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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 Kelsey Stocker at 2012-12-05 17:18:06 -0500
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9
10
11
12 @techreport{Goddard1998,
13 Author = {Kimura, Y. and Cagin, T. and Goddard III, W.A.},
14 Date-Added = {2012-12-05 22:18:01 +0000},
15 Date-Modified = {2012-12-05 22:18:01 +0000},
16 Institution = {California Institute of Technology},
17 Lastchecked = {January 19, 2011},
18 Number = {003},
19 Title = {The Quantum Sutton-Chen Many Body Potential for Properties of fcc Metals},
20 Url = {http://csdrm.caltech.edu/publications/cit-asci-tr/cit-asci-tr003.pdf},
21 Year = {1998},
22 Bdsk-Url-1 = {http://csdrm.caltech.edu/publications/cit-asci-tr/cit-asci-tr003.pdf}}
23
24 @article{Hase2010,
25 Author = {Yue Zhang and George L. Barnes and Tianying Yan and William L. Hase},
26 Date-Added = {2012-12-05 22:18:01 +0000},
27 Date-Modified = {2012-12-05 22:18:01 +0000},
28 Journal = {Phys. Chem. Chem. Phys.},
29 Keywords = {fcc/hcp, non-equilibrium, thiols},
30 Pages = {4435-4445},
31 Title = {Model non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer},
32 Volume = {12},
33 Year = {2010}}
34
35 @article{Kuang2010,
36 Author = {Shenyu Kuang and J. Daniel Gezelter},
37 Date-Added = {2012-12-05 22:18:01 +0000},
38 Date-Modified = {2012-12-05 22:18:01 +0000},
39 Journal = {J. Chem. Phys.},
40 Keywords = {NIVS, RNEMD, NIVS-RNEMD},
41 Month = {October},
42 Pages = {164101-1 - 164101-9},
43 Title = {A gentler approach to RNEMD: Nonisotropic velocity scaling for computing thermal conductivity and shear viscosity},
44 Volume = {133},
45 Year = {2010}}
46
47 @article{Kuang2011,
48 Author = {Shenyu Kuang and J. Daniel Gezelter},
49 Date-Added = {2012-12-05 22:18:01 +0000},
50 Date-Modified = {2012-12-05 22:18:01 +0000},
51 Journal = {J. Phys. Chem. C},
52 Keywords = {thiols, RNEMD},
53 Month = {October},
54 Pages = {22475-22483},
55 Title = {Simulating Interfacial Thermal Conductance at Metal-Solvent Interfaces: The Role of Chemical Capping Agents},
56 Volume = {115},
57 Year = {2011}}
58
59 @article{Kuang2012,
60 Author = {Shenyu Kuang and J. Daniel Gezelter},
61 Date-Added = {2012-12-05 22:18:01 +0000},
62 Date-Modified = {2012-12-05 22:18:01 +0000},
63 Journal = {Mol. Phys.},
64 Keywords = {VSS, RNEMD, VSS-RNEMD},
65 Month = {May},
66 Number = {9-10},
67 Pages = {691-701},
68 Title = {Velocity shearing and scaling RNEMD: a minimally perturbing method for simulating temperature and momentum gradients},
69 Volume = {110},
70 Year = {2012}}
71
72 @misc{open_md,
73 Author = {Shenyu Kuang and Joseph Michalka and Kelsey M. Stocker and James Marr and Teng Lin and Charles F. Vardeman II and Christopher J. Fennell and Xiuquan Sun and Chunlei Li and Kyle Daily and Yang Zheng and Matthew A. Meineke and J. Daniel Gezelter},
74 Date-Added = {2012-12-05 22:18:01 +0000},
75 Date-Modified = {2012-12-05 22:18:01 +0000},
76 Howpublished = {http://openmd.net},
77 Keywords = {OpenMD},
78 Lastchecked = {January 18, 2011},
79 Title = {OpenMD, an open source engine for molecular dynamics},
80 Bdsk-Url-1 = {http://openmd.net}}
81
82 @article{doi:10.1080/0026897031000068578,
83 Abstract = { Using equilibrium and non-equilibrium molecular dynamics simulations, we determine the Kapitza resistance (or thermal contact resistance) at a model liquid-solid interface. The Kapitza resistance (or the associated Kapitza length) can reach appreciable values when the liquid does not wet the solid. The analogy with the hydrodynamic slip length is discussed. },
84 Author = {Barrat, Jean-Louis and Chiaruttini, Fran{\c c}ois},
85 Date-Added = {2011-12-13 17:17:05 -0500},
86 Date-Modified = {2011-12-13 17:17:05 -0500},
87 Doi = {10.1080/0026897031000068578},
88 Eprint = {http://tandfprod.literatumonline.com/doi/pdf/10.1080/0026897031000068578},
89 Journal = {Mol. Phys.},
90 Number = {11},
91 Pages = {1605-1610},
92 Title = {Kapitza resistance at the liquid---solid interface},
93 Url = {http://tandfprod.literatumonline.com/doi/abs/10.1080/0026897031000068578},
94 Volume = {101},
95 Year = {2003},
96 Bdsk-Url-1 = {http://tandfprod.literatumonline.com/doi/abs/10.1080/0026897031000068578},
