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Revision: 3771
Committed: Tue Dec 6 01:26:56 2011 UTC (12 years, 9 months ago) by skuang
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have a rough version of introduction and methodology now

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# User Rev Content
1 skuang 3770 %% This BibTeX bibliography file was created using BibDesk.
2     %% http://bibdesk.sourceforge.net/
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5 skuang 3771 %% Created for Shenyu Kuang at 2011-12-05 18:29:14 -0500
6 skuang 3770
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8     %% Saved with string encoding Unicode (UTF-8)
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10    
11    
12 skuang 3771 @article{Maginn:2010,
13     Abstract = {The reverse nonequilibrium molecular dynamics
14     (RNEMD) method calculates the shear viscosity of a
15     fluid by imposing a nonphysical exchange of momentum
16     and measuring the resulting shear velocity
17     gradient. In this study we investigate the range of
18     momentum flux values over which RNEMD yields usable
19     (linear) velocity gradients. We find that nonlinear
20     velocity profiles result primarily from gradients in
21     fluid temperature and density. The temperature
22     gradient results from conversion of heat into bulk
23     kinetic energy, which is transformed back into heat
24     elsewhere via viscous heating. An expression is
25     derived to predict the temperature profile resulting
26     from a specified momentum flux for a given fluid and
27     simulation cell. Although primarily bounded above,
28     we also describe milder low-flux limitations. RNEMD
29     results for a Lennard-Jones fluid agree with
30     equilibrium molecular dynamics and conventional
31     nonequilibrium molecular dynamics calculations at
32     low shear, but RNEMD underpredicts viscosity
33     relative to conventional NEMD at high shear.},
34     Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
35     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.},
36     Article-Number = {014103},
37     Author = {Tenney, Craig M. and Maginn, Edward J.},
38     Author-Email = {ed@nd.edu},
39     Date-Added = {2011-12-05 18:29:08 -0500},
40     Date-Modified = {2011-12-05 18:29:08 -0500},
41     Doc-Delivery-Number = {542DQ},
42     Doi = {10.1063/1.3276454},
43     Funding-Acknowledgement = {U.S. Department of Energy {[}DE-FG36-08G088020]},
44     Funding-Text = {Support for this work was provided by the U.S. Department of Energy (Grant No. DE-FG36-08G088020)},
45     Issn = {0021-9606},
46     Journal = {J. Chem. Phys.},
47     Journal-Iso = {J. Chem. Phys.},
48     Keywords = {Lennard-Jones potential; molecular dynamics method; Navier-Stokes equations; viscosity},
49     Keywords-Plus = {CURRENT AUTOCORRELATION-FUNCTION; IONIC LIQUID; SIMULATIONS; TEMPERATURE},
50     Language = {English},
51     Month = {JAN 7},
52     Number = {1},
53     Number-Of-Cited-References = {20},
54     Pages = {014103},
55     Publisher = {AMER INST PHYSICS},
56     Subject-Category = {Physics, Atomic, Molecular \& Chemical},
57     Times-Cited = {0},
58     Title = {Limitations and recommendations for the calculation of shear viscosity using reverse nonequilibrium molecular dynamics},
59     Type = {Article},
60     Unique-Id = {ISI:000273472300004},
61     Volume = {132},
62     Year = {2010},
63     Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.3276454}}
64    
65     @article{ISI:000080382700030,
66     Abstract = {A nonequilibrium method for calculating the shear
67     viscosity is presented. It reverses the
68     cause-and-effect picture customarily used in
69     nonequilibrium molecular dynamics: the effect, the
70     momentum flux or stress, is imposed, whereas the
71     cause, the velocity gradient or shear rate, is
72     obtained from the simulation. It differs from other
73     Norton-ensemble methods by the way in which the
74     steady-state momentum flux is maintained. This
75     method involves a simple exchange of particle
76     momenta, which is easy to implement. Moreover, it
77     can be made to conserve the total energy as well as
78     the total linear momentum, so no coupling to an
79     external temperature bath is needed. The resulting
80     raw data, the velocity profile, is a robust and
81     rapidly converging property. The method is tested on
82     the Lennard-Jones fluid near its triple point. It
83     yields a viscosity of 3.2-3.3, in Lennard-Jones
84     reduced units, in agreement with literature
85     results. {[}S1063-651X(99)03105-0].},
86     Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
87     Affiliation = {Muller-Plathe, F (Reprint Author), Max Planck Inst Polymerforsch, Ackermannweg 10, D-55128 Mainz, Germany. Max Planck Inst Polymerforsch, D-55128 Mainz, Germany.},
