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Revision: 3775
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a rought draft of simulation details and a figure added.

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# User Rev Content
1 skuang 3770 %% This BibTeX bibliography file was created using BibDesk.
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11    
12 skuang 3775 @article{TraPPE-UA.thiols,
13     Author = {Lubna, Nusrat and Kamath, Ganesh and Potoff, Jeffrey J. and Rai, Neeraj and Siepmann, J. Ilja},
14     Date-Added = {2011-12-07 15:06:12 -0500},
15     Date-Modified = {2011-12-07 15:06:12 -0500},
16     Doi = {10.1021/jp0549125},
17     Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp0549125},
18     Journal = {J. Phys. Chem. B},
19     Number = {50},
20     Pages = {24100-24107},
21     Title = {Transferable Potentials for Phase Equilibria. 8. United-Atom Description for Thiols, Sulfides, Disulfides, and Thiophene},
22     Url = {http://pubs.acs.org/doi/abs/10.1021/jp0549125},
23     Volume = {109},
24     Year = {2005},
25     Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp0549125},
26     Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp0549125}}
27    
28     @article{TraPPE-UA.alkylbenzenes,
29     Author = {Wick, Collin D. and Martin, Marcus G. and Siepmann, J. Ilja},
30     Date-Added = {2011-12-07 15:06:12 -0500},
31     Date-Modified = {2011-12-07 15:06:12 -0500},
32     Doi = {10.1021/jp001044x},
33     Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp001044x},
34     Journal = {J. Phys. Chem. B},
35     Number = {33},
36     Pages = {8008-8016},
37     Title = {Transferable Potentials for Phase Equilibria. 4. United-Atom Description of Linear and Branched Alkenes and Alkylbenzenes},
38     Url = {http://pubs.acs.org/doi/abs/10.1021/jp001044x},
39     Volume = {104},
40     Year = {2000},
41     Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp001044x},
42     Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp001044x}}
43    
44     @article{TraPPE-UA.alkanes,
45     Author = {Martin, Marcus G. and Siepmann, J. Ilja},
46     Date-Added = {2011-12-07 15:06:12 -0500},
47     Date-Modified = {2011-12-07 15:06:12 -0500},
48     Doi = {10.1021/jp972543+},
49     Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp972543%2B},
50     Journal = {J. Phys. Chem. B},
51     Number = {14},
52     Pages = {2569-2577},
53     Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes},
54     Url = {http://pubs.acs.org/doi/abs/10.1021/jp972543%2B},
55     Volume = {102},
56     Year = {1998},
57     Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp972543+},
58     Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp972543+},
59     Bdsk-Url-3 = {http://pubs.acs.org/doi/abs/10.1021/jp972543%2B}}
60    
61     @article{ISI:000167766600035,
62     Abstract = {Molecular dynamics simulations are used to
63     investigate the separation of water films adjacent
64     to a hot metal surface. The simulations clearly show
65     that the water layers nearest the surface overheat
66     and undergo explosive boiling. For thick films, the
67     expansion of the vaporized molecules near the
68     surface forces the outer water layers to move away
69     from the surface. These results are of interest for
70     mass spectrometry of biological molecules, steam
71     cleaning of surfaces, and medical procedures.},
72     Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
73     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.},
74     Author = {Dou, YS and Zhigilei, LV and Winograd, N and Garrison, BJ},
75     Date-Added = {2011-12-07 15:02:32 -0500},
76     Date-Modified = {2011-12-07 15:02:32 -0500},
77     Doc-Delivery-Number = {416ED},
78     Issn = {1089-5639},
79     Journal = {J. Phys. Chem. A},
80     Journal-Iso = {J. Phys. Chem. A},
81     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},
82     Language = {English},
83     Month = {MAR 29},
84     Number = {12},
85     Number-Of-Cited-References = {65},
86     Pages = {2748-2755},
87     Publisher = {AMER CHEMICAL SOC},
88     Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
89     Times-Cited = {66},
90     Title = {Explosive boiling of water films adjacent to heated surfaces: A microscopic description},
91     Type = {Article},
92     Unique-Id = {ISI:000167766600035},
