group/interfacial/interfacial.bib

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@article{doi:10.1021/la026493y,
        Abstract = { We have studied butanethiol self-assembled monolayers on Au(100) using cyclic voltammetry and in situ scanning tunneling microscopy (STM). The butanethiol adlayer shows ordered domains with a striped structure, the stripes running parallel to the main crystallographic axes of the substrate. After modification the surface reveals a 50% coverage of monoatomic high gold islands, but no vacancy islands were observed. Reductive and oxidative desorption of the film, previously studied by electrochemistry, were monitored by STM. },
        Author = {Loglio, F. and Schweizer, M. and Kolb, D. M.},
        Date-Added = {2011-07-12 17:52:01 -0400},
        Date-Modified = {2011-07-12 17:52:01 -0400},
        Doi = {10.1021/la026493y},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/la026493y},
        Journal = {Langmuir},
        Number = {3},
        Pages = {830-834},
        Title = {In Situ Characterization of Self-Assembled Butanethiol Monolayers on Au(100) Electrodes},
        Url = {http://pubs.acs.org/doi/abs/10.1021/la026493y},
        Volume = {19},
        Year = {2003},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/la026493y},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/la026493y}}

@article{doi:10.1021/j100035a033,
        Author = {McDermott, Christie A. and McDermott, Mark T. and Green, John-Bruce and Porter, Marc D.},
        Date-Added = {2011-07-12 17:51:55 -0400},
        Date-Modified = {2011-07-12 17:51:55 -0400},
        Doi = {10.1021/j100035a033},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/j100035a033},
        Journal = {The Journal of Physical Chemistry},
        Number = {35},
        Pages = {13257-13267},
        Title = {Structural Origins of the Surface Depressions at Alkanethiolate Monolayers on Au(111): A Scanning Tunneling and Atomic Force Microscopic Investigation},
        Url = {http://pubs.acs.org/doi/abs/10.1021/j100035a033},
        Volume = {99},
        Year = {1995},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/j100035a033},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/j100035a033}}

@article{hautman:4994,
        Author = {Joseph Hautman and Michael L. Klein},
        Date-Added = {2011-07-11 18:27:57 -0400},
        Date-Modified = {2011-07-11 18:27:57 -0400},
        Doi = {10.1063/1.457621},
        Journal = {The Journal of Chemical Physics},
        Keywords = {MOLECULAR DYNAMICS CALCULATIONS; SIMULATION; MONOLAYERS; THIOLS; ALKYL COMPOUNDS; CHAINS; SURFACE STRUCTURE; GOLD; SUBSTRATES; CHEMISORPTION; SURFACE PROPERTIES},
        Number = {8},
        Pages = {4994-5001},
        Publisher = {AIP},
        Title = {Simulation of a monolayer of alkyl thiol chains},
        Url = {http://link.aip.org/link/?JCP/91/4994/1},
        Volume = {91},
        Year = {1989},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/91/4994/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.457621}}

@article{landman:1998,
        Abstract = { Equilibrium structures and thermodynamic properties of dodecanethiol self-assembled monolayers on small (Au140) and larger (Au1289) gold nanocrystallites were investigated with the use of molecular dynamics simulations. Compact passivating monolayers are formed on the (111) and (100) facets of the nanocrystallites, with adsorption site geometries differing from those found on extended flat Au(111) and Au(100) surfaces, as well as with higher packing densities. At lower temperatures the passivating molecules organize into preferentially oriented molecular bundles with the molecules in the bundles aligned approximately parallel to each other. Thermal disordering starts at T ≳200 K, initiating at the boundaries of the bundles and involving generation of intramolecular conformational (gauche) defects which occur first at bonds near the chains' outer terminus and propagate inward toward the underlying gold nanocrystalline surface as the temperature is increased. The disordering process culminates in melting of the molecular bundles, resulting in a uniform orientational distribution of the molecules around the gold nanocrystallites. From the inflection points in the calculated caloric curves, melting temperatures were determined as 280 and 294 K for the monolayers adsorbed on the smaller and larger gold nanocrystallites, respectively. These temperatures are significantly lower than the melting temperature estimated for a self-assembled monolayer of dodecanethiol adsorbed on an extended Au(111) surface. The theoretically predicted disordering mechanisms and melting scenario, resulting in a temperature-broadened transition, support recent experimental investigations. },
        Author = {Luedtke, W. D. and Landman, Uzi},
        Date-Added = {2011-07-11 18:22:20 -0400},
        Date-Modified = {2011-07-11 18:22:54 -0400},
        Doi = {10.1021/jp981745i},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp981745i},
        Journal = {The Journal of Physical Chemistry B},
        Number = {34},
        Pages = {6566-6572},
        Title = {Structure and Thermodynamics of Self-Assembled Monolayers on Gold Nanocrystallites},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp981745i},
        Volume = {102},
        Year = {1998},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp981745i},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp981745i}}

@article{hase:2010,
        Abstract = {Model non-equilibrium molecular dynamics (MD) simulations are presented of heat transfer from a hot Au {111} substrate to an alkylthiolate self-assembled monolayer (H-SAM) to assist in obtaining an atomic-level understanding of experiments by Wang et al. (Z. Wang{,} J. A. Carter{,} A. Lagutchev{,} Y. K. Koh{,} N.-H. Seong{,} D. G. Cahill{,} and D. D. Dlott{,} Science{,} 2007{,} 317{,} 787). Different models are considered to determine how they affect the heat transfer dynamics. They include temperature equilibrated (TE) and temperature gradient (TG) thermostat models for the Au(s) surface{,} and soft and stiff S/Au(s) models for bonding of the S-atoms to the Au(s) surface. A detailed analysis of the non-equilibrium heat transfer at the heterogeneous interface is presented. There is a short time temperature gradient within the top layers of the Au(s) surface. The S-atoms heat rapidly{,} much faster than do the C-atoms in the alkylthiolate chains. A high thermal conductivity in the H-SAM{,} perpendicular to the interface{,} results in nearly identical temperatures for the CH2 and CH3 groups versus time. Thermal-induced disorder is analyzed for the Au(s) substrate{,} the S/Au(s) interface and the H-SAM. Before heat transfer occurs from the hot Au(s) substrate to the H-SAM{,} there is disorder at the S/Au(s) interface and within the alkylthiolate chains arising from heat-induced disorder near the surface of hot Au(s). The short-time rapid heating of the S-atoms enhances this disorder. The increasing disorder of H-SAM chains with time results from both disorder at the Au/S interface and heat transfer to the H-SAM chains.},
        Author = {Zhang, Yue and Barnes, George L. and Yan, Tianying and Hase, William L.},
        Date-Added = {2011-07-11 16:02:11 -0400},
        Date-Modified = {2011-07-11 16:06:39 -0400},
        Doi = {10.1039/B923858C},
        Issue = {17},
        Journal = {Phys. Chem. Chem. Phys.},
        Pages = {4435-4445},
        Publisher = {The Royal Society of Chemistry},
        Title = {Model non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer},
        Url = {http://dx.doi.org/10.1039/B923858C},
        Volume = {12},
        Year = {2010},
        Bdsk-Url-1 = {http://dx.doi.org/10.1039/B923858C}}

@article{jiang:2002,
        Abstract = { A review is presented of this group's recent molecular simulation studies of self-assembled monolayers (SAMs) of alkanethiols on Au(111) surfaces. SAMs are very useful for the systematic alteration of the chemical and structural properties of a surface by varying chain length, tail group and composition. The scientific and technological importance of SAMs cannot be overestimated. The present work has been centred on studies of atomic scale surface properties of SAMs. First, configurational-bias Monte Carlo simulations were performed in both semigrand canonical and canonical ensembles to investigate the preferential adsorption and phase behaviour of mixed SAMs on Au(111) surfaces. Second, a novel hybrid molecular simulation technique was developed to simulate atomic force microscopy (AFM) over experimental timescales. The method combines a dynamic element model for the tip-cantilever system in AFM and a molecular dynamics relaxation approach for the sample. The hybrid simulation technique was applied to investigate atomic scale friction and adhesion properties of SAMs as a function of chain length. Third, dual-control-volume grand canonical molecular dynamics (DCV-GCMD) simulations were performed of transport diffusion of liquid water and methanol through a slit pore with both inner walls consisting of Au(111) surfaces covered by SAMs under a chemical potential gradient. Surface hydrophobicity was adjusted by varying the terminal group of CH3 (hydrophobic) or OH (hydrophilic) of the SAMs. Finally, ab initio quantum chemical calculations were performed on both clusters and periodic systems of methylthiols on Au(111) surfaces. Based on the ab initio results, an accurate force field capable of predicting c(4×2) superlattice structures over a wide range of temepratures for alkanethiols on Au(111) was developed. The extension of current work is discussed briefly. },
        Author = {JIANG, SHAOYI},
        Date-Added = {2011-07-08 17:51:59 -0400},
        Date-Modified = {2011-07-11 16:11:38 -0400},
        Doi = {10.1080/00268970210130948},
        Eprint = {http://www.tandfonline.com/doi/pdf/10.1080/00268970210130948},
        Journal = {Molecular Physics},
        Number = {14},
        Pages = {2261-2275},
        Title = {Molecular simulation studies of self-assembled monolayers of alkanethiols on Au(111)},
        Url = {http://www.tandfonline.com/doi/abs/10.1080/00268970210130948},
        Volume = {100},
        Year = {2002},
        Bdsk-Url-1 = {http://www.tandfonline.com/doi/abs/10.1080/00268970210130948},
        Bdsk-Url-2 = {http://dx.doi.org/10.1080/00268970210130948}}

@article{doi:10.1021/la904855s,
        Author = {Alper, Joshua and Hamad-Schifferli, Kimberly},
        Date-Added = {2011-07-08 17:18:53 -0400},
        Date-Modified = {2011-07-08 17:18:53 -0400},
        Doi = {10.1021/la904855s},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/la904855s},
        Journal = {Langmuir},
        Note = {PMID: 20166728},
        Number = {6},
        Pages = {3786-3789},
        Title = {Effect of Ligands on Thermal Dissipation from Gold Nanorods},
        Url = {http://pubs.acs.org/doi/abs/10.1021/la904855s},
        Volume = {26},
        Year = {2010},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/la904855s},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/la904855s}}

@article{doi:10.1021/jp8051888,
        Abstract = { Thermal transport between CTAB passivated gold nanorods and solvent is studied by an optical pump−probe technique. Increasing the free CTAB concentration from 1 mM to 10 mM causes a ∼3× increase in the CTAB layer's effective thermal interface conductance and a corresponding shift in the longitudinal surface plasmon resonance. The transition occurs near the CTAB critical micelle concentration, revealing the importance of the role of free ligand on thermal transport. },
        Author = {Schmidt, Aaron J. and Alper, Joshua D. and Chiesa, Matteo and Chen, Gang and Das, Sarit K. and Hamad-Schifferli, Kimberly},
        Date-Added = {2011-07-08 17:04:34 -0400},
        Date-Modified = {2011-07-08 17:04:34 -0400},
        Doi = {10.1021/jp8051888},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp8051888},
        Journal = {The Journal of Physical Chemistry C},
        Number = {35},
        Pages = {13320-13323},
        Title = {Probing the Gold Nanorod−Ligand−Solvent Interface by Plasmonic Absorption and Thermal Decay},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp8051888},
        Volume = {112},
        Year = {2008},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp8051888},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp8051888}}

