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add more citations for NEMD and EMD background info.

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1 skuang 3527 %% This BibTeX bibliography file was created using BibDesk.
2     %% http://bibdesk.sourceforge.net/
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5 skuang 3591 %% Created for Shenyu Kuang at 2010-04-16 12:38:13 -0400
6 skuang 3527
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11    
12 skuang 3591 @article{hess:209,
13     Author = {Berk Hess},
14     Date-Added = {2010-04-16 12:37:37 -0400},
15     Date-Modified = {2010-04-16 12:37:37 -0400},
16     Doi = {10.1063/1.1421362},
17     Journal = {The Journal of Chemical Physics},
18     Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
19     Number = {1},
20     Pages = {209-217},
21     Publisher = {AIP},
22     Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
23     Url = {http://link.aip.org/link/?JCP/116/209/1},
24     Volume = {116},
25     Year = {2002},
26     Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
27     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}}
28    
29     @article{backer:154503,
30     Author = {J. A. Backer and C. P. Lowe and H. C. J. Hoefsloot and P. D. Iedema},
31     Date-Added = {2010-04-16 12:37:37 -0400},
32     Date-Modified = {2010-04-16 12:37:37 -0400},
33     Doi = {10.1063/1.1883163},
34     Eid = {154503},
35     Journal = {The Journal of Chemical Physics},
36     Keywords = {Poiseuille flow; flow simulation; Lennard-Jones potential; viscosity; boundary layers; computational fluid dynamics},
37     Number = {15},
38     Numpages = {6},
39     Pages = {154503},
40     Publisher = {AIP},
41     Title = {Poiseuille flow to measure the viscosity of particle model fluids},
42     Url = {http://link.aip.org/link/?JCP/122/154503/1},
43     Volume = {122},
44     Year = {2005},
45     Bdsk-Url-1 = {http://link.aip.org/link/?JCP/122/154503/1},
46     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1883163}}
47    
48     @article{daivis:541,
49     Author = {Peter J. Daivis and Denis J. Evans},
50     Date-Added = {2010-04-16 12:05:36 -0400},
51     Date-Modified = {2010-04-16 12:05:36 -0400},
52     Doi = {10.1063/1.466970},
53     Journal = {The Journal of Chemical Physics},
54     Keywords = {SHEAR; DECANE; FLOW MODELS; VOLUME; PRESSURE; NONEQUILIBRIUM; MOLECULAR DYNAMICS CALCULATIONS; COMPARATIVE EVALUATIONS; SIMULATION; STRAIN RATE; VISCOSITY; KUBO FORMULA},
55     Number = {1},
56     Pages = {541-547},
57     Publisher = {AIP},
58     Title = {Comparison of constant pressure and constant volume nonequilibrium simulations of sheared model decane},
59     Url = {http://link.aip.org/link/?JCP/100/541/1},
60     Volume = {100},
61     Year = {1994},
62     Bdsk-Url-1 = {http://link.aip.org/link/?JCP/100/541/1},
63     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.466970}}
64    
65     @article{mondello:9327,
66     Author = {Maurizio Mondello and Gary S. Grest},
67     Date-Added = {2010-04-16 12:05:36 -0400},
68     Date-Modified = {2010-04-16 12:05:36 -0400},
69     Doi = {10.1063/1.474002},
70     Journal = {The Journal of Chemical Physics},
71     Keywords = {organic compounds; viscosity; digital simulation; molecular dynamics method},
72     Number = {22},
73     Pages = {9327-9336},
74     Publisher = {AIP},
75     Title = {Viscosity calculations of [bold n]-alkanes by equilibrium molecular dynamics},
76     Url = {http://link.aip.org/link/?JCP/106/9327/1},
77     Volume = {106},
78     Year = {1997},
79     Bdsk-Url-1 = {http://link.aip.org/link/?JCP/106/9327/1},
80     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.474002}}
81    
82 skuang 3588 @article{ISI:A1988Q205300014,
83     Address = {{ONE GUNDPOWDER SQUARE, LONDON, ENGLAND EC4A 3DE}},
84     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.}},
85     Author = {VOGELSANG, R and HOHEISEL, G and LUCKAS, M},
86     Date-Added = {2010-04-14 16:20:24 -0400},
87     Date-Modified = {2010-04-14 16:20:24 -0400},
88     Doc-Delivery-Number = {{Q2053}},
89     Issn = {{0026-8976}},
90     Journal = {{MOLECULAR PHYSICS}},
91     Journal-Iso = {{Mol. Phys.}},
92     Language = {{English}},
93     Month = {{AUG 20}},
94     Number = {{6}},
95     Number-Of-Cited-References = {{14}},
96     Pages = {{1203-1213}},
97     Publisher = {{TAYLOR \& FRANCIS LTD}},
98     Subject-Category = {{Physics, Atomic, Molecular \& Chemical}},
99     Times-Cited = {{12}},
100     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}},
101     Type = {{Article}},
102     Unique-Id = {{ISI:A1988Q205300014}},
103     Volume = {{64}},
104     Year = {{1988}}}
105    
106 skuang 3587 @article{ISI:000261835100054,
107     Abstract = {{Transport properties of liquid methanol and ethanol are predicted by
108     molecular dynamics simulation. The molecular models for the alcohols
109     are rigid, nonpolarizable, and of united-atom type. They were developed
110     in preceding work using experimental vapor-liquid equilibrium data
111     only. Self- and Maxwell-Stefan diffusion coefficients as well as the
112     shear viscosity of methanol, ethanol, and their binary mixture are
113     determined using equilibrium molecular dynamics and the Green-Kubo
114     formalism. Nonequilibrium molecular dynamics is used for predicting the
115     thermal conductivity of the two pure substances. The transport
116     properties of the fluids are calculated over a wide temperature range
117     at ambient pressure and compared with experimental and simulation data
118     from the literature. Overall, a very good agreement with the experiment
119     is found. For instance, the self-diffusion coefficient and the shear
120     viscosity are predicted with average deviations of less than 8\% for
121     the pure alcohols and 12\% for the mixture. The predicted thermal
122     conductivity agrees on average within 5\% with the experimental data.
