangles in
214     3-space that contain exactly three atoms.
215 gezelter 3640
216 gezelter 3652 The convex hull is the set of facets that have {\it no concave
217     corners} at an atomic site. This eliminates all facets on the
218     interior of the point cloud, leaving only those exposed to the
219     bath. Sites on the convex hull are dynamic. As molecules re-enter the
220     cluster, all interactions between atoms on that molecule and the
221     external bath are removed.
222 gezelter 3640
223 gezelter 3652 For atomic sites in the interior of the point cloud, the equations of
224     motion are simple Newtonian dynamics,
225 gezelter 3640 \begin{equation}
226 gezelter 3652 m_i \dot{\mathbf v}_i(t)=-{\mathbf \nabla}_i U,
227     \label{eq:Newton}
228 gezelter 3640 \end{equation}
229 gezelter 3652 where $m_i$ is the mass of site $i$, ${\mathbf v}_i(t)$ is the
230     instantaneous velocity of site $i$ at time $t$, and $U$ is the total
231     potential energy. For atoms on the exterior of the cluster
232     (i.e. those that occupy one of the vertices of the convex hull), the
233     equation of motion is modified with an external force, ${\mathbf
234     F}_i^{\mathrm ext}$,
235 gezelter 3640 \begin{equation}
236 gezelter 3652 m_i \dot{\mathbf v}_i(t)=-{\mathbf \nabla}_i U + {\mathbf F}_i^{\mathrm ext}.
237 gezelter 3640 \end{equation}
238    
239 gezelter 3652 The external bath interacts directly with the facets of the convex
240     hull. Since each vertex (or atom) provides one corner of a triangular
241     facet, the force on the facets are divided equally to each vertex.
242     However, each vertex can participate in multiple facets, so the resultant
243     force is a sum over all facets $f$ containing vertex $i$:
244 gezelter 3640 \begin{equation}
245     {\mathbf F}_{i}^{\mathrm ext} = \sum_{\begin{array}{c}\mathrm{facets\
246     } f \\ \mathrm{containing\ } i\end{array}} \frac{1}{3}\ {\mathbf
247     F}_f^{\mathrm ext}
248     \end{equation}
249    
250 gezelter 3652 The external pressure bath applies a force to the facets of the convex
251     hull in direct proportion to the area of the facet, while the thermal
252     coupling depends on the solvent temperature, friction and the size and
253     shape of each facet. The thermal interactions are expressed as a
254     typical Langevin description of the forces,
255 gezelter 3640 \begin{equation}
256     \begin{array}{rclclcl}
257     {\mathbf F}_f^{\text{ext}} & = & \text{external pressure} & + & \text{drag force} & + & \text{random force} \\
258     & = & -\hat{n}_f P A_f & - & \Xi_f(t) {\mathbf v}_f(t) & + & {\mathbf R}_f(t)
259     \end{array}
260     \end{equation}
261 gezelter 3652 Here, $P$ is the external pressure, $A_f$ and $\hat{n}_f$ are the area
262     and normal vectors for facet $f$, respectively. ${\mathbf v}_f(t)$ is
263     the velocity of the facet,
264     \begin{equation}
265     {\mathbf v}_f(t) = \frac{1}{3} \sum_{i=1}^{3} {\mathbf v}_i,
266     \end{equation}
267 gezelter 3653 and $\Xi_f(t)$ is an approximate ($3 \times 3$) hydrodynamic tensor
268     that depends on the geometry and surface area of facet $f$ and the
269     viscosity of the fluid (See Appendix A). The hydrodynamic tensor is
270     related to the fluctuations of the random force, $\mathbf{R}(t)$, by
271     the fluctuation-dissipation theorem,
272 gezelter 3640 \begin{eqnarray}
273     \left< {\mathbf R}_f(t) \right> & = & 0 \\
274     \left<{\mathbf R}_f(t) {\mathbf R}_f^T(t^\prime)\right> & = & 2 k_B T\
275 gezelter 3652 \Xi_f(t)\delta(t-t^\prime).