@article{PhysRevB.80.195406,
        Author = {Juv\'e, Vincent and Scardamaglia, Mattia and Maioli, Paolo and Crut, Aur\'elien and Merabia, Samy and Joly, Laurent and Del Fatti, Natalia and Vall\'ee, Fabrice},
        Date-Added = {2011-07-08 16:36:39 -0400},
        Date-Modified = {2011-07-08 16:36:39 -0400},
        Doi = {10.1103/PhysRevB.80.195406},
        Journal = {Phys. Rev. B},
        Month = {Nov},
        Number = {19},
        Numpages = {6},
        Pages = {195406},
        Publisher = {American Physical Society},
        Title = {Cooling dynamics and thermal interface resistance of glass-embedded metal nanoparticles},
        Volume = {80},
        Year = {2009},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.80.195406}}

@article{Wang10082007,
        Abstract = {At the level of individual molecules, familiar concepts of heat transport no longer apply. When large amounts of heat are transported through a molecule, a crucial process in molecular electronic devices, energy is carried by discrete molecular vibrational excitations. We studied heat transport through self-assembled monolayers of long-chain hydrocarbon molecules anchored to a gold substrate by ultrafast heating of the gold with a femtosecond laser pulse. When the heat reached the methyl groups at the chain ends, a nonlinear coherent vibrational spectroscopy technique detected the resulting thermally induced disorder. The flow of heat into the chains was limited by the interface conductance. The leading edge of the heat burst traveled ballistically along the chains at a velocity of 1 kilometer per second. The molecular conductance per chain was 50 picowatts per kelvin.},
        Author = {Wang, Zhaohui and Carter, Jeffrey A. and Lagutchev, Alexei and Koh, Yee Kan and Seong, Nak-Hyun and Cahill, David G. and Dlott, Dana D.},
        Date-Added = {2011-07-08 16:20:05 -0400},
        Date-Modified = {2011-07-08 16:20:05 -0400},
        Doi = {10.1126/science.1145220},
        Eprint = {http://www.sciencemag.org/content/317/5839/787.full.pdf},
        Journal = {Science},
        Number = {5839},
        Pages = {787-790},
        Title = {Ultrafast Flash Thermal Conductance of Molecular Chains},
        Url = {http://www.sciencemag.org/content/317/5839/787.abstract},
        Volume = {317},
        Year = {2007},
        Bdsk-Url-1 = {http://www.sciencemag.org/content/317/5839/787.abstract},
        Bdsk-Url-2 = {http://dx.doi.org/10.1126/science.1145220}}

@article{hase:2011,
        Abstract = { In a previous article (Phys. Chem. Chem. Phys.2010, 12, 4435), nonequilibrium molecular dynamics (MD) simulations of heat transfer from a hot Au{111} substrate to an alkylthiolate self-assembled monolayer (H-SAM) were presented. The simulations were performed for an H-SAM chain length of eight carbon atoms, and a qualitative agreement with the experiments of Wang et al. (Science2007, 317, 787) was found. Here, simulation results are presented for heat transfer to H-SAM surfaces with carbon chain lengths of 10--20 carbon atoms. Relaxation times for heat transfer are extracted, compared with experiment, and a qualitative agreement is obtained. The same relaxation time is found from either the temperature of the H-SAM or the orientational disorder of the H-SAM versus time. For a simulation model with the Au substrate thermally equilibrated, the relaxation times determined from the simulations are approximately a factor of 4 larger than the experimental values. },
        Author = {Manikandan, Paranjothy and Carter, Jeffrey A. and Dlott, Dana D. and Hase, William L.},
        Date-Added = {2011-07-08 13:36:39 -0400},
        Date-Modified = {2011-07-11 16:07:01 -0400},
        Doi = {10.1021/jp200672e},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp200672e},
        Journal = {The Journal of Physical Chemistry C},
        Number = {19},
        Pages = {9622-9628},
        Title = {Effect of Carbon Chain Length on the Dynamics of Heat Transfer at a Gold/Hydrocarbon Interface: Comparison of Simulation with Experiment},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp200672e},
        Volume = {115},
        Year = {2011},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp200672e},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp200672e}}

@article{doi:10.1021/ja00051a040,
        Author = {Rappe, A. K. and Casewit, C. J. and Colwell, K. S. and Goddard, W. A. and Skiff, W. M.},
        Date-Added = {2011-06-29 14:04:33 -0400},
        Date-Modified = {2011-06-29 14:04:33 -0400},
        Doi = {10.1021/ja00051a040},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/ja00051a040},
        Journal = {Journal of the American Chemical Society},
        Number = {25},
        Pages = {10024-10035},
        Title = {UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations},
        Url = {http://pubs.acs.org/doi/abs/10.1021/ja00051a040},
        Volume = {114},
        Year = {1992},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/ja00051a040},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/ja00051a040}}

@article{doi:10.1021/jp034405s,
        Abstract = { We use the universal force field (UFF) developed by Rapp{\'e} et al. (Rapp{\'e}, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M. J. Am. Chem. Soc. 1992, 114, 10024) and the specific classical potentials developed from ab initio calculations for Au−benzenedithiol (BDT) molecule interaction to perform molecular dynamics (MD) simulations of a BDT monolayer on an extended Au(111) surface. The simulation system consists of 100 BDT molecules and three rigid Au layers in a simulation box that is rhombic in the plane of the Au surface. A multiple time scale algorithm, the double-reversible reference system propagator algorithm (double RESPA) based on the Nos{\'e}−Hoover dynamics scheme, and the Ewald summation with a boundary correction term for the treatment of long-range electrostatic interactions in a 2-D slab have been incorporated into the simulation technique. We investigate the local bonding properties of Au−BDT contacts and molecular orientation distributions of BDT molecules. These results show that whereas different basis sets from ab initio calculations may generate different local bonding geometric parameters (the bond length, etc.) the packing structures of BDT molecules maintain approximately the same well-ordered herringbone structure with small peak differences in the probability distributions of global geometric parameters. The methodology developed here opens an avenue for classical simulations of a metal−molecule−metal complex in molecular electronics devices. },
        Author = {Leng and Keffer, David J. and Cummings, Peter T.},
        Date-Added = {2011-04-28 11:23:28 -0400},
        Date-Modified = {2011-04-28 11:23:28 -0400},
        Doi = {10.1021/jp034405s},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp034405s},
        Journal = {The Journal of Physical Chemistry B},
        Number = {43},
        Pages = {11940-11950},
        Title = {Structure and Dynamics of a Benzenedithiol Monolayer on a Au(111) Surface},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp034405s},
        Volume = {107},
        Year = {2003},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp034405s},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp034405s}}

@article{OPLSAA,
        Abstract = {null},
        Annote = {doi: 10.1021/ja9621760},
        Author = {Jorgensen, William L. and Maxwell, David S. and Tirado-Rives, Julian},
        Date = {1996/01/01},
        Date-Added = {2011-02-04 18:54:58 -0500},
        Date-Modified = {2011-02-04 18:54:58 -0500},
        Do = {10.1021/ja9621760},
        Isbn = {0002-7863},
        Journal = {Journal of the American Chemical Society},
        M3 = {doi: 10.1021/ja9621760},
        Month = {01},
        Number = {45},
        Pages = {11225--11236},
        Publisher = {American Chemical Society},
        Title = {Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids},
        Ty = {JOUR},
        Url = {http://dx.doi.org/10.1021/ja9621760},
        Volume = {118},
        Year = {1996},
        Year1 = {1996/01/01},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/ja9621760}}

@article{TraPPE-UA.alkylbenzenes,
        Author = {Wick, Collin D. and Martin, Marcus G. and Siepmann, J. Ilja},
        Date-Added = {2011-02-04 18:31:46 -0500},
        Date-Modified = {2011-02-04 18:32:22 -0500},
        Doi = {10.1021/jp001044x},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp001044x},
        Journal = {The Journal of Physical Chemistry 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 = {2011-02-04 18:01:31 -0500},
        Date-Modified = {2011-02-04 18:02:19 -0500},
        Doi = {10.1021/jp972543+},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp972543%2B},
        Journal = {The Journal of Physical Chemistry 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+}}

@article{TraPPE-UA.thiols,
        Author = {Lubna, Nusrat and Kamath, Ganesh and Potoff, Jeffrey J. and Rai, Neeraj and Siepmann, J. Ilja},
        Date-Added = {2011-02-04 17:51:03 -0500},
        Date-Modified = {2011-02-04 17:54:20 -0500},
        Doi = {10.1021/jp0549125},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp0549125},
        Journal = {The Journal of Physical Chemistry 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{vlugt:cpc2007154,
        Author = {Philipp Schapotschnikow and Ren{\'e} Pool and Thijs J.H. Vlugt},
        Date-Added = {2011-02-01 16:00:11 -0500},
        Date-Modified = {2011-02-04 18:21:59 -0500},
        Doi = {DOI: 10.1016/j.cpc.2007.02.028},
        Issn = {0010-4655},
        Journal = {Computer Physics Communications},
        Keywords = {Gold nanocrystals},
        Note = {Proceedings of the Conference on Computational Physics 2006 - CCP 2006, Conference on Computational Physics 2006},
        Number = {1-2},
        Pages = {154 - 157},
        Title = {Selective adsorption of alkyl thiols on gold in different geometries},
        Url = {http://www.sciencedirect.com/science/article/B6TJ5-4N3WYP0-1/2/66dbe8892f456c230b9b8fcd9c23f456},
        Volume = {177},
        Year = {2007},
        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TJ5-4N3WYP0-1/2/66dbe8892f456c230b9b8fcd9c23f456},
        Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.cpc.2007.02.028}}

@article{packmol,
        Author = {L. Mart\'{\i}nez and R. Andrade and Ernesto G. Birgin and Jos{\'e} Mario Mart\'{\i}nez},
        Bibsource = {DBLP, http://dblp.uni-trier.de},
        Date-Added = {2011-02-01 15:13:02 -0500},
        Date-Modified = {2011-02-01 15:14:25 -0500},
        Ee = {http://dx.doi.org/10.1002/jcc.21224},
        Journal = {Journal of Computational Chemistry},
        Number = {13},
        Pages = {2157-2164},
        Title = {PACKMOL: A package for building initial configurations for molecular dynamics simulations},
        Volume = {30},
        Year = {2009}}

@article{kuang:164101,
        Author = {Shenyu Kuang and J. Daniel Gezelter},
        Date-Added = {2011-01-31 17:12:35 -0500},
        Date-Modified = {2011-01-31 17:12:35 -0500},
        Doi = {10.1063/1.3499947},
        Eid = {164101},
        Journal = {The Journal of Chemical Physics},
        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}}

