trunk/chainLength/thiolsRNEMD.bib

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%% http://bibdesk.sourceforge.net/


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@techreport{Goddard1998,
        Author = {Kimura, Y. and Cagin, T. and Goddard III, W.A.},
        Date-Added = {2012-12-05 22:18:01 +0000},
        Date-Modified = {2012-12-05 22:18:01 +0000},
        Institution = {California Institute of Technology},
        Lastchecked = {January 19, 2011},
        Number = {003},
        Title = {The Quantum Sutton-Chen Many Body Potential for Properties of fcc Metals},
        Url = {http://csdrm.caltech.edu/publications/cit-asci-tr/cit-asci-tr003.pdf},
        Year = {1998},
        Bdsk-Url-1 = {http://csdrm.caltech.edu/publications/cit-asci-tr/cit-asci-tr003.pdf}}

@article{Hase2010,
        Author = {Yue Zhang and George L. Barnes and Tianying Yan and William L. Hase},
        Date-Added = {2012-12-05 22:18:01 +0000},
        Date-Modified = {2012-12-05 22:18:01 +0000},
        Journal = {Phys. Chem. Chem. Phys.},
        Keywords = {fcc/hcp, non-equilibrium, thiols},
        Pages = {4435-4445},
        Title = {Model non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer},
        Volume = {12},
        Year = {2010}}

@article{Kuang2010,
        Author = {Shenyu Kuang and J. Daniel Gezelter},
        Date-Added = {2012-12-05 22:18:01 +0000},
        Date-Modified = {2012-12-05 22:18:01 +0000},
        Journal = {J. Chem. Phys.},
        Keywords = {NIVS, RNEMD, NIVS-RNEMD},
        Month = {October},
        Pages = {164101-1 - 164101-9},
        Title = {A gentler approach to RNEMD: Nonisotropic velocity scaling for computing thermal conductivity and shear viscosity},
        Volume = {133},
        Year = {2010}}

@article{Kuang2011,
        Author = {Shenyu Kuang and J. Daniel Gezelter},
        Date-Added = {2012-12-05 22:18:01 +0000},
        Date-Modified = {2012-12-05 22:18:01 +0000},
        Journal = {J. Phys. Chem. C},
        Keywords = {thiols, RNEMD},
        Month = {October},
        Pages = {22475-22483},
        Title = {Simulating Interfacial Thermal Conductance at Metal-Solvent Interfaces: The Role of Chemical Capping Agents},
        Volume = {115},
        Year = {2011}}

@article{Kuang2012,
        Author = {Shenyu Kuang and J. Daniel Gezelter},
        Date-Added = {2012-12-05 22:18:01 +0000},
        Date-Modified = {2012-12-05 22:18:01 +0000},
        Journal = {Mol. Phys.},
        Keywords = {VSS, RNEMD, VSS-RNEMD},
        Month = {May},
        Number = {9-10},
        Pages = {691-701},
        Title = {Velocity shearing and scaling RNEMD: a minimally perturbing method for simulating temperature and momentum gradients},
        Volume = {110},
        Year = {2012}}

@misc{open_md,
        Author = {Shenyu Kuang and Joseph Michalka and Kelsey M. Stocker and James Marr and Teng Lin and Charles F. Vardeman II and Christopher J. Fennell and Xiuquan Sun and Chunlei Li and Kyle Daily and Yang Zheng and Matthew A. Meineke and J. Daniel Gezelter},
        Date-Added = {2012-12-05 22:18:01 +0000},
        Date-Modified = {2012-12-05 22:18:01 +0000},
        Howpublished = {http://openmd.net},
        Keywords = {OpenMD},
        Lastchecked = {January 18, 2011},
        Title = {OpenMD, an open source engine for molecular dynamics},
        Bdsk-Url-1 = {http://openmd.net}}