276     \label{eq:randomForce}
277 gezelter 3640 \end{eqnarray}
278    
279 gezelter 3652 Once the hydrodynamic tensor is known for a given facet (see Appendix
280     A) obtaining a stochastic vector that has the properties in
281     Eq. (\ref{eq:randomForce}) can be done efficiently by carrying out a
282     one-time Cholesky decomposition to obtain the square root matrix of
283     the resistance tensor,
284     \begin{equation}
285     \Xi_f = {\bf S} {\bf S}^{T},
286     \label{eq:Cholesky}
287     \end{equation}
288     where ${\bf S}$ is a lower triangular matrix.\cite{Schlick2002} A
289     vector with the statistics required for the random force can then be
290     obtained by multiplying ${\bf S}$ onto a random 3-vector ${\bf Z}$ which
291     has elements chosen from a Gaussian distribution, such that:
292     \begin{equation}
293     \langle {\bf Z}_i \rangle = 0, \hspace{1in} \langle {\bf Z}_i \cdot
294     {\bf Z}_j \rangle = \frac{2 k_B T}{\delta t} \delta_{ij},
295     \end{equation}
296     where $\delta t$ is the timestep in use during the simulation. The
297     random force, ${\bf R}_{f} = {\bf S} {\bf Z}$, can be shown to
298     have the correct properties required by Eq. (\ref{eq:randomForce}).
299 gezelter 3640
300 gezelter 3653 Our treatment of the hydrodynamic tensor must be approximate. $\Xi$
301     for a triangular plate would normally be treated as a $6 \times 6$
302     tensor that includes translational and rotational drag as well as
303     translational-rotational coupling. The computation of hydrodynamic
304     tensors for rigid bodies has been detailed
305     elsewhere,\cite{JoseGarciadelaTorre02012000,Garcia-de-la-Torre:2001wd,GarciadelaTorreJ2002,Sun2008}
306     but the standard approach involving bead approximations would be
307     prohibitively expensive if it were recomputed at each step in a
308     molecular dynamics simulation.
309    
310     We are utilizing an approximate hydrodynamic tensor obtained by first
311     constructing the Oseen tensor for the interaction of the centroid of
312     the facet ($f$) with each of the subfacets $j$,
313     \begin{equation}
314     T_{jf}=\frac{A_j}{8\pi\eta R_{jf}}\left(I +
315     \frac{\mathbf{R}_{jf}\mathbf{R}_{jf}^T}{R_{jf}^2}\right)
316     \end{equation}
317     Here, $A_j$ is the area of subfacet $j$ which is a triangle containing
318     two of the vertices of the facet along with the centroid.
319     $\mathbf{R}_{jf}$ is the vector between the centroid of facet $f$ and
320     the centroid of sub-facet $j$, and $I$ is the ($3 \times 3$) identity
321     matrix. $\eta$ is the viscosity of the external bath.
322    
323     \begin{figure}
324     \includegraphics[width=\linewidth]{hydro}
325     \caption{The hydrodynamic tensor $\Xi$ for a facet comprising sites $i$,
326     $j$, and $k$ is constructed using Oseen tensor contributions
327     between the centoid of the facet $f$ and each of the sub-facets
328     ($i,f,j$), ($j,f,k$), and ($k,f,i$). The centroids of the sub-facets
329     are located at $1$, $2$, and $3$, and the area of each sub-facet is
330     easily computed using half the cross product of two of the edges.}
331     \label{hydro}
332     \end{figure}
333    
334     The Oseen tensors for each of the sub-facets are summed, and the
335     resulting matrix is inverted to give a $3 \times 3$ hydrodynamic
336     tensor for translations of the triangular plate,
337     \begin{equation}
338     \Xi_f(t) =\left[\sum_{i=1}^3 T_{if}\right]^{-1}.
339     \end{equation}
340 gezelter 3652 We have implemented this method by extending the Langevin dynamics
341 gezelter 3653 integrator in our group code, OpenMD.\cite{Meineke2005,openmd} There
342     is a moderate penalty for computing the convex hull at each step in
343     the molecular dynamics simulation (HOW MUCH?), but the convex hull is
344     remarkably easy to parallelize on distributed memory machines (see
345     Appendix B).
346 gezelter 3652
347 gezelter 3640 \section{Tests \& Applications}
348 gezelter 3653 \label{sec:tests}
349 gezelter 3640
350     \subsection{Bulk modulus of gold nanoparticles}
351    
352     \begin{figure}
353     \includegraphics[width=\linewidth]{pressure_tb}
354     \caption{Pressure response is rapid (18 \AA gold nanoparticle), target
355     pressure = 4 GPa}
356     \label{pressureResponse}
357     \end{figure}
358    
359     \begin{figure}
360     \includegraphics[width=\linewidth]{temperature_tb}
361     \caption{Temperature equilibration depends on surface area and bath
362     viscosity. Target Temperature = 300K}
363     \label{temperatureResponse}
364     \end{figure}
365    
366     \begin{equation}
367     \kappa_T=-\frac{1}{V_{\mathrm{eq}}}\left(\frac{\partial V}{\partial
368     P}\right)
369     \end{equation}
370    
371     \begin{figure}
372     \includegraphics[width=\linewidth]{compress_tb}
373     \caption{Isothermal Compressibility (18 \AA gold nanoparticle)}
374     \label{temperatureResponse}
375     \end{figure}
376    
377     \subsection{Compressibility of SPC/E water clusters}
378    
379 kstocke1 3649 Both NVT \cite{Glattli2002} and NPT \cite{Motakabbir1990, Pi2009} molecular dynamics simulations of SPC/E water have yielded values for the isothermal compressibility of water that agree well with experiment \cite{Fine1973}. The results of three different methods for computing the isothermal compressibility from Langevin Hull simulations for pressures between 1 and 6500 atm are shown in Fig. 5 along with compressibility values obtained from both other SPC/E simulations and experiment. Compressibility values from all references are for applied pressures within the range 1 - 1000 atm.