@article{muller:014102,
        Author = {Thomas J. Muller and Michael Al-Samman and Florian Muller-Plathe},
        Date-Added = {2010-09-16 19:19:25 -0400},
        Date-Modified = {2010-09-16 19:19:25 -0400},
        Doi = {10.1063/1.2943312},
        Eid = {014102},
        Journal = {The Journal of Chemical Physics},
        Keywords = {intramolecular mechanics; Lennard-Jones potential; molecular dynamics method; thermostats; viscosity},
        Number = {1},
        Numpages = {8},
        Pages = {014102},
        Publisher = {AIP},
        Title = {The influence of thermostats and manostats on reverse nonequilibrium molecular dynamics calculations of fluid viscosities},
        Url = {http://link.aip.org/link/?JCP/129/014102/1},
        Volume = {129},
        Year = {2008},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/129/014102/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2943312}}

@article{wolf:8254,
        Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
        Date-Added = {2010-09-16 19:01:51 -0400},
        Date-Modified = {2010-09-16 19:01:51 -0400},
        Doi = {10.1063/1.478738},
        Journal = {J. Chem. Phys.},
        Keywords = {POTENTIAL ENERGY; COULOMB FIELD; COULOMB ENERGY; LATTICE PARAMETERS; potential energy functions; lattice dynamics; lattice energy},
        Number = {17},
        Pages = {8254-8282},
        Publisher = {AIP},
        Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r[sup -1] summation},
        Url = {http://link.aip.org/link/?JCP/110/8254/1},
        Volume = {110},
        Year = {1999},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/110/8254/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.478738}}

@article{HeX:1993,
        Abstract = {A recently developed non-equilibrium molecular dynamics algorithm for
   heat conduction is used to compute the thermal conductivity, thermal
   diffusion factor, and heat of transfer in binary Lennard-Jones
   mixtures. An internal energy flux is established with local source and
   sink terms for kinetic energy.
   Simulations of isotope mixtures covering a range of densities and mass
   ratios show that the lighter component prefers the hot side of the
   system at stationary state. This implies a positive thermal diffusion
   factor in the definition we have adopted here. The molecular basis for
   the Soret effect is studied by analysing the energy flux through the
   system. In all cases we found that there is a difference in the
   relative contributions when we compare the hot and cold sides of the
   system. The contribution from the lighter component is predominantly
   flux of kinetic energy, and this contribution increases from the cold
   to the hot side. The contribution from the heavier component is
   predominantly energy transfer through molecular interactions, and it
   increases from the hot to the cold side. This explains why the thermal
   diffusion factor is positive; heal is conducted more effectively
   through the system if the lighter component is enriched at the hot
   side. Even for very large heat fluxes, we find a linear or almost
   linear temperature profile through the system, and a constant thermal
   conductivity. The entropy production per unit volume and unit time
   increases from the hot to the cold side.},
        Author = {Hafskjold, B and Ikeshoji, T and Ratkje, SK},
        Date-Added = {2010-09-15 16:52:45 -0400},
        Date-Modified = {2010-09-15 16:54:23 -0400},
        Issn = {{0026-8976}},
        Journal = {Mol. Phys.},
        Month = {DEC},
        Number = {6},
        Pages = {1389-1412},
        Title = {ON THE MOLECULAR MECHANISM OF THERMAL-DIFFUSION IN LIQUIDS},
        Unique-Id = {ISI:A1993MQ34500009},
        Volume = {80},
        Year = {1993}}

@article{HeX:1994,
        Abstract = {This paper presents a new algorithm for non-equilibrium molecular
   dynamics, where a temperature gradient is established in a system with
   periodic boundary conditions. At each time step in the simulation, a
   fixed amount of energy is supplied to a hot region by scaling the
   velocity of each particle in it, subject to conservation of total
   momentum. An equal amount of energy is likewise withdrawn from a cold
   region at each time step. Between the hot and cold regions is a region
   through which an energy flux is established. Two configurations of hot
   and cold regions are proposed. Using a stacked layer structure, the
   instantaneous local energy flux for a 128-particle Lennard-Jones system
   in liquid was found to be in good agreement with the macroscopic theory
   of heat conduction at stationary state, except in and near the hot and
   cold regions. Thermal conductivity calculated for the 128-particle
   system was about 10\% smaller than the literature value obtained by
   molecular dynamics calculations. One run with a 1024-particle system
   showed an agreement with the literature value within statistical error
   (1-2\%). Using a unit cell with a cold spherical region at the centre
   and a hot region in the perimeter of the cube, an initial gaseous state
   of argon was separated into gas and liquid phases. Energy fluxes due to
   intermolecular energy transfer and transport of kinetic energy dominate
   in the liquid and gas phases, respectively.},
        Author = {Ikeshoji, T and Hafskjold, B},
        Date-Added = {2010-09-15 16:52:45 -0400},
        Date-Modified = {2010-09-15 16:54:37 -0400},
        Issn = {0026-8976},
        Journal = {Mol. Phys.},
        Month = {FEB},
        Number = {2},
        Pages = {251-261},
        Title = {NONEQUILIBRIUM MOLECULAR-DYNAMICS CALCULATION OF HEAT-CONDUCTION IN LIQUID AND THROUGH LIQUID-GAS INTERFACE},
        Unique-Id = {ISI:A1994MY17400001},
        Volume = {81},
        Year = {1994}}

@article{plech:195423,
        Author = {A. Plech and V. Kotaidis and S. Gresillon and C. Dahmen and G. von Plessen},
        Date-Added = {2010-08-12 11:34:55 -0400},
        Date-Modified = {2010-08-12 11:34:55 -0400},
        Eid = {195423},
        Journal = {Phys. Rev. B},
        Keywords = {gold; laser materials processing; melting; nanoparticles; time resolved spectra; X-ray scattering; lattice dynamics; high-speed optical techniques; cooling; thermal resistance; thermal conductivity; long-range order},
        Local-Url = {file://localhost/Users/charles/Documents/Papers/PhysRevB_70_195423.pdf},
        Number = {19},
        Numpages = {7},
        Pages = {195423},
        Publisher = {APS},
        Title = {Laser-induced heating and melting of gold nanoparticles studied by time-resolved x-ray scattering},
        Url = {http://link.aps.org/abstract/PRB/v70/e195423},
        Volume = {70},
        Year = {2004},
        Bdsk-Url-1 = {http://link.aps.org/abstract/PRB/v70/e195423}}

@article{Wilson:2002uq,
        Abstract = {We investigate suspensions of 3-10 nm diameter Au, Pt, and AuPd nanoparticles as probes of thermal transport in fluids and determine approximate values for the thermal conductance G of the particle/fluid interfaces. Subpicosecond lambda=770 nm optical pulses from a Ti:sapphire mode-locked laser are used to heat the particles and interrogate the decay of their temperature through time-resolved changes in optical absorption. The thermal decay of alkanethiol-terminated Au nanoparticles in toluene is partially obscured by other effects; we set a lower limit G>20 MW m(-2)K(-1). The thermal decay of citrate-stabilized Pt nanoparticles in water gives Gapproximate to130 MW m(-2) K-1. AuPd alloy nanoparticles in toluene and stabilized by alkanethiol termination give Gapproximate to5 MW m(-2) K-1. The measured G are within a factor of 2 of theoretical estimates based on the diffuse-mismatch model.},
        Author = {Wilson, OM and Hu, XY and Cahill, DG and Braun, PV},
        Date-Added = {2010-08-12 11:31:02 -0400},
        Date-Modified = {2010-08-12 11:31:02 -0400},
        Doi = {ARTN 224301},
        Journal = {Phys. Rev. B},
        Local-Url = {file://localhost/Users/charles/Documents/Papers/e2243010.pdf},
        Title = {Colloidal metal particles as probes of nanoscale thermal transport in fluids},
        Volume = {66},
        Year = {2002},
        Bdsk-Url-1 = {http://dx.doi.org/224301}}

@article{RevModPhys.61.605,
        Author = {Swartz, E. T. and Pohl, R. O.},
        Date-Added = {2010-08-06 17:03:01 -0400},
        Date-Modified = {2010-08-06 17:03:01 -0400},
        Doi = {10.1103/RevModPhys.61.605},
        Journal = {Rev. Mod. Phys.},
        Month = {Jul},
        Number = {3},
        Numpages = {63},
        Pages = {605--668},
        Publisher = {American Physical Society},
        Title = {Thermal boundary resistance},
        Volume = {61},
        Year = {1989},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/RevModPhys.61.605}}

@article{cahill:793,
        Author = {David G. Cahill and Wayne K. Ford and Kenneth E. Goodson and Gerald D. Mahan and Arun Majumdar and Humphrey J. Maris and Roberto Merlin and Simon R. Phillpot},
        Date-Added = {2010-08-06 17:02:22 -0400},
        Date-Modified = {2010-08-06 17:02:22 -0400},
        Doi = {10.1063/1.1524305},
        Journal = {J. Applied Phys.},
        Keywords = {nanostructured materials; reviews; thermal conductivity; interface phenomena; molecular dynamics method; thermal management (packaging); Boltzmann equation; carbon nanotubes; porosity; semiconductor superlattices; thermoreflectance; interface phonons; thermoelectricity; phonon-phonon interactions},
        Number = {2},
        Pages = {793-818},
        Publisher = {AIP},
        Title = {Nanoscale thermal transport},
        Url = {http://link.aip.org/link/?JAP/93/793/1},
        Volume = {93},
        Year = {2003},
        Bdsk-Url-1 = {http://link.aip.org/link/?JAP/93/793/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1524305}}

@inbook{Hoffman:2001sf,
        Address = {New York},
        Annote = {LDR    01107cam  2200253 a 4500
001    12358442
005    20070910074423.0
008    010326s2001    nyua     b    001 0 eng  
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925 0  $aacquire$b2 shelf copies$xpolicy default
955    $ato ASCD pc23 03-26-01; jp20 03-27-01 to subj; jp99 to SL 03-27-01; jp85 to Dewey 03-27-01; aa01 03-28-01$aps02 2001-10-04 bk rec'd, to CIP ver.;$fpv04 2001-10-31 CIP ver to BCCD$ajp01 2001-12-06 c. 2 to BCCD
010    $a  2001028633
020    $a0824704436 (acid-free paper)
040    $aDLC$cDLC$dDLC
050 00 $aQA297$b.H588 2001
082 00 $a519.4$221
100 1  $aHoffman, Joe D.,$d1934-
245 10 $aNumerical methods for engineers and scientists /$cJoe D. Hoffman.
250    $a2nd ed., rev. and expanded.
260    $aNew York :$bMarcel Dekker,$cc2001.
300    $axi, 823 p. :$bill. ;$c26 cm.
504    $aIncludes bibliographical references (p. 775-777) and index.
650  0 $aNumerical analysis.
856 42 $3Publisher description$uhttp://www.loc.gov/catdir/enhancements/fy0743/2001028633-d.html
},
        Author = {Hoffman, Joe D.},
        Call-Number = {QA297},
        Date-Added = {2010-07-15 16:32:02 -0400},
        Date-Modified = {2010-07-19 16:49:37 -0400},
        Dewey-Call-Number = {519.4},
        Edition = {2nd ed., rev. and expanded},
        Genre = {Numerical analysis},
        Isbn = {0824704436 (acid-free paper)},
        Library-Id = {2001028633},
        Pages = {157},
        Publisher = {Marcel Dekker},
        Title = {Numerical methods for engineers and scientists},
        Url = {http://www.loc.gov/catdir/enhancements/fy0743/2001028633-d.html},
        Year = {2001},
        Bdsk-Url-1 = {http://www.loc.gov/catdir/enhancements/fy0743/2001028633-d.html}}

