trunk/fennellDissertation/dissertation.bib

%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/


%% Created for Chris Fennell at 2006-08-06 17:08:39 -0400 


%% Saved with string encoding Western (ASCII) 


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

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

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

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

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

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

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

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

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

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

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

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

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

@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.}}


@article{Ryckaert77,
        Author = {J.-P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
        Date-Added = {2006-08-06 17:05:44 -0400},
        Date-Modified = {2006-08-06 17:08:35 -0400},
        Doi = {10.1016/0021-9991(77)90098-5},
        Journal = {J. Comput. Phys.},
        Month = {March},
        Number = {3},
        Pages = {327-341},
        Title = {Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of {\it n}-alkanes},
        Volume = {23},
        Year = {1977}}

@article{Impey82,
        Author = {R.~W. Impey and P.~A. Madden and I.~R. McDonald},
        Date-Added = {2006-08-03 08:42:21 -0400},
        Date-Modified = {2006-08-03 08:44:06 -0400},
        Journal = {Mol. Phys.},
        Number = {3},
        Pages = {513-539},
        Title = {Spectroscopic and transport properties of water: \uppercase{M}odel calculations and the interpretation of experimental results},
        Volume = {46},
        Year = {1982}}

@article{Laasonen93,
        Author = {K. Laasonen and M. Sprik and M. Parrinello and R. Car},
        Date-Added = {2006-08-02 08:23:46 -0400},
        Date-Modified = {2006-08-02 13:09:18 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Laasonen_AbInitioLiquidWater_93.pdf},
        Number = {11},
        Pages = {9080-9089},
        Title = {``{\it \uppercase{A}b initio}" liquid water},
        Volume = {99},
        Year = {1993}}

@article{Donchev06,
        Author = {A.~G. Donchev and N.~G. Galkin and A.~A. Illarionov and O.~V. Khoruzhii and M.~A. Olevanov and M.~V. Subbotin and V.~I. Tarasov},
        Date-Added = {2006-08-02 08:15:11 -0400},
        Date-Modified = {2006-08-02 08:16:16 -0400},
        Doi = {www.pnas.org/cgi/doi/10.1073/pnas.0602982103},
        Journal = {Proc. Natl. Acad. Sci. USA},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Donchev_QuantumWater_06.pdf},
        Number = {23},
        Pages = {8613-8617},
        Title = {Water properties from first principles: \uppercase{S}imulations by a general-purpose quantum mechanical polarizable force field},
        Volume = {103},
        Year = {2006}}

@article{Malmberg56,
        Author = {G.~G. Malmberg and A.~A. Maryott},
        Date-Added = {2006-08-01 17:19:00 -0400},
        Date-Modified = {2006-08-02 13:16:04 -0400},
        Journal = {J. Res. Natl. Bur. Stand.},
        Number = {1},
        Pages = {1-8},
        Title = {Dielectric constant of Water from 0$^\circ$ to 100$^\circ$\uppercase{C}},
        Volume = {56},
        Year = {1956}}

@article{Neumann80,
        Author = {M. Neumann and O. Steinhauser},
        Date-Added = {2006-08-01 17:17:52 -0400},
        Date-Modified = {2006-08-01 17:18:51 -0400},
        Journal = {Mol. Phys.},
        Number = {2},
        Pages = {437-454},
        Title = {The influence of boundary conditions used in machine simulations on the structure of polar systems},
        Volume = {39},
        Year = {1980}}

@article{Neumann83,
        Author = {M. Neumann},
        Date-Added = {2006-08-01 17:16:51 -0400},
        Date-Modified = {2006-08-01 17:17:45 -0400},
        Journal = {Mol. Phys.},
        Number = {4},
        Pages = {841-858},
        Title = {Dipole moment fluctuation formulas in computer simulations of polar systems},
        Volume = {50},
        Year = {1983}}

@article{Kell75,
        Author = {G.~S. Kell},
        Date-Added = {2006-08-01 16:05:09 -0400},
        Date-Modified = {2006-08-02 13:17:29 -0400},
        Journal = {J. Chem. Eng. Data},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Kell_CompressibilityAndExpansivityOfH2O_75.pdf},
        Number = {1},
        Pages = {91-105},
        Title = {Density, Thermal Expansivity, and Compressibility of Liquid Water from 0$^\circ$ to 150$^\circ$\uppercase{C}: \uppercase{C}orrelations and Tables for Atmospheric Pressure and Saturation Reviewed and Expressed on 1968 Temperature Scale},
        Volume = {20},
        Year = {1975}}

@article{Wagner02,
        Author = {W. Wagner and A. Pru{\ss}},
        Date-Added = {2006-08-01 16:02:31 -0400},
        Date-Modified = {2006-08-02 13:16:50 -0400},
        Journal = {J. Phys. Chem. Ref. Data},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Wagner_ThermodynamicPropertiesOfH2O_03.pdf},
        Number = {2},
        Pages = {387-535},
        Title = {The \uppercase{IAPWS} Formulation 1995 for the Thermodynamic Properties of Ordinary Water Substance for General and Scientific Use},
        Volume = {31},
        Year = {2002}}