123     Additionally, some velocity and shear viscosity autocorrelation
124     functions are presented and discussed. Radial distribution functions
125     for ethanol are also presented. The predicted excess volume, excess
126     enthalpy, and the vapor-liquid equilibrium of the binary mixture
127     methanol + ethanol are assessed and agree well with experimental data.}},
128     Address = {{1155 16TH ST, NW, WASHINGTON, DC 20036 USA}},
129     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.}},
130     Author = {Guevara-Carrion, Gabriela and Nieto-Draghi, Carlos and Vrabec, Jadran and Hasse, Hans},
131     Author-Email = {{vrabec@itt.uni-stuttgart.de}},
132     Date-Added = {2010-04-14 15:43:29 -0400},
133     Date-Modified = {2010-04-14 15:43:29 -0400},
134     Doc-Delivery-Number = {{385SY}},
135     Doi = {{10.1021/jp805584d}},
136     Issn = {{1520-6106}},
137     Journal = {{JOURNAL OF PHYSICAL CHEMISTRY B}},
138     Journal-Iso = {{J. Phys. Chem. B}},
139     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}},
140     Language = {{English}},
141     Month = {{DEC 25}},
142     Number = {{51}},
143     Number-Of-Cited-References = {{86}},
144     Pages = {{16664-16674}},
145     Publisher = {{AMER CHEMICAL SOC}},
146     Subject-Category = {{Chemistry, Physical}},
147     Times-Cited = {{5}},
148     Title = {{Prediction of Transport Properties by Molecular Simulation: Methanol and Ethanol and Their Mixture}},
149     Type = {{Article}},
150     Unique-Id = {{ISI:000261835100054}},
151     Volume = {{112}},
152     Year = {{2008}},
153     Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp805584d%7D}}
154    
155     @article{ISI:000258460400020,
156     Abstract = {{Nonequilibrium molecular dynamics simulations with the nonpolarizable
157     SPC/E (Berendsen et al., J. Phys. Chem. 1987, 91, 6269) and the
158     polarizable COS/G2 (Yu and van Gunsteren, J. Chem. Phys. 2004, 121,
159     9549) force fields have been employed to calculate the thermal
160     conductivity and other associated properties of methane hydrate over a
161     temperature range from 30 to 260 K. The calculated results are compared
162     to experimental data over this same range. The values of the thermal
163     conductivity calculated with the COS/G2 model are closer to the
164     experimental values than are those calculated with the nonpolarizable
165     SPC/E model. The calculations match the temperature trend in the
166     experimental data at temperatures below 50 K; however, they exhibit a
167     slight decrease in thermal conductivity at higher temperatures in
168     comparison to an opposite trend in the experimental data. The
169     calculated thermal conductivity values are found to be relatively
170     insensitive to the occupancy of the cages except at low (T <= 50 K)
171     temperatures, which indicates that the differences between the two
172     lattice structures may have a more dominant role than generally thought
173     in explaining the low thermal conductivity of methane hydrate compared
174     to ice Ih. The introduction of defects into the water lattice is found
175     to cause a reduction in the thermal conductivity but to have a
176     negligible impact on its temperature dependence.}},
177     Address = {{1155 16TH ST, NW, WASHINGTON, DC 20036 USA}},
178     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.}},
179     Author = {Jiang, Hao and Myshakin, Evgeniy M. and Jordan, Kenneth D. and Warzinski, Robert P.},
180     Date-Added = {2010-04-14 15:38:14 -0400},
181     Date-Modified = {2010-04-14 15:38:14 -0400},
182     Doc-Delivery-Number = {{337UG}},
183     Doi = {{10.1021/jp802942v}},
184     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]}},
185     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.}},
186     Issn = {{1520-6106}},
187     Journal = {{JOURNAL OF PHYSICAL CHEMISTRY B}},
188     Journal-Iso = {{J. Phys. Chem. B}},
189     Keywords-Plus = {{LIQUID WATER; CLATHRATE HYDRATE; HEAT-CAPACITY; FORCE-FIELDS; ICE; ANHARMONICITY; SUMMATION; MODELS; SILICA}},
190     Language = {{English}},
191     Month = {{AUG 21}},
192     Number = {{33}},
193     Number-Of-Cited-References = {{51}},
194     Pages = {{10207-10216}},
195     Publisher = {{AMER CHEMICAL SOC}},
196     Subject-Category = {{Chemistry, Physical}},
197     Times-Cited = {{8}},
198     Title = {{Molecular dynamics Simulations of the thermal conductivity of methane hydrate}},
199     Type = {{Article}},
200     Unique-Id = {{ISI:000258460400020}},
201     Volume = {{112}},
202     Year = {{2008}},
203     Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp802942v%7D}}
204    
205 skuang 3585 @article{ISI:000184808400018,
206     Abstract = {{A new non-equilibrium molecular dynamics algorithm is presented based
207     on the original work of Willer-Plathe, (1997, J. chem. Phys., 106,
208     6082), for the non-equilibrium simulation of heat transport maintaining
209     fixed the total momentum as well as the total energy of the system. The
210     presented scheme preserves these properties but, unlike the original
211     algorithm, is able to deal with multicomponent systems, that is with
212     particles of different mass independently of their relative
213     concentration. The main idea behind the new procedure is to consider an
214     exchange of momentum and energy between the particles in the hot and
215     cold regions, to maintain the non-equilibrium conditions, as if they
216     undergo a hypothetical elastic collision. The new algorithm can also be
217     employed in multicomponent systems for molecular fluids and in a wide
218     range of thermodynamic conditions.}},
219     Address = {{4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND}},
220     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.}},
221     Author = {Nieto-Draghi, C and Avalos, JB},
222     Date-Added = {2010-04-14 12:48:08 -0400},
223     Date-Modified = {2010-04-14 12:48:08 -0400},
224     Doc-Delivery-Number = {{712QM}},
225     Doi = {{10.1080/0026897031000154338}},
226     Issn = {{0026-8976}},
227     Journal = {{MOLECULAR PHYSICS}},
228     Journal-Iso = {{Mol. Phys.}},
229     Keywords-Plus = {{BINARY-LIQUID MIXTURES; THERMAL-CONDUCTIVITY; MATTER TRANSPORT; WATER}},
230     Language = {{English}},
231     Month = {{JUL 20}},
232     Number = {{14}},
233     Number-Of-Cited-References = {{20}},
234     Pages = {{2303-2307}},
235     Publisher = {{TAYLOR \& FRANCIS LTD}},
236     Subject-Category = {{Physics, Atomic, Molecular \& Chemical}},
237     Times-Cited = {{13}},
238     Title = {{Non-equilibrium momentum exchange algorithm for molecular dynamics simulation of heat flow in multicomponent systems}},
239     Type = {{Article}},
240     Unique-Id = {{ISI:000184808400018}},
241     Volume = {{101}},
242     Year = {{2003}},
243     Bdsk-Url-1 = {http://dx.doi.org/10.1080/0026897031000154338%7D}}
244    
245     @article{Bedrov:2000-1,
246     Abstract = {{The thermal conductivity of liquid
247     octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) has been
248     determined from imposed heat flux non-equilibrium molecular dynamics
249     (NEMD) simulations using a previously published quantum chemistry-based
250     atomistic potential. The thermal conductivity was determined in the
251     temperature domain 550 less than or equal to T less than or equal to
252     800 K, which corresponds approximately to the existence limits of the
253     liquid phase of HMX at atmospheric pressure. The NEMD predictions,
254     which comprise the first reported values for thermal conductivity of
255     HMX liquid, were found to be consistent with measured values for
256     crystalline HMX. The thermal conductivity of liquid HMX was found to
257     exhibit a much weaker temperature dependence than the shear viscosity
258     and self-diffusion coefficients. (C) 2000 Elsevier Science B.V. All
259     rights reserved.}},
260     Address = {{PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}},
261     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.}},
262     Author = {Bedrov, D and Smith, GD and Sewell, TD},
263     Date-Added = {2010-04-14 12:26:59 -0400},
264     Date-Modified = {2010-04-14 12:27:52 -0400},
265     Doc-Delivery-Number = {{330PF}},
266     Issn = {{0009-2614}},
267     Journal = {{CHEMICAL PHYSICS LETTERS}},
268     Journal-Iso = {{Chem. Phys. Lett.}},
269     Keywords-Plus = {{FORCE-FIELD}},
270     Language = {{English}},
271     Month = {{JUN 30}},
272     Number = {{1-3}},
273     Number-Of-Cited-References = {{17}},
274     Pages = {{64-68}},
275     Publisher = {{ELSEVIER SCIENCE BV}},
276     Subject-Category = {{Chemistry, Physical; Physics, Atomic, Molecular \& Chemical}},
277     Times-Cited = {{19}},
278     Title = {{Thermal conductivity of liquid octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) from molecular dynamics simulations}},
279     Type = {{Article}},
280     Unique-Id = {{ISI:000087969900011}},
281     Volume = {{324}},
282     Year = {{2000}}}
283    
284     @article{ISI:000258840700015,
285     Abstract = {{By using the embedded-atom method (EAM), a series of molecular dynamics
286     (MD) simulations are carried out to calculate the viscosity and
287     self-diffusion coefficient of liquid copper from the normal to the
288     undercooled states. The simulated results are in reasonable agreement
289     with the experimental values available above the melting temperature
290     that is also predicted from a solid-liquid-solid sandwich structure.