93     Volume = {105},
94     Year = {2001}}
95    
96     @article{Chen90,
97     Author = {A.~P. Sutton and J. Chen},
98     Date-Added = {2011-12-07 15:01:59 -0500},
99     Date-Modified = {2011-12-07 15:01:59 -0500},
100     Journal = {Philos. Mag. Lett.},
101     Pages = {139-146},
102     Title = {Long-Range Finnis Sinclair Potentials},
103     Volume = 61,
104     Year = {1990}}
105    
106     @article{PhysRevB.59.3527,
107     Author = {Qi, Yue and \c{C}a\v{g}in, Tahir and Kimura, Yoshitaka and {Goddard III}, William A.},
108     Date-Added = {2011-12-07 15:01:36 -0500},
109     Date-Modified = {2011-12-07 15:01:36 -0500},
110     Doi = {10.1103/PhysRevB.59.3527},
111     Journal = {Phys. Rev. B},
112     Local-Url = {file://localhost/Users/charles/Documents/Papers/Qi/1999.pdf},
113     Month = {Feb},
114     Number = {5},
115     Numpages = {6},
116     Pages = {3527-3533},
117     Publisher = {American Physical Society},
118     Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals:\quad{}{C}u-{A}g and {C}u-{N}i},
119     Volume = {59},
120     Year = {1999},
121     Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.59.3527}}
122    
123     @article{Bedrov:2000,
124     Abstract = {We have applied a new nonequilibrium molecular
125     dynamics (NEMD) method {[}F. Muller-Plathe,
126     J. Chem. Phys. 106, 6082 (1997)] previously applied
127     to monatomic Lennard-Jones fluids in the
128     determination of the thermal conductivity of
129     molecular fluids. The method was modified in order
130     to be applicable to systems with holonomic
131     constraints. Because the method involves imposing a
132     known heat flux it is particularly attractive for
133     systems involving long-range and many-body
134     interactions where calculation of the microscopic
135     heat flux is difficult. The predicted thermal
136     conductivities of liquid n-butane and water using
137     the imposed-flux NEMD method were found to be in a
138     good agreement with previous simulations and
139     experiment. (C) 2000 American Institute of
140     Physics. {[}S0021-9606(00)50841-1].},
141     Address = {2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA},
142     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.},
143     Author = {Bedrov, D and Smith, GD},
144     Date-Added = {2011-12-07 15:00:27 -0500},
145     Date-Modified = {2011-12-07 15:00:27 -0500},
146     Doc-Delivery-Number = {369BF},
147     Issn = {0021-9606},
148     Journal = {J. Chem. Phys.},
149     Journal-Iso = {J. Chem. Phys.},
150     Keywords-Plus = {EFFECTIVE PAIR POTENTIALS; TRANSPORT-PROPERTIES; CANONICAL ENSEMBLE; NORMAL-BUTANE; ALGORITHMS; SHAKE; WATER},
151     Language = {English},
152     Month = {NOV 8},
153     Number = {18},
154     Number-Of-Cited-References = {26},
155     Pages = {8080-8084},
156     Publisher = {AMER INST PHYSICS},
157     Read = {1},
158     Subject-Category = {Physics, Atomic, Molecular \& Chemical},
159     Times-Cited = {23},
160     Title = {Thermal conductivity of molecular fluids from molecular dynamics simulations: Application of a new imposed-flux method},
161     Type = {Article},
162     Unique-Id = {ISI:000090151400044},
163     Volume = {113},
164     Year = {2000}}
165    
166     @article{10.1063/1.3330544,
167     Author = {Miguel Angel Gonz{\'a}lez and Jos{\'e} L. F. Abascal},
168     Coden = {JCPSA6},
169     Date-Added = {2011-12-07 14:59:20 -0500},
170     Date-Modified = {2011-12-07 14:59:20 -0500},
171     Doi = {DOI:10.1063/1.3330544},
172     Eissn = {10897690},
173     Issn = {00219606},
174     Keywords = {shear strength; viscosity;},
175     Number = {9},
176     Pages = {096101},
177     Publisher = {AIP},
178     Title = {The shear viscosity of rigid water models},
179     Url = {http://dx.doi.org/doi/10.1063/1.3330544},
180     Volume = {132},
181     Year = {2010},
182     Bdsk-Url-1 = {http://dx.doi.org/doi/10.1063/1.3330544},
183     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3330544}}
184    
185     @article{Medina2011,
186     Abstract = {
187     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.},
188     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},
189     Date-Added = {2011-12-07 14:59:14 -0500},
190     Date-Modified = {2011-12-07 14:59:14 -0500},
191     Doi = {DOI: 10.1016/j.chemphys.2011.07.001},