@article{Neumann84,
        Author = {M. Neumann and O. Steinhauser and G.~S. Pawley},
        Date-Added = {2006-07-31 10:22:39 -0400},
        Date-Modified = {2006-07-31 10:24:17 -0400},
        Journal = {Mol. Phys.},
        Number = {1},
        Pages = {97-113},
        Title = {Consistent calculation of the static and frequency-dependent dielectric constant in computer simulations},
        Volume = {52},
        Year = {1984}}

@article{Neumann85,
        Author = {M. Neumann},
        Date-Added = {2006-07-31 10:19:17 -0400},
        Date-Modified = {2006-08-02 13:17:58 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/DielectricConst./Neumann_H2ODielConst_85.pdf},
        Number = {12},
        Pages = {5663-5672},
        Title = {The dielectric constant of water. \uppercase{C}omputer simulations with the \uppercase{MCY} potential},
        Volume = {82},
        Year = {1985}}

@book{Berry00,
        Address = {New York},
        Author = {R. Stephen Berry and Stuart A. Rice and John Ross},
        Date-Added = {2006-07-30 14:49:40 -0400},
        Date-Modified = {2006-07-30 14:53:08 -0400},
        Edition = {Second},
        Editor = {Donald G. Truhlar},
        Publisher = {Oxford University Press, Inc.},
        Series = {Topics in Physical Chemistry},
        Title = {Physical Chemistry},
        Year = {2000}}

@article{Sorenson00,
        Author = {J.~M. Sorenson and G. Hura and R.~M. Glaeser and T. Head-Gordon},
        Date-Added = {2006-07-21 11:41:31 -0400},
        Date-Modified = {2006-07-21 11:44:44 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/THGord_X-RayRadial_2000.pdf},
        Number = {20},
        Pages = {9149-9161},
        Title = {What can x-ray scattering tell us about the radial distribution functions of water?},
        Volume = {113},
        Year = {2000}}

@book{CRC80,
        Address = {Boca Raton, FL},
        Date-Added = {2006-07-21 09:20:17 -0400},
        Date-Modified = {2006-07-21 09:20:17 -0400},
        Edition = 60,
        Editor = {R.~C. Weast},
        Publisher = {CRC Press, Inc.},
        Title = {CRC Handbook of Chemistry and Physics},
        Year = 1980}

@article{Shi06,
        Author = {Q. Shi and S. Izvekov and G.~A. Voth},
        Date-Added = {2006-07-20 15:28:29 -0400},
        Date-Modified = {2006-07-20 15:29:45 -0400},
        Doi = {10.1021/jp062700h},
        Journal = {J. Phys. Chem. B},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Shi_MixedAtomisticCGIonChannel_06.pdf},
        Title = {Mixed Atomistic and Coarse-Grained Molecular Dynamics: Simulation of a Membrane-Bound Ion Channel},
        Year = {2006}}

@article{Weis06,
        Author = {J.-J. Weis and D. Levesque},
        Date-Added = {2006-07-20 15:22:45 -0400},
        Date-Modified = {2006-07-20 15:24:22 -0400},
        Doi = {10.1063/1.2215614},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Weis_OrientationalOrderHardSphereDipole_06.pdf},
        Number = {3},
        Pages = {034504},
        Title = {Orientational order in high density dipolar hard sphere fluids},
        Volume = {125},
        Year = {2006}}

@article{Rick04,
        Author = {S.~W. Rick},
        Date-Added = {2006-07-18 10:49:48 -0400},
        Date-Modified = {2006-07-18 14:23:07 -0400},
        Doi = {10.1063/1.1652434},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Rick_TIP5P-Ew_04.pdf},
        Number = {13},
        Pages = {6085-6093},
        Title = {A reoptimization of the five-site water potential (\uppercase{TIP5P}) for use with \uppercase{E}wald sums},
        Volume = {120},
        Year = {2004}}

@article{Horn04,
        Author = {H.~W. Horn and W.~C. Swope and J.~W. Pitera and J.~D. Madura and T.~J. Dick and G.~L. Hura and T. Head-Gordon},
        Date-Added = {2006-07-18 10:18:42 -0400},
        Date-Modified = {2006-07-18 14:21:48 -0400},
        Doi = {10.1063/1.1683075},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Horn_TIP4P-Ew_04.pdf},
        Number = {20},
        Pages = {9665-9678},
        Title = {Development of an improved four-site water model for biomolecular simulations: \uppercase{TIP4P-E}w},
        Volume = {120},
        Year = {2004}}