291     The relationship between the viscosity and the self-diffusion
292     coefficient is evaluated. It is found that the Stokes-Einstein and
293     Sutherland-Einstein relations qualitatively describe this relationship
294     within the simulation temperature range. However, the predicted
295     constant from MD simulation is close to 1/(3 pi), which is larger than
296     the constants of the Stokes-Einstein and Sutherland-Einstein relations.}},
297     Address = {{233 SPRING ST, NEW YORK, NY 10013 USA}},
298     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.}},
299     Author = {Han, X. J. and Chen, M. and Lue, Y. J.},
300     Author-Email = {{mchen@tsinghua.edu.cn}},
301     Date-Added = {2010-04-14 12:00:38 -0400},
302     Date-Modified = {2010-04-14 12:00:38 -0400},
303     Doc-Delivery-Number = {{343GH}},
304     Doi = {{10.1007/s10765-008-0489-7}},
305     Funding-Acknowledgement = {{China Postdoctoral Science Foundation ; National Natural Science Foundation of China {[}50395101, 50371043]}},
306     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.}},
307     Issn = {{0195-928X}},
308     Journal = {{INTERNATIONAL JOURNAL OF THERMOPHYSICS}},
309     Journal-Iso = {{Int. J. Thermophys.}},
310     Keywords = {{copper; molecular simulation; self-diffusion coefficient; viscosity; undercooled}},
311     Keywords-Plus = {{EMBEDDED-ATOM MODEL; THERMOPHYSICAL PROPERTIES; COMPUTER-SIMULATION; TRANSITION-METALS; SHEAR VISCOSITY; ALLOYS; TEMPERATURE; DIFFUSION; BINDING; SURFACE}},
312     Language = {{English}},
313     Month = {{AUG}},
314     Number = {{4}},
315     Number-Of-Cited-References = {{39}},
316     Pages = {{1408-1421}},
317     Publisher = {{SPRINGER/PLENUM PUBLISHERS}},
318     Subject-Category = {{Thermodynamics; Chemistry, Physical; Mechanics; Physics, Applied}},
319     Times-Cited = {{2}},
320     Title = {{Transport properties of undercooled liquid copper: A molecular dynamics study}},
321     Type = {{Article}},
322     Unique-Id = {{ISI:000258840700015}},
323     Volume = {{29}},
324     Year = {{2008}},
325     Bdsk-Url-1 = {http://dx.doi.org/10.1007/s10765-008-0489-7%7D}}
326    
327     @article{Muller-Plathe:2008,
328     Abstract = {{Reverse nonequilibrium molecular dynamics and equilibrium molecular
329     dynamics simulations were carried out to compute the shear viscosity of
330     the pure ionic liquid system {[}bmim]{[}PF6] at 300 K. The two methods
331     yielded consistent results which were also compared to experiments. The
332     results showed that the reverse nonequilibrium molecular dynamics
333     (RNEMD) methodology can successfully be applied to computation of
334     highly viscous ionic liquids. Moreover, this study provides a
335     validation of the atomistic force-field developed by Bhargava and
336     Balasubramanian (J. Chem. Phys. 2007, 127, 114510) for dynamic
337     properties.}},
338     Address = {{1155 16TH ST, NW, WASHINGTON, DC 20036 USA}},
339     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.}},
340     Author = {Wei Zhao and Leroy, Frederic and Balasubramanian, Sundaram and Mueller-Plathe, Florian},
341     Author-Email = {{w.zhao@theo.chemie.tu-darmstadt.de}},
342     Date-Added = {2010-04-14 11:53:37 -0400},
343     Date-Modified = {2010-04-14 11:54:20 -0400},
344     Doc-Delivery-Number = {{321VS}},
345     Doi = {{10.1021/jp8017869}},
346     Issn = {{1520-6106}},
347     Journal = {{JOURNAL OF PHYSICAL CHEMISTRY B}},
348     Journal-Iso = {{J. Phys. Chem. B}},
349     Keywords-Plus = {{TRANSPORT-PROPERTIES; FORCE-FIELD; TEMPERATURE; SIMULATION; IMIDAZOLIUM; FLUIDS; MODEL; BIS(TRIFLUOROMETHANESULFONYL)IMIDE; PYRIDINIUM; CHLORIDE}},
350     Language = {{English}},
351     Month = {{JUL 10}},
352     Number = {{27}},
353     Number-Of-Cited-References = {{49}},
354     Pages = {{8129-8133}},
355     Publisher = {{AMER CHEMICAL SOC}},
356     Subject-Category = {{Chemistry, Physical}},
357     Times-Cited = {{2}},
358     Title = {{Shear viscosity of the ionic liquid 1-n-butyl 3-methylimidazolium hexafluorophosphate {[}bmim]{[}PF6] computed by reverse nonequilibrium molecular dynamics}},
359     Type = {{Article}},
360     Unique-Id = {{ISI:000257335200022}},
361     Volume = {{112}},
362     Year = {{2008}},
363     Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp8017869%7D}}
364    
365     @article{Muller-Plathe:2002,
366     Abstract = {{The reverse nonequilibrium molecular dynamics {[}F. Muller-Plathe,
367     Phys. Rev. E 49, 359 (1999)] presented for the calculation of the shear
368     viscosity of Lennard-Jones liquids has been extended to atomistic
369     models of molecular liquids. The method is improved to overcome the
370     problems due to the detailed molecular models. The new technique is
371     besides a test with a Lennard-Jones fluid, applied on different
372     realistic systems: liquid nitrogen, water, and hexane, in order to
373     cover a large range of interactions and systems/architectures. We show
374     that all the advantages of the method itemized previously are still
375     valid, and that it has a very good efficiency and accuracy making it
376     very competitive. (C) 2002 American Institute of Physics.}},
377     Address = {{CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA}},
378     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.}},
379     Author = {Bordat, P and Muller-Plathe, F},
380     Date-Added = {2010-04-14 11:34:42 -0400},
381     Date-Modified = {2010-04-14 11:35:35 -0400},
382     Doc-Delivery-Number = {{521QV}},
383     Doi = {{10.1063/1.1436124}},
384     Issn = {{0021-9606}},
385     Journal = {{JOURNAL OF CHEMICAL PHYSICS}},
386     Journal-Iso = {{J. Chem. Phys.}},
387     Keywords-Plus = {{TRANSPORT-PROPERTIES; PHYSICAL-PROPERTIES; LIQUID ALKANES; N-HEPTADECANE; SIMULATION; WATER; FLOW; MIXTURES; BUTANE; NITROGEN}},
388     Language = {{English}},
389     Month = {{FEB 22}},
390     Number = {{8}},
391     Number-Of-Cited-References = {{47}},
392     Pages = {{3362-3369}},
393     Publisher = {{AMER INST PHYSICS}},
394     Subject-Category = {{Physics, Atomic, Molecular \& Chemical}},
395     Times-Cited = {{33}},
396     Title = {{The shear viscosity of molecular fluids: A calculation by reverse nonequilibrium molecular dynamics}},
397     Type = {{Article}},
398     Unique-Id = {{ISI:000173853600023}},
399     Volume = {{116}},
400     Year = {{2002}},
401     Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1436124%7D}}
402    
403 skuang 3580 @article{ISI:000207079300006,