@article{doi:10.1080/0026897031000068578,
        Abstract = { Using equilibrium and non-equilibrium molecular dynamics simulations, we determine the Kapitza resistance (or thermal contact resistance) at a model liquid-solid interface. The Kapitza resistance (or the associated Kapitza length) can reach appreciable values when the liquid does not wet the solid. The analogy with the hydrodynamic slip length is discussed. },
        Author = {Barrat, Jean-Louis and Chiaruttini, Fran{\c c}ois},
        Date-Added = {2011-12-13 17:17:05 -0500},
        Date-Modified = {2011-12-13 17:17:05 -0500},
        Doi = {10.1080/0026897031000068578},
        Eprint = {http://tandfprod.literatumonline.com/doi/pdf/10.1080/0026897031000068578},
        Journal = {Mol. Phys.},
        Number = {11},
        Pages = {1605-1610},
        Title = {Kapitza resistance at the liquid---solid interface},
        Url = {http://tandfprod.literatumonline.com/doi/abs/10.1080/0026897031000068578},
        Volume = {101},
        Year = {2003},
        Bdsk-Url-1 = {http://tandfprod.literatumonline.com/doi/abs/10.1080/0026897031000068578},
        Bdsk-Url-2 = {http://dx.doi.org/10.1080/0026897031000068578}}

@article{Medina2011,
        Abstract = {Molecular dynamics (MD) simulations are carried out on a system of rigid or flexible water molecules at a series of temperatures between 273 and 368&#xa0;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.},
        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},
        Date-Added = {2011-12-13 17:08:34 -0500},
        Date-Modified = {2011-12-13 17:08:49 -0500},
        Doi = {10.1016/j.chemphys.2011.07.001},
        Issn = {0301-0104},
        Journal = {Chemical Physics},
        Keywords = {Viscosity calculations},
        Number = {1-3},
        Pages = {9 - 18},
        Title = {Molecular dynamics simulations of rigid and flexible water models: Temperature dependence of viscosity},
        Url = {http://www.sciencedirect.com/science/article/pii/S0301010411002813},
        Volume = {388},
        Year = {2011},
        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0301010411002813},
        Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.chemphys.2011.07.001}}

@book{WagnerKruse,
        Address = {Berlin},
        Author = {W. Wagner and A. Kruse},
        Date-Added = {2011-12-13 14:57:08 -0500},
        Date-Modified = {2011-12-13 14:57:08 -0500},
        Publisher = {Springer-Verlag},
        Title = {Properties of Water and Steam, the Industrial Standard IAPWS-IF97 for the Thermodynamic Properties and Supplementary Equations for Other Properties},
        Year = {1998}}

@article{garde:PhysRevLett2009,
        Author = {Shenogina, Natalia and Godawat, Rahul and Keblinski, Pawel and Garde, Shekhar},
        Date-Added = {2011-12-13 12:48:51 -0500},
        Date-Modified = {2011-12-13 12:48:51 -0500},
        Doi = {10.1103/PhysRevLett.102.156101},
        Journal = {Phys. Rev. Lett.},
        Month = {Apr},
        Number = {15},
        Numpages = {4},
        Pages = {156101},
        Publisher = {American Physical Society},
        Title = {How Wetting and Adhesion Affect Thermal Conductance of a Range of Hydrophobic to Hydrophilic Aqueous Interfaces},
        Volume = {102},
        Year = {2009},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.102.156101}}