97 Bdsk-Url-2 = {http://dx.doi.org/10.1080/0026897031000068578}}
98
99 @article{Medina2011,
100 Abstract = {Molecular dynamics (MD) simulations are carried out on a system of rigid or flexible water molecules at a series of temperatures between 273 and 368 K. Collective transport coefficients, such as shear and bulk viscosities are calculated, and their behavior is systematically investigated as a function of flexibility and temperature. It is found that by including the intramolecular terms in the potential the calculated viscosity values are in overall much better agreement, compared to earlier and recent available experimental data, than those obtained with the rigid SPC/E model. The effect of the intramolecular degrees of freedom on transport properties of liquid water is analyzed and the incorporation of polarizability is discussed for further improvements. To our knowledge the present study constitutes the first compendium of results on viscosities for pure liquid water, including flexible models, that has been assembled.},
101 Author = {J.S. Medina and R. Prosmiti and P. Villarreal and G. Delgado-Barrio and G. Winter and B. Gonz{\'a}lez and J.V. Alem{\'a}n and C. Collado},
102 Date-Added = {2011-12-13 17:08:34 -0500},
103 Date-Modified = {2011-12-13 17:08:49 -0500},
104 Doi = {10.1016/j.chemphys.2011.07.001},
105 Issn = {0301-0104},
106 Journal = {Chemical Physics},
107 Keywords = {Viscosity calculations},
108 Number = {1-3},
109 Pages = {9 - 18},
110 Title = {Molecular dynamics simulations of rigid and flexible water models: Temperature dependence of viscosity},
111 Url = {http://www.sciencedirect.com/science/article/pii/S0301010411002813},
112 Volume = {388},
113 Year = {2011},
114 Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0301010411002813},
115 Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.chemphys.2011.07.001}}
116
117 @book{WagnerKruse,
118 Address = {Berlin},
119 Author = {W. Wagner and A. Kruse},
120 Date-Added = {2011-12-13 14:57:08 -0500},
121 Date-Modified = {2011-12-13 14:57:08 -0500},
122 Publisher = {Springer-Verlag},
123 Title = {Properties of Water and Steam, the Industrial Standard IAPWS-IF97 for the Thermodynamic Properties and Supplementary Equations for Other Properties},
124 Year = {1998}}
125
126 @article{garde:PhysRevLett2009,
127 Author = {Shenogina, Natalia and Godawat, Rahul and Keblinski, Pawel and Garde, Shekhar},
128 Date-Added = {2011-12-13 12:48:51 -0500},
129 Date-Modified = {2011-12-13 12:48:51 -0500},
130 Doi = {10.1103/PhysRevLett.102.156101},
131 Journal = {Phys. Rev. Lett.},
132 Month = {Apr},
133 Number = {15},
134 Numpages = {4},
135 Pages = {156101},
136 Publisher = {American Physical Society},
137 Title = {How Wetting and Adhesion Affect Thermal Conductance of a Range of Hydrophobic to Hydrophilic Aqueous Interfaces},
138 Volume = {102},
139 Year = {2009},
140 Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.102.156101}}
141
142 @article{garde:nl2005,
143 Abstract = { Systems with nanoscopic features contain a high density of interfaces. Thermal transport in such systems can be governed by the resistance to heat transfer, the Kapitza resistance (RK), at the interface. Although soft interfaces, such as those between immiscible liquids or between a biomolecule and solvent, are ubiquitous, few studies of thermal transport at such interfaces have been reported. Here we characterize the interfacial conductance, 1/RK, of soft interfaces as a function of molecular architecture, chemistry, and the strength of cross-interfacial intermolecular interactions through detailed molecular dynamics simulations. The conductance of various interfaces studied here, for example, water−organic liquid, water−surfactant, surfactant−organic liquid, is relatively high (in the range of 65−370 MW/m2 K) compared to that for solid−liquid interfaces (∼10 MW/m2 K). Interestingly, the dependence of interfacial conductance on the chemistry and molecular architecture cannot be explained solely in terms of either bulk property mismatch or the strength of intermolecular attraction between the two phases. The observed trends can be attributed to a combination of strong cross-interface intermolecular interactions and good thermal coupling via soft vibration modes present at liquid−liquid interfaces. },