404 skuang 3585 Abstract = {Non-equilibrium Molecular Dynamics Simulation
405 gezelter 3583 methods have been used to study the ability of
406     Embedded Atom Method models of the metals copper and
407     gold to reproduce the equilibrium and
408     non-equilibrium behavior of metals at a stationary
409     and at a moving solid/liquid interface. The
410     equilibrium solid/vapor interface was shown to
411     display a simple termination of the bulk until the
412     temperature of the solid reaches approximate to 90\%
413     of the bulk melting point. At and above such
414     temperatures the systems exhibit a surface
415     disodering known as surface melting. Non-equilibrium
416     simulations emulating the action of a picosecond
417     laser on the metal were performed to determine the
418     regrowth velocity. For copper, the action of a 20 ps
419     laser with an absorbed energy of 2-5 mJ/cm(2)
420     produced a regrowth velocity of 83-100 m/s, in
421     reasonable agreement with the value obtained by
422     experiment (>60 m/s). For gold, similar conditions
423     produced a slower regrowth velocity of 63 m/s at an
424     absorbed energy of 5 mJ/cm(2). This is almost a
425     factor of two too low in comparison to experiment
426     (>100 m/s). The regrowth velocities of the metals
427     seems unexpectedly close to experiment considering
428     that the free-electron contribution is ignored in
429     the Embeeded Atom Method models used.},
430 skuang 3585 Address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND},
431     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.},
432     Author = {Richardson, Clifton F. and Clancy, Paulette},
433     Date-Added = {2010-04-07 11:24:36 -0400},
434     Date-Modified = {2010-04-07 11:24:36 -0400},
435     Doc-Delivery-Number = {V04SY},
436     Issn = {0892-7022},
437     Journal = {MOLECULAR SIMULATION},
438     Journal-Iso = {Mol. Simul.},
439     Keywords = {Non-equilibrium computer simulation; molecular dynamics; crystal growth; Embedded Atom Method models of metals},
440     Language = {English},
441     Number = {5-6},
442     Number-Of-Cited-References = {36},
443     Pages = {335-355},
444     Publisher = {TAYLOR \& FRANCIS LTD},
445     Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
446     Times-Cited = {7},
447     Title = {PICOSECOND LASER PROCESSING OF COPPER AND GOLD: A COMPUTER SIMULATION STUDY},
448     Type = {Article},
449     Unique-Id = {ISI:000207079300006},
450     Volume = {7},
451     Year = {1991}}
452 skuang 3580
453 skuang 3573 @article{ISI:000167766600035,
454 skuang 3585 Abstract = {Molecular dynamics simulations are used to
455 gezelter 3583 investigate the separation of water films adjacent
456     to a hot metal surface. The simulations clearly show
457     that the water layers nearest the surface overheat
458     and undergo explosive boiling. For thick films, the
459     expansion of the vaporized molecules near the
460     surface forces the outer water layers to move away
461     from the surface. These results are of interest for
462     mass spectrometry of biological molecules, steam
463     cleaning of surfaces, and medical procedures.},
464 skuang 3585 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
465     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.},
466     Author = {Dou, YS and Zhigilei, LV and Winograd, N and Garrison, BJ},
467     Date-Added = {2010-03-11 15:32:14 -0500},
468     Date-Modified = {2010-03-11 15:32:14 -0500},
469     Doc-Delivery-Number = {416ED},
470     Issn = {1089-5639},
471     Journal = {J. Phys. Chem. A},
472     Journal-Iso = {J. Phys. Chem. A},
473     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},
474     Language = {English},
475     Month = {MAR 29},
476     Number = {12},
477     Number-Of-Cited-References = {65},
478     Pages = {2748-2755},
479     Publisher = {AMER CHEMICAL SOC},
480     Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
481     Times-Cited = {66},
482     Title = {Explosive boiling of water films adjacent to heated surfaces: A microscopic description},
483     Type = {Article},
484     Unique-Id = {ISI:000167766600035},
485     Volume = {105},
486     Year = {2001}}
487 skuang 3573
488 skuang 3585 @article{Maginn:2010,
489     Abstract = {The reverse nonequilibrium molecular dynamics
490 gezelter 3583 (RNEMD) method calculates the shear viscosity of a
491     fluid by imposing a nonphysical exchange of momentum
492     and measuring the resulting shear velocity
493     gradient. In this study we investigate the range of
494     momentum flux values over which RNEMD yields usable
495     (linear) velocity gradients. We find that nonlinear
496     velocity profiles result primarily from gradients in
497     fluid temperature and density. The temperature
498     gradient results from conversion of heat into bulk
499     kinetic energy, which is transformed back into heat
500     elsewhere via viscous heating. An expression is
501     derived to predict the temperature profile resulting
502     from a specified momentum flux for a given fluid and
503     simulation cell. Although primarily bounded above,
504     we also describe milder low-flux limitations. RNEMD
505     results for a Lennard-Jones fluid agree with
506     equilibrium molecular dynamics and conventional
507     nonequilibrium molecular dynamics calculations at
508     low shear, but RNEMD underpredicts viscosity
509     relative to conventional NEMD at high shear.},
510 skuang 3585 Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
511     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.},
512     Article-Number = {014103},
513     Author = {Tenney, Craig M. and Maginn, Edward J.},
514     Author-Email = {ed@nd.edu},
515     Date-Added = {2010-03-09 13:08:41 -0500},
516     Date-Modified = {2010-04-14 12:51:13 -0400},
517     Doc-Delivery-Number = {542DQ},
518     Doi = {10.1063/1.3276454},
519     Funding-Acknowledgement = {U.S. Department of Energy {[}DE-FG36-08G088020]},
520     Funding-Text = {Support for this work was provided by the U.S. Department of Energy (Grant No. DE-FG36-08G088020)},
521     Issn = {0021-9606},
522     Journal = {J. Chem. Phys.},
523     Journal-Iso = {J. Chem. Phys.},
524     Keywords = {Lennard-Jones potential; molecular dynamics method; Navier-Stokes equations; viscosity},
525     Keywords-Plus = {CURRENT AUTOCORRELATION-FUNCTION; IONIC LIQUID; SIMULATIONS; TEMPERATURE},
526     Language = {English},
527     Month = {JAN 7},
528     Number = {1},
529     Number-Of-Cited-References = {20},
