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1 %% This BibTeX bibliography file was created using BibDesk.
2 %% http://bibdesk.sourceforge.net/
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5 %% Created for Shenyu Kuang at 2011-04-28 11:23:43 -0400
6
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8 %% Saved with string encoding Unicode (UTF-8)
9
10
11
12 @article{doi:10.1021/jp034405s,
13 Abstract = { We use the universal force field (UFF) developed by Rapp{\'e} et al. (Rapp{\'e}, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M. J. Am. Chem. Soc. 1992, 114, 10024) and the specific classical potentials developed from ab initio calculations for Au−benzenedithiol (BDT) molecule interaction to perform molecular dynamics (MD) simulations of a BDT monolayer on an extended Au(111) surface. The simulation system consists of 100 BDT molecules and three rigid Au layers in a simulation box that is rhombic in the plane of the Au surface. A multiple time scale algorithm, the double-reversible reference system propagator algorithm (double RESPA) based on the Nos{\'e}−Hoover dynamics scheme, and the Ewald summation with a boundary correction term for the treatment of long-range electrostatic interactions in a 2-D slab have been incorporated into the simulation technique. We investigate the local bonding properties of Au−BDT contacts and molecular orientation distributions of BDT molecules. These results show that whereas different basis sets from ab initio calculations may generate different local bonding geometric parameters (the bond length, etc.) the packing structures of BDT molecules maintain approximately the same well-ordered herringbone structure with small peak differences in the probability distributions of global geometric parameters. The methodology developed here opens an avenue for classical simulations of a metal−molecule−metal complex in molecular electronics devices. },
14 Author = {Leng and Keffer, David J. and Cummings, Peter T.},
15 Date-Added = {2011-04-28 11:23:28 -0400},
16 Date-Modified = {2011-04-28 11:23:28 -0400},
17 Doi = {10.1021/jp034405s},
18 Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp034405s},
19 Journal = {The Journal of Physical Chemistry B},
20 Number = {43},
21 Pages = {11940-11950},
22 Title = {Structure and Dynamics of a Benzenedithiol Monolayer on a Au(111) Surface},
23 Url = {http://pubs.acs.org/doi/abs/10.1021/jp034405s},
24 Volume = {107},
25 Year = {2003},
26 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp034405s},
27 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp034405s}}
28
29 @article{OPLSAA,
30 Abstract = {null},
31 Annote = {doi: 10.1021/ja9621760},
32 Author = {Jorgensen, William L. and Maxwell, David S. and Tirado-Rives, Julian},
33 Date = {1996/01/01},
34 Date-Added = {2011-02-04 18:54:58 -0500},
35 Date-Modified = {2011-02-04 18:54:58 -0500},
36 Do = {10.1021/ja9621760},
37 Isbn = {0002-7863},
38 Journal = {Journal of the American Chemical Society},
39 M3 = {doi: 10.1021/ja9621760},
40 Month = {01},
41 Number = {45},
42 Pages = {11225--11236},
43 Publisher = {American Chemical Society},
44 Title = {Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids},
45 Ty = {JOUR},
46 Url = {http://dx.doi.org/10.1021/ja9621760},
47 Volume = {118},
48 Year = {1996},
49 Year1 = {1996/01/01},
50 Bdsk-Url-1 = {http://dx.doi.org/10.1021/ja9621760}}
51
52 @article{TraPPE-UA.alkylbenzenes,
53 Author = {Wick, Collin D. and Martin, Marcus G. and Siepmann, J. Ilja},
54 Date-Added = {2011-02-04 18:31:46 -0500},
55 Date-Modified = {2011-02-04 18:32:22 -0500},
56 Doi = {10.1021/jp001044x},
57 Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp001044x},
58 Journal = {The Journal of Physical Chemistry B},
59 Number = {33},
60 Pages = {8008-8016},
61 Title = {Transferable Potentials for Phase Equilibria. 4. United-Atom Description of Linear and Branched Alkenes and Alkylbenzenes},
62 Url = {http://pubs.acs.org/doi/abs/10.1021/jp001044x},
63 Volume = {104},
64 Year = {2000},
65 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp001044x},
66 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp001044x}}
67
68 @article{TraPPE-UA.alkanes,
69 Author = {Martin, Marcus G. and Siepmann, J. Ilja},
70 Date-Added = {2011-02-04 18:01:31 -0500},
71 Date-Modified = {2011-02-04 18:02:19 -0500},
72 Doi = {10.1021/jp972543+},
73 Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp972543%2B},
74 Journal = {The Journal of Physical Chemistry B},
75 Number = {14},
76 Pages = {2569-2577},
77 Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes},
78 Url = {http://pubs.acs.org/doi/abs/10.1021/jp972543%2B},
79 Volume = {102},
80 Year = {1998},
81 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp972543+},
82 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp972543+}}
83
84 @article{TraPPE-UA.thiols,
85 Author = {Lubna, Nusrat and Kamath, Ganesh and Potoff, Jeffrey J. and Rai, Neeraj and Siepmann, J. Ilja},
86 Date-Added = {2011-02-04 17:51:03 -0500},
87 Date-Modified = {2011-02-04 17:54:20 -0500},
88 Doi = {10.1021/jp0549125},
89 Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp0549125},
90 Journal = {The Journal of Physical Chemistry B},
91 Number = {50},
92 Pages = {24100-24107},
93 Title = {Transferable Potentials for Phase Equilibria. 8. United-Atom Description for Thiols, Sulfides, Disulfides, and Thiophene},
94 Url = {http://pubs.acs.org/doi/abs/10.1021/jp0549125},
95 Volume = {109},
96 Year = {2005},
97 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp0549125},
98 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp0549125}}
99
100 @article{vlugt:cpc2007154,
101 Author = {Philipp Schapotschnikow and Ren{\'e} Pool and Thijs J.H. Vlugt},
102 Date-Added = {2011-02-01 16:00:11 -0500},
103 Date-Modified = {2011-02-04 18:21:59 -0500},
104 Doi = {DOI: 10.1016/j.cpc.2007.02.028},
105 Issn = {0010-4655},
106 Journal = {Computer Physics Communications},
107 Keywords = {Gold nanocrystals},
108 Note = {Proceedings of the Conference on Computational Physics 2006 - CCP 2006, Conference on Computational Physics 2006},
109 Number = {1-2},
110 Pages = {154 - 157},
111 Title = {Selective adsorption of alkyl thiols on gold in different geometries},
112 Url = {http://www.sciencedirect.com/science/article/B6TJ5-4N3WYP0-1/2/66dbe8892f456c230b9b8fcd9c23f456},
113 Volume = {177},
114 Year = {2007},
115 Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TJ5-4N3WYP0-1/2/66dbe8892f456c230b9b8fcd9c23f456},
116 Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.cpc.2007.02.028}}
117
118 @article{packmol,
119 Author = {L. Mart\'{\i}nez and R. Andrade and Ernesto G. Birgin and Jos{\'e} Mario Mart\'{\i}nez},
120 Bibsource = {DBLP, http://dblp.uni-trier.de},
121 Date-Added = {2011-02-01 15:13:02 -0500},
122 Date-Modified = {2011-02-01 15:14:25 -0500},
123 Ee = {http://dx.doi.org/10.1002/jcc.21224},
124 Journal = {Journal of Computational Chemistry},
125 Number = {13},
126 Pages = {2157-2164},
127 Title = {PACKMOL: A package for building initial configurations for molecular dynamics simulations},
128 Volume = {30},
129 Year = {2009}}
130
131 @article{kuang:164101,
132 Author = {Shenyu Kuang and J. Daniel Gezelter},
133 Date-Added = {2011-01-31 17:12:35 -0500},
134 Date-Modified = {2011-01-31 17:12:35 -0500},
135 Doi = {10.1063/1.3499947},
136 Eid = {164101},
137 Journal = {The Journal of Chemical Physics},
138 Keywords = {linear momentum; molecular dynamics method; thermal conductivity; total energy; viscosity},
139 Number = {16},
140 Numpages = {9},
141 Pages = {164101},
142 Publisher = {AIP},
143 Title = {A gentler approach to RNEMD: Nonisotropic velocity scaling for computing thermal conductivity and shear viscosity},
144 Url = {http://link.aip.org/link/?JCP/133/164101/1},
145 Volume = {133},
146 Year = {2010},
147 Bdsk-Url-1 = {http://link.aip.org/link/?JCP/133/164101/1},
148 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3499947}}
149
150 @article{muller:014102,
151 Author = {Thomas J. Muller and Michael Al-Samman and Florian Muller-Plathe},
152 Date-Added = {2010-09-16 19:19:25 -0400},
153 Date-Modified = {2010-09-16 19:19:25 -0400},
154 Doi = {10.1063/1.2943312},
155 Eid = {014102},
156 Journal = {The Journal of Chemical Physics},
157 Keywords = {intramolecular mechanics; Lennard-Jones potential; molecular dynamics method; thermostats; viscosity},
158 Number = {1},
159 Numpages = {8},
160 Pages = {014102},
161 Publisher = {AIP},
162 Title = {The influence of thermostats and manostats on reverse nonequilibrium molecular dynamics calculations of fluid viscosities},
163 Url = {http://link.aip.org/link/?JCP/129/014102/1},
164 Volume = {129},
165 Year = {2008},
166 Bdsk-Url-1 = {http://link.aip.org/link/?JCP/129/014102/1},
167 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2943312}}
168
169 @article{wolf:8254,
170 Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
171 Date-Added = {2010-09-16 19:01:51 -0400},
172 Date-Modified = {2010-09-16 19:01:51 -0400},
173 Doi = {10.1063/1.478738},
174 Journal = {J. Chem. Phys.},
175 Keywords = {POTENTIAL ENERGY; COULOMB FIELD; COULOMB ENERGY; LATTICE PARAMETERS; potential energy functions; lattice dynamics; lattice energy},
176 Number = {17},
177 Pages = {8254-8282},
178 Publisher = {AIP},
179 Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r[sup -1] summation},
180 Url = {http://link.aip.org/link/?JCP/110/8254/1},
181 Volume = {110},
182 Year = {1999},
183 Bdsk-Url-1 = {http://link.aip.org/link/?JCP/110/8254/1},
184 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.478738}}
185
186 @article{HeX:1993,
187 Abstract = {A recently developed non-equilibrium molecular dynamics algorithm for
188 heat conduction is used to compute the thermal conductivity, thermal
189 diffusion factor, and heat of transfer in binary Lennard-Jones
190 mixtures. An internal energy flux is established with local source and
191 sink terms for kinetic energy.