144 Author = {Patel, Harshit A. and Garde, Shekhar and Keblinski, Pawel},
145 Date-Added = {2011-12-13 12:48:51 -0500},
146 Date-Modified = {2011-12-13 12:48:51 -0500},
147 Doi = {10.1021/nl051526q},
148 Eprint = {http://pubs.acs.org/doi/pdf/10.1021/nl051526q},
149 Journal = {Nano Lett.},
150 Note = {PMID: 16277458},
151 Number = {11},
152 Pages = {2225-2231},
153 Title = {Thermal Resistance of Nanoscopic Liquid−Liquid Interfaces:  Dependence on Chemistry and Molecular Architecture},
154 Url = {http://pubs.acs.org/doi/abs/10.1021/nl051526q},
155 Volume = {5},
156 Year = {2005},
157 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/nl051526q},
158 Bdsk-Url-2 = {http://dx.doi.org/10.1021/nl051526q}}
159
160 @article{melchionna93,
161 Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
162 Date-Added = {2011-12-12 17:52:15 -0500},
163 Date-Modified = {2011-12-12 17:52:15 -0500},
164 Journal = {Mol. Phys.},
165 Pages = {533-544},
166 Title = {Hoover {\sc npt} dynamics for systems varying in shape and size},
167 Volume = 78,
168 Year = 1993}
169
170 @article{TraPPE-UA.thiols,
171 Author = {Lubna, Nusrat and Kamath, Ganesh and Potoff, Jeffrey J. and Rai, Neeraj and Siepmann, J. Ilja},
172 Date-Added = {2011-12-07 15:06:12 -0500},
173 Date-Modified = {2011-12-07 15:06:12 -0500},
174 Doi = {10.1021/jp0549125},
175 Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp0549125},
176 Journal = {J. Phys. Chem. B},
177 Number = {50},
178 Pages = {24100-24107},
179 Title = {Transferable Potentials for Phase Equilibria. 8. United-Atom Description for Thiols, Sulfides, Disulfides, and Thiophene},
180 Url = {http://pubs.acs.org/doi/abs/10.1021/jp0549125},
181 Volume = {109},
182 Year = {2005},
183 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp0549125},
184 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp0549125}}
185
186 @article{TraPPE-UA.alkylbenzenes,
187 Author = {Wick, Collin D. and Martin, Marcus G. and Siepmann, J. Ilja},
188 Date-Added = {2011-12-07 15:06:12 -0500},
189 Date-Modified = {2011-12-07 15:06:12 -0500},
190 Doi = {10.1021/jp001044x},
191 Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp001044x},
192 Journal = {J. Phys. Chem. B},
193 Number = {33},
194 Pages = {8008-8016},
195 Title = {Transferable Potentials for Phase Equilibria. 4. United-Atom Description of Linear and Branched Alkenes and Alkylbenzenes},
196 Url = {http://pubs.acs.org/doi/abs/10.1021/jp001044x},
197 Volume = {104},
198 Year = {2000},
199 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp001044x},
200 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp001044x}}
201
202 @article{TraPPE-UA.alkanes,
203 Author = {Martin, Marcus G. and Siepmann, J. Ilja},
204 Date-Added = {2011-12-07 15:06:12 -0500},
205 Date-Modified = {2011-12-07 15:06:12 -0500},
206 Doi = {10.1021/jp972543+},
207 Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp972543%2B},
208 Journal = {J. Phys. Chem. B},
209 Number = {14},
210 Pages = {2569-2577},
211 Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes},
212 Url = {http://pubs.acs.org/doi/abs/10.1021/jp972543%2B},
213 Volume = {102},
214 Year = {1998},
215 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp972543+},
216 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp972543+},
217 Bdsk-Url-3 = {http://pubs.acs.org/doi/abs/10.1021/jp972543%2B}}
218
219 @article{ISI:000167766600035,
220 Abstract = {Molecular dynamics simulations are used to
221 investigate the separation of water films adjacent
222 to a hot metal surface. The simulations clearly show
223 that the water layers nearest the surface overheat
224 and undergo explosive boiling. For thick films, the
225 expansion of the vaporized molecules near the
226 surface forces the outer water layers to move away
227 from the surface. These results are of interest for
228 mass spectrometry of biological molecules, steam
229 cleaning of surfaces, and medical procedures.},
230 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
231 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.},