@article{Vardeman:2008fk,
        Abstract = {Using molecular dynamics simulations, we have simulated the rapid cooling experienced by bimetallic nanoparticles following laser excitation at the plasmon resonance and find evidence that glassy beads, specifically Ag-Cu bimetallic particles at the eutectic composition (60\% Ag, 40\% Cu), can be formed during these experiments. The bimetallic nanoparticles are embedded in an implicit solvent with a viscosity tuned to yield cooling curves that match the experimental cooling behavior as closely as possible. Because the nanoparticles have a large surface-to-volume ratio, experimentally realistic cooling rates are accessible via relatively short simulations. The presence of glassy structural features was verified using bond orientational order parameters that are sensitive to the formation of local icosahedral ordering in condensed phases. As the particles cool from the liquid droplet state into glassy beads, a silver-rich monolayer develops on the outer surface and local icosahedra can develop around the silver atoms in this monolayer. However, we observe a strong preference for the local icosahedral ordering around the copper atoms in the particles. As the particles cool, these local icosahedral structures grow to include a larger fraction of the atoms in the nanoparticle, eventually leading to a glassy nanosphere.},
        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
        Author = {{Vardeman II}, Charles F. and Gezelter, J. Daniel},
        Date-Added = {2010-07-13 11:48:22 -0400},
        Date-Modified = {2010-07-19 16:20:01 -0400},
        Doi = {DOI 10.1021/jp710063g},
        Isi = {000253512400021},
        Isi-Recid = {160903603},
        Isi-Ref-Recids = {144152922 81445483 98913099 146167982 55512304 50985260 52031423 29272311 151055545 134895634 130292830 101988637 100757730 98524559 123952006 6025131 59492217 2078548 135495737 136941603 90709964 160903604 130558416 113800688 30137926 117888234 63632785 38926953 158293976 135246439 125693419 125789026 155583142 156430464 65888620 130160487 97576420 109490154 150229560 116057234 134425927 142869781 121706070 89390336 119150946 143383743 64066027 171282998 142688207 51429664 84591083 127696312 58160909 155366996 155654757 137551818 128633299 109033408 120457571 171282999 124947095 126857514 49630702 64115284 84689627 71842426 96309965 79034659 92658330 146168029 119238036 144824430 132319357 160903607 171283000 100274448},
        Journal = {J. Phys. Chem. C},
        Month = mar,
        Number = {9},
        Pages = {3283-3293},
        Publisher = {AMER CHEMICAL SOC},
        Times-Cited = {0},
        Title = {Simulations of laser-induced glass formation in Ag-Cu nanoparticles},
        Volume = {112},
        Year = {2008},
        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000253512400021}}

@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 = {2010-07-13 11:44:08 -0400},
        Date-Modified = {2010-07-13 11:44:08 -0400},
        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{Medasani:2007uq,
        Abstract = {We employ first-principles and empirical computational methods to study the surface energy and surface stress of silver nanoparticles. The structures, cohesive energies, and lattice contractions of spherical Ag nanoclusters in the size range 0.5-5.5 nm are analyzed using two different theoretical approaches: an ab initio density functional pseudopotential technique combined with the generalized gradient approximation and the embedded atom method. The surface energies and stresses obtained via the embedded atom method are found to be in good agreement with those predicted by the gradient-corrected ab initio density functional formalism. We estimate the surface energy of Ag nanoclusters to be in the range of 1.0-2.2 J/m(2). Our values are close to the bulk surface energy of silver, but are significantly lower than the recently reported value of 7.2 J/m(2) for free Ag nanoparticles derived from the Kelvin equation.},
        Author = {Medasani, Bharat and Park, Young Ho and Vasiliev, Igor},
        Date-Added = {2010-07-13 11:43:15 -0400},
        Date-Modified = {2010-07-13 11:43:15 -0400},
        Doi = {ARTN 235436},
        Journal = {Phys. Rev. B},
        Local-Url = {file://localhost/Users/charles/Documents/Papers/PhysRevB_75_235436.pdf},
        Title = {Theoretical study of the surface energy, stress, and lattice contraction of silver nanoparticles},
        Volume = {75},
        Year = {2007},
        Bdsk-Url-1 = {http://dx.doi.org/235436}}

@article{Wang:2005qy,
        Abstract = {The surface structures of cubo-octahedral Pt-Mo nanoparticles have been investigated using the Monte Carlo method and modified embedded atom method potentials that we developed for Pt-Mo alloys. The cubo-octahedral Pt-Mo nanoparticles are constructed with disordered fcc configurations, with sizes from 2.5 to 5.0 nm, and with Pt concentrations from 60 to 90 atom \%. The equilibrium Pt-Mo nanoparticle configurations were generated through Monte Carlo simulations allowing both atomic displacements and element exchanges at 600 K. We predict that the Pt atoms weakly segregate to the surfaces of such nanoparticles. The Pt concentrations in the surface are calculated to be 5-14 atom \% higher than the Pt concentrations of the nanoparticles. Moreover, the Pt atoms preferentially segregate to the facet sites of the surface, while the Pt and Mo atoms tend to alternate along the edges and vertexes of these nanoparticles. We found that decreasing the size or increasing the Pt concentration leads to higher Pt concentrations but fewer Pt-Mo pairs in the Pt-Mo nanoparticle surfaces.},
        Author = {Wang, GF and Van Hove, MA and Ross, PN and Baskes, MI},
        Date-Added = {2010-07-13 11:42:50 -0400},
        Date-Modified = {2010-07-13 11:42:50 -0400},
        Doi = {DOI 10.1021/jp050116n},
        Journal = {J. Phys. Chem. B},
        Pages = {11683-11692},
        Title = {Surface structures of cubo-octahedral Pt-Mo catalyst nanoparticles from Monte Carlo simulations},
        Volume = {109},
        Year = {2005},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp050116n}}

@article{Chui:2003fk,
        Abstract = {Molecular dynamics simulations of a platinum nanocluster consisting 250 atoms were performed at different temperatures between 70 K and 298 K. The semi-empirical, many-body Sutton-Chen (SC) potential was used to model the interatomic interaction in the metallic system. Regions of core or bulk-like atoms and surface atoms can be defined from analyses of structures, atomic coordination, and the local density function of atoms as defined in the SC potential. The core atoms in the nanoparticle behave as bulk-like metal atoms with a predominant face centered cubic (fcc) packing. The interface between surface atoms and core atoms is marked by a peak in the local density function and corresponds to near surface atoms. The near surface atoms and surface atoms prefer a hexagonal closed packing (hcp). The temperature and size effects on structures of the nanoparticle and the dynamics of the surface region and the core region are discussed.},
        Author = {Chui, YH and Chan, KY},
        Date-Added = {2010-07-13 11:42:32 -0400},
        Date-Modified = {2010-07-13 11:42:32 -0400},
        Doi = {DOI 10.1039/b302122j},
        Journal = {Phys. Chem. Chem. Phys.},
        Pages = {2869-2874},
        Title = {Analyses of surface and core atoms in a platinum nanoparticle},
        Volume = {5},
        Year = {2003},
        Bdsk-Url-1 = {http://dx.doi.org/10.1039/b302122j}}

@article{Sankaranarayanan:2005lr,
        Abstract = {Bimetallic nanoclusters are of interest because of their utility in catalysis and sensors, The thermal characteristics of bimetallic Pt-Pd nanoclusters of different sizes and compositions were investigated through molecular dynamics simulations using quantum Sutton-Chen (QSC) many-body potentials, Monte Carlo simulations employing the bond order simulation model were used to generate minimum energy configurations, which were utilized as the starting point for molecular dynamics simulations. The calculated initial configurations of the Pt-Pd system consisted of surface segregated Pd atoms and a Pt-rich core, Melting characteristics were studied by following the changes in potential energy and heat capacity as functions of temperature, Structural changes accompanying the thermal evolution were studied by the bond order parameter method. The Pt-Pd clusters exhibited a two-stage melting: surface melting of the external Pd atoms followed by homogeneous melting of the Pt core. These transitions were found to depend on the composition and size of the nanocluster. Melting temperatures of the nanoclusters were found to be much lower than those of bulk Pt and Pd. Bulk melting temperatures of Pd and Pt simulated using periodic boundary conditions compare well with experimental values, thus providing justification for the use of QSC potentials in these simulations. Deformation parameters were calculated to characterize the structural evolution resulting from diffusion of Pd and Pt atoms, The results indicate that in Pd-Pt clusters, Pd atoms prefer to remain at the surface even after melting. In addition, Pt also tends to diffuse to the surface after melting due to reduction of its surface energy with temperature. This mixing pattern is different from those reported in some of the earlier Studies on melting of bimetallics.},
        Author = {Sankaranarayanan, SKRS and Bhethanabotla, VR and Joseph, B},
        Date-Added = {2010-07-13 11:42:13 -0400},
        Date-Modified = {2010-07-13 11:42:13 -0400},
        Doi = {ARTN 195415},
        Journal = {Phys. Rev. B},
        Title = {Molecular dynamics simulation study of the melting of Pd-Pt nanoclusters},
        Volume = {71},
        Year = {2005},
        Bdsk-Url-1 = {http://dx.doi.org/195415}}

@article{Vardeman-II:2001jn,
        Author = {C.~F. {Vardeman II} and J.~D. Gezelter},
        Date-Added = {2010-07-13 11:41:50 -0400},
        Date-Modified = {2010-07-13 11:41:50 -0400},
        Journal = {J. Phys. Chem. A},
        Local-Url = {file://localhost/Users/charles/Documents/Papers/Vardeman%20II/2001.pdf},
        Number = {12},
        Pages = {2568},
        Title = {Comparing models for diffusion in supercooled liquids: The eutectic composition of the {A}g-{C}u alloy},
        Volume = {105},
        Year = {2001}}

@article{ShibataT._ja026764r,
        Author = {Shibata, T. and Bunker, B.A. and Zhang, Z. and Meisel, D. and Vardeman, C.F. and Gezelter, J.D.},
        Date-Added = {2010-07-13 11:41:36 -0400},
        Date-Modified = {2010-07-13 11:41:36 -0400},
        Journal = {J. Amer. Chem. Soc.},
        Local-Url = {file://localhost/Users/charles/Documents/Papers/ja026764r.pdf},
        Number = {40},
        Pages = {11989-11996},
        Title = {Size-Dependent Spontaneous Alloying of {A}u-{A}g Nanoparticles},
        Url = {http://dx.doi.org/10.1021/ja026764r},
        Volume = {124},
        Year = {2002},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/ja026764r}}

@article{Chen90,
        Author = {A.~P. Sutton and J. Chen},
        Date-Added = {2010-07-13 11:40:48 -0400},
        Date-Modified = {2010-07-13 11:40:48 -0400},
        Journal = {Phil. Mag. Lett.},
        Pages = {139-146},
        Title = {Long-Range Finnis Sinclair Potentials},
        Volume = 61,
        Year = {1990}}