192 Simulations of isotope mixtures covering a range of densities and mass
193 ratios show that the lighter component prefers the hot side of the
194 system at stationary state. This implies a positive thermal diffusion
195 factor in the definition we have adopted here. The molecular basis for
196 the Soret effect is studied by analysing the energy flux through the
197 system. In all cases we found that there is a difference in the
198 relative contributions when we compare the hot and cold sides of the
199 system. The contribution from the lighter component is predominantly
200 flux of kinetic energy, and this contribution increases from the cold
201 to the hot side. The contribution from the heavier component is
202 predominantly energy transfer through molecular interactions, and it
203 increases from the hot to the cold side. This explains why the thermal
204 diffusion factor is positive; heal is conducted more effectively
205 through the system if the lighter component is enriched at the hot
206 side. Even for very large heat fluxes, we find a linear or almost
207 linear temperature profile through the system, and a constant thermal
208 conductivity. The entropy production per unit volume and unit time
209 increases from the hot to the cold side.},
210 Author = {Hafskjold, B and Ikeshoji, T and Ratkje, SK},
211 Date-Added = {2010-09-15 16:52:45 -0400},
212 Date-Modified = {2010-09-15 16:54:23 -0400},
213 Issn = {{0026-8976}},
214 Journal = {Mol. Phys.},
215 Month = {DEC},
216 Number = {6},
217 Pages = {1389-1412},
218 Title = {ON THE MOLECULAR MECHANISM OF THERMAL-DIFFUSION IN LIQUIDS},
219 Unique-Id = {ISI:A1993MQ34500009},
220 Volume = {80},
221 Year = {1993}}
222
223 @article{HeX:1994,
224 Abstract = {This paper presents a new algorithm for non-equilibrium molecular
225 dynamics, where a temperature gradient is established in a system with
226 periodic boundary conditions. At each time step in the simulation, a
227 fixed amount of energy is supplied to a hot region by scaling the
228 velocity of each particle in it, subject to conservation of total
229 momentum. An equal amount of energy is likewise withdrawn from a cold
230 region at each time step. Between the hot and cold regions is a region
231 through which an energy flux is established. Two configurations of hot
232 and cold regions are proposed. Using a stacked layer structure, the
233 instantaneous local energy flux for a 128-particle Lennard-Jones system
234 in liquid was found to be in good agreement with the macroscopic theory
235 of heat conduction at stationary state, except in and near the hot and
236 cold regions. Thermal conductivity calculated for the 128-particle
237 system was about 10\% smaller than the literature value obtained by
238 molecular dynamics calculations. One run with a 1024-particle system
239 showed an agreement with the literature value within statistical error
240 (1-2\%). Using a unit cell with a cold spherical region at the centre
241 and a hot region in the perimeter of the cube, an initial gaseous state
242 of argon was separated into gas and liquid phases. Energy fluxes due to
243 intermolecular energy transfer and transport of kinetic energy dominate
244 in the liquid and gas phases, respectively.},
245 Author = {Ikeshoji, T and Hafskjold, B},
246 Date-Added = {2010-09-15 16:52:45 -0400},
247 Date-Modified = {2010-09-15 16:54:37 -0400},
248 Issn = {0026-8976},
249 Journal = {Mol. Phys.},
250 Month = {FEB},
251 Number = {2},
252 Pages = {251-261},
253 Title = {NONEQUILIBRIUM MOLECULAR-DYNAMICS CALCULATION OF HEAT-CONDUCTION IN LIQUID AND THROUGH LIQUID-GAS INTERFACE},
254 Unique-Id = {ISI:A1994MY17400001},
255 Volume = {81},
256 Year = {1994}}
257
258 @article{plech:195423,
259 Author = {A. Plech and V. Kotaidis and S. Gresillon and C. Dahmen and G. von Plessen},
260 Date-Added = {2010-08-12 11:34:55 -0400},
261 Date-Modified = {2010-08-12 11:34:55 -0400},
262 Eid = {195423},
263 Journal = {Phys. Rev. B},
264 Keywords = {gold; laser materials processing; melting; nanoparticles; time resolved spectra; X-ray scattering; lattice dynamics; high-speed optical techniques; cooling; thermal resistance; thermal conductivity; long-range order},
265 Local-Url = {file://localhost/Users/charles/Documents/Papers/PhysRevB_70_195423.pdf},
266 Number = {19},
267 Numpages = {7},
268 Pages = {195423},
269 Publisher = {APS},
270 Title = {Laser-induced heating and melting of gold nanoparticles studied by time-resolved x-ray scattering},
271 Url = {http://link.aps.org/abstract/PRB/v70/e195423},
272 Volume = {70},
273 Year = {2004},
274 Bdsk-Url-1 = {http://link.aps.org/abstract/PRB/v70/e195423}}
275
276 @article{Wilson:2002uq,
277 Abstract = {We investigate suspensions of 3-10 nm diameter Au, Pt, and AuPd nanoparticles as probes of thermal transport in fluids and determine approximate values for the thermal conductance G of the particle/fluid interfaces. Subpicosecond lambda=770 nm optical pulses from a Ti:sapphire mode-locked laser are used to heat the particles and interrogate the decay of their temperature through time-resolved changes in optical absorption. The thermal decay of alkanethiol-terminated Au nanoparticles in toluene is partially obscured by other effects; we set a lower limit G>20 MW m(-2)K(-1). The thermal decay of citrate-stabilized Pt nanoparticles in water gives Gapproximate to130 MW m(-2) K-1. AuPd alloy nanoparticles in toluene and stabilized by alkanethiol termination give Gapproximate to5 MW m(-2) K-1. The measured G are within a factor of 2 of theoretical estimates based on the diffuse-mismatch model.},
278 Author = {Wilson, OM and Hu, XY and Cahill, DG and Braun, PV},
279 Date-Added = {2010-08-12 11:31:02 -0400},
280 Date-Modified = {2010-08-12 11:31:02 -0400},
281 Doi = {ARTN 224301},
282 Journal = {Phys. Rev. B},
283 Local-Url = {file://localhost/Users/charles/Documents/Papers/e2243010.pdf},
284 Title = {Colloidal metal particles as probes of nanoscale thermal transport in fluids},
285 Volume = {66},
286 Year = {2002},
287 Bdsk-Url-1 = {http://dx.doi.org/224301}}
288
289 @article{RevModPhys.61.605,
290 Author = {Swartz, E. T. and Pohl, R. O.},
291 Date-Added = {2010-08-06 17:03:01 -0400},
292 Date-Modified = {2010-08-06 17:03:01 -0400},
293 Doi = {10.1103/RevModPhys.61.605},
294 Journal = {Rev. Mod. Phys.},
295 Month = {Jul},
296 Number = {3},
297 Numpages = {63},
298 Pages = {605--668},
299 Publisher = {American Physical Society},
300 Title = {Thermal boundary resistance},
301 Volume = {61},
302 Year = {1989},
303 Bdsk-Url-1 = {http://dx.doi.org/10.1103/RevModPhys.61.605}}
304
305 @article{cahill:793,
306 Author = {David G. Cahill and Wayne K. Ford and Kenneth E. Goodson and Gerald D. Mahan and Arun Majumdar and Humphrey J. Maris and Roberto Merlin and Simon R. Phillpot},
307 Date-Added = {2010-08-06 17:02:22 -0400},
308 Date-Modified = {2010-08-06 17:02:22 -0400},
309 Doi = {10.1063/1.1524305},
310 Journal = {J. Applied Phys.},
311 Keywords = {nanostructured materials; reviews; thermal conductivity; interface phenomena; molecular dynamics method; thermal management (packaging); Boltzmann equation; carbon nanotubes; porosity; semiconductor superlattices; thermoreflectance; interface phonons; thermoelectricity; phonon-phonon interactions},
312 Number = {2},
313 Pages = {793-818},
314 Publisher = {AIP},
315 Title = {Nanoscale thermal transport},
316 Url = {http://link.aip.org/link/?JAP/93/793/1},
317 Volume = {93},
318 Year = {2003},
319 Bdsk-Url-1 = {http://link.aip.org/link/?JAP/93/793/1},
320 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1524305}}
321
322 @inbook{Hoffman:2001sf,
323 Address = {New York},
324 Annote = {LDR 01107cam 2200253 a 4500
325 001 12358442
326 005 20070910074423.0
327 008 010326s2001 nyua b 001 0 eng
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329 925 0 $aacquire$b2 shelf copies$xpolicy default
330 955 $ato ASCD pc23 03-26-01; jp20 03-27-01 to subj; jp99 to SL 03-27-01; jp85 to Dewey 03-27-01; aa01 03-28-01$aps02 2001-10-04 bk rec'd, to CIP ver.;$fpv04 2001-10-31 CIP ver to BCCD$ajp01 2001-12-06 c. 2 to BCCD
331 010 $a 2001028633
332 020 $a0824704436 (acid-free paper)
333 040 $aDLC$cDLC$dDLC
334 050 00 $aQA297$b.H588 2001
335 082 00 $a519.4$221
336 100 1 $aHoffman, Joe D.,$d1934-
337 245 10 $aNumerical methods for engineers and scientists /$cJoe D. Hoffman.
338 250 $a2nd ed., rev. and expanded.
339 260 $aNew York :$bMarcel Dekker,$cc2001.
340 300 $axi, 823 p. :$bill. ;$c26 cm.
341 504 $aIncludes bibliographical references (p. 775-777) and index.
342 650 0 $aNumerical analysis.
343 856 42 $3Publisher description$uhttp://www.loc.gov/catdir/enhancements/fy0743/2001028633-d.html
344 },
345 Author = {Hoffman, Joe D.},
346 Call-Number = {QA297},
347 Date-Added = {2010-07-15 16:32:02 -0400},
348 Date-Modified = {2010-07-19 16:49:37 -0400},
349 Dewey-Call-Number = {519.4},
350 Edition = {2nd ed., rev. and expanded},
351 Genre = {Numerical analysis},
352 Isbn = {0824704436 (acid-free paper)},
353 Library-Id = {2001028633},
354 Pages = {157},
355 Publisher = {Marcel Dekker},
356 Title = {Numerical methods for engineers and scientists},
357 Url = {http://www.loc.gov/catdir/enhancements/fy0743/2001028633-d.html},
358 Year = {2001},
359 Bdsk-Url-1 = {http://www.loc.gov/catdir/enhancements/fy0743/2001028633-d.html}}
360
361 @article{Vardeman:2008fk,
362 Abstract = {Using molecular dynamics simulations, we have simulated the rapid cooling experienced by bimetallic nanoparticles following laser excitation at the plasmon resonance and find evidence that glassy beads, specifically Ag-Cu bimetallic particles at the eutectic composition (60\% Ag, 40\% Cu), can be formed during these experiments. The bimetallic nanoparticles are embedded in an implicit solvent with a viscosity tuned to yield cooling curves that match the experimental cooling behavior as closely as possible. Because the nanoparticles have a large surface-to-volume ratio, experimentally realistic cooling rates are accessible via relatively short simulations. The presence of glassy structural features was verified using bond orientational order parameters that are sensitive to the formation of local icosahedral ordering in condensed phases. As the particles cool from the liquid droplet state into glassy beads, a silver-rich monolayer develops on the outer surface and local icosahedra can develop around the silver atoms in this monolayer. However, we observe a strong preference for the local icosahedral ordering around the copper atoms in the particles. As the particles cool, these local icosahedral structures grow to include a larger fraction of the atoms in the nanoparticle, eventually leading to a glassy nanosphere.},
363 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
364 Author = {{Vardeman II}, Charles F. and Gezelter, J. Daniel},
365 Date-Added = {2010-07-13 11:48:22 -0400},
366 Date-Modified = {2010-07-19 16:20:01 -0400},
367 Doi = {DOI 10.1021/jp710063g},
368 Isi = {000253512400021},
369 Isi-Recid = {160903603},
370 Isi-Ref-Recids = {144152922 81445483 98913099 146167982 55512304 50985260 52031423 29272311 151055545 134895634 130292830 101988637 100757730 98524559 123952006 6025131 59492217 2078548 135495737 136941603 90709964 160903604 130558416 113800688 30137926 117888234 63632785 38926953 158293976 135246439 125693419 125789026 155583142 156430464 65888620 130160487 97576420 109490154 150229560 116057234 134425927 142869781 121706070 89390336 119150946 143383743 64066027 171282998 142688207 51429664 84591083 127696312 58160909 155366996 155654757 137551818 128633299 109033408 120457571 171282999 124947095 126857514 49630702 64115284 84689627 71842426 96309965 79034659 92658330 146168029 119238036 144824430 132319357 160903607 171283000 100274448},
371 Journal = {J. Phys. Chem. C},
372 Month = mar,
373 Number = {9},
374 Pages = {3283-3293},
375 Publisher = {AMER CHEMICAL SOC},
376 Times-Cited = {0},
377 Title = {Simulations of laser-induced glass formation in Ag-Cu nanoparticles},
378 Volume = {112},
379 Year = {2008},
380 Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000253512400021}}
381
382 @article{PhysRevB.59.3527,