@article{garde:nl2005,
        Abstract = { Systems with nanoscopic features contain a high density of interfaces. Thermal transport in such systems can be governed by the resistance to heat transfer, the Kapitza resistance (RK), at the interface. Although soft interfaces, such as those between immiscible liquids or between a biomolecule and solvent, are ubiquitous, few studies of thermal transport at such interfaces have been reported. Here we characterize the interfacial conductance, 1/RK, of soft interfaces as a function of molecular architecture, chemistry, and the strength of cross-interfacial intermolecular interactions through detailed molecular dynamics simulations. The conductance of various interfaces studied here, for example, water−organic liquid, water−surfactant, surfactant−organic liquid, is relatively high (in the range of 65−370 MW/m2 K) compared to that for solid−liquid interfaces (∼10 MW/m2 K). Interestingly, the dependence of interfacial conductance on the chemistry and molecular architecture cannot be explained solely in terms of either bulk property mismatch or the strength of intermolecular attraction between the two phases. The observed trends can be attributed to a combination of strong cross-interface intermolecular interactions and good thermal coupling via soft vibration modes present at liquid−liquid interfaces. },
        Author = {Patel, Harshit A. and Garde, Shekhar and Keblinski, Pawel},
        Date-Added = {2011-12-13 12:48:51 -0500},
        Date-Modified = {2011-12-13 12:48:51 -0500},
        Doi = {10.1021/nl051526q},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/nl051526q},
        Journal = {Nano Lett.},
        Note = {PMID: 16277458},
        Number = {11},
        Pages = {2225-2231},
        Title = {Thermal Resistance of Nanoscopic Liquid−Liquid Interfaces:  Dependence on Chemistry and Molecular Architecture},
        Url = {http://pubs.acs.org/doi/abs/10.1021/nl051526q},
        Volume = {5},
        Year = {2005},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/nl051526q},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/nl051526q}}

@article{melchionna93,
        Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
        Date-Added = {2011-12-12 17:52:15 -0500},
        Date-Modified = {2011-12-12 17:52:15 -0500},
        Journal = {Mol. Phys.},
        Pages = {533-544},
        Title = {Hoover {\sc npt} dynamics for systems varying in shape and size},
        Volume = 78,
        Year = 1993}

@article{TraPPE-UA.thiols,
        Author = {Lubna, Nusrat and Kamath, Ganesh and Potoff, Jeffrey J. and Rai, Neeraj and Siepmann, J. Ilja},
        Date-Added = {2011-12-07 15:06:12 -0500},
        Date-Modified = {2011-12-07 15:06:12 -0500},
        Doi = {10.1021/jp0549125},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp0549125},
        Journal = {J. Phys. Chem. B},
        Number = {50},
        Pages = {24100-24107},
        Title = {Transferable Potentials for Phase Equilibria. 8. United-Atom Description for Thiols, Sulfides, Disulfides, and Thiophene},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp0549125},
        Volume = {109},
        Year = {2005},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp0549125},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp0549125}}

@article{TraPPE-UA.alkylbenzenes,
        Author = {Wick, Collin D. and Martin, Marcus G. and Siepmann, J. Ilja},
        Date-Added = {2011-12-07 15:06:12 -0500},
        Date-Modified = {2011-12-07 15:06:12 -0500},
        Doi = {10.1021/jp001044x},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp001044x},
        Journal = {J. Phys. Chem. B},
        Number = {33},
        Pages = {8008-8016},
        Title = {Transferable Potentials for Phase Equilibria. 4. United-Atom Description of Linear and Branched Alkenes and Alkylbenzenes},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp001044x},
        Volume = {104},
        Year = {2000},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp001044x},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp001044x}}

@article{TraPPE-UA.alkanes,
        Author = {Martin, Marcus G. and Siepmann, J. Ilja},
        Date-Added = {2011-12-07 15:06:12 -0500},
        Date-Modified = {2011-12-07 15:06:12 -0500},
        Doi = {10.1021/jp972543+},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp972543%2B},
        Journal = {J. Phys. Chem. B},
        Number = {14},
        Pages = {2569-2577},
        Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp972543%2B},
        Volume = {102},
        Year = {1998},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp972543+},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp972543+},
        Bdsk-Url-3 = {http://pubs.acs.org/doi/abs/10.1021/jp972543%2B}}