@article{PhysRevB.33.7983,
        Author = {Foiles, S. M. and Baskes, M. I. and Daw, M. S.},
        Date-Added = {2010-07-13 11:40:28 -0400},
        Date-Modified = {2010-07-13 11:40:28 -0400},
        Doi = {10.1103/PhysRevB.33.7983},
        Journal = {Phys. Rev. B},
        Local-Url = {file://localhost/Users/charles/Documents/Papers/p7983_1.pdf},
        Month = {Jun},
        Number = {12},
        Numpages = {8},
        Pages = {7983-7991},
        Publisher = {American Physical Society},
        Title = {Embedded-atom-method functions for the fcc metals {C}u, {A}g, {A}u, {N}i, {P}d, {P}t, and their alloys},
        Volume = {33},
        Year = {1986},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.33.7983}}

@article{hoover85,
        Author = {W.~G. Hoover},
        Date-Added = {2010-07-13 11:24:30 -0400},
        Date-Modified = {2010-07-13 11:24:30 -0400},
        Journal = pra,
        Pages = 1695,
        Title = {Canonical dynamics: Equilibrium phase-space distributions},
        Volume = 31,
        Year = 1985}

@article{melchionna93,
        Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
        Date-Added = {2010-07-13 11:22:17 -0400},
        Date-Modified = {2010-07-13 11:22:17 -0400},
        Journal = {Mol. Phys.},
        Pages = {533-544},
        Title = {Hoover {\sc npt} dynamics for systems varying in shape and size},
        Volume = 78,
        Year = 1993}

@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 = {2010-07-13 11:16:00 -0400},
        Date-Modified = {2010-07-19 16:27:45 -0400},
        Howpublished = {Available at {\tt http://openmd.net}},
        Title = {{OpenMD, an open source engine for molecular dynamics}}}

@inbook{AshcroftMermin,
        Address = {Belmont, CA},
        Author = {Neil W. Ashcroft and N.~David Mermin},
        Date-Added = {2010-07-12 14:26:49 -0400},
        Date-Modified = {2010-07-22 13:37:20 -0400},
        Pages = {21},
        Publisher = {Brooks Cole},
        Title = {Solid State Physics},
        Year = {1976}}

@book{WagnerKruse,
        Address = {Berlin},
        Author = {W. Wagner and A. Kruse},
        Date-Added = {2010-07-12 14:10:29 -0400},
        Date-Modified = {2010-07-12 14:13:44 -0400},
        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{ISI:000266247600008,
        Abstract = {Temperature dependence of viscosity of butyl-3-methylimidazolium
   hexafluorophosphate is investigated by non-equilibrium molecular
   dynamics simulations with cosine-modulated force in the temperature
   range from 360 to 480K. It is shown that this method is able to
   correctly predict the shear viscosity. The simulation setting and
   choice of the force field are discussed in detail. The all-atom force
   field exhibits a bad convergence and the shear viscosity is
   overestimated, while the simple united atom model predicts the kinetics
   very well. The results are compared with the equilibrium molecular
   dynamics simulations. The relationship between the diffusion
   coefficient and viscosity is examined by means of the hydrodynamic
   radii calculated from the Stokes-Einstein equation and the solvation
   properties are discussed.},
        Address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND},
        Affiliation = {Kolafa, J (Reprint Author), Prague Inst Chem Technol, Dept Phys Chem, CR-16628 Prague, Czech Republic. {[}Picalek, Jan; Kolafa, Jiri] Prague Inst Chem Technol, Dept Phys Chem, CR-16628 Prague, Czech Republic.},
        Author = {Picalek, Jan and Kolafa, Jiri},
        Author-Email = {jiri.kolafa@vscht.cz},
        Date-Added = {2010-04-16 13:19:12 -0400},
        Date-Modified = {2010-04-16 13:19:12 -0400},
        Doc-Delivery-Number = {448FD},
        Doi = {10.1080/08927020802680703},
        Funding-Acknowledgement = {Czech Science Foundation {[}203/07/1006]; Czech Ministry of Education {[}LC512]},
        Funding-Text = {We gratefully acknowledge a support from the Czech Science Foundation (project 203/07/1006) and the computing facilities from the Czech Ministry of Education (Center for Biomolecules and Complex Molecular Systems, project LC512).},
        Issn = {0892-7022},
        Journal = {Mol. Simul.},
        Journal-Iso = {Mol. Simul.},
        Keywords = {room temperature ionic liquids; viscosity; non-equilibrium molecular dynamics; solvation; imidazolium},
        Keywords-Plus = {1-N-BUTYL-3-METHYLIMIDAZOLIUM HEXAFLUOROPHOSPHATE; PHYSICOCHEMICAL PROPERTIES; COMPUTER-SIMULATION; PHYSICAL-PROPERTIES; IMIDAZOLIUM CATION; FORCE-FIELD; AB-INITIO; TEMPERATURE; CHLORIDE; CONDUCTIVITY},
        Language = {English},
        Number = {8},
        Number-Of-Cited-References = {50},
        Pages = {685-690},
        Publisher = {TAYLOR \& FRANCIS LTD},
        Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
        Times-Cited = {2},
        Title = {Shear viscosity of ionic liquids from non-equilibrium molecular dynamics simulation},
        Type = {Article},
        Unique-Id = {ISI:000266247600008},
        Volume = {35},
        Year = {2009},
        Bdsk-Url-1 = {http://dx.doi.org/10.1080/08927020802680703%7D}}

@article{Vasquez:2004fk,
        Abstract = {A method for fast calculation of viscosity from molecular dynamics simulation is revisited. The method consists of using a steady-state periodic perturbation. A methodology to choose the amplitude of the external perturbation, which is one of the major practical issues in the original technique of Gosling et al. {$[$}Mol. Phys. 26: 1475 (1973){$]$} is proposed. The amplitude of the perturbation required for fast caculations and the viscosity values for wide ranges of temperature and density of the Lennard-Jones (LJ) model fluid are reported. The viscosity results are in agreement with recent LJ viscosity calculations. Additionally, the simulations demonstrate that the proposed approach is suitable to efficiently generate viscosity data of good quality.},
        Author = {Vasquez, V. R. and Macedo, E. A. and Zabaloy, M. S.},
        Date = {2004/11/02/},
        Date-Added = {2010-04-16 13:18:48 -0400},
        Date-Modified = {2010-04-16 13:18:48 -0400},
        Day = {02},
        Journal = {Int. J. Thermophys.},
        M3 = {10.1007/s10765-004-7736-3},
        Month = {11},
        Number = {6},
        Pages = {1799--1818},
        Title = {Lennard-Jones Viscosities in Wide Ranges of Temperature and Density: Fast Calculations Using a Steady--State Periodic Perturbation Method},
        Ty = {JOUR},
        Url = {http://dx.doi.org/10.1007/s10765-004-7736-3},
        Volume = {25},
        Year = {2004},
        Bdsk-Url-1 = {http://dx.doi.org/10.1007/s10765-004-7736-3}}

@article{hess:209,
        Author = {Berk Hess},
        Date-Added = {2010-04-16 12:37:37 -0400},
        Date-Modified = {2010-04-16 12:37:37 -0400},
        Doi = {10.1063/1.1421362},
        Journal = {J. Chem. Phys.},
        Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
        Number = {1},
        Pages = {209-217},
        Publisher = {AIP},
        Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
        Url = {http://link.aip.org/link/?JCP/116/209/1},
        Volume = {116},
        Year = {2002},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}}

@article{backer:154503,
        Author = {J. A. Backer and C. P. Lowe and H. C. J. Hoefsloot and P. D. Iedema},
        Date-Added = {2010-04-16 12:37:37 -0400},
        Date-Modified = {2010-04-16 12:37:37 -0400},
        Doi = {10.1063/1.1883163},
        Eid = {154503},
        Journal = {J. Chem. Phys.},
        Keywords = {Poiseuille flow; flow simulation; Lennard-Jones potential; viscosity; boundary layers; computational fluid dynamics},
        Number = {15},
        Numpages = {6},
        Pages = {154503},
        Publisher = {AIP},
        Title = {Poiseuille flow to measure the viscosity of particle model fluids},
        Url = {http://link.aip.org/link/?JCP/122/154503/1},
        Volume = {122},
        Year = {2005},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/122/154503/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1883163}}

@article{daivis:541,
        Author = {Peter J. Daivis and Denis J. Evans},
        Date-Added = {2010-04-16 12:05:36 -0400},
        Date-Modified = {2010-04-16 12:05:36 -0400},
        Doi = {10.1063/1.466970},
        Journal = {J. Chem. Phys.},
        Keywords = {SHEAR; DECANE; FLOW MODELS; VOLUME; PRESSURE; NONEQUILIBRIUM; MOLECULAR DYNAMICS CALCULATIONS; COMPARATIVE EVALUATIONS; SIMULATION; STRAIN RATE; VISCOSITY; KUBO FORMULA},
        Number = {1},
        Pages = {541-547},
        Publisher = {AIP},
        Title = {Comparison of constant pressure and constant volume nonequilibrium simulations of sheared model decane},
        Url = {http://link.aip.org/link/?JCP/100/541/1},
        Volume = {100},
        Year = {1994},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/100/541/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.466970}}

@article{mondello:9327,
        Author = {Maurizio Mondello and Gary S. Grest},
        Date-Added = {2010-04-16 12:05:36 -0400},
        Date-Modified = {2010-04-16 12:05:36 -0400},
        Doi = {10.1063/1.474002},
        Journal = {J. Chem. Phys.},
        Keywords = {organic compounds; viscosity; digital simulation; molecular dynamics method},
        Number = {22},
        Pages = {9327-9336},
        Publisher = {AIP},
        Title = {Viscosity calculations of [bold n]-alkanes by equilibrium molecular dynamics},
        Url = {http://link.aip.org/link/?JCP/106/9327/1},
        Volume = {106},
        Year = {1997},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/106/9327/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.474002}}

@article{ISI:A1988Q205300014,
        Address = {ONE GUNDPOWDER SQUARE, LONDON, ENGLAND EC4A 3DE},
        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.},
        Author = {Vogelsang, R and Hoheisel, G and Luckas, M},
        Date-Added = {2010-04-14 16:20:24 -0400},
        Date-Modified = {2010-04-14 16:20:24 -0400},
        Doc-Delivery-Number = {Q2053},
        Issn = {0026-8976},
        Journal = {Mol. Phys.},
        Journal-Iso = {Mol. Phys.},
        Language = {English},
        Month = {AUG 20},
        Number = {6},
        Number-Of-Cited-References = {14},
        Pages = {1203-1213},
        Publisher = {TAYLOR \& FRANCIS LTD},
        Subject-Category = {Physics, Atomic, Molecular \& Chemical},
        Times-Cited = {12},
        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},
        Type = {Article},
        Unique-Id = {ISI:A1988Q205300014},
        Volume = {64},
        Year = {1988}}