530     Publisher = {AMER INST PHYSICS},
531     Subject-Category = {Physics, Atomic, Molecular \& Chemical},
532     Times-Cited = {0},
533     Title = {Limitations and recommendations for the calculation of shear viscosity using reverse nonequilibrium molecular dynamics},
534     Type = {Article},
535     Unique-Id = {ISI:000273472300004},
536     Volume = {132},
537     Year = {2010},
538     Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.3276454}}
539 skuang 3565
540 skuang 3582 @article{Clancy:1992,
541 skuang 3585 Abstract = {The regrowth velocity of a crystal from a melt
542 gezelter 3583 depends on contributions from the thermal
543     conductivity, heat gradient, and latent heat. The
544     relative contributions of these terms to the
545     regrowth velocity of the pure metals copper and gold
546     during liquid-phase epitaxy are evaluated. These
547     results are used to explain how results from
548     previous nonequilibrium molecular-dynamics
549     simulations using classical potentials are able to
550     predict regrowth velocities that are close to the
551     experimental values. Results from equilibrium
552     molecular dynamics showing the nature of the
553     solid-vapor interface of an
554     embedded-atom-method-modeled Cu57Ni43 alloy at a
555     temperature corresponding to 62\% of the melting
556     point are presented. The regrowth of this alloy
557     following a simulation of a laser-processing
558     experiment is also given, with use of nonequilibrium
559     molecular-dynamics techniques. The thermal
560     conductivity and temperature gradient in the
561     simulation of the alloy are compared to those for
562     the pure metals.},
563 skuang 3585 Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
564     Affiliation = {CORNELL UNIV,SCH CHEM ENGN,ITHACA,NY 14853.},
565     Author = {Richardson, C.~F. and Clancy, P},
566     Date-Added = {2010-01-12 16:17:33 -0500},
567     Date-Modified = {2010-04-08 17:18:25 -0400},
568     Doc-Delivery-Number = {HX378},
569     Issn = {0163-1829},
570     Journal = {Phys. Rev. B},
571     Journal-Iso = {Phys. Rev. B},
572     Keywords-Plus = {SURFACE SEGREGATION; MOLECULAR-DYNAMICS; TRANSITION-METALS; SOLIDIFICATION; GROWTH; CU; NI},
573     Language = {English},
574     Month = {JUN 1},
575     Number = {21},
576     Number-Of-Cited-References = {24},
577     Pages = {12260-12268},
578     Publisher = {AMERICAN PHYSICAL SOC},
579     Subject-Category = {Physics, Condensed Matter},
580     Times-Cited = {11},
581     Title = {CONTRIBUTION OF THERMAL-CONDUCTIVITY TO THE CRYSTAL-REGROWTH VELOCITY OF EMBEDDED-ATOM-METHOD-MODELED METALS AND METAL-ALLOYS},
582     Type = {Article},
583     Unique-Id = {ISI:A1992HX37800010},
584     Volume = {45},
585     Year = {1992}}
586 skuang 3563
587 skuang 3585 @article{Bedrov:2000,
588     Abstract = {We have applied a new nonequilibrium molecular
589 gezelter 3583 dynamics (NEMD) method {[}F. Muller-Plathe,
590     J. Chem. Phys. 106, 6082 (1997)] previously applied
591     to monatomic Lennard-Jones fluids in the
592     determination of the thermal conductivity of
593     molecular fluids. The method was modified in order
594     to be applicable to systems with holonomic
595     constraints. Because the method involves imposing a
596     known heat flux it is particularly attractive for
597     systems involving long-range and many-body
598     interactions where calculation of the microscopic
599     heat flux is difficult. The predicted thermal
600     conductivities of liquid n-butane and water using
601     the imposed-flux NEMD method were found to be in a
602     good agreement with previous simulations and
603     experiment. (C) 2000 American Institute of
604     Physics. {[}S0021-9606(00)50841-1].},
605 skuang 3585 Address = {2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA},
606     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.},
607     Author = {Bedrov, D and Smith, GD},
608     Date-Added = {2009-11-05 18:21:18 -0500},
609     Date-Modified = {2010-04-14 11:50:48 -0400},
610     Doc-Delivery-Number = {369BF},
611     Issn = {0021-9606},
612     Journal = {J. Chem. Phys.},
613     Journal-Iso = {J. Chem. Phys.},
614     Keywords-Plus = {EFFECTIVE PAIR POTENTIALS; TRANSPORT-PROPERTIES; CANONICAL ENSEMBLE; NORMAL-BUTANE; ALGORITHMS; SHAKE; WATER},
615     Language = {English},
616     Month = {NOV 8},
617     Number = {18},
618     Number-Of-Cited-References = {26},
619     Pages = {8080-8084},
620     Publisher = {AMER INST PHYSICS},
621     Subject-Category = {Physics, Atomic, Molecular \& Chemical},
622     Times-Cited = {23},
623     Title = {Thermal conductivity of molecular fluids from molecular dynamics simulations: Application of a new imposed-flux method},
624     Type = {Article},
625     Unique-Id = {ISI:000090151400044},
626     Volume = {113},
627     Year = {2000}}
628 skuang 3563
629     @article{ISI:000231042800044,
630 skuang 3585 Abstract = {The reverse nonequilibrium molecular dynamics
631 gezelter 3583 method for thermal conductivities is adapted to the
632     investigation of molecular fluids. The method
633     generates a heat flux through the system by suitably
634     exchanging velocities of particles located in
635     different regions. From the resulting temperature
636     gradient, the thermal conductivity is then
637     calculated. Different variants of the algorithm and
638     their combinations with other system parameters are
639     tested: exchange of atomic velocities versus
640     exchange of molecular center-of-mass velocities,
641     different exchange frequencies, molecular models
642     with bond constraints versus models with flexible
643     bonds, united-atom versus all-atom models, and
644     presence versus absence of a thermostat. To help
645     establish the range of applicability, the algorithm
646     is tested on different models of benzene,
647     cyclohexane, water, and n-hexane. We find that the
648     algorithm is robust and that the calculated thermal
649     conductivities are insensitive to variations in its
650     control parameters. The force field, in contrast,
651     has a major influence on the value of the thermal
652     conductivity. While calculated and experimental
653     thermal conductivities fall into the same order of
654     magnitude, in most cases the calculated values are
655     systematically larger. United-atom force fields seem
656     to do better than all-atom force fields, possibly
657     because they remove high-frequency degrees of
