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# Line 195 | Line 195 | We have developed a new method which uses a constant p
195   \section{Methodology}
196   \label{sec:meth}
197  
198 < 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.
198 > We have developed a new method which uses an external bath at a fixed
199 > constant pressure ($P$) and temperature ($T$).  This bath interacts
200 > only with the objects on the exterior hull of the system.  Defining
201 > the hull of the simulation is done in a manner similar to the approach
202 > of Kohanoff, Caro and Finnis.\cite{Kohanoff:2005qm} That is, any
203 > instantaneous configuration of the atoms in the system is considered
204 > as a point cloud in three dimensional space.  Delaunay triangulation
205 > is used to find all facets between coplanar neighbors.\cite{DELAUNAY}
206 > In highly symmetric point clouds, facets can contain many atoms, but
207 > in all but the most symmetric of cases the facets are simple triangles
208 > in 3-space that contain exactly three atoms.
209  
208 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
210   The convex hull is the set of facets that have {\it no concave
211    corners} at an atomic site.  This eliminates all facets on the
212   interior of the point cloud, leaving only those exposed to the
213   bath. Sites on the convex hull are dynamic. As molecules re-enter the
214   cluster, all interactions between atoms on that molecule and the
215 < external bath are removed.
215 > external bath are removed.  Since the edge is determined dynamically
216 > as the simulation progresses, no {\it a priori} geometry is
217 > defined. The pressure and temperature bath interacts {\it directly}
218 > with the atoms on the edge and not with atoms interior to the
219 > simulation.
220  
221 < For atomic sites in the interior of the point cloud, the equations of
222 < motion are simple Newtonian dynamics,
221 >
222 > \begin{figure}
223 > \includegraphics[width=\linewidth]{hullSample}
224 > \caption{The external temperature and pressure bath interacts only
225 >  with those atoms on the convex hull (grey surface).  The hull is
226 >  computed dynamically at each time step, and molecules dynamically
227 >  move between the interior (Newtonian) region and the Langevin hull.}
228 > \label{fig:hullSample}
229 > \end{figure}
230 >
231 >
232 > Atomic sites in the interior of the point cloud move under standard
233 > Newtonian dynamics,
234   \begin{equation}
235   m_i \dot{\mathbf v}_i(t)=-{\mathbf \nabla}_i U,
236   \label{eq:Newton}
# Line 237 | Line 246 | hull.  Since each vertex (or atom) provides one corner
246   \end{equation}
247  
248   The external bath interacts directly with the facets of the convex
249 < hull.  Since each vertex (or atom) provides one corner of a triangular
249 > hull. Since each vertex (or atom) provides one corner of a triangular
250   facet, the force on the facets are divided equally to each vertex.
251   However, each vertex can participate in multiple facets, so the resultant
252   force is a sum over all facets $f$ containing vertex $i$:
# Line 249 | Line 258 | coupling depends on the solvent temperature, friction
258  
259   The external pressure bath applies a force to the facets of the convex
260   hull in direct proportion to the area of the facet, while the thermal
261 < coupling depends on the solvent temperature, friction and the size and
262 < shape of each facet. The thermal interactions are expressed as a
263 < typical Langevin description of the forces,
261 > coupling depends on the solvent temperature, viscosity and the size
262 > and shape of each facet. The thermal interactions are expressed as a
263 > standard Langevin description of the forces,
264   \begin{equation}
265   \begin{array}{rclclcl}
266   {\mathbf F}_f^{\text{ext}} & = &  \text{external pressure} & + & \text{drag force} & + & \text{random force} \\
267   & = &  -\hat{n}_f P A_f  & - & \Xi_f(t) {\mathbf v}_f(t)  & + & {\mathbf R}_f(t)
268   \end{array}
269   \end{equation}
270 < Here, $P$ is the external pressure, $A_f$ and $\hat{n}_f$ are the area
271 < and normal vectors for facet $f$, respectively.  ${\mathbf v}_f(t)$ is
272 < the velocity of the facet,
270 > Here, $A_f$ and $\hat{n}_f$ are the area and normal vectors for facet
271 > $f$, respectively.  ${\mathbf v}_f(t)$ is the velocity of the facet
272 > centroid,
273   \begin{equation}
274   {\mathbf v}_f(t) =  \frac{1}{3} \sum_{i=1}^{3} {\mathbf v}_i,
275   \end{equation}
276 < and $\Xi_f(t)$ is an approximate ($3 \times 3$) hydrodynamic tensor
