trunk/nonperiodicVSS/nonperiodicVSS.bib

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@string{acp = {Adv. Chem. Phys.}}

@string{bj = {Biophys. J.}}

@string{ccp5 = {CCP5 Information Quarterly}}

@string{cp = {Chem. Phys.}}

@string{cpl = {Chem. Phys. Lett.}}

@string{ea = {Electrochim. Acta}}

@string{jacs = {J. Am. Chem. Soc.}}

@string{jbc = {J. Biol. Chem.}}

@string{jcat = {J. Catalysis}}

@string{jcc = {J. Comp. Chem.}}

@string{jcop = {J. Comp. Phys.}}

@string{jcp = {J. Chem. Phys.}}

@string{jctc = {J. Chem. Theory Comp.}}

@string{jmc = {J. Med. Chem.}}

@string{jml = {J. Mol. Liq.}}

@string{jmm = {J. Mol. Model.}}

@string{jpc = {J. Phys. Chem.}}

@string{jpca = {J. Phys. Chem. A}}

@string{jpcb = {J. Phys. Chem. B}}

@string{jpcc = {J. Phys. Chem. C}}

@string{jpcl = {J. Phys. Chem. Lett.}}

@string{mp = {Mol. Phys.}}

@string{pams = {Proc. Am. Math Soc.}}

@string{pccp = {Phys. Chem. Chem. Phys.}}

@string{pnas = {Proc. Natl. Acad. Sci. USA}}

@string{pr = {Phys. Rev.}}

@string{pra = {Phys. Rev. A}}

@string{prb = {Phys. Rev. B}}

@string{pre = {Phys. Rev. E}}

@string{prl = {Phys. Rev. Lett.}}

@string{rmp = {Rev. Mod. Phys.}}

@string{ss = {Surf. Sci.}}


@article{Vogelsang:1988qv,
        Author = {Vogelsang, R. and Hoheisel, G. and Luckas, M.},
        Date-Added = {2014-03-13 20:40:44 +0000},
        Date-Modified = {2014-03-13 20:40:58 +0000},
        Doi = {10.1080/00268978800100813},
        Eprint = {http://www.tandfonline.com/doi/pdf/10.1080/00268978800100813},
        Journal = {Molecular Physics},
        Number = {6},
        Pages = {1203-1213},
        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},
        Url = {http://www.tandfonline.com/doi/abs/10.1080/00268978800100813},
        Volume = {64},
        Year = {1988},
        Bdsk-Url-1 = {http://www.tandfonline.com/doi/abs/10.1080/00268978800100813},
        Bdsk-Url-2 = {http://dx.doi.org/10.1080/00268978800100813}}

@article{Berendsen87,
        Author = {Berendsen, H. J. C. and Grigera, J. R. and Straatsma, T. P.},
        Date-Added = {2014-03-13 15:02:07 +0000},
        Date-Modified = {2014-03-13 15:02:07 +0000},
        Doi = {10.1021/j100308a038},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/j100308a038},
        Journal = {The Journal of Physical Chemistry},
        Number = {24},
        Pages = {6269-6271},
        Title = {The missing term in effective pair potentials},
        Url = {http://pubs.acs.org/doi/abs/10.1021/j100308a038},
        Volume = {91},
        Year = {1987},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/j100308a038},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/j100308a038}}

@article{Stocker:2013cl,
        Author = {Stocker, Kelsey M. and Gezelter, J. Daniel},
        Date-Added = {2014-03-13 14:20:18 +0000},
        Date-Modified = {2014-03-13 14:21:57 +0000},
        Doi = {10.1021/jp312734f},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp312734f},
        Journal = {The Journal of Physical Chemistry C},
        Number = {15},
        Pages = {7605-7612},
        Title = {Simulations of Heat Conduction at Thiolate-Capped Gold Surfaces: The Role of Chain Length and Solvent Penetration},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp312734f},
        Volume = {117},
        Year = {2013},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp312734f},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp312734f}}

@article{Picalek:2009rz,
        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 = {2014-03-13 14:11:53 +0000},
        Date-Modified = {2014-03-13 14:12:08 +0000},
        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{Backer:2005sf,
        Author = {J. A. Backer and C. P. Lowe and H. C. J. Hoefsloot and P. D. Iedema},
        Date-Added = {2014-03-13 14:11:38 +0000},
        Date-Modified = {2014-03-13 14:12:08 +0000},
        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{Vasquez:2004ty,
        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 = {2014-03-13 14:11:31 +0000},
        Date-Modified = {2014-03-13 14:12:08 +0000},
        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:2002nr,
        Author = {Berk Hess},
        Date-Added = {2014-03-13 14:11:23 +0000},
        Date-Modified = {2014-03-13 14:12:08 +0000},
        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{Romer2012,
        Author = {R{\"o}mer, Frank and Lervik, Anders and Bresme, Fernando},
        Date-Added = {2014-01-08 20:51:36 +0000},
        Date-Modified = {2014-01-08 20:53:28 +0000},
        Journal = {J. Chem. Phys.},
        Pages = {074503-1 - 8},
        Title = {Nonequilibrium Molecular Dynamics Simulations of the Thermal Conductivity of Water: A Systematic Investigation of the SPC/E and TIP4P/2005 Models},
        Volume = {137},
        Year = {2012}}

@article{Zhang2005,
        Author = {Zhang, Meimei and Lussetti, Enrico and de Souza, Lu{\'\i}s and M\"{u}ller-Plathe, Florian},
        Date-Added = {2014-01-08 20:49:09 +0000},
        Date-Modified = {2014-01-08 20:51:28 +0000},
        Journal = {J. Phys. Chem. B},
        Pages = {15060-15067},
        Title = {Thermal Conductivities of Molecular Liquids by Reverse Nonequilibrium Molecular Dynamics},
        Volume = {109},
        Year = {2005}}

@article{Vardeman2011,
        Author = {Charles F. Vardeman and Kelsey M. Stocker and J. Daniel Gezelter},
        Date-Added = {2013-09-05 23:48:02 +0000},
        Date-Modified = {2013-09-05 23:48:02 +0000},
        Journal = {J. Chem. Theory Comput.},
        Keywords = {Langevin Hull},
        Pages = {834-842},
        Title = {The Langevin Hull: Constant Pressure and Temperature Dynamics for Nonperiodic Systems},
        Volume = {7},
        Year = {2011},
        Bdsk-File-1 = {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}}

@article{EDELSBRUNNER:1994oq,
        Abstract = {Frequently, data in scientific computing is in its abstract form a finite point set in space, and it is sometimes useful or required to compute what one might call the ''shape'' of the set. For that purpose, this article introduces the formal notion of the family of alpha-shapes of a finite point set in R3. Each shape is a well-defined polytope, derived from the Delaunay triangulation of the point set, with a parameter alpha is-an-element-of R controlling the desired level of detail. An algorithm is presented that constructs the entire family of shapes for a given set of size n in time O(n2), worst case. A robust implementation of the algorithm is discussed, and several applications in the area of scientific computing are mentioned.},
        Address = {1515 BROADWAY, NEW YORK, NY 10036},
        Author = {Edelsbrunner, H and Mucke, E.~P.},
        Date = {JAN 1994},
        Date-Added = {2013-09-05 23:47:03 +0000},
        Date-Modified = {2013-09-05 23:47:03 +0000},
        Journal = {ACM Trans. Graphics},
        Keywords = {COMPUTATIONAL GRAPHICS; DELAUNAY TRIANGULATIONS; GEOMETRIC ALGORITHMS; POINT SETS; POLYTOPES; ROBUST IMPLEMENTATION; SCIENTIFIC COMPUTING; SCIENTIFIC VISUALIZATION; SIMPLICIAL COMPLEXES; SIMULATED PERTURBATION; 3-DIMENSIONAL SPACE},
        Pages = {43-72},
        Publisher = {ASSOC COMPUTING MACHINERY},
        Timescited = {270},
        Title = {3-DIMENSIONAL ALPHA-SHAPES},
        Volume = {13},
        Year = {1994}}

@article{Barber96,
        Author = {C.~B. Barber and D.~P. Dobkin and H.~T. Huhdanpaa},
        Date-Added = {2013-09-05 23:46:55 +0000},
        Date-Modified = {2013-09-05 23:46:55 +0000},
        Journal = {ACM Trans. Math. Software},
        Pages = {469-483},
        Title = {The Quickhull Algorithm for Convex Hulls},
        Volume = 22,
        Year = 1996}

@article{Sun2008,
        Author = {Xiuquan Sun and Teng Lin and J. Daniel Gezelter},
        Date-Added = {2013-09-05 20:13:18 +0000},
        Date-Modified = {2013-09-05 20:14:17 +0000},
        Journal = {J. Chem. Phys.},
        Pages = {234107},
        Title = {Langevin Dynamics for Rigid Bodies of Arbitrary Shape},
        Volume = {128},
        Year = {2008}}

@article{Zwanzig,
        Author = {ChihMing Hu and Robert Zwanzig},
        Date-Added = {2013-09-05 20:11:32 +0000},
        Date-Modified = {2013-09-05 20:12:42 +0000},
        Journal = {J. Chem. Phys.},
        Number = {11},
        Pages = {4353-4357},
        Title = {Rotational Friction Coefficients for Spheroids with the Slipping Boundary Condition},
        Volume = {60},
        Year = {1974}}