@article{ISI:000167766600035,
        Abstract = {Molecular dynamics simulations are used to
                  investigate the separation of water films adjacent
                  to a hot metal surface. The simulations clearly show
                  that the water layers nearest the surface overheat
                  and undergo explosive boiling. For thick films, the
                  expansion of the vaporized molecules near the
                  surface forces the outer water layers to move away
                  from the surface. These results are of interest for
                  mass spectrometry of biological molecules, steam
                  cleaning of surfaces, and medical procedures.},
        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
        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.},
        Author = {Dou, YS and Zhigilei, LV and Winograd, N and Garrison, BJ},
        Date-Added = {2011-12-07 15:02:32 -0500},
        Date-Modified = {2011-12-07 15:02:32 -0500},
        Doc-Delivery-Number = {416ED},
        Issn = {1089-5639},
        Journal = {J. Phys. Chem. A},
        Journal-Iso = {J. Phys. Chem. A},
        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},
        Language = {English},
        Month = {MAR 29},
        Number = {12},
        Number-Of-Cited-References = {65},
        Pages = {2748-2755},
        Publisher = {AMER CHEMICAL SOC},
        Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
        Times-Cited = {66},
        Title = {Explosive boiling of water films adjacent to heated surfaces: A microscopic description},
        Type = {Article},
        Unique-Id = {ISI:000167766600035},
        Volume = {105},
        Year = {2001}}

@article{Chen90,
        Author = {A.~P. Sutton and J. Chen},
        Date-Added = {2011-12-07 15:01:59 -0500},
        Date-Modified = {2011-12-07 15:01:59 -0500},
        Journal = {Philos. Mag. Lett.},
        Pages = {139-146},
        Title = {Long-Range Finnis Sinclair Potentials},
        Volume = 61,
        Year = {1990}}

@article{PhysRevB.59.3527,
        Author = {Qi, Yue and \c{C}a\v{g}in, Tahir and Kimura, Yoshitaka and {Goddard III}, William A.},
        Date-Added = {2011-12-07 15:01:36 -0500},
        Date-Modified = {2011-12-07 15:01:36 -0500},
        Doi = {10.1103/PhysRevB.59.3527},
        Journal = {Phys. Rev. B},
        Local-Url = {file://localhost/Users/charles/Documents/Papers/Qi/1999.pdf},
        Month = {Feb},
        Number = {5},
        Numpages = {6},
        Pages = {3527-3533},
        Publisher = {American Physical Society},
        Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals:\quad{}{C}u-{A}g and {C}u-{N}i},
        Volume = {59},
        Year = {1999},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.59.3527}}

@article{Bedrov:2000,
        Abstract = {We have applied a new nonequilibrium molecular
                  dynamics (NEMD) method {[}F. Muller-Plathe,
                  J. Chem. Phys. 106, 6082 (1997)] previously applied
                  to monatomic Lennard-Jones fluids in the
                  determination of the thermal conductivity of
                  molecular fluids. The method was modified in order
                  to be applicable to systems with holonomic
                  constraints. Because the method involves imposing a
                  known heat flux it is particularly attractive for
                  systems involving long-range and many-body
                  interactions where calculation of the microscopic
                  heat flux is difficult. The predicted thermal
                  conductivities of liquid n-butane and water using
                  the imposed-flux NEMD method were found to be in a
                  good agreement with previous simulations and
                  experiment. (C) 2000 American Institute of
                  Physics. {[}S0021-9606(00)50841-1].},
        Address = {2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA},
        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.},
        Author = {Bedrov, D and Smith, GD},
        Date-Added = {2011-12-07 15:00:27 -0500},
        Date-Modified = {2011-12-07 15:00:27 -0500},
        Doc-Delivery-Number = {369BF},
        Issn = {0021-9606},
        Journal = {J. Chem. Phys.},
        Journal-Iso = {J. Chem. Phys.},
        Keywords-Plus = {EFFECTIVE PAIR POTENTIALS; TRANSPORT-PROPERTIES; CANONICAL ENSEMBLE; NORMAL-BUTANE; ALGORITHMS; SHAKE; WATER},
        Language = {English},
        Month = {NOV 8},
        Number = {18},
        Number-Of-Cited-References = {26},
        Pages = {8080-8084},
        Publisher = {AMER INST PHYSICS},
        Read = {1},
        Subject-Category = {Physics, Atomic, Molecular \& Chemical},
        Times-Cited = {23},
        Title = {Thermal conductivity of molecular fluids from molecular dynamics simulations: Application of a new imposed-flux method},
        Type = {Article},
        Unique-Id = {ISI:000090151400044},
        Volume = {113},
        Year = {2000}}