192     Issn = {0301-0104},
193     Journal = {Chemical Physics},
194     Keywords = {Viscosity calculations},
195     Pages = {-},
196     Title = {Molecular dynamics simulations of rigid and flexible water models: Temperature dependence of viscosity},
197     Url = {http://www.sciencedirect.com/science/article/pii/S0301010411002813},
198     Volume = {In Press, Corrected Proof},
199     Year = {2011},
200     Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0301010411002813},
201     Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.chemphys.2011.07.001}}
202    
203     @article{doi:10.1021/jp048434u,
204     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. },
205     Author = {Hirsch, Tomas K. and Ojam{\"a}e, Lars},
206     Date-Added = {2011-12-07 14:38:30 -0500},
207     Date-Modified = {2011-12-07 14:38:30 -0500},
208     Doi = {10.1021/jp048434u},
209     Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp048434u},
210     Journal = {The Journal of Physical Chemistry B},
211     Number = {40},
212     Pages = {15856-15864},
213     Title = {Quantum-Chemical and Force-Field Investigations of Ice Ih:  Computation of Proton-Ordered Structures and Prediction of Their Lattice Energies},
214     Url = {http://pubs.acs.org/doi/abs/10.1021/jp048434u},
215     Volume = {108},
216     Year = {2004},
217     Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp048434u},
218     Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp048434u}}
219    
220     @article{Meineke:2005gd,
221     Abstract = {OOPSE is a new molecular dynamics simulation program
222     that is capable of efficiently integrating equations
223     of motion for atom types with orientational degrees
224     of freedom (e.g. #sticky# atoms and point
225     dipoles). Transition metals can also be simulated
226     using the embedded atom method (EAM) potential
227     included in the code. Parallel simulations are
228     carried out using the force-based decomposition
229     method. Simulations are specified using a very
230     simple C-based meta-data language. A number of
231     advanced integrators are included, and the basic
232     integrator for orientational dynamics provides
233     substantial improvements over older quaternion-based
234     schemes.},
235     Address = {111 RIVER ST, HOBOKEN, NJ 07030 USA},
236     Author = {Meineke, M. A. and Vardeman, C. F. and Lin, T and Fennell, CJ and Gezelter, J. D.},
237     Date-Added = {2011-12-07 13:33:04 -0500},
238     Date-Modified = {2011-12-07 13:33:04 -0500},
239     Doi = {DOI 10.1002/jcc.20161},
240     Isi = {000226558200006},
241     Isi-Recid = {142688207},
242     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},
243     Journal = {J. Comput. Chem.},
244     Keywords = {OOPSE; molecular dynamics},
245     Month = feb,
246     Number = {3},
247     Pages = {252-271},
248     Publisher = {JOHN WILEY \& SONS INC},
249     Times-Cited = {9},
250     Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
251     Volume = {26},
252     Year = {2005},
253     Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000226558200006},
254     Bdsk-Url-2 = {http://dx.doi.org/10.1002/jcc.20161}}
255    
256 skuang 3773 @article{hoover85,
257     Author = {W.~G. Hoover},
258     Date-Added = {2011-12-06 14:23:41 -0500},
259     Date-Modified = {2011-12-06 14:23:41 -0500},
260     Journal = pra,
261     Pages = 1695,
262     Title = {Canonical dynamics: Equilibrium phase-space distributions},
263     Volume = 31,
264     Year = 1985}
265    
266 skuang 3771 @article{Maginn:2010,
267     Abstract = {The reverse nonequilibrium molecular dynamics
268     (RNEMD) method calculates the shear viscosity of a
269     fluid by imposing a nonphysical exchange of momentum
270     and measuring the resulting shear velocity
271     gradient. In this study we investigate the range of
272     momentum flux values over which RNEMD yields usable
273     (linear) velocity gradients. We find that nonlinear
274     velocity profiles result primarily from gradients in
275     fluid temperature and density. The temperature
276     gradient results from conversion of heat into bulk
277     kinetic energy, which is transformed back into heat
278     elsewhere via viscous heating. An expression is
279     derived to predict the temperature profile resulting