@article{ISI:000261835100054,
        Abstract = {Transport properties of liquid methanol and ethanol are predicted by
   molecular dynamics simulation. The molecular models for the alcohols
   are rigid, nonpolarizable, and of united-atom type. They were developed
   in preceding work using experimental vapor-liquid equilibrium data
   only. Self- and Maxwell-Stefan diffusion coefficients as well as the
   shear viscosity of methanol, ethanol, and their binary mixture are
   determined using equilibrium molecular dynamics and the Green-Kubo
   formalism. Nonequilibrium molecular dynamics is used for predicting the
   thermal conductivity of the two pure substances. The transport
   properties of the fluids are calculated over a wide temperature range
   at ambient pressure and compared with experimental and simulation data
   from the literature. Overall, a very good agreement with the experiment
   is found. For instance, the self-diffusion coefficient and the shear
   viscosity are predicted with average deviations of less than 8\% for
   the pure alcohols and 12\% for the mixture. The predicted thermal
   conductivity agrees on average within 5\% with the experimental data.
   Additionally, some velocity and shear viscosity autocorrelation
   functions are presented and discussed. Radial distribution functions
   for ethanol are also presented. The predicted excess volume, excess
   enthalpy, and the vapor-liquid equilibrium of the binary mixture
   methanol + ethanol are assessed and agree well with experimental data.},
        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
        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.},
        Author = {Guevara-Carrion, Gabriela and Nieto-Draghi, Carlos and Vrabec, Jadran and Hasse, Hans},
        Author-Email = {vrabec@itt.uni-stuttgart.de},
        Date-Added = {2010-04-14 15:43:29 -0400},
        Date-Modified = {2010-04-14 15:43:29 -0400},
        Doc-Delivery-Number = {385SY},
        Doi = {10.1021/jp805584d},
        Issn = {1520-6106},
        Journal = {J. Phys. Chem. B},
        Journal-Iso = {J. Phys. Chem. B},
        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},
        Language = {English},
        Month = {DEC 25},
        Number = {51},
        Number-Of-Cited-References = {86},
        Pages = {16664-16674},
        Publisher = {AMER CHEMICAL SOC},
        Subject-Category = {Chemistry, Physical},
        Times-Cited = {5},
        Title = {Prediction of Transport Properties by Molecular Simulation: Methanol and Ethanol and Their Mixture},
        Type = {Article},
        Unique-Id = {ISI:000261835100054},
        Volume = {112},
        Year = {2008},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp805584d%7D}}

@article{ISI:000258460400020,
        Abstract = {Nonequilibrium molecular dynamics simulations with the nonpolarizable
   SPC/E (Berendsen et al., J. Phys. Chem. 1987, 91, 6269) and the
   polarizable COS/G2 (Yu and van Gunsteren, J. Chem. Phys. 2004, 121,
   9549) force fields have been employed to calculate the thermal
   conductivity and other associated properties of methane hydrate over a
   temperature range from 30 to 260 K. The calculated results are compared
   to experimental data over this same range. The values of the thermal
   conductivity calculated with the COS/G2 model are closer to the
   experimental values than are those calculated with the nonpolarizable
   SPC/E model. The calculations match the temperature trend in the
   experimental data at temperatures below 50 K; however, they exhibit a
   slight decrease in thermal conductivity at higher temperatures in
   comparison to an opposite trend in the experimental data. The
   calculated thermal conductivity values are found to be relatively
   insensitive to the occupancy of the cages except at low (T <= 50 K)
   temperatures, which indicates that the differences between the two
   lattice structures may have a more dominant role than generally thought
   in explaining the low thermal conductivity of methane hydrate compared
   to ice Ih. The introduction of defects into the water lattice is found
   to cause a reduction in the thermal conductivity but to have a
   negligible impact on its temperature dependence.},
        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
        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.},
        Author = {Jiang, Hao and Myshakin, Evgeniy M. and Jordan, Kenneth D. and Warzinski, Robert P.},
        Date-Added = {2010-04-14 15:38:14 -0400},
        Date-Modified = {2010-04-14 15:38:14 -0400},
        Doc-Delivery-Number = {337UG},
        Doi = {10.1021/jp802942v},
        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]},
        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.},
        Issn = {1520-6106},
        Journal = {J. Phys. Chem. B},
        Journal-Iso = {J. Phys. Chem. B},
        Keywords-Plus = {LIQUID WATER; CLATHRATE HYDRATE; HEAT-CAPACITY; FORCE-FIELDS; ICE; ANHARMONICITY; SUMMATION; MODELS; SILICA},
        Language = {English},
        Month = {AUG 21},
        Number = {33},
        Number-Of-Cited-References = {51},
        Pages = {10207-10216},
        Publisher = {AMER CHEMICAL SOC},
        Subject-Category = {Chemistry, Physical},
        Times-Cited = {8},
        Title = {Molecular dynamics Simulations of the thermal conductivity of methane hydrate},
        Type = {Article},
        Unique-Id = {ISI:000258460400020},
        Volume = {112},
        Year = {2008},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp802942v%7D}}

@article{ISI:000184808400018,
        Abstract = {A new non-equilibrium molecular dynamics algorithm is presented based
   on the original work of Willer-Plathe, (1997, J. chem. Phys., 106,
   6082), for the non-equilibrium simulation of heat transport maintaining
   fixed the total momentum as well as the total energy of the system. The
   presented scheme preserves these properties but, unlike the original
   algorithm, is able to deal with multicomponent systems, that is with
   particles of different mass independently of their relative
   concentration. The main idea behind the new procedure is to consider an
   exchange of momentum and energy between the particles in the hot and
   cold regions, to maintain the non-equilibrium conditions, as if they
   undergo a hypothetical elastic collision. The new algorithm can also be
   employed in multicomponent systems for molecular fluids and in a wide
   range of thermodynamic conditions.},
        Address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND},
        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.},
        Author = {Nieto-Draghi, C and Avalos, JB},
        Date-Added = {2010-04-14 12:48:08 -0400},
        Date-Modified = {2010-04-14 12:48:08 -0400},
        Doc-Delivery-Number = {712QM},
        Doi = {10.1080/0026897031000154338},
        Issn = {0026-8976},
        Journal = {Mol. Phys.},
        Journal-Iso = {Mol. Phys.},
        Keywords-Plus = {BINARY-LIQUID MIXTURES; THERMAL-CONDUCTIVITY; MATTER TRANSPORT; WATER},
        Language = {English},
        Month = {JUL 20},
        Number = {14},
        Number-Of-Cited-References = {20},
        Pages = {2303-2307},
        Publisher = {TAYLOR \& FRANCIS LTD},
        Subject-Category = {Physics, Atomic, Molecular \& Chemical},
        Times-Cited = {13},
        Title = {Non-equilibrium momentum exchange algorithm for molecular dynamics simulation of heat flow in multicomponent systems},
        Type = {Article},
        Unique-Id = {ISI:000184808400018},
        Volume = {101},
        Year = {2003},
        Bdsk-Url-1 = {http://dx.doi.org/10.1080/0026897031000154338%7D}}

@article{Bedrov:2000-1,
        Abstract = {The thermal conductivity of liquid
   octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) has been
   determined from imposed heat flux non-equilibrium molecular dynamics
   (NEMD) simulations using a previously published quantum chemistry-based
   atomistic potential. The thermal conductivity was determined in the
   temperature domain 550 less than or equal to T less than or equal to
   800 K, which corresponds approximately to the existence limits of the
   liquid phase of HMX at atmospheric pressure. The NEMD predictions,
   which comprise the first reported values for thermal conductivity of
   HMX liquid, were found to be consistent with measured values for
   crystalline HMX. The thermal conductivity of liquid HMX was found to
   exhibit a much weaker temperature dependence than the shear viscosity
   and self-diffusion coefficients. (C) 2000 Elsevier Science B.V. All
   rights reserved.},
        Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
        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.},
        Author = {Bedrov, D and Smith, GD and Sewell, TD},
        Date-Added = {2010-04-14 12:26:59 -0400},
        Date-Modified = {2010-04-14 12:27:52 -0400},
        Doc-Delivery-Number = {330PF},
        Issn = {0009-2614},
        Journal = {Chem. Phys. Lett.},
        Journal-Iso = {Chem. Phys. Lett.},
        Keywords-Plus = {FORCE-FIELD},
        Language = {English},
        Month = {JUN 30},
        Number = {1-3},
        Number-Of-Cited-References = {17},
        Pages = {64-68},
        Publisher = {ELSEVIER SCIENCE BV},
        Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
        Times-Cited = {19},
        Title = {Thermal conductivity of liquid octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) from molecular dynamics simulations},
        Type = {Article},
        Unique-Id = {ISI:000087969900011},
        Volume = {324},
        Year = {2000}}

@article{ISI:000258840700015,
        Abstract = {By using the embedded-atom method (EAM), a series of molecular dynamics
   (MD) simulations are carried out to calculate the viscosity and
   self-diffusion coefficient of liquid copper from the normal to the
   undercooled states. The simulated results are in reasonable agreement
   with the experimental values available above the melting temperature
   that is also predicted from a solid-liquid-solid sandwich structure.
   The relationship between the viscosity and the self-diffusion
   coefficient is evaluated. It is found that the Stokes-Einstein and
   Sutherland-Einstein relations qualitatively describe this relationship
   within the simulation temperature range. However, the predicted
   constant from MD simulation is close to 1/(3 pi), which is larger than
   the constants of the Stokes-Einstein and Sutherland-Einstein relations.},
        Address = {233 SPRING ST, NEW YORK, NY 10013 USA},
        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.},
        Author = {Han, X. J. and Chen, M. and Lue, Y. J.},
        Author-Email = {mchen@tsinghua.edu.cn},
        Date-Added = {2010-04-14 12:00:38 -0400},
        Date-Modified = {2010-04-14 12:00:38 -0400},
        Doc-Delivery-Number = {343GH},
        Doi = {10.1007/s10765-008-0489-7},
        Funding-Acknowledgement = {China Postdoctoral Science Foundation ; National Natural Science Foundation of China {[}50395101, 50371043]},
        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.},
        Issn = {0195-928X},
        Journal = {Int. J. Thermophys.},
        Journal-Iso = {Int. J. Thermophys.},
        Keywords = {copper; molecular simulation; self-diffusion coefficient; viscosity; undercooled},
        Keywords-Plus = {EMBEDDED-ATOM MODEL; THERMOPHYSICAL PROPERTIES; COMPUTER-SIMULATION; TRANSITION-METALS; SHEAR VISCOSITY; ALLOYS; TEMPERATURE; DIFFUSION; BINDING; SURFACE},
        Language = {English},
        Month = {AUG},
        Number = {4},
        Number-Of-Cited-References = {39},
        Pages = {1408-1421},
        Publisher = {SPRINGER/PLENUM PUBLISHERS},
        Subject-Category = {Thermodynamics; Chemistry, Physical; Mechanics; Physics, Applied},
        Times-Cited = {2},
        Title = {Transport properties of undercooled liquid copper: A molecular dynamics study},
        Type = {Article},
        Unique-Id = {ISI:000258840700015},
        Volume = {29},
        Year = {2008},
        Bdsk-Url-1 = {http://dx.doi.org/10.1007/s10765-008-0489-7%7D}}