@article{10.1063/1.3330544,
        Author = {Miguel Angel Gonz{\'a}lez and Jos{\'e} L. F. Abascal},
        Coden = {JCPSA6},
        Date-Added = {2011-12-07 14:59:20 -0500},
        Date-Modified = {2011-12-15 13:10:11 -0500},
        Doi = {DOI:10.1063/1.3330544},
        Eissn = {10897690},
        Issn = {00219606},
        Journal = {J. Chem. Phys.},
        Keywords = {shear strength; viscosity;},
        Number = {9},
        Pages = {096101},
        Publisher = {AIP},
        Title = {The shear viscosity of rigid water models},
        Url = {http://dx.doi.org/doi/10.1063/1.3330544},
        Volume = {132},
        Year = {2010},
        Bdsk-Url-1 = {http://dx.doi.org/doi/10.1063/1.3330544},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3330544}}

@article{doi:10.1021/jp048434u,
        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. },
        Author = {Hirsch, Tomas K. and Ojam{\"a}e, Lars},
        Date-Added = {2011-12-07 14:38:30 -0500},
        Date-Modified = {2011-12-07 14:38:30 -0500},
        Doi = {10.1021/jp048434u},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp048434u},
        Journal = {J. Phys. Chem. B},
        Number = {40},
        Pages = {15856-15864},
        Title = {Quantum-Chemical and Force-Field Investigations of Ice Ih:  Computation of Proton-Ordered Structures and Prediction of Their Lattice Energies},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp048434u},
        Volume = {108},
        Year = {2004},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp048434u},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp048434u}}

@article{Meineke:2005gd,
        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.},
        Address = {111 RIVER ST, HOBOKEN, NJ 07030 USA},
        Author = {Meineke, M. A. and Vardeman, C. F. and Lin, T and Fennell, CJ and Gezelter, J. D.},
        Date-Added = {2011-12-07 13:33:04 -0500},
        Date-Modified = {2011-12-07 13:33:04 -0500},
        Doi = {DOI 10.1002/jcc.20161},
        Isi = {000226558200006},
        Isi-Recid = {142688207},
        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},
        Journal = {J. Comput. Chem.},
        Keywords = {OOPSE; molecular dynamics},
        Month = feb,
        Number = {3},
        Pages = {252-271},
        Publisher = {JOHN WILEY \& SONS INC},
        Times-Cited = {9},
        Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
        Volume = {26},
        Year = {2005},
        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000226558200006},
        Bdsk-Url-2 = {http://dx.doi.org/10.1002/jcc.20161}}

@article{hoover85,
        Author = {W.~G. Hoover},
        Date-Added = {2011-12-06 14:23:41 -0500},
        Date-Modified = {2011-12-06 14:23:41 -0500},
        Journal = {Phys. Rev. A},
        Pages = 1695,
        Title = {Canonical dynamics: Equilibrium phase-space distributions},
        Volume = 31,
        Year = 1985}