280     from a specified momentum flux for a given fluid and
281     simulation cell. Although primarily bounded above,
282     we also describe milder low-flux limitations. RNEMD
283     results for a Lennard-Jones fluid agree with
284     equilibrium molecular dynamics and conventional
285     nonequilibrium molecular dynamics calculations at
286     low shear, but RNEMD underpredicts viscosity
287     relative to conventional NEMD at high shear.},
288     Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
289     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.},
290     Article-Number = {014103},
291     Author = {Tenney, Craig M. and Maginn, Edward J.},
292     Author-Email = {ed@nd.edu},
293     Date-Added = {2011-12-05 18:29:08 -0500},
294     Date-Modified = {2011-12-05 18:29:08 -0500},
295     Doc-Delivery-Number = {542DQ},
296     Doi = {10.1063/1.3276454},
297     Funding-Acknowledgement = {U.S. Department of Energy {[}DE-FG36-08G088020]},
298     Funding-Text = {Support for this work was provided by the U.S. Department of Energy (Grant No. DE-FG36-08G088020)},
299     Issn = {0021-9606},
300     Journal = {J. Chem. Phys.},
301     Journal-Iso = {J. Chem. Phys.},
302     Keywords = {Lennard-Jones potential; molecular dynamics method; Navier-Stokes equations; viscosity},
303     Keywords-Plus = {CURRENT AUTOCORRELATION-FUNCTION; IONIC LIQUID; SIMULATIONS; TEMPERATURE},
304     Language = {English},
305     Month = {JAN 7},
306     Number = {1},
307     Number-Of-Cited-References = {20},
308     Pages = {014103},
309     Publisher = {AMER INST PHYSICS},
310     Subject-Category = {Physics, Atomic, Molecular \& Chemical},
311     Times-Cited = {0},
312     Title = {Limitations and recommendations for the calculation of shear viscosity using reverse nonequilibrium molecular dynamics},
313     Type = {Article},
314     Unique-Id = {ISI:000273472300004},
315     Volume = {132},
316     Year = {2010},
317     Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.3276454}}
318    
319     @article{ISI:000080382700030,
320     Abstract = {A nonequilibrium method for calculating the shear
321     viscosity is presented. It reverses the
322     cause-and-effect picture customarily used in
323     nonequilibrium molecular dynamics: the effect, the
324     momentum flux or stress, is imposed, whereas the
325     cause, the velocity gradient or shear rate, is
326     obtained from the simulation. It differs from other
327     Norton-ensemble methods by the way in which the
328     steady-state momentum flux is maintained. This
329     method involves a simple exchange of particle
330     momenta, which is easy to implement. Moreover, it
331     can be made to conserve the total energy as well as
332     the total linear momentum, so no coupling to an
333     external temperature bath is needed. The resulting
334     raw data, the velocity profile, is a robust and
335     rapidly converging property. The method is tested on
336     the Lennard-Jones fluid near its triple point. It
337     yields a viscosity of 3.2-3.3, in Lennard-Jones
338     reduced units, in agreement with literature
339     results. {[}S1063-651X(99)03105-0].},
340     Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
341     Affiliation = {Muller-Plathe, F (Reprint Author), Max Planck Inst Polymerforsch, Ackermannweg 10, D-55128 Mainz, Germany. Max Planck Inst Polymerforsch, D-55128 Mainz, Germany.},
342     Author = {M\"{u}ller-Plathe, F},
343     Date-Added = {2011-12-05 18:18:37 -0500},
344     Date-Modified = {2011-12-05 18:18:37 -0500},
345     Doc-Delivery-Number = {197TX},
346     Issn = {1063-651X},
347     Journal = {Phys. Rev. E},
348     Journal-Iso = {Phys. Rev. E},
349     Language = {English},
350     Month = {MAY},
351     Number = {5, Part A},
352     Number-Of-Cited-References = {17},
353     Pages = {4894-4898},
354     Publisher = {AMERICAN PHYSICAL SOC},
355     Subject-Category = {Physics, Fluids \& Plasmas; Physics, Mathematical},
356     Times-Cited = {57},
357     Title = {Reversing the perturbation in nonequilibrium molecular dynamics: An easy way to calculate the shear viscosity of fluids},
358     Type = {Article},
359     Unique-Id = {ISI:000080382700030},
360     Volume = {59},
361     Year = {1999}}
362    
363     @article{MullerPlathe:1997xw,
364     Abstract = {A nonequilibrium molecular dynamics method for