@article{hartland2011,
        Author = {Hartland, Gregory V.},
        Date-Added = {2013-02-11 22:54:29 +0000},
        Date-Modified = {2013-02-18 17:56:29 +0000},
        Journal = {Chem. Rev.},
        Pages = {3858-3887},
        Title = {Optical Studies of Dynamics in Noble Metal Nanostructures},
        Volume = {11},
        Year = {2011}}

@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 = {2012-12-25 17:47:40 +0000},
        Date-Modified = {2012-12-25 17:47:40 +0000},
        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{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 = {2012-12-25 17:47:40 +0000},
        Date-Modified = {2013-02-18 17:57:24 +0000},
        Doi = {10.1021/jp200672e},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp200672e},
        Journal = {J. Phys. Chem. 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{RevModPhys.61.605,
        Author = {Swartz, E. T. and Pohl, R. O.},
        Date-Added = {2012-12-21 20:34:12 +0000},
        Date-Modified = {2012-12-21 20:34:12 +0000},
        Doi = {10.1103/RevModPhys.61.605},
        Issue = {3},
        Journal = {Rev. Mod. Phys.},
        Month = {Jul},
        Pages = {605--668},
        Publisher = {American Physical Society},
        Title = {Thermal Boundary Resistance},
        Url = {http://link.aps.org/doi/10.1103/RevModPhys.61.605},
        Volume = {61},
        Year = {1989},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/RevModPhys.61.605},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/RevModPhys.61.605}}

@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 = {2013-02-18 18:01:34 +0000},
        Ee = {http://dx.doi.org/10.1002/jcc.21224},
        Journal = {J. Comput. Chem.},
        Number = {13},
        Pages = {2157-2164},
        Title = {PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations},
        Volume = {30},
        Year = {2009}}

@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, Y. and Keffer, David J. and Cummings, Peter T.},
        Date-Added = {2012-12-17 18:38:38 +0000},
        Date-Modified = {2012-12-17 18:38:38 +0000},
        Doi = {10.1021/jp034405s},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp034405s},
        Journal = {J. Phys. Chem. 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{hautman:4994,
        Author = {Joseph Hautman and Michael L. Klein},
        Date-Added = {2012-12-17 18:38:26 +0000},
        Date-Modified = {2012-12-17 18:38:26 +0000},
        Doi = {10.1063/1.457621},
        Journal = {J. Chem. Phys.},
        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{vlugt:cpc2007154,
        Author = {Philipp Schapotschnikow and Ren{\'e} Pool and Thijs J.H. Vlugt},
        Date-Added = {2012-12-17 18:38:20 +0000},
        Date-Modified = {2013-02-18 18:04:43 +0000},
        Doi = {DOI: 10.1016/j.cpc.2007.02.028},
        Issn = {0010-4655},
        Journal = {Comput. Phys. Commun.},
        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{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 = {2012-12-17 18:38:13 +0000},
        Date-Modified = {2012-12-17 18:38:13 +0000},
        Doi = {10.1021/jp981745i},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp981745i},
        Journal = {J. Phys. Chem. 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{PhysRevLett.96.186101,
        Author = {Ge, Zhenbin and Cahill, David G. and Braun, Paul V.},
        Date-Added = {2012-12-17 17:44:53 +0000},
        Date-Modified = {2012-12-17 17:44:53 +0000},
        Doi = {10.1103/PhysRevLett.96.186101},
        Journal = prl,
        Month = {May},
        Number = {18},
        Numpages = {4},
        Pages = {186101},
        Publisher = {American Physical Society},
        Title = {Thermal Conductance of Hydrophilic and Hydrophobic Interfaces},
        Volume = {96},
        Year = {2006},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.96.186101}}

@article{Larson:2007hw,
        Abstract = {Nanoparticles which consist of a plasmonic layer and an iron oxide moiety could provide a promising platform for development of multimodal imaging and therapy approaches in future medicine. However, the feasibility of this platform has yet to be fully explored. In this study we demonstrated the use of gold-coated iron oxide hybrid nanoparticles for combined molecular specific MRI/optical imaging and photothermal therapy of cancer cells. The gold layer exhibits a surface plasmon resonance that provides optical contrast due to light scattering in the visible region and also presents a convenient surface for conjugating targeting moieties, while the iron oxide cores give strong T-2 (spin-spin relaxation time) contrast. The strong optical absorption of the plasmonic gold layer also makes these nanoparticles a promising agent for photothermal therapy. We synthesized hybrid nanoparticles which specifically target epidermal growth factor receptor (EGFR), a common biomarker for many epithelial cancers. We demonstrated molecular specific MRI and optical imaging in MDA-MB-468 breast cancer cells. Furthermore, we showed that receptor-mediated aggregation of anti-EGFR hybrid nanoparticles allows selective destruction of highly proliferative cancer cells using a nanosecond pulsed laser at 700 nm wavelength, a significant shift from the peak absorbance of isolated hybrid nanoparticles at 532 nm.},
        Address = {DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND},
        Author = {Larson, Timothy A. and Bankson, James and Aaron, Jesse and Sokolov, Konstantin},
        Date = {AUG 15 2007},
        Date-Added = {2012-12-17 17:44:44 +0000},
        Date-Modified = {2013-02-18 17:34:30 +0000},
        Doi = {ARTN 325101},
        Journal = {Nanotechnology},
        Pages = {325101},
        Publisher = {IOP PUBLISHING LTD},
        Timescited = {5},
        Title = {Hybrid Plasmonic Magnetic Nanoparticles as Molecular Specific Agents for MRI/Optical Imaging and Photothermal Therapy of Cancer Cells},
        Volume = {18},
        Year = {2007},
        Bdsk-Url-1 = {http://dx.doi.org/325101}}

@article{Huff:2007ye,
        Abstract = {Plasmon-resonant gold nanorods, which have large absorption cross sections at near-infrared frequencies, are excellent candidates as multifunctional agents for image-guided therapies based on localized hyperthermia. The controlled modification of the surface chemistry of the nanorods is of critical importance, as issues of cell-specific targeting and nonspecific uptake must be addressed prior to clinical evaluation. Nanorods coated with cetyltrimethylammonium bromide (a cationic surfactant used in nanorod synthesis) are internalized within hours into KB cells by a nonspecific uptake pathway, whereas the careful removal of cetyltrimethylammonium bromide from nanorods functionalized with folate results in their accumulation on the cell surface over the same time interval. In either case, the nanorods render the tumor cells highly susceptible to photothermal damage when irradiated at the nanorods' longitudinal plasmon resonance, generating extensive blebbing of the cell membrane at laser fluences as low as 30 J/cm(2).},
        Address = {UNITEC HOUSE, 3RD FLOOR, 2 ALBERT PLACE, FINCHLEY CENTRAL, LONDON, N3 1QB, ENGLAND},
        Author = {Huff, Terry B. and Tong, Ling and Zhao, Yan and Hansen, Matthew N. and Cheng, Ji-Xin and Wei, Alexander},
        Date = {FEB 2007},
        Date-Added = {2012-12-17 17:44:36 +0000},
        Date-Modified = {2012-12-17 17:44:36 +0000},
        Doi = {DOI 10.2217/17435889.2.1.125},
        Journal = {Nanomedicine},
        Keywords = {folate receptor; hyperthermia; imaging; nanorods; nonlinear optical microscopy; plasmon resonance; targeted therapy},
        Pages = {125-132},
        Publisher = {FUTURE MEDICINE LTD},
        Timescited = {13},
        Title = {Hyperthermic Effects of Gold Nanorods on Tumor Cells},
        Volume = {2},
        Year = {2007},
        Bdsk-Url-1 = {http://dx.doi.org/10.2217/17435889.2.1.125}}

@article{Jiang:2008hc,
        Abstract = {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 d 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.},
        Affiliation = {National Energy Technology Laboratory, U.S. Department of Energy, Post Office Box 10940, Pittsburgh, Pennsylvania 15236, Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and Parsons Project Services, Inc., South Park, Pennsylvania 15129},
        Author = {Jiang, Hao and Myshakin, Evgeniy M. and Jordan, Kenneth D. and Warzinski, Robert P.},
        Date-Added = {2012-12-17 16:57:19 +0000},
        Date-Modified = {2014-03-13 14:15:48 +0000},
        Doi = {10.1021/jp802942v},
        Issn = {1520-6106},
        Journal = jpcb,
        Pages = {10207-10216},
        Title = {Molecular Dynamics Simulations of the Thermal Conductivity of Methane Hydrate},
        Volume = {112},
        Year = {2008},
        Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp802942v}}

@article{Schelling:2002dp,
        Author = {Schelling, P. K. and Phillpot, S. R. and Keblinski, P.},
        Date = {APR 1 2002},
        Date-Added = {2012-12-17 16:57:10 +0000},
        Date-Modified = {2014-03-13 14:15:48 +0000},
        Doi = {10.1103/PhysRevB.65.144306},
        Isi = {WOS:000174980300055},
        Issn = {1098-0121},
        Journal = prb,
        Month = {Apr},
        Number = {14},
        Pages = {144306},
        Publication-Type = {J},
        Times-Cited = {288},
        Title = {Comparison of Atomic-Level Simulation Methods for Computing Thermal Conductivity},
        Volume = {65},
        Year = {2002},
        Z8 = {12},
        Z9 = {296},
        Zb = {0},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.65.144306}}