@article{Maginn:2010,
        Abstract = {The reverse nonequilibrium molecular dynamics
                  (RNEMD) method calculates the shear viscosity of a
                  fluid by imposing a nonphysical exchange of momentum
                  and measuring the resulting shear velocity
                  gradient. In this study we investigate the range of
                  momentum flux values over which RNEMD yields usable
                  (linear) velocity gradients. We find that nonlinear
                  velocity profiles result primarily from gradients in
                  fluid temperature and density. The temperature
                  gradient results from conversion of heat into bulk
                  kinetic energy, which is transformed back into heat
                  elsewhere via viscous heating. An expression is
                  derived to predict the temperature profile resulting
                  from a specified momentum flux for a given fluid and
                  simulation cell. Although primarily bounded above,
                  we also describe milder low-flux limitations. RNEMD
                  results for a Lennard-Jones fluid agree with
                  equilibrium molecular dynamics and conventional
                  nonequilibrium molecular dynamics calculations at
                  low shear, but RNEMD underpredicts viscosity
                  relative to conventional NEMD at high shear.},
        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
        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.},
        Article-Number = {014103},
        Author = {Tenney, Craig M. and Maginn, Edward J.},
        Author-Email = {ed@nd.edu},
        Date-Added = {2011-12-05 18:29:08 -0500},
        Date-Modified = {2011-12-05 18:29:08 -0500},
        Doc-Delivery-Number = {542DQ},
        Doi = {10.1063/1.3276454},
        Funding-Acknowledgement = {U.S. Department of Energy {[}DE-FG36-08G088020]},
        Funding-Text = {Support for this work was provided by the U.S. Department of Energy (Grant No. DE-FG36-08G088020)},
        Issn = {0021-9606},
        Journal = {J. Chem. Phys.},
        Journal-Iso = {J. Chem. Phys.},
        Keywords = {Lennard-Jones potential; molecular dynamics method; Navier-Stokes equations; viscosity},
        Keywords-Plus = {CURRENT AUTOCORRELATION-FUNCTION; IONIC LIQUID; SIMULATIONS; TEMPERATURE},
        Language = {English},
        Month = {JAN 7},
        Number = {1},
        Number-Of-Cited-References = {20},
        Pages = {014103},
        Publisher = {AMER INST PHYSICS},
        Subject-Category = {Physics, Atomic, Molecular \& Chemical},
        Times-Cited = {0},
        Title = {Limitations and recommendations for the calculation of shear viscosity using reverse nonequilibrium molecular dynamics},
        Type = {Article},
        Unique-Id = {ISI:000273472300004},
        Volume = {132},
        Year = {2010},
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.3276454}}

@article{ISI:000080382700030,
        Abstract = {A nonequilibrium method for calculating the shear
                  viscosity is presented. It reverses the
                  cause-and-effect picture customarily used in
                  nonequilibrium molecular dynamics: the effect, the
                  momentum flux or stress, is imposed, whereas the
                  cause, the velocity gradient or shear rate, is
                  obtained from the simulation. It differs from other
                  Norton-ensemble methods by the way in which the
                  steady-state momentum flux is maintained. This
                  method involves a simple exchange of particle
                  momenta, which is easy to implement. Moreover, it
                  can be made to conserve the total energy as well as
                  the total linear momentum, so no coupling to an
                  external temperature bath is needed. The resulting
                  raw data, the velocity profile, is a robust and
                  rapidly converging property. The method is tested on
                  the Lennard-Jones fluid near its triple point. It
                  yields a viscosity of 3.2-3.3, in Lennard-Jones
                  reduced units, in agreement with literature
                  results. {[}S1063-651X(99)03105-0].},
        Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
        Affiliation = {Muller-Plathe, F (Reprint Author), Max Planck Inst Polymerforsch, Ackermannweg 10, D-55128 Mainz, Germany. Max Planck Inst Polymerforsch, D-55128 Mainz, Germany.},
        Author = {M\"{u}ller-Plathe, F},
        Date-Added = {2011-12-05 18:18:37 -0500},
        Date-Modified = {2011-12-05 18:18:37 -0500},
        Doc-Delivery-Number = {197TX},
        Issn = {1063-651X},
        Journal = {Phys. Rev. E},
        Journal-Iso = {Phys. Rev. E},
        Language = {English},
        Month = {MAY},
        Number = {5, Part A},
        Number-Of-Cited-References = {17},
        Pages = {4894-4898},
        Publisher = {AMERICAN PHYSICAL SOC},
        Subject-Category = {Physics, Fluids \& Plasmas; Physics, Mathematical},
        Times-Cited = {57},
        Title = {Reversing the perturbation in nonequilibrium molecular dynamics: An easy way to calculate the shear viscosity of fluids},
        Type = {Article},
        Unique-Id = {ISI:000080382700030},
        Volume = {59},
        Year = {1999}}