232 Author = {Dou, YS and Zhigilei, LV and Winograd, N and Garrison, BJ},
233 Date-Added = {2011-12-07 15:02:32 -0500},
234 Date-Modified = {2011-12-07 15:02:32 -0500},
235 Doc-Delivery-Number = {416ED},
236 Issn = {1089-5639},
237 Journal = {J. Phys. Chem. A},
238 Journal-Iso = {J. Phys. Chem. A},
239 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},
240 Language = {English},
241 Month = {MAR 29},
242 Number = {12},
243 Number-Of-Cited-References = {65},
244 Pages = {2748-2755},
245 Publisher = {AMER CHEMICAL SOC},
246 Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
247 Times-Cited = {66},
248 Title = {Explosive boiling of water films adjacent to heated surfaces: A microscopic description},
249 Type = {Article},
250 Unique-Id = {ISI:000167766600035},
251 Volume = {105},
252 Year = {2001}}
253
254 @article{Chen90,
255 Author = {A.~P. Sutton and J. Chen},
256 Date-Added = {2011-12-07 15:01:59 -0500},
257 Date-Modified = {2011-12-07 15:01:59 -0500},
258 Journal = {Philos. Mag. Lett.},
259 Pages = {139-146},
260 Title = {Long-Range Finnis Sinclair Potentials},
261 Volume = 61,
262 Year = {1990}}
263
264 @article{PhysRevB.59.3527,
265 Author = {Qi, Yue and \c{C}a\v{g}in, Tahir and Kimura, Yoshitaka and {Goddard III}, William A.},
266 Date-Added = {2011-12-07 15:01:36 -0500},
267 Date-Modified = {2011-12-07 15:01:36 -0500},
268 Doi = {10.1103/PhysRevB.59.3527},
269 Journal = {Phys. Rev. B},
270 Local-Url = {file://localhost/Users/charles/Documents/Papers/Qi/1999.pdf},
271 Month = {Feb},
272 Number = {5},
273 Numpages = {6},
274 Pages = {3527-3533},
275 Publisher = {American Physical Society},
276 Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals:\quad{}{C}u-{A}g and {C}u-{N}i},
277 Volume = {59},
278 Year = {1999},
279 Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.59.3527}}
280
281 @article{Bedrov:2000,
282 Abstract = {We have applied a new nonequilibrium molecular
283 dynamics (NEMD) method {[}F. Muller-Plathe,
284 J. Chem. Phys. 106, 6082 (1997)] previously applied
285 to monatomic Lennard-Jones fluids in the
286 determination of the thermal conductivity of
287 molecular fluids. The method was modified in order
288 to be applicable to systems with holonomic
289 constraints. Because the method involves imposing a
290 known heat flux it is particularly attractive for
291 systems involving long-range and many-body
292 interactions where calculation of the microscopic
293 heat flux is difficult. The predicted thermal
294 conductivities of liquid n-butane and water using
295 the imposed-flux NEMD method were found to be in a
296 good agreement with previous simulations and
297 experiment. (C) 2000 American Institute of
298 Physics. {[}S0021-9606(00)50841-1].},
299 Address = {2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA},
300 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.},
301 Author = {Bedrov, D and Smith, GD},
302 Date-Added = {2011-12-07 15:00:27 -0500},
303 Date-Modified = {2011-12-07 15:00:27 -0500},
304 Doc-Delivery-Number = {369BF},
305 Issn = {0021-9606},
306 Journal = {J. Chem. Phys.},
307 Journal-Iso = {J. Chem. Phys.},
308 Keywords-Plus = {EFFECTIVE PAIR POTENTIALS; TRANSPORT-PROPERTIES; CANONICAL ENSEMBLE; NORMAL-BUTANE; ALGORITHMS; SHAKE; WATER},
309 Language = {English},
310 Month = {NOV 8},
311 Number = {18},
312 Number-Of-Cited-References = {26},
313 Pages = {8080-8084},
314 Publisher = {AMER INST PHYSICS},
315 Read = {1},
316 Subject-Category = {Physics, Atomic, Molecular \& Chemical},
317 Times-Cited = {23},
318 Title = {Thermal conductivity of molecular fluids from molecular dynamics simulations: Application of a new imposed-flux method},
319 Type = {Article},
320 Unique-Id = {ISI:000090151400044},
321 Volume = {113},
322 Year = {2000}}
323
324 @article{10.1063/1.3330544,
325 Author = {Miguel Angel Gonz{\'a}lez and Jos{\'e} L. F. Abascal},
326 Coden = {JCPSA6},
327 Date-Added = {2011-12-07 14:59:20 -0500},
328 Date-Modified = {2011-12-15 13:10:11 -0500},
329 Doi = {DOI:10.1063/1.3330544},
330 Eissn = {10897690},
331 Issn = {00219606},
332 Journal = {J. Chem. Phys.},
333 Keywords = {shear strength; viscosity;},
334 Number = {9},