@article{Evans:2002tg,
        Author = {Evans, D. J. and Searles, D. J.},
        Date = {NOV 2002},
        Date-Added = {2012-12-17 16:56:59 +0000},
        Date-Modified = {2014-03-13 14:15:48 +0000},
        Doi = {10.1080/00018730210155133},
        Isi = {WOS:000179448200001},
        Issn = {0001-8732},
        Journal = {Adv. Phys.},
        Month = {Nov},
        Number = {7},
        Pages = {1529--1585},
        Publication-Type = {J},
        Times-Cited = {309},
        Title = {The Fluctuation Theorem},
        Volume = {51},
        Year = {2002},
        Z8 = {3},
        Z9 = {311},
        Zb = {9},
        Bdsk-Url-1 = {http://dx.doi.org/10.1080/00018730210155133}}

@article{Berthier:2002ai,
        Author = {Berthier, L. and Barrat, J. L.},
        Date = {APR 8 2002},
        Date-Added = {2012-12-17 16:56:47 +0000},
        Date-Modified = {2014-03-13 14:15:48 +0000},
        Doi = {10.1063/1.1460862},
        Isi = {WOS:000174634200036},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Apr},
        Number = {14},
        Pages = {6228--6242},
        Publication-Type = {J},
        Times-Cited = {172},
        Title = {Nonequilibrium Dynamics and Fluctuation-Dissipation Relation in a Sheared Fluid},
        Volume = {116},
        Year = {2002},
        Z8 = {0},
        Z9 = {172},
        Zb = {1},
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1460862}}

@article{Maginn:1993kl,
        Author = {Maginn, E. J. and Bell, A. T. and Theodorou, D. N.},
        Date = {APR 22 1993},
        Date-Added = {2012-12-17 16:56:40 +0000},
        Date-Modified = {2014-03-13 14:15:48 +0000},
        Doi = {10.1021/j100118a038},
        Isi = {WOS:A1993KY46600039},
        Issn = {0022-3654},
        Journal = jpc,
        Month = {Apr},
        Number = {16},
        Pages = {4173--4181},
        Publication-Type = {J},
        Times-Cited = {198},
        Title = {Transport Diffusivity of Methane in Silicalite from Equilibrium and Nonequilibrium Simulations},
        Volume = {97},
        Year = {1993},
        Z8 = {4},
        Z9 = {201},
        Zb = {0},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/j100118a038}}

@article{Erpenbeck:1984qe,
        Author = {Erpenbeck, J. J.},
        Date = {1984},
        Date-Added = {2012-12-17 16:56:32 +0000},
        Date-Modified = {2014-03-13 14:15:48 +0000},
        Doi = {10.1103/PhysRevLett.52.1333},
        Isi = {WOS:A1984SK96700021},
        Issn = {0031-9007},
        Journal = prl,
        Number = {15},
        Pages = {1333--1335},
        Publication-Type = {J},
        Times-Cited = {189},
        Title = {Shear Viscosity of the Hard-Sphere Fluid via Nonequilibrium Molecular Dynamics},
        Volume = {52},
        Year = {1984},
        Z8 = {0},
        Z9 = {189},
        Zb = {1},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.52.1333}}

@article{Evans:1982oq,
        Author = {Evans, Denis J.},
        Date-Added = {2012-12-17 16:56:24 +0000},
        Date-Modified = {2014-03-13 14:15:48 +0000},
        Journal = {Phys. Lett. A},
        Number = {9},
        Pages = {457--460},
        Title = {Homogeneous NEMD Algorithm for Thermal Conductivity -- Application of Non-Canonical Linear Response Theory},
        Ty = {JOUR},
        Url = {http://www.sciencedirect.com/science/article/B6TVM-46SXM58-S0/1/b270d693318250f3ed0dbce1a535ea50},
        Volume = {91},
        Year = {1982},
        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TVM-46SXM58-S0/1/b270d693318250f3ed0dbce1a535ea50}}

@article{Ashurst:1975eu,
        Author = {Ashurst, W. T. and Hoover, W. G.},
        Date = {1975},
        Date-Added = {2012-12-17 16:56:05 +0000},
        Date-Modified = {2014-03-13 14:15:48 +0000},
        Doi = {10.1103/PhysRevA.11.658},
        Isi = {WOS:A1975V548400036},
        Issn = {1050-2947},
        Journal = pra,
        Number = {2},
        Pages = {658--678},
        Publication-Type = {J},
        Times-Cited = {295},
        Title = {Dense-Fluid Shear Viscosity via Nonequilibrium Molecular Dynamics},
        Volume = {11},
        Year = {1975},
        Z8 = {3},
        Z9 = {298},
        Zb = {1},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.11.658}}

@article{kinaci:014106,
        Author = {A. Kinaci and J. B. Haskins and T. \c{C}a\u{g}in},
        Date-Added = {2012-12-17 16:55:56 +0000},
        Date-Modified = {2012-12-17 16:55:56 +0000},
        Doi = {10.1063/1.4731450},
        Eid = {014106},
        Journal = jcp,
        Keywords = {argon; elemental semiconductors; Ge-Si alloys; molecular dynamics method; nanostructured materials; porous semiconductors; silicon; thermal conductivity},
        Number = {1},
        Numpages = {8},
        Pages = {014106},
        Publisher = {AIP},
        Title = {On Calculation of Thermal Conductivity from Einstein Relation in Equilibrium Molecular Dynamics},
        Url = {http://link.aip.org/link/?JCP/137/014106/1},
        Volume = {137},
        Year = {2012},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/137/014106/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.4731450}}

@article{che:6888,
        Author = {Jianwei Che and Tahir Cagin and Weiqiao Deng and William A. Goddard III},
        Date-Added = {2012-12-17 16:55:48 +0000},
        Date-Modified = {2012-12-17 16:55:48 +0000},
        Doi = {10.1063/1.1310223},
        Journal = jcp,
        Keywords = {diamond; thermal conductivity; digital simulation; vacancies (crystal); Green's function methods; isotope effects},
        Number = {16},
        Pages = {6888-6900},
        Publisher = {AIP},
        Title = {Thermal Conductivity of Diamond and Related Materials from Molecular Dynamics Simulations},
        Url = {http://link.aip.org/link/?JCP/113/6888/1},
        Volume = {113},
        Year = {2000},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/113/6888/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1310223}}

@article{Viscardy:2007rp,
        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 = {MAY 14 2007},
        Date-Added = {2012-12-17 16:55:32 +0000},
        Date-Modified = {2013-02-18 17:58:40 +0000},
        Doi = {ARTN 184513},
        Journal = jcp,
        Pages = {184513},
        Publisher = {AMER INST PHYSICS},
        Timescited = {1},
        Title = {Transport and Helfand Moments in the Lennard-Jones Fluid. II. Thermal Conductivity},
        Volume = {126},
        Year = {2007},
        Bdsk-Url-1 = {http://dx.doi.org/184513}}

@article{PhysRev.119.1,
        Author = {Helfand, Eugene},
        Date-Added = {2012-12-17 16:55:19 +0000},
        Date-Modified = {2012-12-17 16:55:19 +0000},
        Doi = {10.1103/PhysRev.119.1},
        Journal = {Phys. Rev.},
        Month = {Jul},
        Number = {1},
        Numpages = {8},
        Pages = {1--9},
        Publisher = {American Physical Society},
        Title = {Transport Coefficients from Dissipation in a Canonical Ensemble},
        Volume = {119},
        Year = {1960},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.1}}

@article{Evans:1986nx,
        Author = {Evans, Denis J.},
        Date-Added = {2012-12-17 16:55:19 +0000},
        Date-Modified = {2014-03-13 14:15:48 +0000},
        Doi = {10.1103/PhysRevA.34.1449},
        Journal = {Phys. Rev. A},
        Month = {Aug},
        Number = {2},
        Numpages = {4},
        Pages = {1449--1453},
        Publisher = {American Physical Society},
        Title = {Thermal Conductivity of the Lennard-Jones Fluid},
        Volume = {34},
        Year = {1986},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.34.1449}}

@article{MASSOBRIO:1984bl,
        Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
        Author = {Massobrio, C and Ciccotti, G},
        Date = {1984},
        Date-Added = {2012-12-17 16:55:03 +0000},
        Date-Modified = {2012-12-21 22:42:02 +0000},
        Journal = pra,
        Pages = {3191-3197},
        Publisher = {AMERICAN PHYSICAL SOC},
        Timescited = {29},
        Title = {Lennard-Jones Triple-Point Conductivity via Weak External Fields},
        Volume = {30},
        Year = {1984}}