@article{MullerPlathe:1997xw,
        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.},
        Address = {WOODBURY},
        Author = {M\"{u}ller-Plathe, F.},
        Cited-Reference-Count = {13},
        Date = {APR 8},
        Date-Added = {2011-12-05 18:18:37 -0500},
        Date-Modified = {2011-12-05 18:18:37 -0500},
        Document-Type = {Article},
        Isi = {ISI:A1997WR62000032},
        Isi-Document-Delivery-Number = {WR620},
        Iso-Source-Abbreviation = {J. Chem. Phys.},
        Issn = {0021-9606},
        Journal = {J. Chem. Phys.},
        Language = {English},
        Month = {Apr},
        Number = {14},
        Page-Count = {4},
        Pages = {6082--6085},
        Publication-Type = {J},
        Publisher = {AMER INST PHYSICS},
        Publisher-Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999},
        Reprint-Address = {MullerPlathe, F, MAX PLANCK INST POLYMER RES, D-55128 MAINZ, GERMANY.},
        Source = {J CHEM PHYS},
        Subject-Category = {Physics, Atomic, Molecular & Chemical},
        Times-Cited = {106},
        Title = {A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity},
        Volume = {106},
        Year = {1997}}

@article{priezjev:204704,
        Author = {Nikolai V. Priezjev},
        Date-Added = {2011-11-28 14:39:18 -0500},
        Date-Modified = {2011-11-28 14:39:18 -0500},
        Doi = {10.1063/1.3663384},
        Eid = {204704},
        Journal = {J. Chem. Phys.},
        Keywords = {channel flow; diffusion; flow simulation; hydrodynamics; molecular dynamics method; pattern formation; random processes; shear flow; slip flow; wetting},
        Number = {20},
        Numpages = {9},
        Pages = {204704},
        Publisher = {AIP},
        Title = {Molecular diffusion and slip boundary conditions at smooth surfaces with periodic and random nanoscale textures},
        Url = {http://link.aip.org/link/?JCP/135/204704/1},
        Volume = {135},
        Year = {2011},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/135/204704/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3663384}}

@article{bryk:10258,
        Author = {Taras Bryk and A. D. J. Haymet},
        Date-Added = {2011-11-22 17:06:35 -0500},
        Date-Modified = {2011-11-22 17:06:35 -0500},
        Doi = {10.1063/1.1519538},
        Journal = {J. Chem. Phys.},
        Keywords = {liquid structure; molecular dynamics method; water; ice; interface structure},
        Number = {22},
        Pages = {10258-10268},
        Publisher = {AIP},
        Title = {Ice 1h/water interface of the SPC/E model: Molecular dynamics simulations of the equilibrium basal and prism interfaces},
        Url = {http://link.aip.org/link/?JCP/117/10258/1},
        Volume = {117},
        Year = {2002},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/117/10258/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1519538}}

@article{kuang:164101,
        Author = {Shenyu Kuang and J. Daniel Gezelter},
        Date-Added = {2011-11-18 15:32:23 -0500},
        Date-Modified = {2011-11-18 15:32:23 -0500},
        Doi = {10.1063/1.3499947},
        Eid = {164101},
        Journal = {J. Chem. Phys.},
        Keywords = {linear momentum; molecular dynamics method; thermal conductivity; total energy; viscosity},
        Number = {16},
        Numpages = {9},
        Pages = {164101},
        Publisher = {AIP},
        Title = {A gentler approach to RNEMD: Nonisotropic velocity scaling for computing thermal conductivity and shear viscosity},
        Url = {http://link.aip.org/link/?JCP/133/164101/1},
        Volume = {133},
        Year = {2010},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/133/164101/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3499947}}