88     Author = {M\"{u}ller-Plathe, F},
89     Date-Added = {2011-12-05 18:18:37 -0500},
90     Date-Modified = {2011-12-05 18:18:37 -0500},
91     Doc-Delivery-Number = {197TX},
92     Issn = {1063-651X},
93     Journal = {Phys. Rev. E},
94     Journal-Iso = {Phys. Rev. E},
95     Language = {English},
96     Month = {MAY},
97     Number = {5, Part A},
98     Number-Of-Cited-References = {17},
99     Pages = {4894-4898},
100     Publisher = {AMERICAN PHYSICAL SOC},
101     Subject-Category = {Physics, Fluids \& Plasmas; Physics, Mathematical},
102     Times-Cited = {57},
103     Title = {Reversing the perturbation in nonequilibrium molecular dynamics: An easy way to calculate the shear viscosity of fluids},
104     Type = {Article},
105     Unique-Id = {ISI:000080382700030},
106     Volume = {59},
107     Year = {1999}}
108    
109     @article{MullerPlathe:1997xw,
110     Abstract = {A nonequilibrium molecular dynamics method for
111     calculating the thermal conductivity is
112     presented. It reverses the usual cause and effect
113     picture. The ''effect,'' the heat flux, is imposed
114     on the system and the ''cause,'' the temperature
115     gradient is obtained from the simulation. Besides
116     being very simple to implement, the scheme offers
117     several advantages such as compatibility with
118     periodic boundary conditions, conservation of total
119     energy and total linear momentum, and the sampling
120     of a rapidly converging quantity (temperature
121     gradient) rather than a slowly converging one (heat
122     flux). The scheme is tested on the Lennard-Jones
123     fluid. (C) 1997 American Institute of Physics.},
124     Address = {WOODBURY},
125     Author = {M\"{u}ller-Plathe, F.},
126     Cited-Reference-Count = {13},
127     Date = {APR 8},
128     Date-Added = {2011-12-05 18:18:37 -0500},
129     Date-Modified = {2011-12-05 18:18:37 -0500},
130     Document-Type = {Article},
131     Isi = {ISI:A1997WR62000032},
132     Isi-Document-Delivery-Number = {WR620},
133     Iso-Source-Abbreviation = {J. Chem. Phys.},
134     Issn = {0021-9606},
135     Journal = {J. Chem. Phys.},
136     Language = {English},
137     Month = {Apr},
138     Number = {14},
139     Page-Count = {4},
140     Pages = {6082--6085},
141     Publication-Type = {J},
142     Publisher = {AMER INST PHYSICS},
143     Publisher-Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999},
144     Reprint-Address = {MullerPlathe, F, MAX PLANCK INST POLYMER RES, D-55128 MAINZ, GERMANY.},
145     Source = {J CHEM PHYS},
146     Subject-Category = {Physics, Atomic, Molecular & Chemical},
147     Times-Cited = {106},
148     Title = {A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity},
149     Volume = {106},
150     Year = {1997}}
151    
152 skuang 3770 @article{priezjev:204704,
153     Author = {Nikolai V. Priezjev},
154     Date-Added = {2011-11-28 14:39:18 -0500},
155     Date-Modified = {2011-11-28 14:39:18 -0500},
156     Doi = {10.1063/1.3663384},
157     Eid = {204704},
158     Journal = {The Journal of Chemical Physics},
159     Keywords = {channel flow; diffusion; flow simulation; hydrodynamics; molecular dynamics method; pattern formation; random processes; shear flow; slip flow; wetting},
160     Number = {20},
161     Numpages = {9},
162     Pages = {204704},
163     Publisher = {AIP},
164     Title = {Molecular diffusion and slip boundary conditions at smooth surfaces with periodic and random nanoscale textures},
165     Url = {http://link.aip.org/link/?JCP/135/204704/1},
166     Volume = {135},
167     Year = {2011},
168     Bdsk-Url-1 = {http://link.aip.org/link/?JCP/135/204704/1},
169     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3663384}}
170    
171     @article{bryk:10258,
172     Author = {Taras Bryk and A. D. J. Haymet},
173     Date-Added = {2011-11-22 17:06:35 -0500},
174     Date-Modified = {2011-11-22 17:06:35 -0500},
175     Doi = {10.1063/1.1519538},
176     Journal = {The Journal of Chemical Physics},
177     Keywords = {liquid structure; molecular dynamics method; water; ice; interface structure},
178     Number = {22},
179     Pages = {10258-10268},
180     Publisher = {AIP},
181     Title = {Ice 1h/water interface of the SPC/E model: Molecular dynamics simulations of the equilibrium basal and prism interfaces},
182     Url = {http://link.aip.org/link/?JCP/117/10258/1},
183     Volume = {117},
184     Year = {2002},
185     Bdsk-Url-1 = {http://link.aip.org/link/?JCP/117/10258/1},
186     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1519538}}
187    
188     @article{kuang:164101,
189     Author = {Shenyu Kuang and J. Daniel Gezelter},
190     Date-Added = {2011-11-18 15:32:23 -0500},
191     Date-Modified = {2011-11-18 15:32:23 -0500},
192     Doi = {10.1063/1.3499947},