@article{PhysRevB.37.5677,
        Author = {Heyes, David M.},
        Date-Added = {2012-12-17 16:54:55 +0000},
        Date-Modified = {2012-12-17 16:54:55 +0000},
        Doi = {10.1103/PhysRevB.37.5677},
        Journal = prb,
        Month = {Apr},
        Number = {10},
        Numpages = {19},
        Pages = {5677--5696},
        Publisher = {American Physical Society},
        Title = {Transport Coefficients of Lennard-Jones Fluids: A Molecular-Dynamics and Effective-Hard-Sphere Treatment},
        Volume = {37},
        Year = {1988},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.37.5677}}

@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 = {2012-12-17 16:54:55 +0000},
        Date-Modified = {2012-12-17 16:54:55 +0000},
        Doi = {10.1103/PhysRevB.80.195406},
        Journal = prb,
        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 = {2012-12-17 16:54:31 +0000},
        Date-Modified = {2012-12-17 16:54:31 +0000},
        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{doi:10.1021/la904855s,
        Annote = {PMID: 20166728},
        Author = {Alper, Joshua and Hamad-Schifferli, Kimberly},
        Date-Added = {2012-12-17 16:54:12 +0000},
        Date-Modified = {2013-02-18 17:57:03 +0000},
        Doi = {10.1021/la904855s},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/la904855s},
        Journal = {Langmuir},
        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/jp048375k,
        Abstract = { Water- and alcohol-soluble AuPd nanoparticles have been investigated to determine the effect of the organic stabilizing group on the thermal conductance G of the particle/fluid interface. The thermal decays of tiopronin-stabilized 3−5-nm diameter AuPd alloy nanoparticles, thioalkylated ethylene glycol-stabilized 3−5-nm diameter AuPd nanoparticles, and cetyltrimethylammonium bromide-stabilized 22-nm diameter Au-core/AuPd-shell nanoparticles give thermal conductances G ≈ 100−300 MW m-2 K-1 for the particle/water interfaces, approximately an order of magnitude larger than the conductance of the interfaces between alkanethiol-terminated AuPd nanoparticles and toluene. The similar values of G for particles ranging in size from 3 to 24 nm with widely varying surface chemistry indicate that the thermal coupling between AuPd nanoparticles and water is strong regardless of the self-assembled stabilizing group. },
        Author = {Ge, Zhenbin and Cahill, David G. and Braun, Paul V.},
        Date-Added = {2012-12-17 16:54:03 +0000},
        Date-Modified = {2012-12-17 16:54:03 +0000},
        Doi = {10.1021/jp048375k},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp048375k},
        Journal = jpcb,
        Number = {49},
        Pages = {18870-18875},
        Title = {AuPd Metal Nanoparticles as Probes of Nanoscale Thermal Transport in Aqueous Solution},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp048375k},
        Volume = {108},
        Year = {2004},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp048375k},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp048375k}}

@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 = {2012-12-17 16:54:03 +0000},
        Date-Modified = {2013-02-18 17:54:59 +0000},
        Doi = {10.1021/jp8051888},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp8051888},
        Journal = jpcc,
        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.67.054302,
        Author = {Costescu, Ruxandra M. and Wall, Marcel A. and Cahill, David G.},
        Date-Added = {2012-12-17 16:53:48 +0000},
        Date-Modified = {2012-12-17 16:53:48 +0000},
        Doi = {10.1103/PhysRevB.67.054302},
        Journal = prb,
        Month = {Feb},
        Number = {5},
        Numpages = {5},
        Pages = {054302},
        Publisher = {American Physical Society},
        Title = {Thermal Conductance of Epitaxial Interfaces},
        Volume = {67},
        Year = {2003},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.67.054302}}

@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 = {2012-12-17 16:53:36 +0000},
        Date-Modified = {2012-12-17 16:53:36 +0000},
        Doi = {10.1063/1.1524305},
        Journal = {J. Appl. 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}}

@article{Eapen:2007mw,
        Abstract = {In a well-dispersed nanofluid with strong cluster-fluid attraction, thermal conduction paths can arise through percolating amorphouslike interfacial structures. This results in a thermal conductivity enhancement beyond the Maxwell limit of 3 phi, with phi being the nanoparticle volume fraction. Our findings from nonequilibrium molecular dynamics simulations, which are amenable to experimental verification, can provide a theoretical basis for the development of future nanofluids.},
        Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
        Author = {Eapen, Jacob and Li, Ju and Yip, Sidney},
        Date = {DEC 2007},
        Date-Added = {2012-12-17 16:53:30 +0000},
        Date-Modified = {2013-02-18 17:48:08 +0000},
        Doi = {ARTN 062501},
        Journal = pre,
        Pages = {062501},
        Publisher = {AMER PHYSICAL SOC},
        Timescited = {0},
        Title = {Beyond the Maxwell Limit: Thermal Conduction in Nanofluids with Percolating Fluid Structures},
        Volume = {76},
        Year = {2007},
        Bdsk-Url-1 = {http://dx.doi.org/062501}}

@article{Xue:2003ya,
        Abstract = {Using nonequilibrium molecular dynamics simulations in which a temperature gradient is imposed, we determine the thermal resistance of a model liquid-solid interface. Our simulations reveal that the strength of the bonding between liquid and solid atoms plays a key role in determining interfacial thermal resistance. Moreover, we find that the functional dependence of the thermal resistance on the strength of the liquid-solid interactions exhibits two distinct regimes: (i) exponential dependence for weak bonding (nonwetting liquid) and (ii) power law dependence for strong bonding (wetting liquid). The identification of the two regimes of the Kapitza resistance has profound implications for understanding and designing the thermal properties of nanocomposite materials. (C) 2003 American Institute of Physics.},
        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
        Author = {Xue, L and Keblinski, P and Phillpot, SR and Choi, SUS and Eastman, JA},
        Date = {JAN 1 2003},
        Date-Added = {2012-12-17 16:53:22 +0000},
        Date-Modified = {2012-12-17 16:53:22 +0000},
        Doi = {DOI 10.1063/1.1525806},
        Journal = jcp,
        Pages = {337-339},
        Publisher = {AMER INST PHYSICS},
        Timescited = {19},
        Title = {Two Regimes of Thermal Resistance at a Liquid-Solid Interface},
        Volume = {118},
        Year = {2003},
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1525806}}

@article{Xue:2004oa,
        Abstract = {Using non-equilibrium molecular dynamics simulations in which a temperature gradient is imposed, we study how the ordering of the liquid at the liquid-solid interface affects the interfacial thermal resistance. Our simulations of a simple monoatomic liquid show no effect on the thermal transport either normal to the surface or parallel to the surface. Even for of a liquid that is highly confined between two solids, we find no effect on thermal conductivity. This contrasts with well-known significant effect of confinement on the viscoelastic response. Our findings suggest that the experimentally observed large enhancement of thermal conductivity in suspensions of solid nanosized particles (nanofluids) can not be explained by altered thermal transport properties of the layered liquid. (C) 2004 Elsevier Ltd. All rights reserved.},
        Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
        Author = {Xue, L and Keblinski, P and Phillpot, SR and Choi, SUS and Eastman, JA},
        Date = {SEP 2004},
        Date-Added = {2012-12-17 16:53:22 +0000},
        Date-Modified = {2013-02-18 17:47:37 +0000},
        Doi = {DOI 10.1016/ijheatmasstransfer.2004.05.016},
        Journal = {Int. J. Heat Mass Tran.},
        Keywords = {interfacial Thermal Resistance; liquid-solid interface; molecular dynamics simulations; nanofluids},
        Pages = {4277-4284},
        Publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
        Timescited = {29},
        Title = {Effect of Liquid Layering at the Liquid-Solid Interface on Thermal Transport},
        Volume = {47},
        Year = {2004},
        Bdsk-Url-1 = {http://dx.doi.org/10.1016/ijheatmasstransfer.2004.05.016}}

@article{Lee:1999ct,
        Abstract = {Oxide nanofluids were produced and their thermal conductivities were measured by a transient hot-wire method. The experimental results show that these nanofluids, containing a small amount of nanoparticles, have substantially higher thermal conductivities than the same liquids without nanoparticles. Comparisons between experiments and the Hamilton and Crosser model show that the model can predict the thermal conductivity of nanofluids containing large agglomerated Al2O3 particles. However, the model appears to be inadequate for nanofluids containing CuO particles. This suggests that not only particle shape but size is considered to be dominant in enhancing the thermal conductivity of nanofluids.},
        Address = {345 E 47TH ST, NEW YORK, NY 10017 USA},
        Author = {Lee, S and Choi, SUS and Li, S and Eastman, JA},
        Date = {MAY 1999},
        Date-Added = {2012-12-17 16:53:15 +0000},
        Date-Modified = {2013-02-18 17:46:57 +0000},
        Journal = {J. Heat Transf.},
        Keywords = {conduction; enhancement; heat transfer; nanoscale; two-phase},
        Pages = {280-289},
        Publisher = {ASME-AMER SOC MECHANICAL ENG},
        Timescited = {183},
        Title = {Measuring Thermal Conductivity of Fluids Containing Oxide Nanoparticles},
        Volume = {121},
        Year = {1999}}