277 < that depends on the geometry and surface area of facet $f$ and the
278 < viscosity of the fluid (See Appendix A).  The hydrodynamic tensor is
279 < related to the fluctuations of the random force, $\mathbf{R}(t)$, by
280 < the fluctuation-dissipation theorem,
276 > and $\Xi_f(t)$ is an approximate ($3 \times 3$) resistance tensor that
277 > depends on the geometry and surface area of facet $f$ and the
278 > viscosity of the fluid.  The resistance tensor is related to the
279 > fluctuations of the random force, $\mathbf{R}(t)$, by the
280 > fluctuation-dissipation theorem,
281   \begin{eqnarray}
282   \left< {\mathbf R}_f(t) \right> & = & 0 \\
283   \left<{\mathbf R}_f(t) {\mathbf R}_f^T(t^\prime)\right> & = & 2 k_B T\
# Line 276 | Line 285 | Once the hydrodynamic tensor is known for a given face
285   \label{eq:randomForce}
286   \end{eqnarray}
287  
288 < Once the hydrodynamic tensor is known for a given facet (see Appendix
289 < A) obtaining a stochastic vector that has the properties in
290 < Eq. (\ref{eq:randomForce}) can be done efficiently by carrying out a
291 < one-time Cholesky decomposition to obtain the square root matrix of
283 < the resistance tensor,
288 > Once the resistance tensor is known for a given facet a stochastic
289 > vector that has the properties in Eq. (\ref{eq:randomForce}) can be
290 > done efficiently by carrying out a Cholesky decomposition to obtain
291 > the square root matrix of the resistance tensor,
292   \begin{equation}
293   \Xi_f = {\bf S} {\bf S}^{T},
294   \label{eq:Cholesky}
# Line 297 | Line 305 | Our treatment of the hydrodynamic tensor must be appro
305   random force, ${\bf R}_{f} = {\bf S} {\bf Z}$, can be shown to
306   have the correct properties required by Eq. (\ref{eq:randomForce}).
307  
308 < Our treatment of the hydrodynamic tensor must be approximate.  $\Xi$
309 < for a triangular plate would normally be treated as a $6 \times 6$
308 > Our treatment of the resistance tensor is approximate.  $\Xi$ for a
309 > rigid triangular plate would normally be treated as a $6 \times 6$
310   tensor that includes translational and rotational drag as well as
311 < translational-rotational coupling. The computation of hydrodynamic
311 > translational-rotational coupling. The computation of resistance
312   tensors for rigid bodies has been detailed
313 < elsewhere,\cite{JoseGarciadelaTorre02012000,Garcia-de-la-Torre:2001wd,GarciadelaTorreJ2002,Sun2008}
313 > elsewhere,\cite{JoseGarciadelaTorre02012000,Garcia-de-la-Torre:2001wd,GarciadelaTorreJ2002,Sun:2008fk}
314   but the standard approach involving bead approximations would be
315   prohibitively expensive if it were recomputed at each step in a
316   molecular dynamics simulation.
317  
318 < We are utilizing an approximate hydrodynamic tensor obtained by first
318 > We are utilizing an approximate resistance tensor obtained by first
319   constructing the Oseen tensor for the interaction of the centroid of
320   the facet ($f$) with each of the subfacets $j$,
321   \begin{equation}
# Line 322 | Line 330 | matrix.  $\eta$ is the viscosity of the external bath.
330  
331   \begin{figure}
332   \includegraphics[width=\linewidth]{hydro}
333 < \caption{The hydrodynamic tensor $\Xi$ for a facet comprising sites $i$,
334 <  $j$, and $k$ is constructed using Oseen tensor contributions
335 <  between the centoid of the facet $f$ and each of the sub-facets
336 <  ($i,f,j$), ($j,f,k$), and ($k,f,i$). The centroids of the sub-facets
337 <  are located at $1$, $2$, and $3$, and the area of each sub-facet is
333 > \caption{The resistance tensor $\Xi$ for a facet comprising sites $i$,
334 >  $j$, and $k$ is constructed using Oseen tensor contributions between
335 >  the centoid of the facet $f$ and each of the sub-facets ($i,f,j$),
336 >  ($j,f,k$), and ($k,f,i$). The centroids of the sub-facets are
337 >  located at $1$, $2$, and $3$, and the area of each sub-facet is
338    easily computed using half the cross product of two of the edges.}
339   \label{hydro}
340   \end{figure}
341  
342 < The Oseen tensors for each of the sub-facets are summed, and the
343 < resulting matrix is inverted to give a $3 \times 3$ hydrodynamic
344 < tensor for translations of the triangular plate,
342 > The Oseen tensors for each of the sub-facets are added together, and
343 > the resulting matrix is inverted to give a $3 \times 3$ resistance
344 > tensor for translations of the triangular facet,
345   \begin{equation}
346   \Xi_f(t) =\left[\sum_{i=1}^3 T_{if}\right]^{-1}.