@article{Muller-Plathe:2008,
        Abstract = {Reverse nonequilibrium molecular dynamics and equilibrium molecular
   dynamics simulations were carried out to compute the shear viscosity of
   the pure ionic liquid system {[}bmim]{[}PF6] at 300 K. The two methods
   yielded consistent results which were also compared to experiments. The
   results showed that the reverse nonequilibrium molecular dynamics
   (RNEMD) methodology can successfully be applied to computation of
   highly viscous ionic liquids. Moreover, this study provides a
   validation of the atomistic force-field developed by Bhargava and
   Balasubramanian (J. Chem. Phys. 2007, 127, 114510) for dynamic
   properties.},
        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
        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.},
        Author = {Wei Zhao and Leroy, Frederic and Balasubramanian, Sundaram and M\"{u}ller-Plathe, Florian},
        Author-Email = {w.zhao@theo.chemie.tu-darmstadt.de},
        Date-Added = {2010-04-14 11:53:37 -0400},
        Date-Modified = {2010-04-14 11:54:20 -0400},
        Doc-Delivery-Number = {321VS},
        Doi = {10.1021/jp8017869},
        Issn = {1520-6106},
        Journal = {J. Phys. Chem. B},
        Journal-Iso = {J. Phys. Chem. B},
        Keywords-Plus = {TRANSPORT-PROPERTIES; FORCE-FIELD; TEMPERATURE; SIMULATION; IMIDAZOLIUM; FLUIDS; MODEL; BIS(TRIFLUOROMETHANESULFONYL)IMIDE; PYRIDINIUM; CHLORIDE},
        Language = {English},
        Month = {JUL 10},
        Number = {27},
        Number-Of-Cited-References = {49},
        Pages = {8129-8133},
        Publisher = {AMER CHEMICAL SOC},
        Subject-Category = {Chemistry, Physical},
        Times-Cited = {2},
        Title = {Shear viscosity of the ionic liquid 1-n-butyl 3-methylimidazolium hexafluorophosphate {[}bmim]{[}PF6] computed by reverse nonequilibrium molecular dynamics},
        Type = {Article},
        Unique-Id = {ISI:000257335200022},
        Volume = {112},
        Year = {2008},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp8017869%7D}}

@article{Muller-Plathe:2002,
        Abstract = {The reverse nonequilibrium molecular dynamics {[}F. Muller-Plathe,
   Phys. Rev. E 49, 359 (1999)] presented for the calculation of the shear
   viscosity of Lennard-Jones liquids has been extended to atomistic
   models of molecular liquids. The method is improved to overcome the
   problems due to the detailed molecular models. The new technique is
   besides a test with a Lennard-Jones fluid, applied on different
   realistic systems: liquid nitrogen, water, and hexane, in order to
   cover a large range of interactions and systems/architectures. We show
   that all the advantages of the method itemized previously are still
   valid, and that it has a very good efficiency and accuracy making it
   very competitive. (C) 2002 American Institute of Physics.},
        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
        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.},
        Author = {Bordat, P and M\"{u}ller-Plathe, F},
        Date-Added = {2010-04-14 11:34:42 -0400},
        Date-Modified = {2010-04-14 11:35:35 -0400},
        Doc-Delivery-Number = {521QV},
        Doi = {10.1063/1.1436124},
        Issn = {0021-9606},
        Journal = {J. Chem. Phys.},
        Journal-Iso = {J. Chem. Phys.},
        Keywords-Plus = {TRANSPORT-PROPERTIES; PHYSICAL-PROPERTIES; LIQUID ALKANES; N-HEPTADECANE; SIMULATION; WATER; FLOW; MIXTURES; BUTANE; NITROGEN},
        Language = {English},
        Month = {FEB 22},
        Number = {8},
        Number-Of-Cited-References = {47},
        Pages = {3362-3369},
        Publisher = {AMER INST PHYSICS},
        Subject-Category = {Physics, Atomic, Molecular \& Chemical},
        Times-Cited = {33},
        Title = {The shear viscosity of molecular fluids: A calculation by reverse nonequilibrium molecular dynamics},
        Type = {Article},
        Unique-Id = {ISI:000173853600023},
        Volume = {116},
        Year = {2002},
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1436124%7D}}

@article{ISI:000207079300006,
        Abstract = {Non-equilibrium Molecular Dynamics Simulation
                  methods have been used to study the ability of
                  Embedded Atom Method models of the metals copper and
                  gold to reproduce the equilibrium and
                  non-equilibrium behavior of metals at a stationary
                  and at a moving solid/liquid interface. The
                  equilibrium solid/vapor interface was shown to
                  display a simple termination of the bulk until the
                  temperature of the solid reaches approximate to 90\%
                  of the bulk melting point. At and above such
                  temperatures the systems exhibit a surface
                  disodering known as surface melting. Non-equilibrium
                  simulations emulating the action of a picosecond
                  laser on the metal were performed to determine the
                  regrowth velocity. For copper, the action of a 20 ps
                  laser with an absorbed energy of 2-5 mJ/cm(2)
                  produced a regrowth velocity of 83-100 m/s, in
                  reasonable agreement with the value obtained by
                  experiment (>60 m/s). For gold, similar conditions
                  produced a slower regrowth velocity of 63 m/s at an
                  absorbed energy of 5 mJ/cm(2). This is almost a
                  factor of two too low in comparison to experiment
                  (>100 m/s). The regrowth velocities of the metals
                  seems unexpectedly close to experiment considering
                  that the free-electron contribution is ignored in
                  the Embeeded Atom Method models used.},
        Address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND},
        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.},
        Author = {Richardson, Clifton F. and Clancy, Paulette},
        Date-Added = {2010-04-07 11:24:36 -0400},
        Date-Modified = {2010-04-07 11:24:36 -0400},
        Doc-Delivery-Number = {V04SY},
        Issn = {0892-7022},
        Journal = {Mol. Simul.},
        Journal-Iso = {Mol. Simul.},
        Keywords = {Non-equilibrium computer simulation; molecular dynamics; crystal growth; Embedded Atom Method models of metals},
        Language = {English},
        Number = {5-6},
        Number-Of-Cited-References = {36},
        Pages = {335-355},
        Publisher = {TAYLOR \& FRANCIS LTD},
        Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
        Times-Cited = {7},
        Title = {PICOSECOND LASER PROCESSING OF COPPER AND GOLD: A COMPUTER SIMULATION STUDY},
        Type = {Article},
        Unique-Id = {ISI:000207079300006},
        Volume = {7},
        Year = {1991}}

@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 = {2010-03-11 15:32:14 -0500},
        Date-Modified = {2010-03-11 15:32:14 -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{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 = {2010-03-09 13:08:41 -0500},
        Date-Modified = {2010-07-19 16:21:35 -0400},
        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{Clancy:1992,
        Abstract = {The regrowth velocity of a crystal from a melt
                  depends on contributions from the thermal
                  conductivity, heat gradient, and latent heat. The
                  relative contributions of these terms to the
                  regrowth velocity of the pure metals copper and gold
                  during liquid-phase epitaxy are evaluated. These
                  results are used to explain how results from
                  previous nonequilibrium molecular-dynamics
                  simulations using classical potentials are able to
                  predict regrowth velocities that are close to the
                  experimental values. Results from equilibrium
                  molecular dynamics showing the nature of the
                  solid-vapor interface of an
                  embedded-atom-method-modeled Cu57Ni43 alloy at a
                  temperature corresponding to 62\% of the melting
                  point are presented. The regrowth of this alloy
                  following a simulation of a laser-processing
                  experiment is also given, with use of nonequilibrium
                  molecular-dynamics techniques. The thermal
                  conductivity and temperature gradient in the
                  simulation of the alloy are compared to those for
                  the pure metals.},
        Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
        Affiliation = {CORNELL UNIV,SCH CHEM ENGN,ITHACA,NY 14853.},
        Author = {Richardson, C.~F. and Clancy, P},
        Date-Added = {2010-01-12 16:17:33 -0500},
        Date-Modified = {2010-04-08 17:18:25 -0400},
        Doc-Delivery-Number = {HX378},
        Issn = {0163-1829},
        Journal = {Phys. Rev. B},
        Journal-Iso = {Phys. Rev. B},
        Keywords-Plus = {SURFACE SEGREGATION; MOLECULAR-DYNAMICS; TRANSITION-METALS; SOLIDIFICATION; GROWTH; CU; NI},
        Language = {English},
        Month = {JUN 1},
        Number = {21},
        Number-Of-Cited-References = {24},
        Pages = {12260-12268},
        Publisher = {AMERICAN PHYSICAL SOC},
        Subject-Category = {Physics, Condensed Matter},
        Times-Cited = {11},
        Title = {CONTRIBUTION OF THERMAL-CONDUCTIVITY TO THE CRYSTAL-REGROWTH VELOCITY OF EMBEDDED-ATOM-METHOD-MODELED METALS AND METAL-ALLOYS},
        Type = {Article},
        Unique-Id = {ISI:A1992HX37800010},
        Volume = {45},
        Year = {1992}}

@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 = {2009-11-05 18:21:18 -0500},
        Date-Modified = {2010-04-14 11:50:48 -0400},
        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},
        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{ISI:000231042800044,
        Abstract = {The reverse nonequilibrium molecular dynamics
                  method for thermal conductivities is adapted to the
                  investigation of molecular fluids. The method
                  generates a heat flux through the system by suitably
                  exchanging velocities of particles located in
                  different regions. From the resulting temperature
                  gradient, the thermal conductivity is then
                  calculated. Different variants of the algorithm and
                  their combinations with other system parameters are
                  tested: exchange of atomic velocities versus
                  exchange of molecular center-of-mass velocities,
                  different exchange frequencies, molecular models
                  with bond constraints versus models with flexible
                  bonds, united-atom versus all-atom models, and
                  presence versus absence of a thermostat. To help
                  establish the range of applicability, the algorithm
                  is tested on different models of benzene,
                  cyclohexane, water, and n-hexane. We find that the
                  algorithm is robust and that the calculated thermal
                  conductivities are insensitive to variations in its
                  control parameters. The force field, in contrast,
                  has a major influence on the value of the thermal
                  conductivity. While calculated and experimental
                  thermal conductivities fall into the same order of
                  magnitude, in most cases the calculated values are
                  systematically larger. United-atom force fields seem
                  to do better than all-atom force fields, possibly
                  because they remove high-frequency degrees of
                  freedom from the simulation, which, in nature, are
                  quantum-mechanical oscillators in their ground state
                  and do not contribute to heat conduction.},
        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
        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.},
        Author = {Zhang, MM and Lussetti, E and de Souza, LES and M\"{u}ller-Plathe, F},
        Date-Added = {2009-11-05 18:17:33 -0500},
        Date-Modified = {2009-11-05 18:17:33 -0500},
        Doc-Delivery-Number = {952YQ},
        Doi = {10.1021/jp0512255},
        Issn = {1520-6106},
        Journal = {J. Phys. Chem. B},
        Journal-Iso = {J. Phys. Chem. B},
        Keywords-Plus = {LENNARD-JONES LIQUIDS; TRANSPORT-COEFFICIENTS; SWOLLEN POLYMERS; SHEAR VISCOSITY; MODEL SYSTEMS; SIMULATION; BENZENE; FLUIDS; POTENTIALS; DIFFUSION},
        Language = {English},
        Month = {AUG 11},
        Number = {31},
        Number-Of-Cited-References = {42},
        Pages = {15060-15067},
        Publisher = {AMER CHEMICAL SOC},
        Subject-Category = {Chemistry, Physical},
        Times-Cited = {17},
        Title = {Thermal conductivities of molecular liquids by reverse nonequilibrium molecular dynamics},
        Type = {Article},
        Unique-Id = {ISI:000231042800044},
        Volume = {109},
        Year = {2005},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp0512255%7D}}

