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@article{Meineke:2005gd, |
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Abstract = {OOPSE is a new molecular dynamics simulation program that is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based meta-data language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.}, |
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Address = {111 RIVER ST, HOBOKEN, NJ 07030 USA}, |
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Author = {Meineke, MA and Vardeman, CF and Lin, T and Fennell, CJ and Gezelter, JD}, |
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Date-Added = {2009-10-01 18:43:03 -0400}, |
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Date-Modified = {2009-10-01 18:43:03 -0400}, |
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Doi = {DOI 10.1002/jcc.20161}, |
| 19 |
Isi = {000226558200006}, |
| 20 |
Isi-Recid = {142688207}, |
| 21 |
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}, |
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Journal = {Journal of Computational Chemistry}, |
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Keywords = {OOPSE; molecular dynamics}, |
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Month = feb, |
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Number = {3}, |
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Pages = {252-271}, |
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Publisher = {JOHN WILEY \& SONS INC}, |
| 28 |
Times-Cited = {9}, |
| 29 |
Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics}, |
| 30 |
Volume = {26}, |
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Year = {2005}, |
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Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000226558200006}} |
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|
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@article{ISI:000080382700030, |
| 35 |
Abstract = {{A nonequilibrium method for calculating the shear viscosity is |
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presented. It reverses the cause-and-effect picture customarily used in |
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nonequilibrium molecular dynamics: the effect, the momentum flux or |
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stress, is imposed, whereas the cause, the velocity gradient or shear |
| 39 |
rate, is obtained from the simulation. It differs from other |
| 40 |
Norton-ensemble methods by the way in which the steady-state momentum |
| 41 |
flux is maintained. This method involves a simple exchange of particle |
| 42 |
momenta, which is easy to implement. Moreover, it can be made to |
| 43 |
conserve the total energy as well as the total linear momentum, so no |
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coupling to an external temperature bath is needed. The resulting raw |
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data, the velocity profile, is a robust and rapidly converging |
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property. The method is tested on the Lennard-Jones fluid near its |
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triple point. It yields a viscosity of 3.2-3.3, in Lennard-Jones |
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reduced units, in agreement with literature results. |
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{[}S1063-651X(99)03105-0].}}, |
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Address = {{ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA}}, |
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Affiliation = {{Muller-Plathe, F (Reprint Author), Max Planck Inst Polymerforsch, Ackermannweg 10, D-55128 Mainz, Germany. Max Planck Inst Polymerforsch, D-55128 Mainz, Germany.}}, |
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Author = {Muller-Plathe, F}, |
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Date-Added = {2009-10-01 14:07:30 -0400}, |
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Date-Modified = {2009-10-01 14:07:30 -0400}, |
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Doc-Delivery-Number = {{197TX}}, |
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Issn = {{1063-651X}}, |
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Journal = {{PHYSICAL REVIEW E}}, |
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Journal-Iso = {{Phys. Rev. E}}, |
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Language = {{English}}, |
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Month = {{MAY}}, |
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Number = {{5, Part A}}, |
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Number-Of-Cited-References = {{17}}, |
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Pages = {{4894-4898}}, |
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Publisher = {{AMERICAN PHYSICAL SOC}}, |
| 65 |
Subject-Category = {{Physics, Fluids \& Plasmas; Physics, Mathematical}}, |
| 66 |
Times-Cited = {{57}}, |
| 67 |
Title = {{Reversing the perturbation in nonequilibrium molecular dynamics: An easy way to calculate the shear viscosity of fluids}}, |
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Type = {{Article}}, |
| 69 |
Unique-Id = {{ISI:000080382700030}}, |
| 70 |
Volume = {{59}}, |
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Year = {{1999}}} |
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|
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@article{ISI:000246190100032, |
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Abstract = {{Atomistic simulations are conducted to examine the dependence of the |
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viscosity of 1-ethyl-3-methylimidazolium |
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bis(trifluoromethanesulfonyl)imide on temperature and water content. A |