380    
381 gezelter 3640 \begin{figure}
382 kstocke1 3649 \includegraphics[width=\linewidth]{new_isothermal}
383     \caption{Compressibility of SPC/E water}
384     \label{compWater}
385 gezelter 3640 \end{figure}
386    
387 kstocke1 3655 The volume of a three-dimensional point cloud is not an obvious property to calculate. In order to calculate the isothermal compressibility we adapted the classic compressibility formula so that the compressibility could be calculated using information about the local density instead of the total volume of the convex hull.
388 kstocke1 3649
389 gezelter 3640 \begin{equation}
390 kstocke1 3649 \kappa_{T} = -\frac{1}{V} \left ( \frac{\partial V}{\partial P} \right )_{T}
391     \end{equation}
392    
393    
394 kstocke1 3655 Assuming a uniform density, we can use the relationship $\rho = \frac{N}{V}$ to rewrite the isothermal compressibility formula as
395 kstocke1 3649
396     \begin{equation}
397 kstocke1 3655 \kappa_{T} = \frac{1}{N} \left ( \frac{\partial N}{\partial P} \right )_{T}
398 kstocke1 3649 \end{equation}
399    
400 kstocke1 3655 Isothermal compressibility values calculated using this modified expression are in good agreement with the reference values throughout the 1 - 1000 atm pressure regime. Regardless of the difficulty in obtaining accurate hull volumes at low temperature and pressures, the Langevin Hull NPT method provides reasonable isothermal compressibility values for water through a large range of pressures.
401 kstocke1 3649
402 kstocke1 3655 We initially used the classic compressibility formula to calculate the the isothermal compressibility at each target pressure. These calculations yielded compressibility values that were dramatically higher than both previous simulations and experiment. The particular compressibility expression used requires the calculation of both a volume and pressure differential, thereby stipulating that the data from at least two simulations at different pressures must be used to calculate the isothermal compressibility at one pressure.
403 kstocke1 3649
404 kstocke1 3655 Per the fluctuation dissipation theorem \cite{Debenedetti1986}, the hull volume fluctuation in any given simulation can be used to calculated the isothermal compressibility at that particular pressure
405    
406 kstocke1 3649 \begin{equation}
407 kstocke1 3655 \kappa_{T} = \frac{\left \langle V^{2} \right \rangle - \left \langle V \right \rangle ^{2}}{V \, k_{B} \, T}
408 kstocke1 3649 \end{equation}
409    
410 kstocke1 3655 Thus, the compressibility of each simulation run can be calculated entirely independently from all other trajectories. However, the resulting compressibilities were still as much as an order of magnitude larger than the reference values. The effect was particularly pronounced at the low end of the pressure range. At ambient temperature and low pressures, there exists an equilibrium between vapor and liquid phases. Vapor molecules are naturally more diffuse around the exterior of the cluster, causing artificially large cluster volumes. Any compressibility calculation that relies on the hull volume will suffer these effects.
411 kstocke1 3649
412 kstocke1 3655
413 kstocke1 3649 \subsection{Molecular orientation distribution at cluster boundary}
414    
415     In order for non-periodic boundary conditions to be widely applicable, they must be constructed in such a way that they allow a finite, usually small, simulated system to replicate the properties of an infinite bulk system. Naturally, this requirement has spawned many methods for inserting boundaries into simulated systems [REF... ?]. Of particular interest to our characterization of the Langevin Hull is the orientation of water molecules included in the geometric hull. Ideally, all molecules in the cluster will have the same orientational distribution as bulk water.