335 Pages = {096101},
336 Publisher = {AIP},
337 Title = {The shear viscosity of rigid water models},
338 Url = {http://dx.doi.org/doi/10.1063/1.3330544},
339 Volume = {132},
340 Year = {2010},
341 Bdsk-Url-1 = {http://dx.doi.org/doi/10.1063/1.3330544},
342 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3330544}}
343
344 @article{doi:10.1021/jp048434u,
345 Abstract = { The different possible proton-ordered structures of ice Ih for an orthorombic unit cell with 8 water molecules were derived. The number of unique structures was found to be 16. The crystallographic coordinates of these are reported. The energetics of the different polymorphs were investigated by quantum-mechanical density-functional theory calculations and for comparison by molecular-mechanics analytical potential models. The polymorphs were found to be close in energy, i.e., within approximately 0.25 kcal/mol H2O, on the basis of the quantum-chemical DFT methods. At 277 K, the different energy levels are about evenly populated, but at a lower temperature, a transition to an ordered form is expected. This form was found to agree with the ice phase XI. The difference in lattice energies among the polymorphs was rationalized in terms of structural characteristics. The most important parameters to determine the lattice energies were found to be the distributions of water dimer H-bonded pair conformations, in an intricate manner. },
346 Author = {Hirsch, Tomas K. and Ojam{\"a}e, Lars},
347 Date-Added = {2011-12-07 14:38:30 -0500},
348 Date-Modified = {2011-12-07 14:38:30 -0500},
349 Doi = {10.1021/jp048434u},
350 Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp048434u},
351 Journal = {J. Phys. Chem. B},
352 Number = {40},
353 Pages = {15856-15864},
354 Title = {Quantum-Chemical and Force-Field Investigations of Ice Ih:  Computation of Proton-Ordered Structures and Prediction of Their Lattice Energies},
355 Url = {http://pubs.acs.org/doi/abs/10.1021/jp048434u},
356 Volume = {108},
357 Year = {2004},
358 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp048434u},
359 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp048434u}}
360
361 @article{Meineke:2005gd,
362 Abstract = {OOPSE is a new molecular dynamics simulation program
363 that is capable of efficiently integrating equations
364 of motion for atom types with orientational degrees
365 of freedom (e.g. #sticky# atoms and point
366 dipoles). Transition metals can also be simulated
367 using the embedded atom method (EAM) potential
368 included in the code. Parallel simulations are
369 carried out using the force-based decomposition
370 method. Simulations are specified using a very
371 simple C-based meta-data language. A number of
372 advanced integrators are included, and the basic
373 integrator for orientational dynamics provides
374 substantial improvements over older quaternion-based
375 schemes.},
376 Address = {111 RIVER ST, HOBOKEN, NJ 07030 USA},
377 Author = {Meineke, M. A. and Vardeman, C. F. and Lin, T and Fennell, CJ and Gezelter, J. D.},
378 Date-Added = {2011-12-07 13:33:04 -0500},
379 Date-Modified = {2011-12-07 13:33:04 -0500},
380 Doi = {DOI 10.1002/jcc.20161},
381 Isi = {000226558200006},
382 Isi-Recid = {142688207},
383 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},
384 Journal = {J. Comput. Chem.},
385 Keywords = {OOPSE; molecular dynamics},
386 Month = feb,
387 Number = {3},
388 Pages = {252-271},
389 Publisher = {JOHN WILEY \& SONS INC},
390 Times-Cited = {9},
391 Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
392 Volume = {26},
393 Year = {2005},
394 Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000226558200006},
395 Bdsk-Url-2 = {http://dx.doi.org/10.1002/jcc.20161}}
396
397 @article{hoover85,
398 Author = {W.~G. Hoover},
399 Date-Added = {2011-12-06 14:23:41 -0500},
400 Date-Modified = {2011-12-06 14:23:41 -0500},
401 Journal = {Phys. Rev. A},
402 Pages = 1695,
403 Title = {Canonical dynamics: Equilibrium phase-space distributions},
404 Volume = 31,
405 Year = 1985}
406
407 @article{Maginn:2010,
408 Abstract = {The reverse nonequilibrium molecular dynamics
409 (RNEMD) method calculates the shear viscosity of a