@article{ISI:A1997YC32200056,
        Abstract = {Equilibrium molecular dynamics simulations have
                  been carried out in the microcanonical ensemble at
                  300 and 255 K on the extended simple point charge
                  (SPC/E) model of water {[}Berendsen et al.,
                  J. Phys. Chem. 91, 6269 (1987)]. In addition to a
                  number of static and dynamic properties, thermal
                  conductivity lambda has been calculated via
                  Green-Kubo integration of the heat current time
                  correlation functions (CF's) in the atomic and
                  molecular formalism, at wave number k=0. The
                  calculated values (0.67 +/- 0.04 W/mK at 300 K and
                  0.52 +/- 0.03 W/mK at 255 K) are in good agreement
                  with the experimental data (0.61 W/mK at 300 K and
                  0.49 W/mK at 255 K). A negative long-time tail of
                  the heat current CF, more apparent at 255 K, is
                  responsible for the anomalous decrease of lambda
                  with temperature. An analysis of the dynamical modes
                  contributing to lambda has shown that its value is
                  due to two low-frequency exponential-like modes, a
                  faster collisional mode, with positive contribution,
                  and a slower one, which determines the negative
                  long-time tail. A comparison of the molecular and
                  atomic spectra of the heat current CF has suggested
                  that higher-frequency modes should not contribute to
                  lambda in this temperature range. Generalized
                  thermal diffusivity D-T(k) decreases as a function
                  of k, after an initial minor increase at k =
                  k(min). The k dependence of the generalized
                  thermodynamic properties has been calculated in the
                  atomic and molecular formalisms. The observed
                  differences have been traced back to intramolecular
                  or intermolecular rotational effects and related to
                  the partial structure functions. Finally, from the
                  results we calculated it appears that the SPC/E
                  model gives results in better agreement with
                  experimental data than the transferable
                  intermolecular potential with four points TIP4P
                  water model {[}Jorgensen et al., J. Chem. Phys. 79,
                  926 (1983)], with a larger improvement for, e.g.,
                  diffusion, viscosities, and dielectric properties
                  and a smaller one for thermal conductivity. The
                  SPC/E model shares, to a smaller extent, the
                  insufficient slowing down of dynamics at low
                  temperature already found for the TIP4P water
                  model.},
        Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
        Affiliation = {UNIV PISA,DIPARTIMENTO CHIM \& CHIM IND,I-56126 PISA,ITALY. CNR,IST FIS ATOM \& MOL,I-56127 PISA,ITALY.},
        Author = {Bertolini, D and Tani, A},
        Date-Added = {2009-10-30 15:41:21 -0400},
        Date-Modified = {2009-10-30 15:41:21 -0400},
        Doc-Delivery-Number = {YC322},
        Issn = {1063-651X},
        Journal = {Phys. Rev. E},
        Journal-Iso = {Phys. Rev. E},
        Keywords-Plus = {TIME-CORRELATION-FUNCTIONS; LENNARD-JONES LIQUID; TRANSPORT-PROPERTIES; SUPERCOOLED WATER; DENSITY; SIMULATIONS; RELAXATION; VELOCITY; ELECTRON; FLUIDS},
        Language = {English},
        Month = {OCT},
        Number = {4},
        Number-Of-Cited-References = {35},
        Pages = {4135-4151},
        Publisher = {AMERICAN PHYSICAL SOC},
        Subject-Category = {Physics, Fluids \& Plasmas; Physics, Mathematical},
        Times-Cited = {18},
        Title = {Thermal conductivity of water: Molecular dynamics and generalized hydrodynamics results},
        Type = {Article},
        Unique-Id = {ISI:A1997YC32200056},
        Volume = {56},
        Year = {1997}}

@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 = {2009-10-01 18:43:03 -0400},
        Date-Modified = {2010-04-13 09:11:16 -0400},
        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. Comp. 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{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 = {2009-10-01 14:07:30 -0400},
        Date-Modified = {2009-10-01 14:07:30 -0400},
        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{Maginn:2007,
        Abstract = {Atomistic simulations are conducted to examine the
                  dependence of the viscosity of
                  1-ethyl-3-methylimidazolium
                  bis(trifluoromethanesulfonyl)imide on temperature
                  and water content. A nonequilibrium molecular
                  dynamics procedure is utilized along with an
                  established fixed charge force field. It is found
                  that the simulations quantitatively capture the
                  temperature dependence of the viscosity as well as
                  the drop in viscosity that occurs with increasing
                  water content. Using mixture viscosity models, we
                  show that the relative drop in viscosity with water
                  content is actually less than that that would be
                  predicted for an ideal system. This finding is at
                  odds with the popular notion that small amounts of
                  water cause an unusually large drop in the viscosity
                  of ionic liquids. The simulations suggest that, due
                  to preferential association of water with anions and
                  the formation of water clusters, the excess molar
                  volume is negative. This means that dissolved water
                  is actually less effective at lowering the viscosity
                  of these mixtures when compared to a solute obeying
                  ideal mixing behavior. The use of a nonequilibrium
                  simulation technique enables diffusive behavior to
                  be observed on the time scale of the simulations,
                  and standard equilibrium molecular dynamics resulted
                  in sub-diffusive behavior even over 2 ns of
                  simulation time.},
        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
        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.},
        Author = {Kelkar, Manish S. and Maginn, Edward J.},
        Author-Email = {ed@nd.edu},
        Date-Added = {2009-09-29 17:07:17 -0400},
        Date-Modified = {2010-04-14 12:51:02 -0400},
        Doc-Delivery-Number = {163VA},
        Doi = {10.1021/jp0686893},
        Issn = {1520-6106},
        Journal = {J. Phys. Chem. B},
        Journal-Iso = {J. Phys. Chem. B},
        Keywords-Plus = {MOLECULAR-DYNAMICS SIMULATION; MOMENTUM IMPULSE RELAXATION; FORCE-FIELD; TRANSPORT-PROPERTIES; PHYSICAL-PROPERTIES; SIMPLE FLUID; CHLORIDE; MODEL; SALTS; ARCHITECTURE},
        Language = {English},
        Month = {MAY 10},
        Number = {18},
        Number-Of-Cited-References = {57},
        Pages = {4867-4876},
        Publisher = {AMER CHEMICAL SOC},
        Subject-Category = {Chemistry, Physical},
        Times-Cited = {35},
        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},
        Type = {Article},
        Unique-Id = {ISI:000246190100032},
        Volume = {111},
        Year = {2007},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp0686893%7D},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp0686893}}

@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 = {2009-09-21 16:51:21 -0400},
        Date-Modified = {2009-09-21 16:51:21 -0400},
        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{Muller-Plathe:1999ek,
        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.},
        Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
        Author = {M\"{u}ller-Plathe, F and Reith, D},
        Date-Added = {2009-09-21 16:47:07 -0400},
        Date-Modified = {2009-09-21 16:47:07 -0400},
        Isi = {000082266500004},
        Isi-Recid = {111564960},
        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},
        Journal = {Computational and Theoretical Polymer Science},
        Keywords = {viscosity; Ludwig-Soret effect; thermal conductivity; Onsager coefficents; non-equilibrium molecular dynamics},
        Number = {3-4},
        Pages = {203-209},
        Publisher = {ELSEVIER SCI LTD},
        Times-Cited = {15},
        Title = {Cause and effect reversed in non-equilibrium molecular dynamics: an easy route to transport coefficients},
        Volume = {9},
        Year = {1999},
        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000082266500004}}

@article{Viscardy:2007lq,
        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.},
        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
        Author = {Viscardy, S. and Servantie, J. and Gaspard, P.},
        Date-Added = {2009-09-21 16:37:20 -0400},
        Date-Modified = {2010-07-19 16:18:44 -0400},
        Doi = {DOI 10.1063/1.2724821},
        Isi = {000246453900035},
        Isi-Recid = {156192451},
        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},
        Journal = {J. Chem. Phys.},
        Month = may,
        Number = {18},
        Pages = {184513},
        Publisher = {AMER INST PHYSICS},
        Times-Cited = {3},
        Title = {Transport and Helfand moments in the Lennard-Jones fluid. II. Thermal conductivity},
        Volume = {126},
        Year = {2007},
        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000246453900035},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2724821}}

@article{Viscardy:2007bh,
        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.},
        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
        Author = {Viscardy, S. and Servantie, J. and Gaspard, P.},
        Date-Added = {2009-09-21 16:37:19 -0400},
        Date-Modified = {2010-07-19 16:19:03 -0400},
        Doi = {DOI 10.1063/1.2724820},
        Isi = {000246453900034},
        Isi-Recid = {156192449},
        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},
        Journal = {J. Chem. Phys.},
        Month = may,
        Number = {18},
        Pages = {184512},
        Publisher = {AMER INST PHYSICS},
        Times-Cited = {1},
        Title = {Transport and Helfand moments in the Lennard-Jones fluid. I. Shear viscosity},
        Volume = {126},
        Year = {2007},
        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000246453900034},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2724820}}

@inproceedings{384119,
        Address = {New York, NY, USA},
        Author = {Fortune, Steven},
        Booktitle = {ISSAC '01: Proceedings of the 2001 international symposium on Symbolic and algebraic computation},
        Doi = {http://doi.acm.org/10.1145/384101.384119},
        Isbn = {1-58113-417-7},
        Location = {London, Ontario, Canada},
        Pages = {121--128},
        Publisher = {ACM},
        Title = {Polynomial root finding using iterated Eigenvalue computation},
        Year = {2001},
        Bdsk-Url-1 = {http://doi.acm.org/10.1145/384101.384119}}

@article{Fennell06,
        Author = {C.~J. Fennell and J.~D. Gezelter},
        Date-Added = {2006-08-24 09:49:57 -0400},
        Date-Modified = {2006-08-24 09:49:57 -0400},
        Doi = {10.1063/1.2206581},
        Journal = {J. Chem. Phys.},
        Number = {23},
        Pages = {234104(12)},
        Rating = {5},
        Read = {Yes},
        Title = {Is the \uppercase{E}wald summation still necessary? \uppercase{P}airwise alternatives to the accepted standard for long-range electrostatics},
        Volume = {124},
        Year = {2006},
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2206581}}

@book{Sommese2005,
        Address = {Singapore},
        Author = {Andrew J. Sommese and Charles W. Wampler},
        Publisher = {World Scientific Press},
        Title = {The numerical solution of systems of polynomials arising in engineering and science},
        Year = 2005}
Revision:	3737
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