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nonequilibrium molecular dynamics procedure is utilized along with an |
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established fixed charge force field. It is found that the simulations |
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quantitatively capture the temperature dependence of the viscosity as |
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well as the drop in viscosity that occurs with increasing water |
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content. Using mixture viscosity models, we show that the relative drop |
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in viscosity with water content is actually less than that that would |
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be predicted for an ideal system. This finding is at odds with the |
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popular notion that small amounts of water cause an unusually large |
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drop in the viscosity of ionic liquids. The simulations suggest that, |
| 86 |
due to preferential association of water with anions and the formation |
| 87 |
of water clusters, the excess molar volume is negative. This means that |
| 88 |
dissolved water is actually less effective at lowering the viscosity of |
| 89 |
these mixtures when compared to a solute obeying ideal mixing behavior. |
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The use of a nonequilibrium simulation technique enables diffusive |
| 91 |
behavior to be observed on the time scale of the simulations, and |
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standard equilibrium molecular dynamics resulted in sub-diffusive |
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behavior even over 2 ns of simulation time.}}, |
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Address = {{1155 16TH ST, NW, WASHINGTON, DC 20036 USA}}, |
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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.}}, |
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Author = {Kelkar, Manish S. and Maginn, Edward J.}, |
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Author-Email = {{ed@nd.edu}}, |
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Date-Added = {2009-09-29 17:07:17 -0400}, |
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Date-Modified = {2009-09-29 17:07:17 -0400}, |
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Doc-Delivery-Number = {{163VA}}, |
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Doi = {{10.1021/jp0686893}}, |
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Issn = {{1520-6106}}, |
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Journal = {{JOURNAL OF PHYSICAL CHEMISTRY B}}, |
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Journal-Iso = {{J. Phys. Chem. B}}, |
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Keywords-Plus = {{MOLECULAR-DYNAMICS SIMULATION; MOMENTUM IMPULSE RELAXATION; FORCE-FIELD; TRANSPORT-PROPERTIES; PHYSICAL-PROPERTIES; SIMPLE FLUID; CHLORIDE; MODEL; SALTS; ARCHITECTURE}}, |
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Language = {{English}}, |
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Month = {{MAY 10}}, |
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Number = {{18}}, |
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Number-Of-Cited-References = {{57}}, |
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Pages = {{4867-4876}}, |
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Publisher = {{AMER CHEMICAL SOC}}, |
| 112 |
Subject-Category = {{Chemistry, Physical}}, |
| 113 |
Times-Cited = {{35}}, |
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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}}, |
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Type = {{Article}}, |
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Unique-Id = {{ISI:000246190100032}}, |
| 117 |
Volume = {{111}}, |
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Year = {{2007}}, |
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Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp0686893%7D}} |
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|
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@article{MullerPlathe:1997xw, |
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Abstract = {A nonequilibrium molecular dynamics method for calculating the thermal conductivity is presented. It reverses the usual cause and effect picture. The ''effect,'' the heat flux, is imposed on the system and the ''cause,'' the temperature gradient is obtained from the simulation. Besides being very simple to implement, the scheme offers several advantages such as compatibility with periodic boundary conditions, conservation of total energy and total linear momentum, and the sampling of a rapidly converging quantity (temperature gradient) rather than a slowly converging one (heat flux). The scheme is tested on the Lennard-Jones fluid. (C) 1997 American Institute of Physics.}, |
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Address = {WOODBURY}, |
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Author = {MullerPlathe, F.}, |
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Cited-Reference-Count = {13}, |
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Date = {APR 8}, |
| 127 |
Date-Added = {2009-09-21 16:51:21 -0400}, |
| 128 |
Date-Modified = {2009-09-21 16:51:21 -0400}, |
| 129 |
Document-Type = {Article}, |
| 130 |
Isi = {ISI:A1997WR62000032}, |
| 131 |
Isi-Document-Delivery-Number = {WR620}, |
| 132 |
Iso-Source-Abbreviation = {J. Chem. Phys.}, |
| 133 |
Issn = {0021-9606}, |
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Journal = {JOURNAL OF CHEMICAL PHYSICS}, |
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Language = {English}, |
| 136 |
Month = {Apr}, |
| 137 |
Number = {14}, |
| 138 |
Page-Count = {4}, |