416    
417     The orientation of molecules at the edges of a simulated cluster has long been a concern when performing simulations of explicitly non-periodic systems. Early work led to the surface constrained soft sphere dipole model (SCSSD) \cite{Warshel1978} in which the surface molecules are fixed in a random orientation representative of the bulk solvent structural properties. Belch, et al \cite{Belch1985} simulated clusters of TIPS2 water surrounded by a hydrophobic bounding potential. The spherical hydrophobic boundary induced dangling hydrogen bonds at the surface that propagated deep into the cluster, affecting 70\% of the 100 molecules in the simulation. This result echoes an earlier study which showed that an extended planar hydrophobic surface caused orientational preference at the surface which extended 7 \r{A} into the liquid simulation cell \cite{Lee1984}. The surface constrained all-atom solvent (SCAAS) model \cite{King1989} improved upon its SCSSD predecessor. The SCAAS model utilizes a polarization constraint which is applied to the surface molecules to maintain bulk-like structure at the cluster surface. A radial constraint is used to maintain the desired bulk density of the liquid. Both constraint forces are applied only to a pre-determined number of the outermost molecules.
418    
419     In contrast, the Langevin Hull does not require that the orientation of molecules be fixed, nor does it utilize an explicitly hydrophobic boundary, orientational constraint or radial constraint. The number and identity of the molecules included on the convex hull are dynamic properties, thus avoiding the formation of an artificial solvent boundary layer. The hope is that the water molecules on the surface of the cluster, if left to their own devices in the absence of orientational and radial constraints, will maintain a bulk-like orientational distribution.
420    
421     To determine the extent of these effects demonstrated by the Langevin Hull, we examined the orientations exhibited by SPC/E water in a cluster of 1372 molecules at 300 K and at pressures ranging from 1 - 1000 atm.
422    
423     The orientation of a water molecule is described by
424    
425     \begin{equation}
426 gezelter 3640 \cos{\theta}=\frac{\vec{r}_i\cdot\vec{\mu}_i}{|\vec{r}_i||\vec{\mu}_i|}
427     \end{equation}
428    
429 kstocke1 3649 where $\vec{r}_{i}$ is the vector between molecule {\it i}'s center of mass and the cluster center of mass and $\vec{\mu}_{i}$ is the vector bisecting the H-O-H angle of molecule {\it i}.
430    
431 gezelter 3640 \begin{figure}
432 kstocke1 3649 \includegraphics[width=\linewidth]{g_r_theta}
433     \caption{Definition of coordinates}
434     \label{coords}
435     \end{figure}
436    
437     Fig. 7 shows the probability of each value of $\cos{\theta}$ for molecules in the interior of the cluster (squares) and for molecules included in the convex hull (circles).
438    
439     \begin{figure}
440 gezelter 3640 \includegraphics[width=\linewidth]{pAngle}
441     \caption{SPC/E water clusters: only minor dewetting at the boundary}
442     \label{pAngle}
443     \end{figure}
444    
445 kstocke1 3649 As expected, interior molecules (those not included in the convex hull) maintain a bulk-like structure with a uniform distribution of orientations. Molecules included in the convex hull show a slight preference for values of $\cos{\theta} < 0.$ These values correspond to molecules with a hydrogen directed toward the exterior of the cluster, forming a dangling hydrogen bond.
446 gezelter 3640
447 kstocke1 3649 In the absence of an electrostatic contribution from the exterior bath, the orientational distribution of water molecules included in the Langevin Hull will slightly resemble the distribution at a neat water liquid/vapor interface. Previous molecular dynamics simulations of SPC/E water \cite{Taylor1996} have shown that molecules at the liquid/vapor interface favor an orientation where one hydrogen protrudes from the liquid phase. This behavior is demonstrated by experiments \cite{Du1994} \cite{Scatena2001} showing that approximately one-quarter of water molecules at the liquid/vapor interface form dangling hydrogen bonds. The negligible preference shown in these cluster simulations could be removed through the introduction of an implicit solvent model, which would provide the missing electrostatic interactions between the cluster molecules and the surrounding temperature/pressure bath.
448    
449     The orientational preference exhibited by hull molecules is significantly weaker than the preference caused by an explicit hydrophobic bounding potential. Additionally, the Langevin Hull does not require that the orientation of any molecules be fixed in order to maintain bulk-like structure, even at the cluster surface.
450    
451    
452 gezelter 3640 \subsection{Heterogeneous nanoparticle / water mixtures}
453    
454    
455     \section{Appendix A: Hydrodynamic tensor for triangular facets}
456    
457     \section{Appendix B: Computing Convex Hulls on Parallel Computers}
458    
459     \section{Acknowledgments}
460     Support for this project was provided by the
461     National Science Foundation under grant CHE-0848243. Computational
462     time was provided by the Center for Research Computing (CRC) at the
463     University of Notre Dame.
464    
465     \newpage
466    
467     \bibliography{langevinHull}
468    
469     \end{doublespace}
470     \end{document}