658     freedom from the simulation, which, in nature, are
659     quantum-mechanical oscillators in their ground state
660     and do not contribute to heat conduction.},
661 skuang 3585 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
662     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.},
663     Author = {Zhang, MM and Lussetti, E and de Souza, LES and M\"{u}ller-Plathe, F},
664     Date-Added = {2009-11-05 18:17:33 -0500},
665     Date-Modified = {2009-11-05 18:17:33 -0500},
666     Doc-Delivery-Number = {952YQ},
667     Doi = {10.1021/jp0512255},
668     Issn = {1520-6106},
669     Journal = {J. Phys. Chem. B},
670     Journal-Iso = {J. Phys. Chem. B},
671     Keywords-Plus = {LENNARD-JONES LIQUIDS; TRANSPORT-COEFFICIENTS; SWOLLEN POLYMERS; SHEAR VISCOSITY; MODEL SYSTEMS; SIMULATION; BENZENE; FLUIDS; POTENTIALS; DIFFUSION},
672     Language = {English},
673     Month = {AUG 11},
674     Number = {31},
675     Number-Of-Cited-References = {42},
676     Pages = {15060-15067},
677     Publisher = {AMER CHEMICAL SOC},
678     Subject-Category = {Chemistry, Physical},
679     Times-Cited = {17},
680     Title = {Thermal conductivities of molecular liquids by reverse nonequilibrium molecular dynamics},
681     Type = {Article},
682     Unique-Id = {ISI:000231042800044},
683     Volume = {109},
684     Year = {2005},
685     Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp0512255%7D}}
686 skuang 3563
687     @article{ISI:A1997YC32200056,
688 skuang 3585 Abstract = {Equilibrium molecular dynamics simulations have
689 gezelter 3583 been carried out in the microcanonical ensemble at
690     300 and 255 K on the extended simple point charge
691     (SPC/E) model of water {[}Berendsen et al.,
692     J. Phys. Chem. 91, 6269 (1987)]. In addition to a
693     number of static and dynamic properties, thermal
694     conductivity lambda has been calculated via
695     Green-Kubo integration of the heat current time
696     correlation functions (CF's) in the atomic and
697     molecular formalism, at wave number k=0. The
698     calculated values (0.67 +/- 0.04 W/mK at 300 K and
699     0.52 +/- 0.03 W/mK at 255 K) are in good agreement
700     with the experimental data (0.61 W/mK at 300 K and
701     0.49 W/mK at 255 K). A negative long-time tail of
702     the heat current CF, more apparent at 255 K, is
703     responsible for the anomalous decrease of lambda
704     with temperature. An analysis of the dynamical modes
705     contributing to lambda has shown that its value is
706     due to two low-frequency exponential-like modes, a
707     faster collisional mode, with positive contribution,
708     and a slower one, which determines the negative
709     long-time tail. A comparison of the molecular and
710     atomic spectra of the heat current CF has suggested
711     that higher-frequency modes should not contribute to
712     lambda in this temperature range. Generalized
713     thermal diffusivity D-T(k) decreases as a function
714     of k, after an initial minor increase at k =
715     k(min). The k dependence of the generalized
716     thermodynamic properties has been calculated in the
717     atomic and molecular formalisms. The observed
718     differences have been traced back to intramolecular
719     or intermolecular rotational effects and related to
720     the partial structure functions. Finally, from the
721     results we calculated it appears that the SPC/E
722     model gives results in better agreement with
723     experimental data than the transferable
724     intermolecular potential with four points TIP4P
725     water model {[}Jorgensen et al., J. Chem. Phys. 79,
726     926 (1983)], with a larger improvement for, e.g.,
727     diffusion, viscosities, and dielectric properties
728     and a smaller one for thermal conductivity. The
729     SPC/E model shares, to a smaller extent, the
730     insufficient slowing down of dynamics at low
731     temperature already found for the TIP4P water
732     model.},
733 skuang 3585 Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
734     Affiliation = {UNIV PISA,DIPARTIMENTO CHIM \& CHIM IND,I-56126 PISA,ITALY. CNR,IST FIS ATOM \& MOL,I-56127 PISA,ITALY.},
735     Author = {Bertolini, D and Tani, A},
736     Date-Added = {2009-10-30 15:41:21 -0400},
737     Date-Modified = {2009-10-30 15:41:21 -0400},
738     Doc-Delivery-Number = {YC322},
739     Issn = {1063-651X},
740     Journal = {Phys. Rev. E},
741     Journal-Iso = {Phys. Rev. E},
742     Keywords-Plus = {TIME-CORRELATION-FUNCTIONS; LENNARD-JONES LIQUID; TRANSPORT-PROPERTIES; SUPERCOOLED WATER; DENSITY; SIMULATIONS; RELAXATION; VELOCITY; ELECTRON; FLUIDS},
743     Language = {English},
744     Month = {OCT},
745     Number = {4},
746     Number-Of-Cited-References = {35},
747     Pages = {4135-4151},
748     Publisher = {AMERICAN PHYSICAL SOC},
749     Subject-Category = {Physics, Fluids \& Plasmas; Physics, Mathematical},
750     Times-Cited = {18},
751     Title = {Thermal conductivity of water: Molecular dynamics and generalized hydrodynamics results},
752     Type = {Article},
753     Unique-Id = {ISI:A1997YC32200056},
754     Volume = {56},
755     Year = {1997}}
756 skuang 3563
757 skuang 3532 @article{Meineke:2005gd,
758 skuang 3585 Abstract = {OOPSE is a new molecular dynamics simulation program
759 gezelter 3583 that is capable of efficiently integrating equations
760     of motion for atom types with orientational degrees
761     of freedom (e.g. #sticky# atoms and point
762     dipoles). Transition metals can also be simulated
763     using the embedded atom method (EAM) potential
764     included in the code. Parallel simulations are
765     carried out using the force-based decomposition
766     method. Simulations are specified using a very
767     simple C-based meta-data language. A number of
768     advanced integrators are included, and the basic
769     integrator for orientational dynamics provides
770     substantial improvements over older quaternion-based
771     schemes.},
772 skuang 3585 Address = {111 RIVER ST, HOBOKEN, NJ 07030 USA},
773     Author = {Meineke, M. A. and Vardeman, C. F. and Lin, T and Fennell, CJ and Gezelter, J. D.},
774     Date-Added = {2009-10-01 18:43:03 -0400},
775     Date-Modified = {2010-04-13 09:11:16 -0400},
776     Doi = {DOI 10.1002/jcc.20161},
777     Isi = {000226558200006},
778     Isi-Recid = {142688207},
779     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},
780     Journal = {J. Comp. Chem.},
781     Keywords = {OOPSE; molecular dynamics},
782     Month = feb,