@article{Keblinski:2002bx,
        Abstract = {Recent measurements on nanofluids have demonstrated that the thermal conductivity increases with decreasing grain size. However, Such increases cannot be explained by existing theories. We explore four possible explanations for this anomalous increase: Brownian motion of the particles, molecular-level layering of the liquid at the liquid/particle interface, the nature of heat transport in the nanoparticles. and the effects of nanoparticle clustering. We show that the key factors in understanding thermal properties of nanofluids are the ballistic, rather than diffusive, nature of heat transport in the nanoparticles, combined with direct or fluid-mediated clustering effects that provide paths for rapid heat transport. (C) 2001 Elsevier Science Ltd. All rights reserved.},
        Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
        Author = {Keblinski, P and Phillpot, SR and Choi, SUS and Eastman, JA},
        Date = {FEB 2002},
        Date-Added = {2012-12-17 16:53:06 +0000},
        Date-Modified = {2013-02-18 17:41:04 +0000},
        Journal = {Int. J. Heat Mass Tran.},
        Keywords = {thermal conductivity; nanofluids; molecular dynamics simulations; ballistic heat transport},
        Pages = {855-863},
        Publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
        Timescited = {161},
        Title = {Mechanisms of Heat Flow in Suspensions of Nano-Sized Particles (Nanofluids)},
        Volume = {45},
        Year = {2002}}

@article{Eastman:2001wb,
        Abstract = {It is shown that a "nanofluid" consisting of copper nanometer-sized particles dispersed in ethylene glycol has a much higher effective thermal conductivity than either pure ethylene glycol or ethylene glycol containing the same volume fraction of dispersed oxide nanoparticles. The effective thermal conductivity of ethylene glycol is shown to be increased by up to 40\% for a nanofluid consisting of ethylene glycol containing approximately 0.3 vol \% Cu nanoparticles of mean diameter < 10 nm. The results are anomalous based on previous theoretical calculations that had predicted a strong effect of particle shape on effective nanofluid thermal conductivity, but no effect of either particle size or particle thermal conductivity. (C) 2001 American Institute of Physics.},
        Address = {2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA},
        Author = {Eastman, JA and Choi, SUS and Li, S and Yu, W and Thompson, LJ},
        Date = {FEB 5 2001},
        Date-Added = {2012-12-17 16:52:55 +0000},
        Date-Modified = {2013-02-18 17:40:41 +0000},
        Journal = {Appl. Phys. Lett.},
        Pages = {718-720},
        Publisher = {AMER INST PHYSICS},
        Timescited = {246},
        Title = {Anomalously Increased Effective Thermal Conductivities of Ethylene Glycol-Based Nanofluids Containing Copper Nanoparticles},
        Volume = {78},
        Year = {2001}}

@article{Eapen:2007th,
        Abstract = {Transient hot-wire data on thermal conductivity of suspensions of silica and perfluorinated particles show agreement with the mean-field theory of Maxwell but not with the recently postulated microconvection mechanism. The influence of interfacial thermal resistance, convective effects at microscales, and the possibility of thermal conductivity enhancements beyond the Maxwell limit are discussed.},
        Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
        Author = {Eapen, Jacob and Williams, Wesley C. and Buongiorno, Jacopo and Hu, Lin-Wen and Yip, Sidney and Rusconi, Roberto and Piazza, Roberto},
        Date = {AUG 31 2007},
        Date-Added = {2012-12-17 16:52:46 +0000},
        Date-Modified = {2013-02-18 17:40:15 +0000},
        Doi = {ARTN 095901},
        Journal = prl,
        Pages = {095901},
        Publisher = {AMER PHYSICAL SOC},
        Timescited = {8},
        Title = {Mean-Field Versus Microconvection Effects in Nanofluid Thermal Conduction},
        Volume = {99},
        Year = {2007},
        Bdsk-Url-1 = {http://dx.doi.org/095901}}

@article{Plech:2005kx,
        Abstract = {The transient structural response of laser excited gold nanoparticle sols has been recorded by pulsed X-ray scattering. Time resolved wide angle and small angle scattering (SAXS) record the changes in structure both of the nanoparticles and the water environment subsequent to femtosecond laser excitation. Within the first nanosecond after the excitation of the nanoparticles, the water phase shows a signature of compression, induced by a heat-induced evaporation of the water shell close to the heated nanoparticles. The particles themselves undergo a melting transition and are fragmented to Form new clusters in the nanometer range. (C) 2004 Elsevier B.V. All rights reserved.},
        Author = {Plech, A and Kotaidis, V and Lorenc, M and Wulff, M},
        Date-Added = {2012-12-17 16:52:34 +0000},
        Date-Modified = {2012-12-17 16:52:34 +0000},
        Doi = {DOI 10.1016/j.cplett.2004.11.072},
        Journal = cpl,
        Local-Url = {file://localhost/Users/charles/Documents/Papers/sdarticle3.pdf},
        Pages = {565-569},
        Title = {Thermal Dynamics in Laser Excited Metal Nanoparticles},
        Volume = {401},
        Year = {2005},
        Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.11.072}}

@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 = {2012-12-17 16:52:22 +0000},
        Date-Modified = {2013-02-18 17:34:52 +0000},
        Doi = {ARTN 224301},
        Journal = {Phys. Rev. B},
        Local-Url = {file://localhost/Users/charles/Documents/Papers/e2243010.pdf},
        Pages = {224301},
        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{Mazzaglia:2008to,
        Abstract = {Amphiphilic cyclodextrins (CDs) modified in the upper rim with thiohexyl groups and in the lower rim with oligoethylene amino (SC6NH2) or oligoethylene hydroxyl groups (SC6OH) can bind gold colloids, yielding Au/CD particles with an average hydrodynamic radius (RH) of 2 and 25 rim in water solution. The systems were investigated by UV-vis, quasi-elastic light scattering, and FTIR-ATR techniques. The concentration of amphiphiles was kept above the concentration of gold colloids to afford complete covering. In the case of SC6NH2, basic conditions (Et3N, pH 11) yield promptly the decoration of Au, which can be stabilized by linkage of CD amino and/or thioether groups. The critical aggregation concentration of SC6NH2 was measured (similar to 4 mu M) by surface tension measurements, pointing out that about 50\% of CDs are present in nonaggregated form. Whereas Au/SC6NH2 colloids were stable in size and morphology for at least one month, the size of the Au/SC6OH system increases remarkably, forming nanoaggregates of 20 and 80 rim in two hours. Under physiological conditions, the gold/amino amphiphiles system can internalize in HeLa cells, as shown by extinction spectra registered on the immobilized cells. The gold delivered by cyclodextrins can induce photothermal damage upon irradiation, doubling the cell mortality with respect to uncovered gold colloids. These findings can open useful perspectives to the application of these self-assembled systems in cancer photothermal therapy.},
        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
        Author = {Mazzaglia, Antonino and Trapani, Mariachiara and Villari, Valentina and Micali, Norberto and Merlo, Francesca Marino and Zaccaria, Daniela and Sciortino, Maria Teresa and Previti, Francesco and Patane, Salvatore and Scolaro, Luigi Monsu},
        Date = {MAY 1 2008},
        Date-Added = {2012-12-17 16:52:15 +0000},
        Date-Modified = {2012-12-17 16:52:15 +0000},
        Doi = {DOI 10.1021/jp7120033},
        Journal = jpcc,
        Pages = {6764-6769},
        Publisher = {AMER CHEMICAL SOC},
        Timescited = {0},
        Title = {Amphiphilic Cyclodextrins as Capping Agents for Gold Colloids: A Spectroscopic Investigation with Perspectives in Photothermal Therapy},
        Volume = {112},
        Year = {2008},
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp7120033}}

@article{Gnyawali:2008lp,
        Abstract = {Tissue surface temperature distribution on the treatment site can serve as an indicator for the effectiveness of a photothermal therapy. In this study, both infrared thermography and theoretical simulation were used to determine the surface temperature distribution during laser irradiation of both gel phantom and animal tumors. Selective photothermal interaction was attempted by using intratumoral indocyanine green enhancement and irradiation via a near-infrared laser. An immunoadjuvant was also used to enhance immunological responses during tumor treatment. Monte Carlo method for tissue absorption of light and finite difference method for heat diffusion in tissue were used to simulate the temperature distribution during the selective laser photothermal interaction. An infrared camera was used to capture the thermal images during the laser treatment and the surface temperature was determined. Our findings show that the theoretical and experimental results are in good agreement and that the surface temperature of irradiated tissue can be controlled with appropriate dye and adjuvant enhancement. These results can be used to control the laser tumor treatment parameters and to optimize the treatment outcome. More importantly, when used with immunotherapy as a precursor of immunological responses, the selective photothermal treatment can be guided by the tissue temperature profiles both in the tumor and on the surface.},
        Address = {TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY},
        Author = {Gnyawali, Surya C. and Chen, Yicho and Wu, Feng and Bartels, Kenneth E. and Wicksted, James P. and Liu, Hong and Sen, Chandan K. and Chen, Wei R.},
        Date = {FEB 2008},
        Date-Added = {2012-12-17 16:52:08 +0000},
        Date-Modified = {2013-02-18 17:32:43 +0000},
        Doi = {DOI 10.1007/s11517-007-0251-5},
        Journal = {Med. Biol. Eng. Comput.},
        Keywords = {infrared thermography; indocyanine green; glycated chitosan; surface temperature; Monte Carlo simulation},
        Pages = {159-168},
        Publisher = {SPRINGER HEIDELBERG},
        Timescited = {0},
        Title = {Temperature Measurement on Tissue Surface During Laser Irradiation},
        Volume = {46},
        Year = {2008},
        Bdsk-Url-1 = {http://dx.doi.org/10.1007/s11517-007-0251-5}}