365     calculating the thermal conductivity is
366     presented. It reverses the usual cause and effect
367     picture. The ''effect,'' the heat flux, is imposed
368     on the system and the ''cause,'' the temperature
369     gradient is obtained from the simulation. Besides
370     being very simple to implement, the scheme offers
371     several advantages such as compatibility with
372     periodic boundary conditions, conservation of total
373     energy and total linear momentum, and the sampling
374     of a rapidly converging quantity (temperature
375     gradient) rather than a slowly converging one (heat
376     flux). The scheme is tested on the Lennard-Jones
377     fluid. (C) 1997 American Institute of Physics.},
378     Address = {WOODBURY},
379     Author = {M\"{u}ller-Plathe, F.},
380     Cited-Reference-Count = {13},
381     Date = {APR 8},
382     Date-Added = {2011-12-05 18:18:37 -0500},
383     Date-Modified = {2011-12-05 18:18:37 -0500},
384     Document-Type = {Article},
385     Isi = {ISI:A1997WR62000032},
386     Isi-Document-Delivery-Number = {WR620},
387     Iso-Source-Abbreviation = {J. Chem. Phys.},
388     Issn = {0021-9606},
389     Journal = {J. Chem. Phys.},
390     Language = {English},
391     Month = {Apr},
392     Number = {14},
393     Page-Count = {4},
394     Pages = {6082--6085},
395     Publication-Type = {J},
396     Publisher = {AMER INST PHYSICS},
397     Publisher-Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999},
398     Reprint-Address = {MullerPlathe, F, MAX PLANCK INST POLYMER RES, D-55128 MAINZ, GERMANY.},
399     Source = {J CHEM PHYS},
400     Subject-Category = {Physics, Atomic, Molecular & Chemical},
401     Times-Cited = {106},
402     Title = {A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity},
403     Volume = {106},
404     Year = {1997}}
405    
406 skuang 3770 @article{priezjev:204704,
407     Author = {Nikolai V. Priezjev},
408     Date-Added = {2011-11-28 14:39:18 -0500},
409     Date-Modified = {2011-11-28 14:39:18 -0500},
410     Doi = {10.1063/1.3663384},
411     Eid = {204704},
412     Journal = {The Journal of Chemical Physics},
413     Keywords = {channel flow; diffusion; flow simulation; hydrodynamics; molecular dynamics method; pattern formation; random processes; shear flow; slip flow; wetting},
414     Number = {20},
415     Numpages = {9},
416     Pages = {204704},
417     Publisher = {AIP},
418     Title = {Molecular diffusion and slip boundary conditions at smooth surfaces with periodic and random nanoscale textures},
419     Url = {http://link.aip.org/link/?JCP/135/204704/1},
420     Volume = {135},
421     Year = {2011},
422     Bdsk-Url-1 = {http://link.aip.org/link/?JCP/135/204704/1},
423     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3663384}}
424    
425     @article{bryk:10258,
426     Author = {Taras Bryk and A. D. J. Haymet},
427     Date-Added = {2011-11-22 17:06:35 -0500},
428     Date-Modified = {2011-11-22 17:06:35 -0500},
429     Doi = {10.1063/1.1519538},
430     Journal = {The Journal of Chemical Physics},
431     Keywords = {liquid structure; molecular dynamics method; water; ice; interface structure},
432     Number = {22},
433     Pages = {10258-10268},
434     Publisher = {AIP},
435     Title = {Ice 1h/water interface of the SPC/E model: Molecular dynamics simulations of the equilibrium basal and prism interfaces},
436     Url = {http://link.aip.org/link/?JCP/117/10258/1},
437     Volume = {117},
438     Year = {2002},
439     Bdsk-Url-1 = {http://link.aip.org/link/?JCP/117/10258/1},
440     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1519538}}
441    
442     @article{kuang:164101,
443     Author = {Shenyu Kuang and J. Daniel Gezelter},
444     Date-Added = {2011-11-18 15:32:23 -0500},
445     Date-Modified = {2011-11-18 15:32:23 -0500},
446     Doi = {10.1063/1.3499947},
447     Eid = {164101},
448     Journal = {J. Chem. Phys.},
449     Keywords = {linear momentum; molecular dynamics method; thermal conductivity; total energy; viscosity},
450     Number = {16},
451     Numpages = {9},
452     Pages = {164101},
453     Publisher = {AIP},
454     Title = {A gentler approach to RNEMD: Nonisotropic velocity scaling for computing thermal conductivity and shear viscosity},
455     Url = {http://link.aip.org/link/?JCP/133/164101/1},
456     Volume = {133},