383 Author = {Qi, Yue and \c{C}a\v{g}in, Tahir and Kimura, Yoshitaka and {Goddard III}, William A.},
384 Date-Added = {2010-07-13 11:44:08 -0400},
385 Date-Modified = {2010-07-13 11:44:08 -0400},
386 Doi = {10.1103/PhysRevB.59.3527},
387 Journal = {Phys. Rev. B},
388 Local-Url = {file://localhost/Users/charles/Documents/Papers/Qi/1999.pdf},
389 Month = {Feb},
390 Number = {5},
391 Numpages = {6},
392 Pages = {3527-3533},
393 Publisher = {American Physical Society},
394 Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals:\quad{}{C}u-{A}g and {C}u-{N}i},
395 Volume = {59},
396 Year = {1999},
397 Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.59.3527}}
398
399 @article{Medasani:2007uq,
400 Abstract = {We employ first-principles and empirical computational methods to study the surface energy and surface stress of silver nanoparticles. The structures, cohesive energies, and lattice contractions of spherical Ag nanoclusters in the size range 0.5-5.5 nm are analyzed using two different theoretical approaches: an ab initio density functional pseudopotential technique combined with the generalized gradient approximation and the embedded atom method. The surface energies and stresses obtained via the embedded atom method are found to be in good agreement with those predicted by the gradient-corrected ab initio density functional formalism. We estimate the surface energy of Ag nanoclusters to be in the range of 1.0-2.2 J/m(2). Our values are close to the bulk surface energy of silver, but are significantly lower than the recently reported value of 7.2 J/m(2) for free Ag nanoparticles derived from the Kelvin equation.},
401 Author = {Medasani, Bharat and Park, Young Ho and Vasiliev, Igor},
402 Date-Added = {2010-07-13 11:43:15 -0400},
403 Date-Modified = {2010-07-13 11:43:15 -0400},
404 Doi = {ARTN 235436},
405 Journal = {Phys. Rev. B},
406 Local-Url = {file://localhost/Users/charles/Documents/Papers/PhysRevB_75_235436.pdf},
407 Title = {Theoretical study of the surface energy, stress, and lattice contraction of silver nanoparticles},
408 Volume = {75},
409 Year = {2007},
410 Bdsk-Url-1 = {http://dx.doi.org/235436}}
411
412 @article{Wang:2005qy,
413 Abstract = {The surface structures of cubo-octahedral Pt-Mo nanoparticles have been investigated using the Monte Carlo method and modified embedded atom method potentials that we developed for Pt-Mo alloys. The cubo-octahedral Pt-Mo nanoparticles are constructed with disordered fcc configurations, with sizes from 2.5 to 5.0 nm, and with Pt concentrations from 60 to 90 atom \%. The equilibrium Pt-Mo nanoparticle configurations were generated through Monte Carlo simulations allowing both atomic displacements and element exchanges at 600 K. We predict that the Pt atoms weakly segregate to the surfaces of such nanoparticles. The Pt concentrations in the surface are calculated to be 5-14 atom \% higher than the Pt concentrations of the nanoparticles. Moreover, the Pt atoms preferentially segregate to the facet sites of the surface, while the Pt and Mo atoms tend to alternate along the edges and vertexes of these nanoparticles. We found that decreasing the size or increasing the Pt concentration leads to higher Pt concentrations but fewer Pt-Mo pairs in the Pt-Mo nanoparticle surfaces.},
414 Author = {Wang, GF and Van Hove, MA and Ross, PN and Baskes, MI},
415 Date-Added = {2010-07-13 11:42:50 -0400},
416 Date-Modified = {2010-07-13 11:42:50 -0400},
417 Doi = {DOI 10.1021/jp050116n},
418 Journal = {J. Phys. Chem. B},
419 Pages = {11683-11692},
420 Title = {Surface structures of cubo-octahedral Pt-Mo catalyst nanoparticles from Monte Carlo simulations},
421 Volume = {109},
422 Year = {2005},
423 Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp050116n}}
424
425 @article{Chui:2003fk,
426 Abstract = {Molecular dynamics simulations of a platinum nanocluster consisting 250 atoms were performed at different temperatures between 70 K and 298 K. The semi-empirical, many-body Sutton-Chen (SC) potential was used to model the interatomic interaction in the metallic system. Regions of core or bulk-like atoms and surface atoms can be defined from analyses of structures, atomic coordination, and the local density function of atoms as defined in the SC potential. The core atoms in the nanoparticle behave as bulk-like metal atoms with a predominant face centered cubic (fcc) packing. The interface between surface atoms and core atoms is marked by a peak in the local density function and corresponds to near surface atoms. The near surface atoms and surface atoms prefer a hexagonal closed packing (hcp). The temperature and size effects on structures of the nanoparticle and the dynamics of the surface region and the core region are discussed.},
427 Author = {Chui, YH and Chan, KY},
428 Date-Added = {2010-07-13 11:42:32 -0400},
429 Date-Modified = {2010-07-13 11:42:32 -0400},
430 Doi = {DOI 10.1039/b302122j},
431 Journal = {Phys. Chem. Chem. Phys.},
432 Pages = {2869-2874},
433 Title = {Analyses of surface and core atoms in a platinum nanoparticle},
434 Volume = {5},
435 Year = {2003},
436 Bdsk-Url-1 = {http://dx.doi.org/10.1039/b302122j}}
437
438 @article{Sankaranarayanan:2005lr,
439 Abstract = {Bimetallic nanoclusters are of interest because of their utility in catalysis and sensors, The thermal characteristics of bimetallic Pt-Pd nanoclusters of different sizes and compositions were investigated through molecular dynamics simulations using quantum Sutton-Chen (QSC) many-body potentials, Monte Carlo simulations employing the bond order simulation model were used to generate minimum energy configurations, which were utilized as the starting point for molecular dynamics simulations. The calculated initial configurations of the Pt-Pd system consisted of surface segregated Pd atoms and a Pt-rich core, Melting characteristics were studied by following the changes in potential energy and heat capacity as functions of temperature, Structural changes accompanying the thermal evolution were studied by the bond order parameter method. The Pt-Pd clusters exhibited a two-stage melting: surface melting of the external Pd atoms followed by homogeneous melting of the Pt core. These transitions were found to depend on the composition and size of the nanocluster. Melting temperatures of the nanoclusters were found to be much lower than those of bulk Pt and Pd. Bulk melting temperatures of Pd and Pt simulated using periodic boundary conditions compare well with experimental values, thus providing justification for the use of QSC potentials in these simulations. Deformation parameters were calculated to characterize the structural evolution resulting from diffusion of Pd and Pt atoms, The results indicate that in Pd-Pt clusters, Pd atoms prefer to remain at the surface even after melting. In addition, Pt also tends to diffuse to the surface after melting due to reduction of its surface energy with temperature. This mixing pattern is different from those reported in some of the earlier Studies on melting of bimetallics.},
440 Author = {Sankaranarayanan, SKRS and Bhethanabotla, VR and Joseph, B},
441 Date-Added = {2010-07-13 11:42:13 -0400},
442 Date-Modified = {2010-07-13 11:42:13 -0400},
443 Doi = {ARTN 195415},
444 Journal = {Phys. Rev. B},
445 Title = {Molecular dynamics simulation study of the melting of Pd-Pt nanoclusters},
446 Volume = {71},
447 Year = {2005},
448 Bdsk-Url-1 = {http://dx.doi.org/195415}}
449
450 @article{Vardeman-II:2001jn,
451 Author = {C.~F. {Vardeman II} and J.~D. Gezelter},
452 Date-Added = {2010-07-13 11:41:50 -0400},
453 Date-Modified = {2010-07-13 11:41:50 -0400},
454 Journal = {J. Phys. Chem. A},
455 Local-Url = {file://localhost/Users/charles/Documents/Papers/Vardeman%20II/2001.pdf},
456 Number = {12},
457 Pages = {2568},
458 Title = {Comparing models for diffusion in supercooled liquids: The eutectic composition of the {A}g-{C}u alloy},
459 Volume = {105},
460 Year = {2001}}
461
462 @article{ShibataT._ja026764r,
463 Author = {Shibata, T. and Bunker, B.A. and Zhang, Z. and Meisel, D. and Vardeman, C.F. and Gezelter, J.D.},
464 Date-Added = {2010-07-13 11:41:36 -0400},
465 Date-Modified = {2010-07-13 11:41:36 -0400},
466 Journal = {J. Amer. Chem. Soc.},
467 Local-Url = {file://localhost/Users/charles/Documents/Papers/ja026764r.pdf},
468 Number = {40},
469 Pages = {11989-11996},
470 Title = {Size-Dependent Spontaneous Alloying of {A}u-{A}g Nanoparticles},
471 Url = {http://dx.doi.org/10.1021/ja026764r},
472 Volume = {124},
473 Year = {2002},
474 Bdsk-Url-1 = {http://dx.doi.org/10.1021/ja026764r}}
475
476 @article{Chen90,
477 Author = {A.~P. Sutton and J. Chen},
478 Date-Added = {2010-07-13 11:40:48 -0400},
479 Date-Modified = {2010-07-13 11:40:48 -0400},
480 Journal = {Phil. Mag. Lett.},
481 Pages = {139-146},
482 Title = {Long-Range Finnis Sinclair Potentials},
483 Volume = 61,
484 Year = {1990}}
485
486 @article{PhysRevB.33.7983,
487 Author = {Foiles, S. M. and Baskes, M. I. and Daw, M. S.},
488 Date-Added = {2010-07-13 11:40:28 -0400},
489 Date-Modified = {2010-07-13 11:40:28 -0400},
490 Doi = {10.1103/PhysRevB.33.7983},
491 Journal = {Phys. Rev. B},
492 Local-Url = {file://localhost/Users/charles/Documents/Papers/p7983_1.pdf},
493 Month = {Jun},
494 Number = {12},
495 Numpages = {8},
496 Pages = {7983-7991},
497 Publisher = {American Physical Society},
498 Title = {Embedded-atom-method functions for the fcc metals {C}u, {A}g, {A}u, {N}i, {P}d, {P}t, and their alloys},
499 Volume = {33},
500 Year = {1986},
501 Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.33.7983}}
502
503 @article{hoover85,
504 Author = {W.~G. Hoover},
505 Date-Added = {2010-07-13 11:24:30 -0400},
506 Date-Modified = {2010-07-13 11:24:30 -0400},
507 Journal = pra,
508 Pages = 1695,
509 Title = {Canonical dynamics: Equilibrium phase-space distributions},
510 Volume = 31,
511 Year = 1985}
512
513 @article{melchionna93,
514 Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
515 Date-Added = {2010-07-13 11:22:17 -0400},
516 Date-Modified = {2010-07-13 11:22:17 -0400},
517 Journal = {Mol. Phys.},
518 Pages = {533-544},
519 Title = {Hoover {\sc npt} dynamics for systems varying in shape and size},
520 Volume = 78,
521 Year = 1993}
522
523 @misc{openmd,
524 Author = {J. Daniel Gezelter and Shenyu Kuang and James Marr and Kelsey Stocker and Chunlei Li and Charles F. Vardeman and Teng Lin and Christopher J. Fennell and Xiuquan Sun and Kyle Daily and Yang Zheng and Matthew A. Meineke},
525 Date-Added = {2010-07-13 11:16:00 -0400},
526 Date-Modified = {2010-07-19 16:27:45 -0400},
527 Howpublished = {Available at {\tt http://openmd.net}},
528 Title = {{OpenMD, an open source engine for molecular dynamics}}}
529
530 @inbook{AshcroftMermin,
531 Address = {Belmont, CA},
532 Author = {Neil W. Ashcroft and N.~David Mermin},
533 Date-Added = {2010-07-12 14:26:49 -0400},
534 Date-Modified = {2010-07-22 13:37:20 -0400},
535 Pages = {21},
536 Publisher = {Brooks Cole},
537 Title = {Solid State Physics},
538 Year = {1976}}
539
540 @book{WagnerKruse,
541 Address = {Berlin},
542 Author = {W. Wagner and A. Kruse},
543 Date-Added = {2010-07-12 14:10:29 -0400},
544 Date-Modified = {2010-07-12 14:13:44 -0400},
545 Publisher = {Springer-Verlag},
546 Title = {Properties of Water and Steam, the Industrial Standard IAPWS-IF97 for the Thermodynamic Properties and Supplementary Equations for Other Properties},
547 Year = {1998}}
548
549 @article{ISI:000266247600008,
550 Abstract = {Temperature dependence of viscosity of butyl-3-methylimidazolium
551 hexafluorophosphate is investigated by non-equilibrium molecular
552 dynamics simulations with cosine-modulated force in the temperature
553 range from 360 to 480K. It is shown that this method is able to
554 correctly predict the shear viscosity. The simulation setting and
555 choice of the force field are discussed in detail. The all-atom force
556 field exhibits a bad convergence and the shear viscosity is
557 overestimated, while the simple united atom model predicts the kinetics
558 very well. The results are compared with the equilibrium molecular
559 dynamics simulations. The relationship between the diffusion