@article{Petrova:2007ad,
        Abstract = {This paper describes our recent time-resolved spectroscopy studies of the properties of gold particles at high laser excitation levels. In these experiments, an intense pump laser pulse rapidly heats the particle, creating very high lattice temperatures - up to the melting point of bulk gold. These high temperatures can have dramatic effects on the particle and the surroundings. The lattice temperature created is determined by observing the coherently excited the vibrational modes of the particles. The periods of these modes depend on temperature, thus, they act as an internal thermometer. We have used these experiments to provide values for the threshold temperatures for explosive boiling of the solvent surrounding the particles, and laser induced structural transformations in non-spherical particles. The results of these experiments are relevant to the use of metal nanoparticles in photothermal therapy, where laser induced heating is used to selectively kill cells.},
        Address = {LEKTORAT MINT, POSTFACH 80 13 60, D-81613 MUNICH, GERMANY},
        Author = {Petrova, Hristina and Hu, Min and Hartland, Gregory V.},
        Date = {2007},
        Date-Added = {2012-12-17 16:52:01 +0000},
        Date-Modified = {2013-02-18 17:32:23 +0000},
        Doi = {DOI 10.1524/zpch.2007.221.3.361},
        Journal = {Z Phys. Chem.},
        Keywords = {metal nanoparticles; phonon modes; photothermal properties; laser-induced heating},
        Pages = {361-376},
        Publisher = {OLDENBOURG VERLAG},
        Timescited = {2},
        Title = {Photothermal Properties of Gold Nanoparticles},
        Volume = {221},
        Year = {2007},
        Bdsk-Url-1 = {http://dx.doi.org/10.1524/zpch.2007.221.3.361}}

@article{Jain:2007ux,
        Abstract = {Noble metal, especially gold (Au) and silver (Ag) nanoparticles exhibit unique and tunable optical properties on account of their surface plasmon resonance (SPR). In this review, we discuss the SPR-enhanced optical properties of noble metal nanoparticles, with an emphasis on the recent advances in the utility of these plasmonic properties in molecular-specific imaging and sensing, photo-diagnostics, and selective photothermal therapy. The strongly enhanced SPR scattering from Au nanoparticles makes them useful as bright optical tags for molecular-specific biological imaging and detection using simple dark-field optical microscopy. On the other hand, the SPR absorption of the nanoparticles has allowed their use in the selective laser photothermal therapy of cancer. We also discuss the sensitivity of the nanoparticle SPR frequency to the local medium dielectric constant, which has been successfully exploited for the optical sensing of chemical and biological analytes. Plasmon coupling between metal nanoparticle pairs is also discussed, which forms the basis for nanoparticle assembly-based biodiagnostics and the plasmon ruler for dynamic measurement of nanoscale distances in biological systems.},
        Address = {233 SPRING STREET, NEW YORK, NY 10013 USA},
        Author = {Jain, Prashant K. and Huang, Xiaohua and El-Sayed, Ivan H. and El-Sayad, Mostafa A.},
        Date = {SEP 2007},
        Date-Added = {2012-12-17 16:51:52 +0000},
        Date-Modified = {2013-02-18 17:25:37 +0000},
        Doi = {DOI 10.1007/s11468-007-9031-1},
        Journal = {Plasmonics},
        Keywords = {surface plasmon resonance (SPR); SPR sensing; Mie scattering; metal nanocrystals for biodiagnostics; photothermal therapy; plasmon coupling},
        Number = {3},
        Pages = {107-118},
        Publisher = {SPRINGER},
        Timescited = {2},
        Title = {Review of Some Interesting Surface Plasmon Resonance-Enhanced Properties of Noble Metal Nanoparticles and Their Applications to Biosystems},
        Volume = {2},
        Year = {2007},
        Bdsk-Url-1 = {http://dx.doi.org/10.1007/s11468-007-9031-1}}

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

@article{Kuang:2010if,
        Author = {Shenyu Kuang and J. Daniel Gezelter},
        Date-Added = {2012-12-05 22:18:01 +0000},
        Date-Modified = {2014-03-13 14:21:57 +0000},
        Journal = {J. Chem. Phys.},
        Keywords = {NIVS, RNEMD, NIVS-RNEMD},
        Month = {October},
        Pages = {164101-1 - 164101-9},
        Title = {A Gentler Approach to RNEMD: Nonisotropic Velocity Scaling for Computing Thermal Conductivity and Shear Viscosity},
        Volume = {133},
        Year = {2010}}

@article{Kuang:2012fe,
        Author = {Shenyu Kuang and J. Daniel Gezelter},
        Date-Added = {2012-12-05 22:18:01 +0000},
        Date-Modified = {2014-03-13 14:21:57 +0000},
        Journal = {Mol. Phys.},
        Keywords = {VSS, RNEMD, VSS-RNEMD},
        Month = {May},
        Number = {9-10},
        Pages = {691-701},
        Title = {Velocity Shearing and Scaling RNEMD: A Minimally Perturbing Method for Simulating Temperature and Momentum Gradients},
        Volume = {110},
        Year = {2012}}

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

@article{Medina2011,
        Abstract = {Molecular dynamics (MD) simulations are carried out on a system of rigid or flexible water molecules at a series of temperatures between 273 and 368&#xa0;K. Collective transport coefficients, such as shear and bulk viscosities are calculated, and their behavior is systematically investigated as a function of flexibility and temperature. It is found that by including the intramolecular terms in the potential the calculated viscosity values are in overall much better agreement, compared to earlier and recent available experimental data, than those obtained with the rigid SPC/E model. The effect of the intramolecular degrees of freedom on transport properties of liquid water is analyzed and the incorporation of polarizability is discussed for further improvements. To our knowledge the present study constitutes the first compendium of results on viscosities for pure liquid water, including flexible models, that has been assembled.},
        Author = {J.S. Medina and R. Prosmiti and P. Villarreal and G. Delgado-Barrio and G. Winter and B. Gonz{\'a}lez and J.V. Alem{\'a}n and C. Collado},
        Date-Added = {2011-12-13 17:08:34 -0500},
        Date-Modified = {2011-12-13 17:08:49 -0500},
        Doi = {10.1016/j.chemphys.2011.07.001},
        Issn = {0301-0104},
        Journal = {Chemical Physics},
        Keywords = {Viscosity calculations},
        Number = {1-3},
        Pages = {9 - 18},
        Title = {Molecular Dynamics Simulations of Rigid and Flexible Water Models: Temperature Dependence of Viscosity},
        Url = {http://www.sciencedirect.com/science/article/pii/S0301010411002813},
        Volume = {388},
        Year = {2011},
        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0301010411002813},
        Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.chemphys.2011.07.001}}

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

@article{Shenogina:2009ix,
        Author = {Shenogina, Natalia and Godawat, Rahul and Keblinski, Pawel and Garde, Shekhar},
        Date-Added = {2011-12-13 12:48:51 -0500},
        Date-Modified = {2014-03-13 14:21:57 +0000},
        Doi = {10.1103/PhysRevLett.102.156101},
        Journal = {Phys. Rev. Lett.},
        Month = {Apr},
        Number = {15},
        Numpages = {4},
        Pages = {156101},
        Publisher = {American Physical Society},
        Title = {How Wetting and Adhesion Affect Thermal Conductance of a Range of Hydrophobic to Hydrophilic Aqueous Interfaces},
        Volume = {102},
        Year = {2009},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.102.156101}}

@article{Patel:2005zm,
        Abstract = { Systems with nanoscopic features contain a high density of interfaces. Thermal transport in such systems can be governed by the resistance to heat transfer, the Kapitza resistance (RK), at the interface. Although soft interfaces, such as those between immiscible liquids or between a biomolecule and solvent, are ubiquitous, few studies of thermal transport at such interfaces have been reported. Here we characterize the interfacial conductance, 1/RK, of soft interfaces as a function of molecular architecture, chemistry, and the strength of cross-interfacial intermolecular interactions through detailed molecular dynamics simulations. The conductance of various interfaces studied here, for example, water−organic liquid, water−surfactant, surfactant−organic liquid, is relatively high (in the range of 65−370 MW/m2 K) compared to that for solid−liquid interfaces (∼10 MW/m2 K). Interestingly, the dependence of interfacial conductance on the chemistry and molecular architecture cannot be explained solely in terms of either bulk property mismatch or the strength of intermolecular attraction between the two phases. The observed trends can be attributed to a combination of strong cross-interface intermolecular interactions and good thermal coupling via soft vibration modes present at liquid−liquid interfaces. },
        Annote = {PMID: 16277458},
        Author = {Patel, Harshit A. and Garde, Shekhar and Keblinski, Pawel},
        Date-Added = {2011-12-13 12:48:51 -0500},
        Date-Modified = {2014-03-13 20:42:07 +0000},
        Doi = {10.1021/nl051526q},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/nl051526q},
        Journal = {Nano Lett.},
        Number = {11},
        Pages = {2225-2231},
        Title = {Thermal Resistance of Nanoscopic Liquid-Liquid Interfaces: Dependence on Chemistry and Molecular Architecture},
        Url = {http://pubs.acs.org/doi/abs/10.1021/nl051526q},
        Volume = {5},
        Year = {2005},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/nl051526q},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/nl051526q}}