457     Year = {2010},
458     Bdsk-Url-1 = {http://link.aip.org/link/?JCP/133/164101/1},
459     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3499947}}
460    
461     @misc{openmd,
462     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},
463     Date-Added = {2011-11-18 15:32:23 -0500},
464     Date-Modified = {2011-11-18 15:32:23 -0500},
465     Howpublished = {Available at {\tt http://openmd.net}},
466     Title = {{OpenMD, an open source engine for molecular dynamics}}}
467    
468 skuang 3771 @article{kuang:AuThl,
469 skuang 3770 Author = {Kuang, Shenyu and Gezelter, J. Daniel},
470     Date-Added = {2011-11-18 13:03:06 -0500},
471 skuang 3771 Date-Modified = {2011-12-05 17:58:01 -0500},
472 skuang 3770 Doi = {10.1021/jp2073478},
473     Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp2073478},
474     Journal = {The Journal of Physical Chemistry C},
475     Number = {45},
476     Pages = {22475-22483},
477     Title = {Simulating Interfacial Thermal Conductance at Metal-Solvent Interfaces: The Role of Chemical Capping Agents},
478     Url = {http://pubs.acs.org/doi/abs/10.1021/jp2073478},
479     Volume = {115},
480     Year = {2011},
481     Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp2073478},
482     Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp2073478}}
483    
484     @article{10.1063/1.2772547,
485     Author = {Hideo Kaburaki and Ju Li and Sidney Yip and Hajime Kimizuka},
486     Coden = {JAPIAU},
487     Date-Added = {2011-11-01 16:46:32 -0400},
488     Date-Modified = {2011-11-01 16:46:32 -0400},
489     Doi = {DOI:10.1063/1.2772547},
490     Eissn = {10897550},
491     Issn = {00218979},
492     Keywords = {argon; Lennard-Jones potential; phonons; thermal conductivity;},
493     Number = {4},
494     Pages = {043514},
495     Publisher = {AIP},
496     Title = {Dynamical thermal conductivity of argon crystal},
497     Url = {http://dx.doi.org/10.1063/1.2772547},
498     Volume = {102},
499     Year = {2007},
500     Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2772547}}
501    
502     @article{PhysRevLett.82.4671,
503     Author = {Barrat, Jean-Louis and Bocquet, Lyd\'eric},
504     Date-Added = {2011-11-01 16:44:29 -0400},
505     Date-Modified = {2011-11-01 16:44:29 -0400},
506     Doi = {10.1103/PhysRevLett.82.4671},
507     Issue = {23},
508     Journal = {Phys. Rev. Lett.},
509     Month = {Jun},
510     Pages = {4671--4674},
511     Publisher = {American Physical Society},
512     Title = {Large Slip Effect at a Nonwetting Fluid-Solid Interface},
513     Url = {http://link.aps.org/doi/10.1103/PhysRevLett.82.4671},
514     Volume = {82},
515     Year = {1999},
516     Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevLett.82.4671},
517     Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevLett.82.4671}}
518    
519     @article{10.1063/1.1610442,
520     Author = {J. R. Schmidt and J. L. Skinner},
521     Coden = {JCPSA6},
522     Date-Added = {2011-10-13 16:28:43 -0400},
523     Date-Modified = {2011-10-13 16:28:43 -0400},
524     Doi = {DOI:10.1063/1.1610442},
525     Eissn = {10897690},
526     Issn = {00219606},
527     Keywords = {hydrodynamics; Brownian motion; molecular dynamics method; diffusion;},
528     Number = {15},
529     Pages = {8062-8068},
530     Publisher = {AIP},
531     Title = {Hydrodynamic boundary conditions, the Stokes?Einstein law, and long-time tails in the Brownian limit},
532     Url = {http://dx.doi.org/10.1063/1.1610442},
533     Volume = {119},
534     Year = {2003},
535     Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}
536    
537     @article{10.1063/1.3274802,
538     Author = {Ting Chen and Berend Smit and Alexis T. Bell},
539     Coden = {JCPSA6},
540     Doi = {DOI:10.1063/1.3274802},
541     Eissn = {10897690},
542     Issn = {00219606},
543     Keywords = {fluctuations; molecular dynamics method; viscosity;},
544     Number = {24},
545     Pages = {246101},
546     Publisher = {AIP},
547     Title = {Are pressure fluctuation-based equilibrium methods really worse than nonequilibrium methods for calculating viscosities?},
548     Url = {http://dx.doi.org/doi/10.1063/1.3274802},
549     Volume = {131},
550     Year = {2009},
551     Bdsk-Url-1 = {http://dx.doi.org/doi/10.1063/1.3274802},
552     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3274802}}