560 coefficient and viscosity is examined by means of the hydrodynamic
561 radii calculated from the Stokes-Einstein equation and the solvation
562 properties are discussed.},
563 Address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND},
564 Affiliation = {Kolafa, J (Reprint Author), Prague Inst Chem Technol, Dept Phys Chem, CR-16628 Prague, Czech Republic. {[}Picalek, Jan; Kolafa, Jiri] Prague Inst Chem Technol, Dept Phys Chem, CR-16628 Prague, Czech Republic.},
565 Author = {Picalek, Jan and Kolafa, Jiri},
566 Author-Email = {jiri.kolafa@vscht.cz},
567 Date-Added = {2010-04-16 13:19:12 -0400},
568 Date-Modified = {2010-04-16 13:19:12 -0400},
569 Doc-Delivery-Number = {448FD},
570 Doi = {10.1080/08927020802680703},
571 Funding-Acknowledgement = {Czech Science Foundation {[}203/07/1006]; Czech Ministry of Education {[}LC512]},
572 Funding-Text = {We gratefully acknowledge a support from the Czech Science Foundation (project 203/07/1006) and the computing facilities from the Czech Ministry of Education (Center for Biomolecules and Complex Molecular Systems, project LC512).},
573 Issn = {0892-7022},
574 Journal = {Mol. Simul.},
575 Journal-Iso = {Mol. Simul.},
576 Keywords = {room temperature ionic liquids; viscosity; non-equilibrium molecular dynamics; solvation; imidazolium},
577 Keywords-Plus = {1-N-BUTYL-3-METHYLIMIDAZOLIUM HEXAFLUOROPHOSPHATE; PHYSICOCHEMICAL PROPERTIES; COMPUTER-SIMULATION; PHYSICAL-PROPERTIES; IMIDAZOLIUM CATION; FORCE-FIELD; AB-INITIO; TEMPERATURE; CHLORIDE; CONDUCTIVITY},
578 Language = {English},
579 Number = {8},
580 Number-Of-Cited-References = {50},
581 Pages = {685-690},
582 Publisher = {TAYLOR \& FRANCIS LTD},
583 Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
584 Times-Cited = {2},
585 Title = {Shear viscosity of ionic liquids from non-equilibrium molecular dynamics simulation},
586 Type = {Article},
587 Unique-Id = {ISI:000266247600008},
588 Volume = {35},
589 Year = {2009},
590 Bdsk-Url-1 = {http://dx.doi.org/10.1080/08927020802680703%7D}}
591
592 @article{Vasquez:2004fk,
593 Abstract = {A method for fast calculation of viscosity from molecular dynamics simulation is revisited. The method consists of using a steady-state periodic perturbation. A methodology to choose the amplitude of the external perturbation, which is one of the major practical issues in the original technique of Gosling et al. {$[$}Mol. Phys. 26: 1475 (1973){$]$} is proposed. The amplitude of the perturbation required for fast caculations and the viscosity values for wide ranges of temperature and density of the Lennard-Jones (LJ) model fluid are reported. The viscosity results are in agreement with recent LJ viscosity calculations. Additionally, the simulations demonstrate that the proposed approach is suitable to efficiently generate viscosity data of good quality.},
594 Author = {Vasquez, V. R. and Macedo, E. A. and Zabaloy, M. S.},
595 Date = {2004/11/02/},
596 Date-Added = {2010-04-16 13:18:48 -0400},
597 Date-Modified = {2010-04-16 13:18:48 -0400},
598 Day = {02},
599 Journal = {Int. J. Thermophys.},
600 M3 = {10.1007/s10765-004-7736-3},
601 Month = {11},
602 Number = {6},
603 Pages = {1799--1818},
604 Title = {Lennard-Jones Viscosities in Wide Ranges of Temperature and Density: Fast Calculations Using a Steady--State Periodic Perturbation Method},
605 Ty = {JOUR},
606 Url = {http://dx.doi.org/10.1007/s10765-004-7736-3},
607 Volume = {25},
608 Year = {2004},
609 Bdsk-Url-1 = {http://dx.doi.org/10.1007/s10765-004-7736-3}}
610
611 @article{hess:209,
612 Author = {Berk Hess},
613 Date-Added = {2010-04-16 12:37:37 -0400},
614 Date-Modified = {2010-04-16 12:37:37 -0400},
615 Doi = {10.1063/1.1421362},
616 Journal = {J. Chem. Phys.},
617 Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
618 Number = {1},
619 Pages = {209-217},
620 Publisher = {AIP},
621 Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
622 Url = {http://link.aip.org/link/?JCP/116/209/1},
623 Volume = {116},
624 Year = {2002},
625 Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
626 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}}
627
628 @article{backer:154503,
629 Author = {J. A. Backer and C. P. Lowe and H. C. J. Hoefsloot and P. D. Iedema},
630 Date-Added = {2010-04-16 12:37:37 -0400},
631 Date-Modified = {2010-04-16 12:37:37 -0400},
632 Doi = {10.1063/1.1883163},
633 Eid = {154503},
634 Journal = {J. Chem. Phys.},
635 Keywords = {Poiseuille flow; flow simulation; Lennard-Jones potential; viscosity; boundary layers; computational fluid dynamics},
636 Number = {15},
637 Numpages = {6},
638 Pages = {154503},
639 Publisher = {AIP},
640 Title = {Poiseuille flow to measure the viscosity of particle model fluids},
641 Url = {http://link.aip.org/link/?JCP/122/154503/1},
642 Volume = {122},
643 Year = {2005},
644 Bdsk-Url-1 = {http://link.aip.org/link/?JCP/122/154503/1},
645 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1883163}}
646
647 @article{daivis:541,
648 Author = {Peter J. Daivis and Denis J. Evans},
649 Date-Added = {2010-04-16 12:05:36 -0400},
650 Date-Modified = {2010-04-16 12:05:36 -0400},
651 Doi = {10.1063/1.466970},
652 Journal = {J. Chem. Phys.},
653 Keywords = {SHEAR; DECANE; FLOW MODELS; VOLUME; PRESSURE; NONEQUILIBRIUM; MOLECULAR DYNAMICS CALCULATIONS; COMPARATIVE EVALUATIONS; SIMULATION; STRAIN RATE; VISCOSITY; KUBO FORMULA},
654 Number = {1},
655 Pages = {541-547},
656 Publisher = {AIP},
657 Title = {Comparison of constant pressure and constant volume nonequilibrium simulations of sheared model decane},
658 Url = {http://link.aip.org/link/?JCP/100/541/1},
659 Volume = {100},
660 Year = {1994},
661 Bdsk-Url-1 = {http://link.aip.org/link/?JCP/100/541/1},
662 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.466970}}
663
664 @article{mondello:9327,
665 Author = {Maurizio Mondello and Gary S. Grest},
666 Date-Added = {2010-04-16 12:05:36 -0400},
667 Date-Modified = {2010-04-16 12:05:36 -0400},
668 Doi = {10.1063/1.474002},
669 Journal = {J. Chem. Phys.},
670 Keywords = {organic compounds; viscosity; digital simulation; molecular dynamics method},
671 Number = {22},
672 Pages = {9327-9336},
673 Publisher = {AIP},
674 Title = {Viscosity calculations of [bold n]-alkanes by equilibrium molecular dynamics},
675 Url = {http://link.aip.org/link/?JCP/106/9327/1},
676 Volume = {106},
677 Year = {1997},
678 Bdsk-Url-1 = {http://link.aip.org/link/?JCP/106/9327/1},
679 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.474002}}
680
681 @article{ISI:A1988Q205300014,
682 Address = {ONE GUNDPOWDER SQUARE, LONDON, ENGLAND EC4A 3DE},
683 Affiliation = {VOGELSANG, R (Reprint Author), RUHR UNIV BOCHUM,UNIV STR 150,D-4630 BOCHUM,FED REP GER. UNIV DUISBURG,THERMODYNAM,D-4100 DUISBURG,FED REP GER.},
684 Author = {Vogelsang, R and Hoheisel, G and Luckas, M},
685 Date-Added = {2010-04-14 16:20:24 -0400},
686 Date-Modified = {2010-04-14 16:20:24 -0400},
687 Doc-Delivery-Number = {Q2053},
688 Issn = {0026-8976},
689 Journal = {Mol. Phys.},
690 Journal-Iso = {Mol. Phys.},
691 Language = {English},
692 Month = {AUG 20},
693 Number = {6},
694 Number-Of-Cited-References = {14},
695 Pages = {1203-1213},
696 Publisher = {TAYLOR \& FRANCIS LTD},
697 Subject-Category = {Physics, Atomic, Molecular \& Chemical},
698 Times-Cited = {12},
699 Title = {SHEAR VISCOSITY AND THERMAL-CONDUCTIVITY OF THE LENNARD-JONES LIQUID COMPUTED USING MOLECULAR-DYNAMICS AND PREDICTED BY A MEMORY FUNCTION MODEL FOR A LARGE NUMBER OF STATES},
700 Type = {Article},
701 Unique-Id = {ISI:A1988Q205300014},
702 Volume = {64},
703 Year = {1988}}
704
705 @article{ISI:000261835100054,
706 Abstract = {Transport properties of liquid methanol and ethanol are predicted by
707 molecular dynamics simulation. The molecular models for the alcohols
708 are rigid, nonpolarizable, and of united-atom type. They were developed
709 in preceding work using experimental vapor-liquid equilibrium data
710 only. Self- and Maxwell-Stefan diffusion coefficients as well as the
711 shear viscosity of methanol, ethanol, and their binary mixture are
712 determined using equilibrium molecular dynamics and the Green-Kubo
713 formalism. Nonequilibrium molecular dynamics is used for predicting the
714 thermal conductivity of the two pure substances. The transport
715 properties of the fluids are calculated over a wide temperature range
716 at ambient pressure and compared with experimental and simulation data
717 from the literature. Overall, a very good agreement with the experiment
718 is found. For instance, the self-diffusion coefficient and the shear
719 viscosity are predicted with average deviations of less than 8\% for
720 the pure alcohols and 12\% for the mixture. The predicted thermal
721 conductivity agrees on average within 5\% with the experimental data.
722 Additionally, some velocity and shear viscosity autocorrelation
723 functions are presented and discussed. Radial distribution functions
724 for ethanol are also presented. The predicted excess volume, excess
725 enthalpy, and the vapor-liquid equilibrium of the binary mixture
726 methanol + ethanol are assessed and agree well with experimental data.},
727 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
728 Affiliation = {Vrabec, J (Reprint Author), Univ Stuttgart, Inst Thermodynam \& Thermal Proc Engn, D-70550 Stuttgart, Germany. {[}Vrabec, Jadran] Univ Stuttgart, Inst Thermodynam \& Thermal Proc Engn, D-70550 Stuttgart, Germany. {[}Guevara-Carrion, Gabriela; Hasse, Hans] Univ Kaiserslautern, Lab Engn Thermodynam, D-67663 Kaiserslautern, Germany. {[}Nieto-Draghi, Carlos] Inst Francais Petr, F-92852 Rueil Malmaison, France.},
729 Author = {Guevara-Carrion, Gabriela and Nieto-Draghi, Carlos and Vrabec, Jadran and Hasse, Hans},
730 Author-Email = {vrabec@itt.uni-stuttgart.de},
731 Date-Added = {2010-04-14 15:43:29 -0400},
732 Date-Modified = {2010-04-14 15:43:29 -0400},
733 Doc-Delivery-Number = {385SY},
734 Doi = {10.1021/jp805584d},
735 Issn = {1520-6106},
736 Journal = {J. Phys. Chem. B},
737 Journal-Iso = {J. Phys. Chem. B},
738 Keywords-Plus = {STEFAN DIFFUSION-COEFFICIENTS; MONTE-CARLO CALCULATIONS; ATOM FORCE-FIELD; SELF-DIFFUSION; DYNAMICS SIMULATION; PHASE-EQUILIBRIA; LIQUID METHANOL; TEMPERATURE-DEPENDENCE; COMPUTER-SIMULATION; MONOHYDRIC ALCOHOLS},
739 Language = {English},
740 Month = {DEC 25},
741 Number = {51},
742 Number-Of-Cited-References = {86},
743 Pages = {16664-16674},
744 Publisher = {AMER CHEMICAL SOC},
745 Subject-Category = {Chemistry, Physical},
746 Times-Cited = {5},
747 Title = {Prediction of Transport Properties by Molecular Simulation: Methanol and Ethanol and Their Mixture},
748 Type = {Article},
749 Unique-Id = {ISI:000261835100054},
750 Volume = {112},
751 Year = {2008},
752 Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp805584d%7D}}
753
754 @article{ISI:000258460400020,
755 Abstract = {Nonequilibrium molecular dynamics simulations with the nonpolarizable
756 SPC/E (Berendsen et al., J. Phys. Chem. 1987, 91, 6269) and the
757 polarizable COS/G2 (Yu and van Gunsteren, J. Chem. Phys. 2004, 121,
758 9549) force fields have been employed to calculate the thermal
759 conductivity and other associated properties of methane hydrate over a
760 temperature range from 30 to 260 K. The calculated results are compared
761 to experimental data over this same range. The values of the thermal
762 conductivity calculated with the COS/G2 model are closer to the
763 experimental values than are those calculated with the nonpolarizable
764 SPC/E model. The calculations match the temperature trend in the
765 experimental data at temperatures below 50 K; however, they exhibit a
766 slight decrease in thermal conductivity at higher temperatures in
767 comparison to an opposite trend in the experimental data. The
768 calculated thermal conductivity values are found to be relatively
769 insensitive to the occupancy of the cages except at low (T <= 50 K)
770 temperatures, which indicates that the differences between the two
771 lattice structures may have a more dominant role than generally thought
772 in explaining the low thermal conductivity of methane hydrate compared
773 to ice Ih. The introduction of defects into the water lattice is found