410 fluid by imposing a nonphysical exchange of momentum
411 and measuring the resulting shear velocity
412 gradient. In this study we investigate the range of
413 momentum flux values over which RNEMD yields usable
414 (linear) velocity gradients. We find that nonlinear
415 velocity profiles result primarily from gradients in
416 fluid temperature and density. The temperature
417 gradient results from conversion of heat into bulk
418 kinetic energy, which is transformed back into heat
419 elsewhere via viscous heating. An expression is
420 derived to predict the temperature profile resulting
421 from a specified momentum flux for a given fluid and
422 simulation cell. Although primarily bounded above,
423 we also describe milder low-flux limitations. RNEMD
424 results for a Lennard-Jones fluid agree with
425 equilibrium molecular dynamics and conventional
426 nonequilibrium molecular dynamics calculations at
427 low shear, but RNEMD underpredicts viscosity
428 relative to conventional NEMD at high shear.},
429 Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
430 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.},
431 Article-Number = {014103},
432 Author = {Tenney, Craig M. and Maginn, Edward J.},
433 Author-Email = {ed@nd.edu},
434 Date-Added = {2011-12-05 18:29:08 -0500},
435 Date-Modified = {2011-12-05 18:29:08 -0500},
436 Doc-Delivery-Number = {542DQ},
437 Doi = {10.1063/1.3276454},
438 Funding-Acknowledgement = {U.S. Department of Energy {[}DE-FG36-08G088020]},
439 Funding-Text = {Support for this work was provided by the U.S. Department of Energy (Grant No. DE-FG36-08G088020)},
440 Issn = {0021-9606},
441 Journal = {J. Chem. Phys.},
442 Journal-Iso = {J. Chem. Phys.},
443 Keywords = {Lennard-Jones potential; molecular dynamics method; Navier-Stokes equations; viscosity},
444 Keywords-Plus = {CURRENT AUTOCORRELATION-FUNCTION; IONIC LIQUID; SIMULATIONS; TEMPERATURE},
445 Language = {English},
446 Month = {JAN 7},
447 Number = {1},
448 Number-Of-Cited-References = {20},
449 Pages = {014103},
450 Publisher = {AMER INST PHYSICS},
451 Subject-Category = {Physics, Atomic, Molecular \& Chemical},
452 Times-Cited = {0},
453 Title = {Limitations and recommendations for the calculation of shear viscosity using reverse nonequilibrium molecular dynamics},
454 Type = {Article},
455 Unique-Id = {ISI:000273472300004},
456 Volume = {132},
457 Year = {2010},
458 Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.3276454}}
459
460 @article{ISI:000080382700030,
461 Abstract = {A nonequilibrium method for calculating the shear
462 viscosity is presented. It reverses the
463 cause-and-effect picture customarily used in
464 nonequilibrium molecular dynamics: the effect, the
465 momentum flux or stress, is imposed, whereas the
466 cause, the velocity gradient or shear rate, is
467 obtained from the simulation. It differs from other
468 Norton-ensemble methods by the way in which the
469 steady-state momentum flux is maintained. This
470 method involves a simple exchange of particle
471 momenta, which is easy to implement. Moreover, it
472 can be made to conserve the total energy as well as
473 the total linear momentum, so no coupling to an
474 external temperature bath is needed. The resulting
475 raw data, the velocity profile, is a robust and
476 rapidly converging property. The method is tested on
477 the Lennard-Jones fluid near its triple point. It
478 yields a viscosity of 3.2-3.3, in Lennard-Jones
479 reduced units, in agreement with literature
480 results. {[}S1063-651X(99)03105-0].},
481 Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
482 Affiliation = {Muller-Plathe, F (Reprint Author), Max Planck Inst Polymerforsch, Ackermannweg 10, D-55128 Mainz, Germany. Max Planck Inst Polymerforsch, D-55128 Mainz, Germany.},
483 Author = {M\"{u}ller-Plathe, F},
484 Date-Added = {2011-12-05 18:18:37 -0500},
485 Date-Modified = {2011-12-05 18:18:37 -0500},
486 Doc-Delivery-Number = {197TX},
487 Issn = {1063-651X},
488 Journal = {Phys. Rev. E},
489 Journal-Iso = {Phys. Rev. E},
490 Language = {English},
491 Month = {MAY},
492 Number = {5, Part A},
493 Number-Of-Cited-References = {17},
494 Pages = {4894-4898},