193     Eid = {164101},
194     Journal = {J. Chem. Phys.},
195     Keywords = {linear momentum; molecular dynamics method; thermal conductivity; total energy; viscosity},
196     Number = {16},
197     Numpages = {9},
198     Pages = {164101},
199     Publisher = {AIP},
200     Title = {A gentler approach to RNEMD: Nonisotropic velocity scaling for computing thermal conductivity and shear viscosity},
201     Url = {http://link.aip.org/link/?JCP/133/164101/1},
202     Volume = {133},
203     Year = {2010},
204     Bdsk-Url-1 = {http://link.aip.org/link/?JCP/133/164101/1},
205     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3499947}}
206    
207     @misc{openmd,
208     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},
209     Date-Added = {2011-11-18 15:32:23 -0500},
210     Date-Modified = {2011-11-18 15:32:23 -0500},
211     Howpublished = {Available at {\tt http://openmd.net}},
212     Title = {{OpenMD, an open source engine for molecular dynamics}}}
213    
214 skuang 3771 @article{kuang:AuThl,
215 skuang 3770 Author = {Kuang, Shenyu and Gezelter, J. Daniel},
216     Date-Added = {2011-11-18 13:03:06 -0500},
217 skuang 3771 Date-Modified = {2011-12-05 17:58:01 -0500},
218 skuang 3770 Doi = {10.1021/jp2073478},
219     Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp2073478},
220     Journal = {The Journal of Physical Chemistry C},
221     Number = {45},
222     Pages = {22475-22483},
223     Title = {Simulating Interfacial Thermal Conductance at Metal-Solvent Interfaces: The Role of Chemical Capping Agents},
224     Url = {http://pubs.acs.org/doi/abs/10.1021/jp2073478},
225     Volume = {115},
226     Year = {2011},
227     Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp2073478},
228     Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp2073478}}
229    
230     @article{10.1063/1.2772547,
231     Author = {Hideo Kaburaki and Ju Li and Sidney Yip and Hajime Kimizuka},
232     Coden = {JAPIAU},
233     Date-Added = {2011-11-01 16:46:32 -0400},
234     Date-Modified = {2011-11-01 16:46:32 -0400},
235     Doi = {DOI:10.1063/1.2772547},
236     Eissn = {10897550},
237     Issn = {00218979},
238     Keywords = {argon; Lennard-Jones potential; phonons; thermal conductivity;},
239     Number = {4},
240     Pages = {043514},
241     Publisher = {AIP},
242     Title = {Dynamical thermal conductivity of argon crystal},
243     Url = {http://dx.doi.org/10.1063/1.2772547},
244     Volume = {102},
245     Year = {2007},
246     Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2772547}}
247    
248     @article{PhysRevLett.82.4671,
249     Author = {Barrat, Jean-Louis and Bocquet, Lyd\'eric},
250     Date-Added = {2011-11-01 16:44:29 -0400},
251     Date-Modified = {2011-11-01 16:44:29 -0400},
252     Doi = {10.1103/PhysRevLett.82.4671},
253     Issue = {23},
254     Journal = {Phys. Rev. Lett.},
255     Month = {Jun},
256     Pages = {4671--4674},
257     Publisher = {American Physical Society},
258     Title = {Large Slip Effect at a Nonwetting Fluid-Solid Interface},
259     Url = {http://link.aps.org/doi/10.1103/PhysRevLett.82.4671},
260     Volume = {82},
261     Year = {1999},
262     Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevLett.82.4671},
263     Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevLett.82.4671}}
264    
265     @article{10.1063/1.1610442,
266     Author = {J. R. Schmidt and J. L. Skinner},
267     Coden = {JCPSA6},
268     Date-Added = {2011-10-13 16:28:43 -0400},
269     Date-Modified = {2011-10-13 16:28:43 -0400},
270     Doi = {DOI:10.1063/1.1610442},
271     Eissn = {10897690},
272     Issn = {00219606},
273     Keywords = {hydrodynamics; Brownian motion; molecular dynamics method; diffusion;},
274     Number = {15},
275     Pages = {8062-8068},
276     Publisher = {AIP},
277     Title = {Hydrodynamic boundary conditions, the Stokes?Einstein law, and long-time tails in the Brownian limit},
278     Url = {http://dx.doi.org/10.1063/1.1610442},
279     Volume = {119},
280     Year = {2003},
281     Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}
282    
283     @article{10.1063/1.3274802,
284     Author = {Ting Chen and Berend Smit and Alexis T. Bell},
285     Coden = {JCPSA6},
286     Doi = {DOI:10.1063/1.3274802},
287     Eissn = {10897690},
288     Issn = {00219606},
289     Keywords = {fluctuations; molecular dynamics method; viscosity;},
290     Number = {24},
291     Pages = {246101},
292     Publisher = {AIP},
293     Title = {Are pressure fluctuation-based equilibrium methods really worse than nonequilibrium methods for calculating viscosities?},
294     Url = {http://dx.doi.org/doi/10.1063/1.3274802},
295     Volume = {131},
296     Year = {2009},
297     Bdsk-Url-1 = {http://dx.doi.org/doi/10.1063/1.3274802},
298     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3274802}}