774 to cause a reduction in the thermal conductivity but to have a
775 negligible impact on its temperature dependence.},
776 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
777 Affiliation = {Jordan, KD (Reprint Author), US DOE, Natl Energy Technol Lab, POB 10940, Pittsburgh, PA 15236 USA. {[}Jiang, Hao; Myshakin, Evgeniy M.; Jordan, Kenneth D.; Warzinski, Robert P.] US DOE, Natl Energy Technol Lab, Pittsburgh, PA 15236 USA. {[}Jiang, Hao; Jordan, Kenneth D.] Univ Pittsburgh, Dept Chem, Pittsburgh, PA 15260 USA. {[}Jiang, Hao; Jordan, Kenneth D.] Univ Pittsburgh, Ctr Mol \& Mat Simulat, Pittsburgh, PA 15260 USA. {[}Myshakin, Evgeniy M.] Parsons Project Serv Inc, South Pk, PA 15129 USA.},
778 Author = {Jiang, Hao and Myshakin, Evgeniy M. and Jordan, Kenneth D. and Warzinski, Robert P.},
779 Date-Added = {2010-04-14 15:38:14 -0400},
780 Date-Modified = {2010-04-14 15:38:14 -0400},
781 Doc-Delivery-Number = {337UG},
782 Doi = {10.1021/jp802942v},
783 Funding-Acknowledgement = {E.M.M. ; National Energy Technology Laboratory's Office of Research and Development {[}41817.660.01.03]; ORISE Part-Time Faculty Program ; {[}DE-AM26-04NT41817]; {[}41817.606.06.03]},
784 Funding-Text = {We thank Drs. John Tse, Niall English, and Alan McGaughey for their comments. H.J. and K.D.J. performed this work under Contract DE-AM26-04NT41817, Subtask 41817.606.06.03, and E.M.M. performed this work under the same contract, Subtask 41817.660.01.03, in support of the National Energy Technology Laboratory's Office of Research and Development. K.D.J. was also supported at NETL by the ORISE Part-Time Faculty Program during the early stages of this work.},
785 Issn = {1520-6106},
786 Journal = {J. Phys. Chem. B},
787 Journal-Iso = {J. Phys. Chem. B},
788 Keywords-Plus = {LIQUID WATER; CLATHRATE HYDRATE; HEAT-CAPACITY; FORCE-FIELDS; ICE; ANHARMONICITY; SUMMATION; MODELS; SILICA},
789 Language = {English},
790 Month = {AUG 21},
791 Number = {33},
792 Number-Of-Cited-References = {51},
793 Pages = {10207-10216},
794 Publisher = {AMER CHEMICAL SOC},
795 Subject-Category = {Chemistry, Physical},
796 Times-Cited = {8},
797 Title = {Molecular dynamics Simulations of the thermal conductivity of methane hydrate},
798 Type = {Article},
799 Unique-Id = {ISI:000258460400020},
800 Volume = {112},
801 Year = {2008},
802 Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp802942v%7D}}
803
804 @article{ISI:000184808400018,
805 Abstract = {A new non-equilibrium molecular dynamics algorithm is presented based
806 on the original work of Willer-Plathe, (1997, J. chem. Phys., 106,
807 6082), for the non-equilibrium simulation of heat transport maintaining
808 fixed the total momentum as well as the total energy of the system. The
809 presented scheme preserves these properties but, unlike the original
810 algorithm, is able to deal with multicomponent systems, that is with
811 particles of different mass independently of their relative
812 concentration. The main idea behind the new procedure is to consider an
813 exchange of momentum and energy between the particles in the hot and
814 cold regions, to maintain the non-equilibrium conditions, as if they
815 undergo a hypothetical elastic collision. The new algorithm can also be
816 employed in multicomponent systems for molecular fluids and in a wide
817 range of thermodynamic conditions.},
818 Address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND},
819 Affiliation = {Nieto-Draghi, C (Reprint Author), Univ Rovira \& Virgili, ETSEQ, Dept Engn Quim, Avda Paisos Catalans 26, Tarragona 43007, Spain. Univ Rovira \& Virgili, ETSEQ, Dept Engn Quim, Tarragona 43007, Spain.},
820 Author = {Nieto-Draghi, C and Avalos, JB},
821 Date-Added = {2010-04-14 12:48:08 -0400},
822 Date-Modified = {2010-04-14 12:48:08 -0400},
823 Doc-Delivery-Number = {712QM},
824 Doi = {10.1080/0026897031000154338},
825 Issn = {0026-8976},
826 Journal = {Mol. Phys.},
827 Journal-Iso = {Mol. Phys.},
828 Keywords-Plus = {BINARY-LIQUID MIXTURES; THERMAL-CONDUCTIVITY; MATTER TRANSPORT; WATER},
829 Language = {English},
830 Month = {JUL 20},
831 Number = {14},
832 Number-Of-Cited-References = {20},
833 Pages = {2303-2307},
834 Publisher = {TAYLOR \& FRANCIS LTD},
835 Subject-Category = {Physics, Atomic, Molecular \& Chemical},
836 Times-Cited = {13},
837 Title = {Non-equilibrium momentum exchange algorithm for molecular dynamics simulation of heat flow in multicomponent systems},
838 Type = {Article},
839 Unique-Id = {ISI:000184808400018},
840 Volume = {101},
841 Year = {2003},
842 Bdsk-Url-1 = {http://dx.doi.org/10.1080/0026897031000154338%7D}}
843
844 @article{Bedrov:2000-1,
845 Abstract = {The thermal conductivity of liquid
846 octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) has been
847 determined from imposed heat flux non-equilibrium molecular dynamics
848 (NEMD) simulations using a previously published quantum chemistry-based
849 atomistic potential. The thermal conductivity was determined in the
850 temperature domain 550 less than or equal to T less than or equal to
851 800 K, which corresponds approximately to the existence limits of the
852 liquid phase of HMX at atmospheric pressure. The NEMD predictions,
853 which comprise the first reported values for thermal conductivity of
854 HMX liquid, were found to be consistent with measured values for
855 crystalline HMX. The thermal conductivity of liquid HMX was found to
856 exhibit a much weaker temperature dependence than the shear viscosity
857 and self-diffusion coefficients. (C) 2000 Elsevier Science B.V. All
858 rights reserved.},
859 Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
860 Affiliation = {Bedrov, D (Reprint Author), Univ Utah, Dept Mat Sci \& Engn, 122 S Cent Campus Dr,Room 304, Salt Lake City, UT 84112 USA. Univ Utah, Dept Mat Sci \& Engn, Salt Lake City, UT 84112 USA. Univ Utah, Dept Chem \& Fuels Engn, Salt Lake City, UT 84112 USA. Univ Calif Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA.},
861 Author = {Bedrov, D and Smith, GD and Sewell, TD},
862 Date-Added = {2010-04-14 12:26:59 -0400},
863 Date-Modified = {2010-04-14 12:27:52 -0400},
864 Doc-Delivery-Number = {330PF},
865 Issn = {0009-2614},
866 Journal = {Chem. Phys. Lett.},
867 Journal-Iso = {Chem. Phys. Lett.},
868 Keywords-Plus = {FORCE-FIELD},
869 Language = {English},
870 Month = {JUN 30},
871 Number = {1-3},
872 Number-Of-Cited-References = {17},
873 Pages = {64-68},
874 Publisher = {ELSEVIER SCIENCE BV},
875 Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
876 Times-Cited = {19},
877 Title = {Thermal conductivity of liquid octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) from molecular dynamics simulations},
878 Type = {Article},
879 Unique-Id = {ISI:000087969900011},
880 Volume = {324},
881 Year = {2000}}
882
883 @article{ISI:000258840700015,
884 Abstract = {By using the embedded-atom method (EAM), a series of molecular dynamics
885 (MD) simulations are carried out to calculate the viscosity and
886 self-diffusion coefficient of liquid copper from the normal to the
887 undercooled states. The simulated results are in reasonable agreement
888 with the experimental values available above the melting temperature
889 that is also predicted from a solid-liquid-solid sandwich structure.
890 The relationship between the viscosity and the self-diffusion
891 coefficient is evaluated. It is found that the Stokes-Einstein and
892 Sutherland-Einstein relations qualitatively describe this relationship
893 within the simulation temperature range. However, the predicted
894 constant from MD simulation is close to 1/(3 pi), which is larger than
895 the constants of the Stokes-Einstein and Sutherland-Einstein relations.},
896 Address = {233 SPRING ST, NEW YORK, NY 10013 USA},
897 Affiliation = {Chen, M (Reprint Author), Tsinghua Univ, Dept Engn Mech, Beijing 100084, Peoples R China. {[}Han, X. J.; Chen, M.; Lue, Y. J.] Tsinghua Univ, Dept Engn Mech, Beijing 100084, Peoples R China.},
898 Author = {Han, X. J. and Chen, M. and Lue, Y. J.},
899 Author-Email = {mchen@tsinghua.edu.cn},
900 Date-Added = {2010-04-14 12:00:38 -0400},
901 Date-Modified = {2010-04-14 12:00:38 -0400},
902 Doc-Delivery-Number = {343GH},
903 Doi = {10.1007/s10765-008-0489-7},
904 Funding-Acknowledgement = {China Postdoctoral Science Foundation ; National Natural Science Foundation of China {[}50395101, 50371043]},
905 Funding-Text = {This work was financially supported by China Postdoctoral Science Foundation and the National Natural Science Foundation of China under grant Nos. of 50395101 and 50371043. The computations are carried out at the Tsinghua National Laboratory for Information Science and Technology, China. The authors are grateful to Mr. D. Q. Yu for valuable discussions.},
906 Issn = {0195-928X},
907 Journal = {Int. J. Thermophys.},
908 Journal-Iso = {Int. J. Thermophys.},
909 Keywords = {copper; molecular simulation; self-diffusion coefficient; viscosity; undercooled},
910 Keywords-Plus = {EMBEDDED-ATOM MODEL; THERMOPHYSICAL PROPERTIES; COMPUTER-SIMULATION; TRANSITION-METALS; SHEAR VISCOSITY; ALLOYS; TEMPERATURE; DIFFUSION; BINDING; SURFACE},
911 Language = {English},
912 Month = {AUG},
913 Number = {4},
914 Number-Of-Cited-References = {39},
915 Pages = {1408-1421},
916 Publisher = {SPRINGER/PLENUM PUBLISHERS},
917 Subject-Category = {Thermodynamics; Chemistry, Physical; Mechanics; Physics, Applied},
918 Times-Cited = {2},
919 Title = {Transport properties of undercooled liquid copper: A molecular dynamics study},
920 Type = {Article},
921 Unique-Id = {ISI:000258840700015},
922 Volume = {29},
923 Year = {2008},
924 Bdsk-Url-1 = {http://dx.doi.org/10.1007/s10765-008-0489-7%7D}}
925
926 @article{Muller-Plathe:2008,
927 Abstract = {Reverse nonequilibrium molecular dynamics and equilibrium molecular
928 dynamics simulations were carried out to compute the shear viscosity of
929 the pure ionic liquid system {[}bmim]{[}PF6] at 300 K. The two methods
930 yielded consistent results which were also compared to experiments. The
931 results showed that the reverse nonequilibrium molecular dynamics
932 (RNEMD) methodology can successfully be applied to computation of
933 highly viscous ionic liquids. Moreover, this study provides a
934 validation of the atomistic force-field developed by Bhargava and
935 Balasubramanian (J. Chem. Phys. 2007, 127, 114510) for dynamic
936 properties.},
937 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
938 Affiliation = {Wei, Z (Reprint Author), Tech Univ Darmstadt, Petersenstr 30, D-64287 Darmstadt, Germany. {[}Wei Zhao; Leroy, Frederic; Mueller-Plathe, Florian] Tech Univ Darmstadt, D-64287 Darmstadt, Germany. {[}Balasubramanian, Sundaram] Indian Inst Sci, Jawaharlal Nehru Ctr Adv Sci Res, Chem \& Phys Mat Unit, Bangalore 560064, Karnataka, India.},
939 Author = {Wei Zhao and Leroy, Frederic and Balasubramanian, Sundaram and M\"{u}ller-Plathe, Florian},
940 Author-Email = {w.zhao@theo.chemie.tu-darmstadt.de},
941 Date-Added = {2010-04-14 11:53:37 -0400},
942 Date-Modified = {2010-04-14 11:54:20 -0400},
943 Doc-Delivery-Number = {321VS},
944 Doi = {10.1021/jp8017869},
945 Issn = {1520-6106},
946 Journal = {J. Phys. Chem. B},
947 Journal-Iso = {J. Phys. Chem. B},
948 Keywords-Plus = {TRANSPORT-PROPERTIES; FORCE-FIELD; TEMPERATURE; SIMULATION; IMIDAZOLIUM; FLUIDS; MODEL; BIS(TRIFLUOROMETHANESULFONYL)IMIDE; PYRIDINIUM; CHLORIDE},
949 Language = {English},
950 Month = {JUL 10},
951 Number = {27},
952 Number-Of-Cited-References = {49},
953 Pages = {8129-8133},
954 Publisher = {AMER CHEMICAL SOC},
955 Subject-Category = {Chemistry, Physical},
956 Times-Cited = {2},
957 Title = {Shear viscosity of the ionic liquid 1-n-butyl 3-methylimidazolium hexafluorophosphate {[}bmim]{[}PF6] computed by reverse nonequilibrium molecular dynamics},
958 Type = {Article},
959 Unique-Id = {ISI:000257335200022},
960 Volume = {112},
961 Year = {2008},
962 Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp8017869%7D}}
963
964 @article{Muller-Plathe:2002,
965 Abstract = {The reverse nonequilibrium molecular dynamics {[}F. Muller-Plathe,
966 Phys. Rev. E 49, 359 (1999)] presented for the calculation of the shear