@article{melchionna93,
        Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
        Date-Added = {2011-12-12 17:52:15 -0500},
        Date-Modified = {2011-12-12 17:52:15 -0500},
        Journal = {Mol. Phys.},
        Pages = {533-544},
        Title = {Hoover {\sc NPT} Dynamics for Systems Varying in Shape and Size},
        Volume = 78,
        Year = 1993}

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

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

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

@article{ISI:000167766600035,
        Abstract = {Molecular dynamics simulations are used to
                  investigate the separation of water films adjacent
                  to a hot metal surface. The simulations clearly show
                  that the water layers nearest the surface overheat
                  and undergo explosive boiling. For thick films, the
                  expansion of the vaporized molecules near the
                  surface forces the outer water layers to move away
                  from the surface. These results are of interest for
                  mass spectrometry of biological molecules, steam
                  cleaning of surfaces, and medical procedures.},
        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
        Affiliation = {Garrison, BJ (Reprint Author), Penn State Univ, Dept Chem, University Pk, PA 16802 USA. Penn State Univ, Dept Chem, University Pk, PA 16802 USA. Penn State Univ, Inst Mat Res, University Pk, PA 16802 USA. Univ Virginia, Dept Mat Sci \& Engn, Charlottesville, VA 22903 USA.},
        Author = {Dou, YS and Zhigilei, LV and Winograd, N and Garrison, BJ},
        Date-Added = {2011-12-07 15:02:32 -0500},
        Date-Modified = {2011-12-07 15:02:32 -0500},
        Doc-Delivery-Number = {416ED},
        Issn = {1089-5639},
        Journal = {J. Phys. Chem. A},
        Journal-Iso = {J. Phys. Chem. A},
        Keywords-Plus = {MOLECULAR-DYNAMICS SIMULATIONS; ASSISTED LASER-DESORPTION; FROZEN AQUEOUS-SOLUTIONS; COMPUTER-SIMULATION; ORGANIC-SOLIDS; VELOCITY DISTRIBUTIONS; PARTICLE BOMBARDMENT; MASS-SPECTROMETRY; PHASE EXPLOSION; LIQUID WATER},
        Language = {English},
        Month = {MAR 29},
        Number = {12},
        Number-Of-Cited-References = {65},
        Pages = {2748-2755},
        Publisher = {AMER CHEMICAL SOC},
        Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
        Times-Cited = {66},
        Title = {Explosive Boiling of Water Films Adjacent to Heated Surfaces: A Microscopic Description},
        Type = {Article},
        Unique-Id = {ISI:000167766600035},
        Volume = {105},
        Year = {2001}}

@article{Chen90,
        Author = {A.~P. Sutton and J. Chen},
        Date-Added = {2011-12-07 15:01:59 -0500},
        Date-Modified = {2013-02-18 18:01:16 +0000},
        Journal = {Phil. Mag. Lett.},
        Pages = {139-146},
        Title = {Long-Range Finnis Sinclair Potentials},
        Volume = 61,
        Year = {1990}}

@article{PhysRevB.59.3527,
        Author = {Qi, Yue and \c{C}a\v{g}in, Tahir and Kimura, Yoshitaka and {Goddard III}, William A.},
        Date-Added = {2011-12-07 15:01:36 -0500},
        Date-Modified = {2013-02-18 18:00:57 +0000},
        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: {C}u-{A}g and {C}u-{N}i},
        Volume = {59},
        Year = {1999},
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.59.3527}}

@article{Bedrov:2000,
        Abstract = {We have applied a new nonequilibrium molecular
                  dynamics (NEMD) method {[}F. Muller-Plathe,
                  J. Chem. Phys. 106, 6082 (1997)] previously applied
                  to monatomic Lennard-Jones fluids in the
                  determination of the thermal conductivity of
                  molecular fluids. The method was modified in order
                  to be applicable to systems with holonomic
                  constraints. Because the method involves imposing a
                  known heat flux it is particularly attractive for
                  systems involving long-range and many-body
                  interactions where calculation of the microscopic
                  heat flux is difficult. The predicted thermal
                  conductivities of liquid n-butane and water using
                  the imposed-flux NEMD method were found to be in a
                  good agreement with previous simulations and
                  experiment. (C) 2000 American Institute of
                  Physics. {[}S0021-9606(00)50841-1].},
        Address = {2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA},
        Affiliation = {Bedrov, D (Reprint Author), Univ Utah, Dept Chem \& Fuels Engn, 122 S Cent Campus Dr,Rm 304, Salt Lake City, UT 84112 USA. Univ Utah, Dept Chem \& Fuels Engn, Salt Lake City, UT 84112 USA. Univ Utah, Dept Mat Sci \& Engn, Salt Lake City, UT 84112 USA.},
        Author = {Bedrov, D and Smith, GD},
        Date-Added = {2011-12-07 15:00:27 -0500},
        Date-Modified = {2011-12-07 15:00:27 -0500},
        Doc-Delivery-Number = {369BF},
        Issn = {0021-9606},
        Journal = {J. Chem. Phys.},
        Journal-Iso = {J. Chem. Phys.},
        Keywords-Plus = {EFFECTIVE PAIR POTENTIALS; TRANSPORT-PROPERTIES; CANONICAL ENSEMBLE; NORMAL-BUTANE; ALGORITHMS; SHAKE; WATER},
        Language = {English},
        Month = {NOV 8},
        Number = {18},
        Number-Of-Cited-References = {26},
        Pages = {8080-8084},
        Publisher = {AMER INST PHYSICS},
        Read = {1},
        Subject-Category = {Physics, Atomic, Molecular \& Chemical},
        Times-Cited = {23},
        Title = {Thermal Conductivity of Molecular Fluids from Molecular Dynamics Simulations: Application of a New Imposed-Flux Method},
        Type = {Article},
        Unique-Id = {ISI:000090151400044},
        Volume = {113},
        Year = {2000}}

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

@article{doi:10.1021/jp048434u,
        Abstract = { The different possible proton-ordered structures of ice Ih for an orthorombic unit cell with 8 water molecules were derived. The number of unique structures was found to be 16. The crystallographic coordinates of these are reported. The energetics of the different polymorphs were investigated by quantum-mechanical density-functional theory calculations and for comparison by molecular-mechanics analytical potential models. The polymorphs were found to be close in energy, i.e., within approximately 0.25 kcal/mol H2O, on the basis of the quantum-chemical DFT methods. At 277 K, the different energy levels are about evenly populated, but at a lower temperature, a transition to an ordered form is expected. This form was found to agree with the ice phase XI. The difference in lattice energies among the polymorphs was rationalized in terms of structural characteristics. The most important parameters to determine the lattice energies were found to be the distributions of water dimer H-bonded pair conformations, in an intricate manner. },
        Author = {Hirsch, Tomas K. and Ojam{\"a}e, Lars},
        Date-Added = {2011-12-07 14:38:30 -0500},
        Date-Modified = {2011-12-07 14:38:30 -0500},
        Doi = {10.1021/jp048434u},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp048434u},
        Journal = {J. Phys. Chem. B},
        Number = {40},
        Pages = {15856-15864},
        Title = {Quantum-Chemical and Force-Field Investigations of Ice Ih:  Computation of Proton-Ordered Structures and Prediction of Their Lattice Energies},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp048434u},
        Volume = {108},
        Year = {2004},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp048434u},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp048434u}}

@article{Meineke:2005gd,
        Abstract = {OOPSE is a new molecular dynamics simulation program
                  that is capable of efficiently integrating equations
                  of motion for atom types with orientational degrees
                  of freedom (e.g. #sticky# atoms and point
                  dipoles). Transition metals can also be simulated
                  using the embedded atom method (EAM) potential
                  included in the code. Parallel simulations are
                  carried out using the force-based decomposition
                  method. Simulations are specified using a very
                  simple C-based meta-data language. A number of
                  advanced integrators are included, and the basic
                  integrator for orientational dynamics provides
                  substantial improvements over older quaternion-based
                  schemes.},
        Address = {111 RIVER ST, HOBOKEN, NJ 07030 USA},
        Author = {Meineke, M. A. and Vardeman, C. F. and Lin, T and Fennell, CJ and Gezelter, J. D.},
        Date-Added = {2011-12-07 13:33:04 -0500},
        Date-Modified = {2011-12-07 13:33:04 -0500},
        Doi = {DOI 10.1002/jcc.20161},
        Isi = {000226558200006},
        Isi-Recid = {142688207},
        Isi-Ref-Recids = {67885400 50663994 64190493 93668415 46699855 89992422 57614458 49016001 61447131 111114169 68770425 52728075 102422498 66381878 32391149 134477335 53221357 9929643 59492217 69681001 99223832 142688208 94600872 91658572 54857943 117365867 69323123 49588888 109970172 101670714 142688209 121603296 94652379 96449138 99938010 112825758 114905670 86802042 121339042 104794914 82674909 72096791 93668384 90513335 142688210 23060767 63731466 109033408 76303716 31384453 97861662 71842426 130707771 125809946 66381889 99676497},
        Journal = {J. Comput. Chem.},
        Keywords = {OOPSE; molecular dynamics},
        Month = feb,
        Number = {3},
        Pages = {252-271},
        Publisher = {JOHN WILEY \& SONS INC},
        Times-Cited = {9},
        Title = {OOPSE: An Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
        Volume = {26},
        Year = {2005},
        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000226558200006},
        Bdsk-Url-2 = {http://dx.doi.org/10.1002/jcc.20161}}