783     Number = {3},
784     Pages = {252-271},
785     Publisher = {JOHN WILEY \& SONS INC},
786     Times-Cited = {9},
787     Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
788     Volume = {26},
789     Year = {2005},
790     Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000226558200006},
791     Bdsk-Url-2 = {http://dx.doi.org/10.1002/jcc.20161}}
792 skuang 3532
793     @article{ISI:000080382700030,
794 skuang 3585 Abstract = {A nonequilibrium method for calculating the shear
795 gezelter 3583 viscosity is presented. It reverses the
796     cause-and-effect picture customarily used in
797     nonequilibrium molecular dynamics: the effect, the
798     momentum flux or stress, is imposed, whereas the
799     cause, the velocity gradient or shear rate, is
800     obtained from the simulation. It differs from other
801     Norton-ensemble methods by the way in which the
802     steady-state momentum flux is maintained. This
803     method involves a simple exchange of particle
804     momenta, which is easy to implement. Moreover, it
805     can be made to conserve the total energy as well as
806     the total linear momentum, so no coupling to an
807     external temperature bath is needed. The resulting
808     raw data, the velocity profile, is a robust and
809     rapidly converging property. The method is tested on
810     the Lennard-Jones fluid near its triple point. It
811     yields a viscosity of 3.2-3.3, in Lennard-Jones
812     reduced units, in agreement with literature
813     results. {[}S1063-651X(99)03105-0].},
814 skuang 3585 Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
815     Affiliation = {Muller-Plathe, F (Reprint Author), Max Planck Inst Polymerforsch, Ackermannweg 10, D-55128 Mainz, Germany. Max Planck Inst Polymerforsch, D-55128 Mainz, Germany.},
816     Author = {M\"{u}ller-Plathe, F},
817     Date-Added = {2009-10-01 14:07:30 -0400},
818     Date-Modified = {2009-10-01 14:07:30 -0400},
819     Doc-Delivery-Number = {197TX},
820     Issn = {1063-651X},
821     Journal = {Phys. Rev. E},
822     Journal-Iso = {Phys. Rev. E},
823     Language = {English},
824     Month = {MAY},
825     Number = {5, Part A},
826     Number-Of-Cited-References = {17},
827     Pages = {4894-4898},
828     Publisher = {AMERICAN PHYSICAL SOC},
829     Subject-Category = {Physics, Fluids \& Plasmas; Physics, Mathematical},
830     Times-Cited = {57},
831     Title = {Reversing the perturbation in nonequilibrium molecular dynamics: An easy way to calculate the shear viscosity of fluids},
832     Type = {Article},
833     Unique-Id = {ISI:000080382700030},
834     Volume = {59},
835     Year = {1999}}
836 skuang 3532
837 skuang 3585 @article{Maginn:2007,
838     Abstract = {Atomistic simulations are conducted to examine the
839 gezelter 3583 dependence of the viscosity of
840     1-ethyl-3-methylimidazolium
841     bis(trifluoromethanesulfonyl)imide on temperature
842     and water content. A nonequilibrium molecular
843     dynamics procedure is utilized along with an
844     established fixed charge force field. It is found
845     that the simulations quantitatively capture the
846     temperature dependence of the viscosity as well as
847     the drop in viscosity that occurs with increasing
848     water content. Using mixture viscosity models, we
849     show that the relative drop in viscosity with water
850     content is actually less than that that would be
851     predicted for an ideal system. This finding is at
852     odds with the popular notion that small amounts of
853     water cause an unusually large drop in the viscosity
854     of ionic liquids. The simulations suggest that, due
855     to preferential association of water with anions and
856     the formation of water clusters, the excess molar
857     volume is negative. This means that dissolved water
858     is actually less effective at lowering the viscosity
859     of these mixtures when compared to a solute obeying
860     ideal mixing behavior. The use of a nonequilibrium
861     simulation technique enables diffusive behavior to
862     be observed on the time scale of the simulations,
863     and standard equilibrium molecular dynamics resulted
864     in sub-diffusive behavior even over 2 ns of
865     simulation time.},
866 skuang 3585 Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
867     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.},
868     Author = {Kelkar, Manish S. and Maginn, Edward J.},
869     Author-Email = {ed@nd.edu},
870     Date-Added = {2009-09-29 17:07:17 -0400},
871     Date-Modified = {2010-04-14 12:51:02 -0400},
872     Doc-Delivery-Number = {163VA},
873     Doi = {10.1021/jp0686893},
874     Issn = {1520-6106},
875     Journal = {J. Phys. Chem. B},
876     Journal-Iso = {J. Phys. Chem. B},
877     Keywords-Plus = {MOLECULAR-DYNAMICS SIMULATION; MOMENTUM IMPULSE RELAXATION; FORCE-FIELD; TRANSPORT-PROPERTIES; PHYSICAL-PROPERTIES; SIMPLE FLUID; CHLORIDE; MODEL; SALTS; ARCHITECTURE},
878     Language = {English},
879     Month = {MAY 10},
880     Number = {18},
881     Number-Of-Cited-References = {57},
882     Pages = {4867-4876},
883     Publisher = {AMER CHEMICAL SOC},
884     Subject-Category = {Chemistry, Physical},
885     Times-Cited = {35},
886     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},
887     Type = {Article},
888     Unique-Id = {ISI:000246190100032},
889     Volume = {111},
890     Year = {2007},
891     Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp0686893%7D},
892     Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp0686893}}
893 skuang 3528
894 skuang 3527 @article{MullerPlathe:1997xw,
895 skuang 3585 Abstract = {A nonequilibrium molecular dynamics method for
896 gezelter 3583 calculating the thermal conductivity is
897     presented. It reverses the usual cause and effect
898     picture. The ''effect,'' the heat flux, is imposed
899     on the system and the ''cause,'' the temperature
900     gradient is obtained from the simulation. Besides
901     being very simple to implement, the scheme offers
902     several advantages such as compatibility with
903     periodic boundary conditions, conservation of total
904     energy and total linear momentum, and the sampling
905     of a rapidly converging quantity (temperature
906     gradient) rather than a slowly converging one (heat
907     flux). The scheme is tested on the Lennard-Jones
908     fluid. (C) 1997 American Institute of Physics.},
909 skuang 3585 Address = {WOODBURY},
910     Author = {M\"{u}ller-Plathe, F.},
911     Cited-Reference-Count = {13},