967 viscosity of Lennard-Jones liquids has been extended to atomistic
968 models of molecular liquids. The method is improved to overcome the
969 problems due to the detailed molecular models. The new technique is
970 besides a test with a Lennard-Jones fluid, applied on different
971 realistic systems: liquid nitrogen, water, and hexane, in order to
972 cover a large range of interactions and systems/architectures. We show
973 that all the advantages of the method itemized previously are still
974 valid, and that it has a very good efficiency and accuracy making it
975 very competitive. (C) 2002 American Institute of Physics.},
976 Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
977 Affiliation = {Bordat, P (Reprint Author), Max Planck Inst Polymer Res, Ackermannweg 10, D-55128 Mainz, Germany. Max Planck Inst Polymer Res, D-55128 Mainz, Germany.},
978 Author = {Bordat, P and M\"{u}ller-Plathe, F},
979 Date-Added = {2010-04-14 11:34:42 -0400},
980 Date-Modified = {2010-04-14 11:35:35 -0400},
981 Doc-Delivery-Number = {521QV},
982 Doi = {10.1063/1.1436124},
983 Issn = {0021-9606},
984 Journal = {J. Chem. Phys.},
985 Journal-Iso = {J. Chem. Phys.},
986 Keywords-Plus = {TRANSPORT-PROPERTIES; PHYSICAL-PROPERTIES; LIQUID ALKANES; N-HEPTADECANE; SIMULATION; WATER; FLOW; MIXTURES; BUTANE; NITROGEN},
987 Language = {English},
988 Month = {FEB 22},
989 Number = {8},
990 Number-Of-Cited-References = {47},
991 Pages = {3362-3369},
992 Publisher = {AMER INST PHYSICS},
993 Subject-Category = {Physics, Atomic, Molecular \& Chemical},
994 Times-Cited = {33},
995 Title = {The shear viscosity of molecular fluids: A calculation by reverse nonequilibrium molecular dynamics},
996 Type = {Article},
997 Unique-Id = {ISI:000173853600023},
998 Volume = {116},
999 Year = {2002},
1000 Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1436124%7D}}
1001
1002 @article{ISI:000207079300006,
1003 Abstract = {Non-equilibrium Molecular Dynamics Simulation
1004 methods have been used to study the ability of
1005 Embedded Atom Method models of the metals copper and
1006 gold to reproduce the equilibrium and
1007 non-equilibrium behavior of metals at a stationary
1008 and at a moving solid/liquid interface. The
1009 equilibrium solid/vapor interface was shown to
1010 display a simple termination of the bulk until the
1011 temperature of the solid reaches approximate to 90\%
1012 of the bulk melting point. At and above such
1013 temperatures the systems exhibit a surface
1014 disodering known as surface melting. Non-equilibrium
1015 simulations emulating the action of a picosecond
1016 laser on the metal were performed to determine the
1017 regrowth velocity. For copper, the action of a 20 ps
1018 laser with an absorbed energy of 2-5 mJ/cm(2)
1019 produced a regrowth velocity of 83-100 m/s, in
1020 reasonable agreement with the value obtained by
1021 experiment (>60 m/s). For gold, similar conditions
1022 produced a slower regrowth velocity of 63 m/s at an
1023 absorbed energy of 5 mJ/cm(2). This is almost a
1024 factor of two too low in comparison to experiment
1025 (>100 m/s). The regrowth velocities of the metals
1026 seems unexpectedly close to experiment considering
1027 that the free-electron contribution is ignored in
1028 the Embeeded Atom Method models used.},
1029 Address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND},
1030 Affiliation = {Clancy, P (Reprint Author), Cornell Univ, Sch Chem Engn, Ithaca, NY 14853 USA. {[}Richardson, Clifton F.; Clancy, Paulette] Cornell Univ, Sch Chem Engn, Ithaca, NY 14853 USA.},
1031 Author = {Richardson, Clifton F. and Clancy, Paulette},
1032 Date-Added = {2010-04-07 11:24:36 -0400},
1033 Date-Modified = {2010-04-07 11:24:36 -0400},
1034 Doc-Delivery-Number = {V04SY},
1035 Issn = {0892-7022},
1036 Journal = {Mol. Simul.},
1037 Journal-Iso = {Mol. Simul.},
1038 Keywords = {Non-equilibrium computer simulation; molecular dynamics; crystal growth; Embedded Atom Method models of metals},
1039 Language = {English},
1040 Number = {5-6},
1041 Number-Of-Cited-References = {36},
1042 Pages = {335-355},
1043 Publisher = {TAYLOR \& FRANCIS LTD},
1044 Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
1045 Times-Cited = {7},
1046 Title = {PICOSECOND LASER PROCESSING OF COPPER AND GOLD: A COMPUTER SIMULATION STUDY},
1047 Type = {Article},
1048 Unique-Id = {ISI:000207079300006},
1049 Volume = {7},
1050 Year = {1991}}
1051
1052 @article{ISI:000167766600035,
1053 Abstract = {Molecular dynamics simulations are used to
1054 investigate the separation of water films adjacent
1055 to a hot metal surface. The simulations clearly show
1056 that the water layers nearest the surface overheat
1057 and undergo explosive boiling. For thick films, the
1058 expansion of the vaporized molecules near the
1059 surface forces the outer water layers to move away
1060 from the surface. These results are of interest for
1061 mass spectrometry of biological molecules, steam
1062 cleaning of surfaces, and medical procedures.},
1063 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
1064 Affiliation = {Garrison, BJ (Reprint Author), Penn State Univ, Dept Chem, University Pk, PA 16802 USA. Penn State Univ, Dept Chem, University Pk, PA 16802 USA. Penn State Univ, Inst Mat Res, University Pk, PA 16802 USA. Univ Virginia, Dept Mat Sci \& Engn, Charlottesville, VA 22903 USA.},
1065 Author = {Dou, YS and Zhigilei, LV and Winograd, N and Garrison, BJ},
1066 Date-Added = {2010-03-11 15:32:14 -0500},
1067 Date-Modified = {2010-03-11 15:32:14 -0500},
1068 Doc-Delivery-Number = {416ED},
1069 Issn = {1089-5639},
1070 Journal = {J. Phys. Chem. A},
1071 Journal-Iso = {J. Phys. Chem. A},
1072 Keywords-Plus = {MOLECULAR-DYNAMICS SIMULATIONS; ASSISTED LASER-DESORPTION; FROZEN AQUEOUS-SOLUTIONS; COMPUTER-SIMULATION; ORGANIC-SOLIDS; VELOCITY DISTRIBUTIONS; PARTICLE BOMBARDMENT; MASS-SPECTROMETRY; PHASE EXPLOSION; LIQUID WATER},
1073 Language = {English},
1074 Month = {MAR 29},
1075 Number = {12},
1076 Number-Of-Cited-References = {65},
1077 Pages = {2748-2755},
1078 Publisher = {AMER CHEMICAL SOC},
1079 Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
1080 Times-Cited = {66},
1081 Title = {Explosive boiling of water films adjacent to heated surfaces: A microscopic description},
1082 Type = {Article},
1083 Unique-Id = {ISI:000167766600035},
1084 Volume = {105},
1085 Year = {2001}}
1086
1087 @article{Maginn:2010,
1088 Abstract = {The reverse nonequilibrium molecular dynamics
1089 (RNEMD) method calculates the shear viscosity of a
1090 fluid by imposing a nonphysical exchange of momentum
1091 and measuring the resulting shear velocity
1092 gradient. In this study we investigate the range of
1093 momentum flux values over which RNEMD yields usable
1094 (linear) velocity gradients. We find that nonlinear
1095 velocity profiles result primarily from gradients in
1096 fluid temperature and density. The temperature
1097 gradient results from conversion of heat into bulk
1098 kinetic energy, which is transformed back into heat
1099 elsewhere via viscous heating. An expression is
1100 derived to predict the temperature profile resulting
1101 from a specified momentum flux for a given fluid and
1102 simulation cell. Although primarily bounded above,
1103 we also describe milder low-flux limitations. RNEMD
1104 results for a Lennard-Jones fluid agree with
1105 equilibrium molecular dynamics and conventional
1106 nonequilibrium molecular dynamics calculations at
1107 low shear, but RNEMD underpredicts viscosity
1108 relative to conventional NEMD at high shear.},
1109 Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
1110 Affiliation = {Tenney, CM (Reprint Author), Univ Notre Dame, Dept Chem \& Biomol Engn, 182 Fitzpatrick Hall, Notre Dame, IN 46556 USA. {[}Tenney, Craig M.; Maginn, Edward J.] Univ Notre Dame, Dept Chem \& Biomol Engn, Notre Dame, IN 46556 USA.},
1111 Article-Number = {014103},
1112 Author = {Tenney, Craig M. and Maginn, Edward J.},
1113 Author-Email = {ed@nd.edu},
1114 Date-Added = {2010-03-09 13:08:41 -0500},
1115 Date-Modified = {2010-07-19 16:21:35 -0400},
1116 Doc-Delivery-Number = {542DQ},
1117 Doi = {10.1063/1.3276454},
1118 Funding-Acknowledgement = {U.S. Department of Energy {[}DE-FG36-08G088020]},
1119 Funding-Text = {Support for this work was provided by the U.S. Department of Energy (Grant No. DE-FG36-08G088020)},
1120 Issn = {0021-9606},
1121 Journal = {J. Chem. Phys.},
1122 Journal-Iso = {J. Chem. Phys.},
1123 Keywords = {Lennard-Jones potential; molecular dynamics method; Navier-Stokes equations; viscosity},
1124 Keywords-Plus = {CURRENT AUTOCORRELATION-FUNCTION; IONIC LIQUID; SIMULATIONS; TEMPERATURE},
1125 Language = {English},
1126 Month = {JAN 7},
1127 Number = {1},
1128 Number-Of-Cited-References = {20},
1129 Pages = {014103},
1130 Publisher = {AMER INST PHYSICS},
1131 Subject-Category = {Physics, Atomic, Molecular \& Chemical},
1132 Times-Cited = {0},
1133 Title = {Limitations and recommendations for the calculation of shear viscosity using reverse nonequilibrium molecular dynamics},
1134 Type = {Article},
1135 Unique-Id = {ISI:000273472300004},
1136 Volume = {132},
1137 Year = {2010},
1138 Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.3276454}}
1139
1140 @article{Clancy:1992,
1141 Abstract = {The regrowth velocity of a crystal from a melt
1142 depends on contributions from the thermal
1143 conductivity, heat gradient, and latent heat. The
1144 relative contributions of these terms to the
1145 regrowth velocity of the pure metals copper and gold
1146 during liquid-phase epitaxy are evaluated. These
1147 results are used to explain how results from
1148 previous nonequilibrium molecular-dynamics
1149 simulations using classical potentials are able to
1150 predict regrowth velocities that are close to the
1151 experimental values. Results from equilibrium
1152 molecular dynamics showing the nature of the
1153 solid-vapor interface of an
1154 embedded-atom-method-modeled Cu57Ni43 alloy at a
1155 temperature corresponding to 62\% of the melting
1156 point are presented. The regrowth of this alloy
1157 following a simulation of a laser-processing
1158 experiment is also given, with use of nonequilibrium
1159 molecular-dynamics techniques. The thermal
1160 conductivity and temperature gradient in the
1161 simulation of the alloy are compared to those for
1162 the pure metals.},
1163 Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
1164 Affiliation = {CORNELL UNIV,SCH CHEM ENGN,ITHACA,NY 14853.},
1165 Author = {Richardson, C.~F. and Clancy, P},
1166 Date-Added = {2010-01-12 16:17:33 -0500},
1167 Date-Modified = {2010-04-08 17:18:25 -0400},
1168 Doc-Delivery-Number = {HX378},
1169 Issn = {0163-1829},
1170 Journal = {Phys. Rev. B},
1171 Journal-Iso = {Phys. Rev. B},
1172 Keywords-Plus = {SURFACE SEGREGATION; MOLECULAR-DYNAMICS; TRANSITION-METALS; SOLIDIFICATION; GROWTH; CU; NI},
1173 Language = {English},
1174 Month = {JUN 1},
1175 Number = {21},
1176 Number-Of-Cited-References = {24},
1177 Pages = {12260-12268},
1178 Publisher = {AMERICAN PHYSICAL SOC},
1179 Subject-Category = {Physics, Condensed Matter},
1180 Times-Cited = {11},
1181 Title = {CONTRIBUTION OF THERMAL-CONDUCTIVITY TO THE CRYSTAL-REGROWTH VELOCITY OF EMBEDDED-ATOM-METHOD-MODELED METALS AND METAL-ALLOYS},
1182 Type = {Article},
1183 Unique-Id = {ISI:A1992HX37800010},
1184 Volume = {45},
1185 Year = {1992}}
1186
1187 @article{Bedrov:2000,
1188 Abstract = {We have applied a new nonequilibrium molecular
1189 dynamics (NEMD) method {[}F. Muller-Plathe,
1190 J. Chem. Phys. 106, 6082 (1997)] previously applied
1191 to monatomic Lennard-Jones fluids in the
1192 determination of the thermal conductivity of
1193 molecular fluids. The method was modified in order
1194 to be applicable to systems with holonomic
1195 constraints. Because the method involves imposing a
1196 known heat flux it is particularly attractive for
1197 systems involving long-range and many-body
1198 interactions where calculation of the microscopic
1199 heat flux is difficult. The predicted thermal
1200 conductivities of liquid n-butane and water using
1201 the imposed-flux NEMD method were found to be in a