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

@article{Tenney:2010rp,
        Abstract = {The reverse nonequilibrium molecular dynamics
                  (RNEMD) method calculates the shear viscosity of a
                  fluid by imposing a nonphysical exchange of momentum
                  and measuring the resulting shear velocity
                  gradient. In this study we investigate the range of
                  momentum flux values over which RNEMD yields usable
                  (linear) velocity gradients. We find that nonlinear
                  velocity profiles result primarily from gradients in
                  fluid temperature and density. The temperature
                  gradient results from conversion of heat into bulk
                  kinetic energy, which is transformed back into heat
                  elsewhere via viscous heating. An expression is
                  derived to predict the temperature profile resulting
                  from a specified momentum flux for a given fluid and
                  simulation cell. Although primarily bounded above,
                  we also describe milder low-flux limitations. RNEMD
                  results for a Lennard-Jones fluid agree with
                  equilibrium molecular dynamics and conventional
                  nonequilibrium molecular dynamics calculations at
                  low shear, but RNEMD underpredicts viscosity
                  relative to conventional NEMD at high shear.},
        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
        Affiliation = {Tenney, CM (Reprint Author), Univ Notre Dame, Dept Chem \& Biomol Engn, 182 Fitzpatrick Hall, Notre Dame, IN 46556 USA. {[}Tenney, Craig M.; Maginn, Edward J.] Univ Notre Dame, Dept Chem \& Biomol Engn, Notre Dame, IN 46556 USA.},
        Article-Number = {014103},
        Author = {Tenney, Craig M. and Maginn, Edward J.},
        Author-Email = {ed@nd.edu},
        Date-Added = {2011-12-05 18:29:08 -0500},
        Date-Modified = {2014-03-13 14:21:57 +0000},
        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{Muller-Plathe:1999ao,
        Abstract = {A nonequilibrium method for calculating the shear
                  viscosity is presented. It reverses the
                  cause-and-effect picture customarily used in
                  nonequilibrium molecular dynamics: the effect, the
                  momentum flux or stress, is imposed, whereas the
                  cause, the velocity gradient or shear rate, is
                  obtained from the simulation. It differs from other
                  Norton-ensemble methods by the way in which the
                  steady-state momentum flux is maintained. This
                  method involves a simple exchange of particle
                  momenta, which is easy to implement. Moreover, it
                  can be made to conserve the total energy as well as
                  the total linear momentum, so no coupling to an
                  external temperature bath is needed. The resulting
                  raw data, the velocity profile, is a robust and
                  rapidly converging property. The method is tested on
                  the Lennard-Jones fluid near its triple point. It
                  yields a viscosity of 3.2-3.3, in Lennard-Jones
                  reduced units, in agreement with literature
                  results. {[}S1063-651X(99)03105-0].},
        Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
        Affiliation = {Muller-Plathe, F (Reprint Author), Max Planck Inst Polymerforsch, Ackermannweg 10, D-55128 Mainz, Germany. Max Planck Inst Polymerforsch, D-55128 Mainz, Germany.},
        Author = {M\"{u}ller-Plathe, F},
        Date-Added = {2011-12-05 18:18:37 -0500},
        Date-Modified = {2014-03-13 14:21:57 +0000},
        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{Muller-Plathe:1997wq,
        Abstract = {A nonequilibrium molecular dynamics method for
                  calculating the thermal conductivity is
                  presented. It reverses the usual cause and effect
                  picture. The ''effect,'' the heat flux, is imposed
                  on the system and the ''cause,'' the temperature
                  gradient is obtained from the simulation. Besides
                  being very simple to implement, the scheme offers
                  several advantages such as compatibility with
                  periodic boundary conditions, conservation of total
                  energy and total linear momentum, and the sampling
                  of a rapidly converging quantity (temperature
                  gradient) rather than a slowly converging one (heat
                  flux). The scheme is tested on the Lennard-Jones
                  fluid. (C) 1997 American Institute of Physics.},
        Address = {WOODBURY},
        Author = {M\"{u}ller-Plathe, F.},
        Cited-Reference-Count = {13},
        Date = {APR 8},
        Date-Added = {2011-12-05 18:18:37 -0500},
        Date-Modified = {2014-03-13 14:21:57 +0000},
        Document-Type = {Article},
        Isi = {ISI:A1997WR62000032},
        Isi-Document-Delivery-Number = {WR620},
        Iso-Source-Abbreviation = {J. Chem. Phys.},
        Issn = {0021-9606},
        Journal = {J. Chem. Phys.},
        Language = {English},
        Month = {Apr},
        Number = {14},
        Page-Count = {4},
        Pages = {6082--6085},
        Publication-Type = {J},
        Publisher = {AMER INST PHYSICS},
        Publisher-Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999},
        Reprint-Address = {MullerPlathe, F, MAX PLANCK INST POLYMER RES, D-55128 MAINZ, GERMANY.},
        Source = {J CHEM PHYS},
        Subject-Category = {Physics, Atomic, Molecular & Chemical},
        Times-Cited = {106},
        Title = {A Simple Nonequilibrium Molecular Dynamics Method for Calculating the Thermal Conductivity},
        Volume = {106},
        Year = {1997}}

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

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

@misc{openmd,
        Author = {J. Daniel Gezelter and Shenyu Kuang and James Marr and Kelsey Stocker and Chunlei Li and Charles F. Vardeman and Teng Lin and Christopher J. Fennell and Xiuquan Sun and Kyle Daily and Yang Zheng and Matthew A. Meineke},
        Date-Added = {2011-11-18 15:32:23 -0500},
        Date-Modified = {2014-03-13 20:42:36 +0000},
        Howpublished = {Available at {\tt http://openmd.org}},
        Title = {{OpenMD, an Open Source Engine for Molecular Dynamics}}}

@article{Kuang:2011ef,
        Author = {Kuang, Shenyu and Gezelter, J. Daniel},
        Date-Added = {2011-11-18 13:03:06 -0500},
        Date-Modified = {2014-03-13 14:21:57 +0000},
        Doi = {10.1021/jp2073478},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp2073478},
        Journal = {J. Phys. Chem. C},
        Number = {45},
        Pages = {22475-22483},
        Title = {Simulating Interfacial Thermal Conductance at Metal-Solvent Interfaces: The Role of Chemical Capping Agents},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp2073478},
        Volume = {115},
        Year = {2011},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp2073478},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp2073478}}

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

@article{PhysRevLett.82.4671,
        Author = {Barrat, Jean-Louis and Bocquet, Lyd\'eric},
        Date-Added = {2011-11-01 16:44:29 -0400},
        Date-Modified = {2011-11-01 16:44:29 -0400},
        Doi = {10.1103/PhysRevLett.82.4671},
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        Title = {Large Slip Effect at a Nonwetting Fluid-Solid Interface},
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        Volume = {82},
        Year = {1999},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevLett.82.4671},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevLett.82.4671}}

@article{10.1063/1.1610442,
        Author = {J. R. Schmidt and J. L. Skinner},
        Coden = {JCPSA6},
        Date-Added = {2011-10-13 16:28:43 -0400},
        Date-Modified = {2011-12-15 13:11:53 -0500},
        Doi = {DOI:10.1063/1.1610442},
        Eissn = {10897690},
        Issn = {00219606},
        Journal = {J. Chem. Phys.},
        Keywords = {hydrodynamics; Brownian motion; molecular dynamics method; diffusion;},
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        Pages = {8062-8068},
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        Title = {Hydrodynamic Boundary Conditions, the Stokes?Einstein Law, and Long-Time Tails in the Brownian Limit},
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        Volume = {119},
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        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}

@article{10.1063/1.3274802,
        Author = {Ting Chen and Berend Smit and Alexis T. Bell},
        Coden = {JCPSA6},
        Doi = {DOI:10.1063/1.3274802},
        Eissn = {10897690},
        Issn = {00219606},
        Keywords = {fluctuations; molecular dynamics method; viscosity;},
        Number = {24},
        Pages = {246101},
        Publisher = {AIP},
        Title = {Are Pressure Fluctuation-Based Equilibrium Methods Really Worse than Nonequilibrium Methods for Calculating Viscosities?},
        Url = {http://dx.doi.org/doi/10.1063/1.3274802},
        Volume = {131},
        Year = {2009},
        Bdsk-Url-1 = {http://dx.doi.org/doi/10.1063/1.3274802},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3274802}}

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Revision:	4064
Committed:	Thu Mar 13 20:44:45 2014 UTC (11 years, 4 months ago) by gezelter
File size:	100817 byte(s)
Log Message:	edits