@misc{openmd,
        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},
        Date-Added = {2011-11-18 15:32:23 -0500},
        Date-Modified = {2011-11-18 15:32:23 -0500},
        Howpublished = {Available at {\tt http://openmd.net}},
        Title = {{OpenMD, an open source engine for molecular dynamics}}}

@article{kuang:AuThl,
        Author = {Kuang, Shenyu and Gezelter, J. Daniel},
        Date-Added = {2011-11-18 13:03:06 -0500},
        Date-Modified = {2011-12-05 17:58:01 -0500},
        Doi = {10.1021/jp2073478},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp2073478},
        Journal = {J. Phys. Chem. C},
        Number = {45},
        Pages = {22475-22483},
        Title = {Simulating Interfacial Thermal Conductance at Metal-Solvent Interfaces: The Role of Chemical Capping Agents},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp2073478},
        Volume = {115},
        Year = {2011},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp2073478},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp2073478}}

@article{10.1063/1.2772547,
        Author = {Hideo Kaburaki and Ju Li and Sidney Yip and Hajime Kimizuka},
        Coden = {JAPIAU},
        Date-Added = {2011-11-01 16:46:32 -0400},
        Date-Modified = {2011-11-01 16:46:32 -0400},
        Doi = {DOI:10.1063/1.2772547},
        Eissn = {10897550},
        Issn = {00218979},
        Keywords = {argon; Lennard-Jones potential; phonons; thermal conductivity;},
        Number = {4},
        Pages = {043514},
        Publisher = {AIP},
        Title = {Dynamical thermal conductivity of argon crystal},
        Url = {http://dx.doi.org/10.1063/1.2772547},
        Volume = {102},
        Year = {2007},
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2772547}}

@article{PhysRevLett.82.4671,
        Author = {Barrat, Jean-Louis and Bocquet, Lyd\'eric},
        Date-Added = {2011-11-01 16:44:29 -0400},
        Date-Modified = {2011-11-01 16:44:29 -0400},
        Doi = {10.1103/PhysRevLett.82.4671},
        Issue = {23},
        Journal = {Phys. Rev. Lett.},
        Month = {Jun},
        Pages = {4671--4674},
        Publisher = {American Physical Society},
        Title = {Large Slip Effect at a Nonwetting Fluid-Solid Interface},
        Url = {http://link.aps.org/doi/10.1103/PhysRevLett.82.4671},
        Volume = {82},
        Year = {1999},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevLett.82.4671},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevLett.82.4671}}

@article{10.1063/1.1610442,
        Author = {J. R. Schmidt and J. L. Skinner},
        Coden = {JCPSA6},
        Date-Added = {2011-10-13 16:28:43 -0400},
        Date-Modified = {2011-12-15 13:11:53 -0500},
        Doi = {DOI:10.1063/1.1610442},
        Eissn = {10897690},
        Issn = {00219606},
        Journal = {J. Chem. Phys.},
        Keywords = {hydrodynamics; Brownian motion; molecular dynamics method; diffusion;},
        Number = {15},
        Pages = {8062-8068},
        Publisher = {AIP},
        Title = {Hydrodynamic boundary conditions, the Stokes?Einstein law, and long-time tails in the Brownian limit},
        Url = {http://dx.doi.org/10.1063/1.1610442},
        Volume = {119},
        Year = {2003},
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}

@article{10.1063/1.3274802,
        Author = {Ting Chen and Berend Smit and Alexis T. Bell},
        Coden = {JCPSA6},
        Doi = {DOI:10.1063/1.3274802},
        Eissn = {10897690},
        Issn = {00219606},
        Keywords = {fluctuations; molecular dynamics method; viscosity;},
        Number = {24},
        Pages = {246101},
        Publisher = {AIP},
        Title = {Are pressure fluctuation-based equilibrium methods really worse than nonequilibrium methods for calculating viscosities?},
        Url = {http://dx.doi.org/doi/10.1063/1.3274802},
        Volume = {131},
        Year = {2009},
        Bdsk-Url-1 = {http://dx.doi.org/doi/10.1063/1.3274802},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3274802}}
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