1202 good agreement with previous simulations and
1203 experiment. (C) 2000 American Institute of
1204 Physics. {[}S0021-9606(00)50841-1].},
1205 Address = {2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA},
1206 Affiliation = {Bedrov, D (Reprint Author), Univ Utah, Dept Chem \& Fuels Engn, 122 S Cent Campus Dr,Rm 304, Salt Lake City, UT 84112 USA. Univ Utah, Dept Chem \& Fuels Engn, Salt Lake City, UT 84112 USA. Univ Utah, Dept Mat Sci \& Engn, Salt Lake City, UT 84112 USA.},
1207 Author = {Bedrov, D and Smith, GD},
1208 Date-Added = {2009-11-05 18:21:18 -0500},
1209 Date-Modified = {2010-04-14 11:50:48 -0400},
1210 Doc-Delivery-Number = {369BF},
1211 Issn = {0021-9606},
1212 Journal = {J. Chem. Phys.},
1213 Journal-Iso = {J. Chem. Phys.},
1214 Keywords-Plus = {EFFECTIVE PAIR POTENTIALS; TRANSPORT-PROPERTIES; CANONICAL ENSEMBLE; NORMAL-BUTANE; ALGORITHMS; SHAKE; WATER},
1215 Language = {English},
1216 Month = {NOV 8},
1217 Number = {18},
1218 Number-Of-Cited-References = {26},
1219 Pages = {8080-8084},
1220 Publisher = {AMER INST PHYSICS},
1221 Subject-Category = {Physics, Atomic, Molecular \& Chemical},
1222 Times-Cited = {23},
1223 Title = {Thermal conductivity of molecular fluids from molecular dynamics simulations: Application of a new imposed-flux method},
1224 Type = {Article},
1225 Unique-Id = {ISI:000090151400044},
1226 Volume = {113},
1227 Year = {2000}}
1228
1229 @article{ISI:000231042800044,
1230 Abstract = {The reverse nonequilibrium molecular dynamics
1231 method for thermal conductivities is adapted to the
1232 investigation of molecular fluids. The method
1233 generates a heat flux through the system by suitably
1234 exchanging velocities of particles located in
1235 different regions. From the resulting temperature
1236 gradient, the thermal conductivity is then
1237 calculated. Different variants of the algorithm and
1238 their combinations with other system parameters are
1239 tested: exchange of atomic velocities versus
1240 exchange of molecular center-of-mass velocities,
1241 different exchange frequencies, molecular models
1242 with bond constraints versus models with flexible
1243 bonds, united-atom versus all-atom models, and
1244 presence versus absence of a thermostat. To help
1245 establish the range of applicability, the algorithm
1246 is tested on different models of benzene,
1247 cyclohexane, water, and n-hexane. We find that the
1248 algorithm is robust and that the calculated thermal
1249 conductivities are insensitive to variations in its
1250 control parameters. The force field, in contrast,
1251 has a major influence on the value of the thermal
1252 conductivity. While calculated and experimental
1253 thermal conductivities fall into the same order of
1254 magnitude, in most cases the calculated values are
1255 systematically larger. United-atom force fields seem
1256 to do better than all-atom force fields, possibly
1257 because they remove high-frequency degrees of
1258 freedom from the simulation, which, in nature, are
1259 quantum-mechanical oscillators in their ground state
1260 and do not contribute to heat conduction.},
1261 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
1262 Affiliation = {Zhang, MM (Reprint Author), Int Univ Bremen, POB 750 561, D-28725 Bremen, Germany. Int Univ Bremen, D-28725 Bremen, Germany. Banco Cent Brasil, Desup, Diesp, BR-01310922 Sao Paulo, Brazil.},
1263 Author = {Zhang, MM and Lussetti, E and de Souza, LES and M\"{u}ller-Plathe, F},
1264 Date-Added = {2009-11-05 18:17:33 -0500},
1265 Date-Modified = {2009-11-05 18:17:33 -0500},
1266 Doc-Delivery-Number = {952YQ},
1267 Doi = {10.1021/jp0512255},
1268 Issn = {1520-6106},
1269 Journal = {J. Phys. Chem. B},
1270 Journal-Iso = {J. Phys. Chem. B},
1271 Keywords-Plus = {LENNARD-JONES LIQUIDS; TRANSPORT-COEFFICIENTS; SWOLLEN POLYMERS; SHEAR VISCOSITY; MODEL SYSTEMS; SIMULATION; BENZENE; FLUIDS; POTENTIALS; DIFFUSION},
1272 Language = {English},
1273 Month = {AUG 11},
1274 Number = {31},
1275 Number-Of-Cited-References = {42},
1276 Pages = {15060-15067},
1277 Publisher = {AMER CHEMICAL SOC},
1278 Subject-Category = {Chemistry, Physical},
1279 Times-Cited = {17},
1280 Title = {Thermal conductivities of molecular liquids by reverse nonequilibrium molecular dynamics},
1281 Type = {Article},
1282 Unique-Id = {ISI:000231042800044},
1283 Volume = {109},
1284 Year = {2005},
1285 Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp0512255%7D}}
1286
1287 @article{ISI:A1997YC32200056,
1288 Abstract = {Equilibrium molecular dynamics simulations have
1289 been carried out in the microcanonical ensemble at
1290 300 and 255 K on the extended simple point charge
1291 (SPC/E) model of water {[}Berendsen et al.,
1292 J. Phys. Chem. 91, 6269 (1987)]. In addition to a
1293 number of static and dynamic properties, thermal
1294 conductivity lambda has been calculated via
1295 Green-Kubo integration of the heat current time
1296 correlation functions (CF's) in the atomic and
1297 molecular formalism, at wave number k=0. The
1298 calculated values (0.67 +/- 0.04 W/mK at 300 K and
1299 0.52 +/- 0.03 W/mK at 255 K) are in good agreement
1300 with the experimental data (0.61 W/mK at 300 K and
1301 0.49 W/mK at 255 K). A negative long-time tail of
1302 the heat current CF, more apparent at 255 K, is
1303 responsible for the anomalous decrease of lambda
1304 with temperature. An analysis of the dynamical modes
1305 contributing to lambda has shown that its value is
1306 due to two low-frequency exponential-like modes, a
1307 faster collisional mode, with positive contribution,
1308 and a slower one, which determines the negative
1309 long-time tail. A comparison of the molecular and
1310 atomic spectra of the heat current CF has suggested
1311 that higher-frequency modes should not contribute to
1312 lambda in this temperature range. Generalized
1313 thermal diffusivity D-T(k) decreases as a function
1314 of k, after an initial minor increase at k =
1315 k(min). The k dependence of the generalized
1316 thermodynamic properties has been calculated in the
1317 atomic and molecular formalisms. The observed
1318 differences have been traced back to intramolecular
1319 or intermolecular rotational effects and related to
1320 the partial structure functions. Finally, from the
1321 results we calculated it appears that the SPC/E
1322 model gives results in better agreement with
1323 experimental data than the transferable
1324 intermolecular potential with four points TIP4P
1325 water model {[}Jorgensen et al., J. Chem. Phys. 79,
1326 926 (1983)], with a larger improvement for, e.g.,
1327 diffusion, viscosities, and dielectric properties
1328 and a smaller one for thermal conductivity. The
1329 SPC/E model shares, to a smaller extent, the
1330 insufficient slowing down of dynamics at low
1331 temperature already found for the TIP4P water
1332 model.},
1333 Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
1334 Affiliation = {UNIV PISA,DIPARTIMENTO CHIM \& CHIM IND,I-56126 PISA,ITALY. CNR,IST FIS ATOM \& MOL,I-56127 PISA,ITALY.},
1335 Author = {Bertolini, D and Tani, A},
1336 Date-Added = {2009-10-30 15:41:21 -0400},
1337 Date-Modified = {2009-10-30 15:41:21 -0400},
1338 Doc-Delivery-Number = {YC322},
1339 Issn = {1063-651X},
1340 Journal = {Phys. Rev. E},
1341 Journal-Iso = {Phys. Rev. E},
1342 Keywords-Plus = {TIME-CORRELATION-FUNCTIONS; LENNARD-JONES LIQUID; TRANSPORT-PROPERTIES; SUPERCOOLED WATER; DENSITY; SIMULATIONS; RELAXATION; VELOCITY; ELECTRON; FLUIDS},
1343 Language = {English},
1344 Month = {OCT},
1345 Number = {4},
1346 Number-Of-Cited-References = {35},
1347 Pages = {4135-4151},
1348 Publisher = {AMERICAN PHYSICAL SOC},
1349 Subject-Category = {Physics, Fluids \& Plasmas; Physics, Mathematical},
1350 Times-Cited = {18},
1351 Title = {Thermal conductivity of water: Molecular dynamics and generalized hydrodynamics results},
1352 Type = {Article},
1353 Unique-Id = {ISI:A1997YC32200056},
1354 Volume = {56},
1355 Year = {1997}}
1356
1357 @article{Meineke:2005gd,
1358 Abstract = {OOPSE is a new molecular dynamics simulation program
1359 that is capable of efficiently integrating equations
1360 of motion for atom types with orientational degrees
1361 of freedom (e.g. #sticky# atoms and point
1362 dipoles). Transition metals can also be simulated
1363 using the embedded atom method (EAM) potential
1364 included in the code. Parallel simulations are
1365 carried out using the force-based decomposition
1366 method. Simulations are specified using a very
1367 simple C-based meta-data language. A number of
1368 advanced integrators are included, and the basic
1369 integrator for orientational dynamics provides
1370 substantial improvements over older quaternion-based
1371 schemes.},
1372 Address = {111 RIVER ST, HOBOKEN, NJ 07030 USA},
1373 Author = {Meineke, M. A. and Vardeman, C. F. and Lin, T and Fennell, CJ and Gezelter, J. D.},
1374 Date-Added = {2009-10-01 18:43:03 -0400},
1375 Date-Modified = {2010-04-13 09:11:16 -0400},
1376 Doi = {DOI 10.1002/jcc.20161},
1377 Isi = {000226558200006},
1378 Isi-Recid = {142688207},
1379 Isi-Ref-Recids = {67885400 50663994 64190493 93668415 46699855 89992422 57614458 49016001 61447131 111114169 68770425 52728075 102422498 66381878 32391149 134477335 53221357 9929643 59492217 69681001 99223832 142688208 94600872 91658572 54857943 117365867 69323123 49588888 109970172 101670714 142688209 121603296 94652379 96449138 99938010 112825758 114905670 86802042 121339042 104794914 82674909 72096791 93668384 90513335 142688210 23060767 63731466 109033408 76303716 31384453 97861662 71842426 130707771 125809946 66381889 99676497},
1380 Journal = {J. Comp. Chem.},
1381 Keywords = {OOPSE; molecular dynamics},
1382 Month = feb,
1383 Number = {3},
1384 Pages = {252-271},
1385 Publisher = {JOHN WILEY \& SONS INC},
1386 Times-Cited = {9},
1387 Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
1388 Volume = {26},
1389 Year = {2005},
1390 Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000226558200006},
1391 Bdsk-Url-2 = {http://dx.doi.org/10.1002/jcc.20161}}
1392
1393 @article{ISI:000080382700030,
1394 Abstract = {A nonequilibrium method for calculating the shear
1395 viscosity is presented. It reverses the
1396 cause-and-effect picture customarily used in
1397 nonequilibrium molecular dynamics: the effect, the
1398 momentum flux or stress, is imposed, whereas the
1399 cause, the velocity gradient or shear rate, is
1400 obtained from the simulation. It differs from other
1401 Norton-ensemble methods by the way in which the
1402 steady-state momentum flux is maintained. This
1403 method involves a simple exchange of particle
1404 momenta, which is easy to implement. Moreover, it
1405 can be made to conserve the total energy as well as
1406 the total linear momentum, so no coupling to an
1407 external temperature bath is needed. The resulting
1408 raw data, the velocity profile, is a robust and
1409 rapidly converging property. The method is tested on
1410 the Lennard-Jones fluid near its triple point. It
1411 yields a viscosity of 3.2-3.3, in Lennard-Jones
1412 reduced units, in agreement with literature
1413 results. {[}S1063-651X(99)03105-0].},
1414 Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
1415 Affiliation = {Muller-Plathe, F (Reprint Author), Max Planck Inst Polymerforsch, Ackermannweg 10, D-55128 Mainz, Germany. Max Planck Inst Polymerforsch, D-55128 Mainz, Germany.},
1416 Author = {M\"{u}ller-Plathe, F},
1417 Date-Added = {2009-10-01 14:07:30 -0400},
1418 Date-Modified = {2009-10-01 14:07:30 -0400},
1419 Doc-Delivery-Number = {197TX},
1420 Issn = {1063-651X},
1421 Journal = {Phys. Rev. E},
1422 Journal-Iso = {Phys. Rev. E},
1423 Language = {English},
1424 Month = {MAY},
1425 Number = {5, Part A},
1426 Number-Of-Cited-References = {17},
1427 Pages = {4894-4898},
1428 Publisher = {AMERICAN PHYSICAL SOC},
1429 Subject-Category = {Physics, Fluids \& Plasmas; Physics, Mathematical},
1430 Times-Cited = {57},
1431 Title = {Reversing the perturbation in nonequilibrium molecular dynamics: An easy way to calculate the shear viscosity of fluids},
1432 Type = {Article},
1433 Unique-Id = {ISI:000080382700030},
1434 Volume = {59},
1435 Year = {1999}}