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Pages = {6082--6085}, |
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Publication-Type = {J}, |
| 141 |
Publisher = {AMER INST PHYSICS}, |
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Publisher-Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999}, |
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Reprint-Address = {MullerPlathe, F, MAX PLANCK INST POLYMER RES, D-55128 MAINZ, GERMANY.}, |
| 144 |
Source = {J CHEM PHYS}, |
| 145 |
Subject-Category = {Physics, Atomic, Molecular & Chemical}, |
| 146 |
Times-Cited = {106}, |
| 147 |
Title = {A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity}, |
| 148 |
Volume = {106}, |
| 149 |
Year = {1997}} |
| 150 |
|
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@article{Muller-Plathe:1999ek, |
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Abstract = {A novel non-equilibrium method for calculating transport coefficients is presented. It reverses the experimental cause-and-effect picture, e.g. for the calculation of viscosities: the effect, the momentum flux or stress, is imposed, whereas the cause, the velocity gradient or shear rates, is obtained from the simulation. It differs from other Norton-ensemble methods by the way, in which the steady-state fluxes are maintained. This method involves a simple exchange of particle momenta, which is easy to implement and to analyse. Moreover, it can be made to conserve the total energy as well as the total linear momentum, so no thermostatting is needed. The resulting raw data are robust and rapidly converging. The method is tested on the calculation of the shear viscosity, the thermal conductivity and the Soret coefficient (thermal diffusion) for the Lennard-Jones (LJ) fluid near its triple point. Possible applications to other transport coefficients and more complicated systems are discussed. (C) 1999 Elsevier Science Ltd. All rights reserved.}, |
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Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND}, |
| 154 |
Author = {Muller-Plathe, F and Reith, D}, |
| 155 |
Date-Added = {2009-09-21 16:47:07 -0400}, |
| 156 |
Date-Modified = {2009-09-21 16:47:07 -0400}, |
| 157 |
Isi = {000082266500004}, |
| 158 |
Isi-Recid = {111564960}, |
| 159 |
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}, |
| 160 |
Journal = {Computational and Theoretical Polymer Science}, |
| 161 |
Keywords = {viscosity; Ludwig-Soret effect; thermal conductivity; Onsager coefficents; non-equilibrium molecular dynamics}, |
| 162 |
Number = {3-4}, |
| 163 |
Pages = {203-209}, |
| 164 |
Publisher = {ELSEVIER SCI LTD}, |
| 165 |
Times-Cited = {15}, |
| 166 |
Title = {Cause and effect reversed in non-equilibrium molecular dynamics: an easy route to transport coefficients}, |
| 167 |
Volume = {9}, |
| 168 |
Year = {1999}, |
| 169 |
Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000082266500004}} |
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|
| 171 |
@article{Viscardy:2007lq, |
| 172 |
Abstract = {The thermal conductivity is calculated with the Helfand-moment method in the Lennard-Jones fluid near the triple point. The Helfand moment of thermal conductivity is here derived for molecular dynamics with periodic boundary conditions. Thermal conductivity is given by a generalized Einstein relation with this Helfand moment. The authors compute thermal conductivity by this new method and compare it with their own values obtained by the standard Green-Kubo method. The agreement is excellent. (C) 2007 American Institute of Physics.}, |
| 173 |
Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA}, |
| 174 |
Author = {Viscardy, S. and Servantie, J. and Gaspard, P.}, |
| 175 |
Date-Added = {2009-09-21 16:37:20 -0400}, |
| 176 |
Date-Modified = {2009-09-21 16:37:20 -0400}, |
| 177 |
Doi = {DOI 10.1063/1.2724821}, |
| 178 |
Isi = {000246453900035}, |
| 179 |
Isi-Recid = {156192451}, |
| 180 |
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}, |
| 181 |
Journal = {Journal of Chemical Physics}, |
| 182 |
Month = may, |
| 183 |
Number = {18}, |
| 184 |
Publisher = {AMER INST PHYSICS}, |
| 185 |
Times-Cited = {3}, |
| 186 |
Title = {Transport and Helfand moments in the Lennard-Jones fluid. II. Thermal conductivity}, |
| 187 |
Volume = {126}, |
| 188 |
Year = {2007}, |
| 189 |
Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000246453900035}} |
| 190 |
|
| 191 |
@article{Viscardy:2007bh, |
| 192 |
Abstract = {The authors propose a new method, the Helfand-moment method, to compute the shear viscosity by equilibrium molecular dynamics in periodic systems. In this method, the shear viscosity is written as an Einstein-type relation in terms of the variance of the so-called Helfand moment. This quantity is modified in order to satisfy systems with periodic boundary conditions usually considered in molecular dynamics. They calculate the shear viscosity in the Lennard-Jones fluid near the triple point thanks to this new technique. They show that the results of the Helfand-moment method are in excellent agreement with the results of the standard Green-Kubo method. (C) 2007 American Institute of Physics.}, |
| 193 |
Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA}, |
| 194 |
Author = {Viscardy, S. and Servantie, J. and Gaspard, P.}, |
| 195 |
Date-Added = {2009-09-21 16:37:19 -0400}, |
| 196 |
Date-Modified = {2009-09-21 16:37:19 -0400}, |
| 197 |
Doi = {DOI 10.1063/1.2724820}, |
| 198 |
Isi = {000246453900034}, |
| 199 |
Isi-Recid = {156192449}, |
| 200 |
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}, |
| 201 |
Journal = {Journal of Chemical Physics}, |
| 202 |
Month = may, |
| 203 |
Number = {18}, |
| 204 |
Publisher = {AMER INST PHYSICS}, |
| 205 |
Times-Cited = {1}, |
| 206 |
Title = {Transport and Helfand moments in the Lennard-Jones fluid. I. Shear viscosity}, |
| 207 |
Volume = {126}, |
| 208 |
Year = {2007}, |
| 209 |
Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000246453900034}} |