347   \end{equation}
348 + Note that this treatment explicitly ignores rotations (and
349 + translational-rotational coupling) of the facet.  In compact systems,
350 + the facets stay relatively fixed in orientation between
351 + configurations, so this appears to be a reasonably good approximation.
352 +
353   We have implemented this method by extending the Langevin dynamics
354 < integrator in our group code, OpenMD.\cite{Meineke2005,openmd} There
355 < is a moderate penalty for computing the convex hull at each step in
356 < the molecular dynamics simulation (HOW MUCH?), but the convex hull is
357 < remarkably easy to parallelize on distributed memory machines (see
358 < Appendix B).
354 > integrator in our code, OpenMD.\cite{Meineke2005,openmd} The Delaunay
355 > triangulation and computation of the convex hull are done using calls
356 > to the qhull library.\cite{Qhull} There is a moderate penalty for
357 > computing the convex hull at each step in the molecular dynamics
358 > simulation (HOW MUCH?), but the convex hull is remarkably easy to
359 > parallelize on distributed memory machines (see Appendix A).
360  
361   \section{Tests \& Applications}
362   \label{sec:tests}
363  
364 + To test the new method, we have carried out simulations using the
365 + Langevin Hull on: 1) a crystalline system (gold nanoparticles), 2) a
366 + liquid droplet (SPC/E water),\cite{SPCE} and 3) a heterogeneous
367 + mixture (gold nanoparticles in a water droplet). In each case, we have
368 + computed properties that depend on the external applied pressure.  Of
369 + particular interest for the single-phase systems is the bulk modulus,
370 + \begin{equation}
371 + \kappa_{T} = -\frac{1}{V} \left ( \frac{\partial V}{\partial P} \right
372 + )_{T}.
373 + \label{eq:BM}
374 + \end{equation}
375 +
376 + One problem with eliminating periodic boundary conditions and
377 + simulation boxes is that the volume of a three-dimensional point cloud
378 + is not well-defined.  In order to compute the compressibility of a
379 + bulk material, we make an assumption that the number density, $\rho =
380 + \frac{N}{V}$, is uniform within some region of the cloud.  The
381 + compressibility can then be expressed in terms of the average number
382 + of particles in that region,
383 + \begin{equation}
384 + \kappa_{T} = \frac{1}{N} \left ( \frac{\partial N}{\partial P} \right
385 + )_{T}
386 + \label{eq:BMN}
387 + \end{equation}
388 + The region we used is a spherical volume of 10 \AA\ radius centered in
389 + the middle of the cluster. $N$ is the average number of molecules
390 + found within this region throughout a given simulation. The geometry
391 + and size of the region is arbitrary, and any bulk-like portion of the
392 + cluster can be used to compute the bulk modulus.
393 +
394 + One might assume that the volume of the convex hull could be taken as
395 + the system volume in the compressibility expression (Eq. \ref{eq:BM}),
396 + but this has implications at lower pressures (which are explored in
397 + detail in the section on water droplets).
398 +
399 + The metallic force field in use for the gold nanoparticles is the
400 + quantum Sutton-Chen (QSC) model.\cite{PhysRevB.59.3527} In all
401 + simulations involving point charges, we utilized damped shifted-force
402 + (DSF) electrostatics\cite{Fennell06} which is a variant of the Wolf
403 + summation\cite{wolf:8254} that has been shown to provide good forces
404 + and torques on molecular models for water in a computationally
405 + efficient manner.\cite{Fennell06} The damping parameter ($\alpha$) was
406 + set to 0.18 \AA$^{-1}$, and the cutoff radius was set to 12 \AA.  The
407 + Spohr potential was adopted in depicting the interaction between metal
408 + atoms and the SPC/E water molecules.\cite{ISI:000167766600035}
409 +
410   \subsection{Bulk modulus of gold nanoparticles}
411  
412 + The bulk modulus is well-known for gold, and it provides a good first
413 + test of how the method compares to other similar methods.  