1436
1437 @article{Maginn:2007,
1438 Abstract = {Atomistic simulations are conducted to examine the
1439 dependence of the viscosity of
1440 1-ethyl-3-methylimidazolium
1441 bis(trifluoromethanesulfonyl)imide on temperature
1442 and water content. A nonequilibrium molecular
1443 dynamics procedure is utilized along with an
1444 established fixed charge force field. It is found
1445 that the simulations quantitatively capture the
1446 temperature dependence of the viscosity as well as
1447 the drop in viscosity that occurs with increasing
1448 water content. Using mixture viscosity models, we
1449 show that the relative drop in viscosity with water
1450 content is actually less than that that would be
1451 predicted for an ideal system. This finding is at
1452 odds with the popular notion that small amounts of
1453 water cause an unusually large drop in the viscosity
1454 of ionic liquids. The simulations suggest that, due
1455 to preferential association of water with anions and
1456 the formation of water clusters, the excess molar
1457 volume is negative. This means that dissolved water
1458 is actually less effective at lowering the viscosity
1459 of these mixtures when compared to a solute obeying
1460 ideal mixing behavior. The use of a nonequilibrium
1461 simulation technique enables diffusive behavior to
1462 be observed on the time scale of the simulations,
1463 and standard equilibrium molecular dynamics resulted
1464 in sub-diffusive behavior even over 2 ns of
1465 simulation time.},
1466 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
1467 Affiliation = {Maginn, EJ (Reprint Author), Univ Notre Dame, Dept Chem \& Biomol Engn, 182 Fitzpatrick Hall, Notre Dame, IN 46556 USA. Univ Notre Dame, Dept Chem \& Biomol Engn, Notre Dame, IN 46556 USA.},
1468 Author = {Kelkar, Manish S. and Maginn, Edward J.},
1469 Author-Email = {ed@nd.edu},
1470 Date-Added = {2009-09-29 17:07:17 -0400},
1471 Date-Modified = {2010-04-14 12:51:02 -0400},
1472 Doc-Delivery-Number = {163VA},
1473 Doi = {10.1021/jp0686893},
1474 Issn = {1520-6106},
1475 Journal = {J. Phys. Chem. B},
1476 Journal-Iso = {J. Phys. Chem. B},
1477 Keywords-Plus = {MOLECULAR-DYNAMICS SIMULATION; MOMENTUM IMPULSE RELAXATION; FORCE-FIELD; TRANSPORT-PROPERTIES; PHYSICAL-PROPERTIES; SIMPLE FLUID; CHLORIDE; MODEL; SALTS; ARCHITECTURE},
1478 Language = {English},
1479 Month = {MAY 10},
1480 Number = {18},
1481 Number-Of-Cited-References = {57},
1482 Pages = {4867-4876},
1483 Publisher = {AMER CHEMICAL SOC},
1484 Subject-Category = {Chemistry, Physical},
1485 Times-Cited = {35},
1486 Title = {Effect of temperature and water content on the shear viscosity of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide as studied by atomistic simulations},
1487 Type = {Article},
1488 Unique-Id = {ISI:000246190100032},
1489 Volume = {111},
1490 Year = {2007},
1491 Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp0686893%7D},
1492 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp0686893}}
1493
1494 @article{MullerPlathe:1997xw,
1495 Abstract = {A nonequilibrium molecular dynamics method for
1496 calculating the thermal conductivity is
1497 presented. It reverses the usual cause and effect
1498 picture. The ''effect,'' the heat flux, is imposed
1499 on the system and the ''cause,'' the temperature
1500 gradient is obtained from the simulation. Besides
1501 being very simple to implement, the scheme offers
1502 several advantages such as compatibility with
1503 periodic boundary conditions, conservation of total
1504 energy and total linear momentum, and the sampling
1505 of a rapidly converging quantity (temperature
1506 gradient) rather than a slowly converging one (heat
1507 flux). The scheme is tested on the Lennard-Jones
1508 fluid. (C) 1997 American Institute of Physics.},
1509 Address = {WOODBURY},
1510 Author = {M\"{u}ller-Plathe, F.},
1511 Cited-Reference-Count = {13},
1512 Date = {APR 8},
1513 Date-Added = {2009-09-21 16:51:21 -0400},
1514 Date-Modified = {2009-09-21 16:51:21 -0400},
1515 Document-Type = {Article},
1516 Isi = {ISI:A1997WR62000032},
1517 Isi-Document-Delivery-Number = {WR620},
1518 Iso-Source-Abbreviation = {J. Chem. Phys.},
1519 Issn = {0021-9606},
1520 Journal = {J. Chem. Phys.},
1521 Language = {English},
1522 Month = {Apr},
1523 Number = {14},
1524 Page-Count = {4},
1525 Pages = {6082--6085},
1526 Publication-Type = {J},
1527 Publisher = {AMER INST PHYSICS},
1528 Publisher-Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999},
1529 Reprint-Address = {MullerPlathe, F, MAX PLANCK INST POLYMER RES, D-55128 MAINZ, GERMANY.},
1530 Source = {J CHEM PHYS},
1531 Subject-Category = {Physics, Atomic, Molecular & Chemical},
1532 Times-Cited = {106},
1533 Title = {A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity},
1534 Volume = {106},
1535 Year = {1997}}
1536
1537 @article{Muller-Plathe:1999ek,
1538 Abstract = {A novel non-equilibrium method for calculating
1539 transport coefficients is presented. It reverses the
1540 experimental cause-and-effect picture, e.g. for the
1541 calculation of viscosities: the effect, the momentum
1542 flux or stress, is imposed, whereas the cause, the
1543 velocity gradient or shear rates, is obtained from
1544 the simulation. It differs from other
1545 Norton-ensemble methods by the way, in which the
1546 steady-state fluxes are maintained. This method
1547 involves a simple exchange of particle momenta,
1548 which is easy to implement and to analyse. Moreover,
1549 it can be made to conserve the total energy as well
1550 as the total linear momentum, so no thermostatting
1551 is needed. The resulting raw data are robust and
1552 rapidly converging. The method is tested on the
1553 calculation of the shear viscosity, the thermal
1554 conductivity and the Soret coefficient (thermal
1555 diffusion) for the Lennard-Jones (LJ) fluid near its
1556 triple point. Possible applications to other
1557 transport coefficients and more complicated systems
1558 are discussed. (C) 1999 Elsevier Science Ltd. All
1559 rights reserved.},
1560 Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
1561 Author = {M\"{u}ller-Plathe, F and Reith, D},
1562 Date-Added = {2009-09-21 16:47:07 -0400},
1563 Date-Modified = {2009-09-21 16:47:07 -0400},
1564 Isi = {000082266500004},
1565 Isi-Recid = {111564960},
1566 Isi-Ref-Recids = {64516210 89773595 53816621 60134000 94875498 60964023 90228608 85968509 86405859 63979644 108048497 87560156 577165 103281654 111564961 83735333 99953572 88476740 110174781 111564963 6599000 75892253},
1567 Journal = {Computational and Theoretical Polymer Science},
1568 Keywords = {viscosity; Ludwig-Soret effect; thermal conductivity; Onsager coefficents; non-equilibrium molecular dynamics},
1569 Number = {3-4},
1570 Pages = {203-209},
1571 Publisher = {ELSEVIER SCI LTD},
1572 Times-Cited = {15},
1573 Title = {Cause and effect reversed in non-equilibrium molecular dynamics: an easy route to transport coefficients},
1574 Volume = {9},
1575 Year = {1999},
1576 Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000082266500004}}
1577
1578 @article{Viscardy:2007lq,
1579 Abstract = {The thermal conductivity is calculated with the
1580 Helfand-moment method in the Lennard-Jones fluid
1581 near the triple point. The Helfand moment of thermal
1582 conductivity is here derived for molecular dynamics
1583 with periodic boundary conditions. Thermal
1584 conductivity is given by a generalized Einstein
1585 relation with this Helfand moment. The authors
1586 compute thermal conductivity by this new method and
1587 compare it with their own values obtained by the
1588 standard Green-Kubo method. The agreement is
1589 excellent. (C) 2007 American Institute of Physics.},
1590 Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
1591 Author = {Viscardy, S. and Servantie, J. and Gaspard, P.},
1592 Date-Added = {2009-09-21 16:37:20 -0400},
1593 Date-Modified = {2010-07-19 16:18:44 -0400},
1594 Doi = {DOI 10.1063/1.2724821},
1595 Isi = {000246453900035},
1596 Isi-Recid = {156192451},
1597 Isi-Ref-Recids = {18794442 84473620 156192452 41891249 90040203 110174972 59859940 47256160 105716249 91804339 93329429 95967319 6199670 1785176 105872066 6325196 65361295 71941152 4307928 23120502 54053395 149068110 4811016 99953572 59859908 132156782 156192449},
1598 Journal = {J. Chem. Phys.},
1599 Month = may,
1600 Number = {18},
1601 Pages = {184513},
1602 Publisher = {AMER INST PHYSICS},
1603 Times-Cited = {3},
1604 Title = {Transport and Helfand moments in the Lennard-Jones fluid. II. Thermal conductivity},
1605 Volume = {126},
1606 Year = {2007},
1607 Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000246453900035},
1608 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2724821}}
1609
1610 @article{Viscardy:2007bh,
1611 Abstract = {The authors propose a new method, the Helfand-moment
1612 method, to compute the shear viscosity by
1613 equilibrium molecular dynamics in periodic
1614 systems. In this method, the shear viscosity is
1615 written as an Einstein-type relation in terms of the
1616 variance of the so-called Helfand moment. This
1617 quantity is modified in order to satisfy systems
1618 with periodic boundary conditions usually considered
1619 in molecular dynamics. They calculate the shear
1620 viscosity in the Lennard-Jones fluid near the triple
1621 point thanks to this new technique. They show that
1622 the results of the Helfand-moment method are in
1623 excellent agreement with the results of the standard
1624 Green-Kubo method. (C) 2007 American Institute of
1625 Physics.},
1626 Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
1627 Author = {Viscardy, S. and Servantie, J. and Gaspard, P.},
1628 Date-Added = {2009-09-21 16:37:19 -0400},
1629 Date-Modified = {2010-07-19 16:19:03 -0400},
1630 Doi = {DOI 10.1063/1.2724820},
1631 Isi = {000246453900034},
1632 Isi-Recid = {156192449},
1633 Isi-Ref-Recids = {18794442 89109900 84473620 86837966 26564374 23367140 83161139 75750220 90040203 110174972 5885 67722779 91461489 42484251 77907850 93329429 95967319 105716249 6199670 1785176 105872066 6325196 129596740 120782555 51131244 65361295 41141868 4307928 21555860 23120502 563068 120721875 142813985 135942402 4811016 86224873 57621419 85506488 89860062 44796632 51381285 132156779 156192450 132156782 156192451},
1634 Journal = {J. Chem. Phys.},
1635 Month = may,
1636 Number = {18},
1637 Pages = {184512},
1638 Publisher = {AMER INST PHYSICS},
1639 Times-Cited = {1},
1640 Title = {Transport and Helfand moments in the Lennard-Jones fluid. I. Shear viscosity},
1641 Volume = {126},
1642 Year = {2007},
1643 Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000246453900034},
1644 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2724820}}
1645
1646 @inproceedings{384119,
1647 Address = {New York, NY, USA},
1648 Author = {Fortune, Steven},
1649 Booktitle = {ISSAC '01: Proceedings of the 2001 international symposium on Symbolic and algebraic computation},
1650 Doi = {http://doi.acm.org/10.1145/384101.384119},
1651 Isbn = {1-58113-417-7},
1652 Location = {London, Ontario, Canada},
1653 Pages = {121--128},
1654 Publisher = {ACM},
1655 Title = {Polynomial root finding using iterated Eigenvalue computation},
1656 Year = {2001},
1657 Bdsk-Url-1 = {http://doi.acm.org/10.1145/384101.384119}}
1658
1659 @article{Fennell06,
1660 Author = {C.~J. Fennell and J.~D. Gezelter},
1661 Date-Added = {2006-08-24 09:49:57 -0400},
1662 Date-Modified = {2006-08-24 09:49:57 -0400},
1663 Doi = {10.1063/1.2206581},
1664 Journal = {J. Chem. Phys.},
1665 Number = {23},
1666 Pages = {234104(12)},
1667 Rating = {5},
1668 Read = {Yes},
1669 Title = {Is the \uppercase{E}wald summation still necessary? \uppercase{P}airwise alternatives to the accepted standard for long-range electrostatics},
1670 Volume = {124},
1671 Year = {2006},
1672 Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2206581}}
1673
1674 @book{Sommese2005,
1675 Address = {Singapore},
1676 Author = {Andrew J. Sommese and Charles W. Wampler},
1677 Publisher = {World Scientific Press},
1678 Title = {The numerical solution of systems of polynomials arising in engineering and science},
1679 Year = 2005}