912     Date = {APR 8},
913     Date-Added = {2009-09-21 16:51:21 -0400},
914     Date-Modified = {2009-09-21 16:51:21 -0400},
915     Document-Type = {Article},
916     Isi = {ISI:A1997WR62000032},
917     Isi-Document-Delivery-Number = {WR620},
918     Iso-Source-Abbreviation = {J. Chem. Phys.},
919     Issn = {0021-9606},
920     Journal = {J. Chem. Phys.},
921     Language = {English},
922     Month = {Apr},
923     Number = {14},
924     Page-Count = {4},
925     Pages = {6082--6085},
926     Publication-Type = {J},
927     Publisher = {AMER INST PHYSICS},
928     Publisher-Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999},
929     Reprint-Address = {MullerPlathe, F, MAX PLANCK INST POLYMER RES, D-55128 MAINZ, GERMANY.},
930     Source = {J CHEM PHYS},
931     Subject-Category = {Physics, Atomic, Molecular & Chemical},
932     Times-Cited = {106},
933     Title = {A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity},
934     Volume = {106},
935     Year = {1997}}
936 skuang 3527
937     @article{Muller-Plathe:1999ek,
938 skuang 3585 Abstract = {A novel non-equilibrium method for calculating
939 gezelter 3583 transport coefficients is presented. It reverses the
940     experimental cause-and-effect picture, e.g. for the
941     calculation of viscosities: the effect, the momentum
942     flux or stress, is imposed, whereas the cause, the
943     velocity gradient or shear rates, is obtained from
944     the simulation. It differs from other
945     Norton-ensemble methods by the way, in which the
946     steady-state fluxes are maintained. This method
947     involves a simple exchange of particle momenta,
948     which is easy to implement and to analyse. Moreover,
949     it can be made to conserve the total energy as well
950     as the total linear momentum, so no thermostatting
951     is needed. The resulting raw data are robust and
952     rapidly converging. The method is tested on the
953     calculation of the shear viscosity, the thermal
954     conductivity and the Soret coefficient (thermal
955     diffusion) for the Lennard-Jones (LJ) fluid near its
956     triple point. Possible applications to other
957     transport coefficients and more complicated systems
958     are discussed. (C) 1999 Elsevier Science Ltd. All
959     rights reserved.},
960 skuang 3585 Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
961     Author = {M\"{u}ller-Plathe, F and Reith, D},
962     Date-Added = {2009-09-21 16:47:07 -0400},
963     Date-Modified = {2009-09-21 16:47:07 -0400},
964     Isi = {000082266500004},
965     Isi-Recid = {111564960},
966     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},
967     Journal = {Computational and Theoretical Polymer Science},
968     Keywords = {viscosity; Ludwig-Soret effect; thermal conductivity; Onsager coefficents; non-equilibrium molecular dynamics},
969     Number = {3-4},
970     Pages = {203-209},
971     Publisher = {ELSEVIER SCI LTD},
972     Times-Cited = {15},
973     Title = {Cause and effect reversed in non-equilibrium molecular dynamics: an easy route to transport coefficients},
974     Volume = {9},
975     Year = {1999},
976     Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000082266500004}}
977 skuang 3527
978     @article{Viscardy:2007lq,
979 skuang 3585 Abstract = {The thermal conductivity is calculated with the
980 gezelter 3583 Helfand-moment method in the Lennard-Jones fluid
981     near the triple point. The Helfand moment of thermal
982     conductivity is here derived for molecular dynamics
983     with periodic boundary conditions. Thermal
984     conductivity is given by a generalized Einstein
985     relation with this Helfand moment. The authors
986     compute thermal conductivity by this new method and
987     compare it with their own values obtained by the
988     standard Green-Kubo method. The agreement is
989     excellent. (C) 2007 American Institute of Physics.},
990 skuang 3585 Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
991     Author = {Viscardy, S. and Servantie, J. and Gaspard, P.},
992     Date-Added = {2009-09-21 16:37:20 -0400},
993     Date-Modified = {2009-09-21 16:37:20 -0400},
994     Doi = {DOI 10.1063/1.2724821},
995     Isi = {000246453900035},
996     Isi-Recid = {156192451},
997     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},
998     Journal = {J. Chem. Phys.},
999     Month = may,
1000     Number = {18},
1001     Publisher = {AMER INST PHYSICS},
1002     Times-Cited = {3},
1003     Title = {Transport and Helfand moments in the Lennard-Jones fluid. II. Thermal conductivity},
1004     Volume = {126},
1005     Year = {2007},
1006     Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000246453900035},
1007     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2724821}}
1008 skuang 3527
1009     @article{Viscardy:2007bh,
1010 skuang 3585 Abstract = {The authors propose a new method, the Helfand-moment
1011 gezelter 3583 method, to compute the shear viscosity by
1012     equilibrium molecular dynamics in periodic
1013     systems. In this method, the shear viscosity is
1014     written as an Einstein-type relation in terms of the
1015     variance of the so-called Helfand moment. This
1016     quantity is modified in order to satisfy systems
1017     with periodic boundary conditions usually considered
1018     in molecular dynamics. They calculate the shear
1019     viscosity in the Lennard-Jones fluid near the triple
1020     point thanks to this new technique. They show that
1021     the results of the Helfand-moment method are in
1022     excellent agreement with the results of the standard
1023     Green-Kubo method. (C) 2007 American Institute of
1024     Physics.},
1025 skuang 3585 Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
1026     Author = {Viscardy, S. and Servantie, J. and Gaspard, P.},
1027     Date-Added = {2009-09-21 16:37:19 -0400},
1028     Date-Modified = {2009-09-21 16:37:19 -0400},
1029     Doi = {DOI 10.1063/1.2724820},
1030     Isi = {000246453900034},
1031     Isi-Recid = {156192449},
1032     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},
1033     Journal = {J. Chem. Phys.},
1034     Month = may,
1035     Number = {18},
1036     Publisher = {AMER INST PHYSICS},
1037     Times-Cited = {1},
1038     Title = {Transport and Helfand moments in the Lennard-Jones fluid. I. Shear viscosity},
1039     Volume = {126},
1040     Year = {2007},
1041     Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000246453900034},
1042     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2724820}}