414 +
415 +
416   \begin{figure}
417   \includegraphics[width=\linewidth]{pressure_tb}
418   \caption{Pressure response is rapid (18 \AA gold nanoparticle), target
# Line 376 | Line 440 | Both NVT \cite{Glattli2002} and NPT \cite{Motakabbir19
440  
441   \subsection{Compressibility of SPC/E water clusters}
442  
443 < 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.
443 > Prior molecular dynamics simulations on SPC/E water (both in
444 > NVT~\cite{Glattli2002} and NPT~\cite{Motakabbir1990, Pi2009}
445 > ensembles) have yielded values for the isothermal compressibility that
446 > agree well with experiment.\cite{Fine1973} The results of two
447 > different approaches for computing the isothermal compressibility from
448 > Langevin Hull simulations for pressures between 1 and 6500 atm are
449 > shown in Fig. \ref{fig:compWater} along with compressibility values
450 > obtained from both other SPC/E simulations and experiment.
451 > Compressibility values from all references are for applied pressures
452 > within the range 1 - 1000 atm.
453  
454   \begin{figure}
455   \includegraphics[width=\linewidth]{new_isothermalN}
456   \caption{Compressibility of SPC/E water}
457 < \label{compWater}
457 > \label{fig:compWater}
458   \end{figure}
459  
460 < 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.
460 > Isothermal compressibility values calculated using the number density
461 > (Eq. \ref{eq:BMN}) expression are in good agreement with experimental
462 > and previous simulation work throughout the 1 - 1000 atm pressure
463 > regime.  Compressibilities computed using the Hull volume, however,
464 > deviate dramatically from the experimental values at low applied
465 > pressures.  The reason for this deviation is quite simple; at low
466 > applied pressures, the liquid is in equilibrium with a vapor phase,
467 > and it is entirely possible for one (or a few) molecules to drift away
468 > from the liquid cluster (see Fig. \ref{fig:coneOfShame}).  At low
469 > pressures, the restoring forces on the facets are very gentle, and
470 > this means that the hulls often take on relatively distorted
471 > geometries which include large volumes of empty space.
472  
473 < \begin{equation}
474 < \kappa_{T} = -\frac{1}{V} \left ( \frac{\partial V}{\partial P} \right )_{T}
475 < \end{equation}
473 > \begin{figure}
474 > \includegraphics[width=\linewidth]{flytest2}
475 > \caption{At low pressures, the liquid is in equilibrium with the vapor
476 >  phase, and isolated molecules can detach from the liquid droplet.
477 >  This is expected behavior, but the reported volume of the convex
478 >  hull includes large regions of empty space.  For this reason,
479 >  compressibilities are computed using local number densities rather
480 >  than hull volumes.}
481 > \label{fig:coneOfShame}
482 > \end{figure}
483  
484 + At higher pressures, the equilibrium favors the liquid phase, and the
485 + hull geometries are much more compact.  Because of the liquid-vapor
486 + effect on the convex hull, the regional number density approach
487 + (Eq. \ref{eq:BMN}) provides more reliable estimates of the bulk
488 + modulus.
489  
394 Assuming a uniform density, we can use the relationship $\rho = \frac{N}{V}$ to rewrite the isothermal compressibility formula as
395
396 \begin{equation}
397 \kappa_{T} = \frac{1}{N} \left ( \frac{\partial N}{\partial P} \right )_{T}
398 \end{equation}
399
400 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
490   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.
491  
492 + Regardless of the difficulty in obtaining accurate hull
493 + volumes at low temperature and pressures, the Langevin Hull NPT method
494 + provides reasonable isothermal compressibility values for water
495 + through a large range of pressures.
496 +
497   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
498  
499   \begin{equation}
# Line 448 | Line 541 | The orientational preference exhibited by hull molecul
541  
542   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.
543  
451
544   \subsection{Heterogeneous nanoparticle / water mixtures}
545  
546  
547 < \section{Appendix A: Hydrodynamic tensor for triangular facets}
547 > \section*{Appendix A: Computing Convex Hulls on Parallel Computers}
548  
549 < \section{Appendix B: Computing Convex Hulls on Parallel Computers}
458 <
459 < \section{Acknowledgments}
549 > \section*{Acknowledgments}
550   Support for this project was provided by the
551   National Science Foundation under grant CHE-0848243. Computational
552   time was provided by the Center for Research Computing (CRC) at the

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