495 Publisher = {AMERICAN PHYSICAL SOC},
496 Subject-Category = {Physics, Fluids \& Plasmas; Physics, Mathematical},
497 Times-Cited = {57},
498 Title = {Reversing the perturbation in nonequilibrium molecular dynamics: An easy way to calculate the shear viscosity of fluids},
499 Type = {Article},
500 Unique-Id = {ISI:000080382700030},
501 Volume = {59},
502 Year = {1999}}
503
504 @article{MullerPlathe:1997xw,
505 Abstract = {A nonequilibrium molecular dynamics method for
506 calculating the thermal conductivity is
507 presented. It reverses the usual cause and effect
508 picture. The ''effect,'' the heat flux, is imposed
509 on the system and the ''cause,'' the temperature
510 gradient is obtained from the simulation. Besides
511 being very simple to implement, the scheme offers
512 several advantages such as compatibility with
513 periodic boundary conditions, conservation of total
514 energy and total linear momentum, and the sampling
515 of a rapidly converging quantity (temperature
516 gradient) rather than a slowly converging one (heat
517 flux). The scheme is tested on the Lennard-Jones
518 fluid. (C) 1997 American Institute of Physics.},
519 Address = {WOODBURY},
520 Author = {M\"{u}ller-Plathe, F.},
521 Cited-Reference-Count = {13},
522 Date = {APR 8},
523 Date-Added = {2011-12-05 18:18:37 -0500},
524 Date-Modified = {2011-12-05 18:18:37 -0500},
525 Document-Type = {Article},
526 Isi = {ISI:A1997WR62000032},
527 Isi-Document-Delivery-Number = {WR620},
528 Iso-Source-Abbreviation = {J. Chem. Phys.},
529 Issn = {0021-9606},
530 Journal = {J. Chem. Phys.},
531 Language = {English},
532 Month = {Apr},
533 Number = {14},
534 Page-Count = {4},
535 Pages = {6082--6085},
536 Publication-Type = {J},
537 Publisher = {AMER INST PHYSICS},
538 Publisher-Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999},
539 Reprint-Address = {MullerPlathe, F, MAX PLANCK INST POLYMER RES, D-55128 MAINZ, GERMANY.},
540 Source = {J CHEM PHYS},
541 Subject-Category = {Physics, Atomic, Molecular & Chemical},
542 Times-Cited = {106},
543 Title = {A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity},
544 Volume = {106},
545 Year = {1997}}
546
547 @article{priezjev:204704,
548 Author = {Nikolai V. Priezjev},
549 Date-Added = {2011-11-28 14:39:18 -0500},
550 Date-Modified = {2011-11-28 14:39:18 -0500},
551 Doi = {10.1063/1.3663384},
552 Eid = {204704},
553 Journal = {J. Chem. Phys.},
554 Keywords = {channel flow; diffusion; flow simulation; hydrodynamics; molecular dynamics method; pattern formation; random processes; shear flow; slip flow; wetting},
555 Number = {20},
556 Numpages = {9},
557 Pages = {204704},
558 Publisher = {AIP},
559 Title = {Molecular diffusion and slip boundary conditions at smooth surfaces with periodic and random nanoscale textures},
560 Url = {http://link.aip.org/link/?JCP/135/204704/1},
561 Volume = {135},
562 Year = {2011},
563 Bdsk-Url-1 = {http://link.aip.org/link/?JCP/135/204704/1},
564 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3663384}}
565
566 @article{bryk:10258,
567 Author = {Taras Bryk and A. D. J. Haymet},
568 Date-Added = {2011-11-22 17:06:35 -0500},
569 Date-Modified = {2011-11-22 17:06:35 -0500},
570 Doi = {10.1063/1.1519538},
571 Journal = {J. Chem. Phys.},
572 Keywords = {liquid structure; molecular dynamics method; water; ice; interface structure},
573 Number = {22},
574 Pages = {10258-10268},
575 Publisher = {AIP},
576 Title = {Ice 1h/water interface of the SPC/E model: Molecular dynamics simulations of the equilibrium basal and prism interfaces},
577 Url = {http://link.aip.org/link/?JCP/117/10258/1},
578 Volume = {117},
579 Year = {2002},
580 Bdsk-Url-1 = {http://link.aip.org/link/?JCP/117/10258/1},
581 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1519538}}
582
583 @article{kuang:164101,
584 Author = {Shenyu Kuang and J. Daniel Gezelter},
585 Date-Added = {2011-11-18 15:32:23 -0500},
586 Date-Modified = {2011-11-18 15:32:23 -0500},
587 Doi = {10.1063/1.3499947},
588 Eid = {164101},
589 Journal = {J. Chem. Phys.},
590 Keywords = {linear momentum; molecular dynamics method; thermal conductivity; total energy; viscosity},
591 Number = {16},
592 Numpages = {9},
593 Pages = {164101},
594 Publisher = {AIP},
595 Title = {A gentler approach to RNEMD: Nonisotropic velocity scaling for computing thermal conductivity and shear viscosity},
596 Url = {http://link.aip.org/link/?JCP/133/164101/1},
597 Volume = {133},
598 Year = {2010},
599 Bdsk-Url-1 = {http://link.aip.org/link/?JCP/133/164101/1},
600 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3499947}}
601
602 @misc{openmd,
603 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},
604 Date-Added = {2011-11-18 15:32:23 -0500},
605 Date-Modified = {2011-11-18 15:32:23 -0500},
606 Howpublished = {Available at {\tt http://openmd.net}},
607 Title = {{OpenMD, an open source engine for molecular dynamics}}}
608
609 @article{kuang:AuThl,
610 Author = {Kuang, Shenyu and Gezelter, J. Daniel},
611 Date-Added = {2011-11-18 13:03:06 -0500},
612 Date-Modified = {2011-12-05 17:58:01 -0500},
613 Doi = {10.1021/jp2073478},
614 Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp2073478},
615 Journal = {J. Phys. Chem. C},
616 Number = {45},
617 Pages = {22475-22483},
618 Title = {Simulating Interfacial Thermal Conductance at Metal-Solvent Interfaces: The Role of Chemical Capping Agents},
619 Url = {http://pubs.acs.org/doi/abs/10.1021/jp2073478},
620 Volume = {115},
621 Year = {2011},
622 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp2073478},
623 Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp2073478}}
624
625 @article{10.1063/1.2772547,
626 Author = {Hideo Kaburaki and Ju Li and Sidney Yip and Hajime Kimizuka},
627 Coden = {JAPIAU},
628 Date-Added = {2011-11-01 16:46:32 -0400},
629 Date-Modified = {2011-11-01 16:46:32 -0400},
630 Doi = {DOI:10.1063/1.2772547},
631 Eissn = {10897550},
632 Issn = {00218979},
633 Keywords = {argon; Lennard-Jones potential; phonons; thermal conductivity;},
634 Number = {4},
635 Pages = {043514},
636 Publisher = {AIP},
637 Title = {Dynamical thermal conductivity of argon crystal},
638 Url = {http://dx.doi.org/10.1063/1.2772547},
639 Volume = {102},
640 Year = {2007},
641 Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2772547}}
642
643 @article{PhysRevLett.82.4671,
644 Author = {Barrat, Jean-Louis and Bocquet, Lyd\'eric},
645 Date-Added = {2011-11-01 16:44:29 -0400},
646 Date-Modified = {2011-11-01 16:44:29 -0400},
647 Doi = {10.1103/PhysRevLett.82.4671},
648 Issue = {23},
649 Journal = {Phys. Rev. Lett.},
650 Month = {Jun},
651 Pages = {4671--4674},
652 Publisher = {American Physical Society},
653 Title = {Large Slip Effect at a Nonwetting Fluid-Solid Interface},
654 Url = {http://link.aps.org/doi/10.1103/PhysRevLett.82.4671},
655 Volume = {82},
656 Year = {1999},
657 Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevLett.82.4671},
658 Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevLett.82.4671}}
659
660 @article{10.1063/1.1610442,
661 Author = {J. R. Schmidt and J. L. Skinner},
662 Coden = {JCPSA6},
663 Date-Added = {2011-10-13 16:28:43 -0400},
664 Date-Modified = {2011-12-15 13:11:53 -0500},
665 Doi = {DOI:10.1063/1.1610442},
666 Eissn = {10897690},
667 Issn = {00219606},
668 Journal = {J. Chem. Phys.},
669 Keywords = {hydrodynamics; Brownian motion; molecular dynamics method; diffusion;},
670 Number = {15},
671 Pages = {8062-8068},
672 Publisher = {AIP},
673 Title = {Hydrodynamic boundary conditions, the Stokes?Einstein law, and long-time tails in the Brownian limit},
674 Url = {http://dx.doi.org/10.1063/1.1610442},
675 Volume = {119},
676 Year = {2003},
677 Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}
678
679 @article{10.1063/1.3274802,
680 Author = {Ting Chen and Berend Smit and Alexis T. Bell},
681 Coden = {JCPSA6},
682 Doi = {DOI:10.1063/1.3274802},
683 Eissn = {10897690},
684 Issn = {00219606},
685 Keywords = {fluctuations; molecular dynamics method; viscosity;},
686 Number = {24},
687 Pages = {246101},
688 Publisher = {AIP},
689 Title = {Are pressure fluctuation-based equilibrium methods really worse than nonequilibrium methods for calculating viscosities?},
690 Url = {http://dx.doi.org/doi/10.1063/1.3274802},
691 Volume = {131},
692 Year = {2009},
693 Bdsk-Url-1 = {http://dx.doi.org/doi/10.1063/1.3274802},
694 Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3274802}}