@article{Brodka04,
        Author = {A. Br\'{o}dka},
        Date-Added = {2006-04-26 09:41:52 -0400},
        Date-Modified = {2006-07-18 14:29:43 -0400},
        Doi = {10.1016/j.cplett.2004.10.086},
        Journal = {Chem. Phys. Lett.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf},
        Pages = {62-67},
        Title = {\uppercase{E}wald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
        Volume = {400},
        Year = {2004}}

@article{deJoannis02,
        Author = {J. {de Joannis} and A. Arnold and C. Holm},
        Date-Added = {2006-04-26 09:40:15 -0400},
        Date-Modified = {2006-07-18 14:35:47 -0400},
        Doi = {10.1063/1.149195},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf},
        Number = {6},
        Pages = {2503-2512},
        Title = {Electrostatics in periodic slab geometries. \uppercase{II}},
        Volume = {117},
        Year = {2002}}

@article{Kawata01,
        Author = {M. Kawata and M. Mikami},
        Date-Added = {2006-04-26 09:38:01 -0400},
        Date-Modified = {2006-07-18 14:31:24 -0400},
        Journal = {Chem. Phys. Lett.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Kawata_Rapid2DEwald_01.pdf},
        Pages = {157-164},
        Title = {Rapid calculation of two-dimensional \uppercase{E}wald summation},
        Volume = {340},
        Year = {2001}}

@article{Arnold02,
        Author = {A. Arnold and J. {de Joannis} and C. Holm},
        Date-Added = {2006-04-26 09:36:09 -0400},
        Date-Modified = {2006-07-18 14:29:18 -0400},
        Doi = {10.1063/1.149195},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Arnold_SlabElectrostatics_02.pdf},
        Number = {6},
        Pages = {2496-2502},
        Title = {Electrostatics in periodic slab geometries. \uppercase{I}},
        Volume = {117},
        Year = {2002}}

@article{Kolafa92,
        Author = {J. Kolafa and J.~W. Perram},
        Date-Added = {2006-03-21 09:41:58 -0500},
        Date-Modified = {2006-07-18 14:41:10 -0400},
        Journal = {Mol. Simul.},
        Pages = {351-368},
        Title = {Cutoff Errors in the \uppercase{E}wald Summation Formulae for Point Charge Systems},
        Volume = {9},
        Year = {1992}}

@article{Karasawa89,
        Author = {N. Karasawa and W.~A. {Goddard III}},
        Date-Added = {2006-03-21 09:11:44 -0500},
        Date-Modified = {2006-03-21 09:13:00 -0500},
        Journal = {J. Phys. Chem.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf},
        Pages = {7320-7327},
        Title = {Acceleration of Convergence for Lattice Sums},
        Volume = {93},
        Year = {1989}}

@article{Roux99,
        Author = {B. Roux and T. Simonson},
        Date-Added = {2006-03-19 20:10:18 -0500},
        Date-Modified = {2006-03-19 20:12:10 -0500},
        Journal = {Biophys. Chem.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Roux_ImplicitSolventModels_99.pdf},
        Pages = {1-20},
        Title = {Implicit solvent models},
        Volume = {78},
        Year = {1999}}

@article{Rokhlin85,
        Author = {V. Rokhlin},
        Date-Added = {2006-03-19 20:02:25 -0500},
        Date-Modified = {2006-03-19 20:04:19 -0500},
        Doi = {10.1016/0021-9991(85)90002-6},
        Journal = {J. Comput. Phys.},
        Month = {September},
        Number = {2},
        Pages = {187-207},
        Title = {Rapid solution of integral equations of classical potential theory},
        Volume = {60},
        Year = {1985}}

@article{Grossfield00,
        Author = {A. Grossfield and J. Sachs and T.~B. Woolf},
        Date-Added = {2006-03-19 19:52:19 -0500},
        Date-Modified = {2006-03-19 19:54:14 -0500},
        Journal = {Proteins},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Membrane/Grossfield_dipoleLatticeMembrane_00.pdf},
        Pages = {211-223},
        Title = {Dipole Lattice Membrane Model for Protein Calculations},
        Volume = {41},
        Year = {2000}}

@article{Born20,
        Author = {M. Born},
        Date-Added = {2006-03-19 18:05:01 -0500},
        Date-Modified = {2006-03-19 18:07:42 -0500},
        Journal = {Z. Physik},
        Pages = {45-48},
        Title = {Volumen und hydratationswame der ionen},
        Volume = {1},
        Year = {1920}}

@article{Luty96,
        Author = {B.~A. Luty and W.~F. {van~Gunsteren}},
        Date-Added = {2006-03-18 20:59:19 -0500},
        Date-Modified = {2006-03-18 21:00:33 -0500},
        Journal = {J. Phys. Chem.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_PPPMElectrostaticCalculations_96.pdf},
        Number = {7},
        Pages = {2581-2587},
        Title = {Calculating Electrostatic Interactions Using the Particle-Particle Particle-Mesh Method with Nonperiodic Long-Range Interactions},
        Volume = {100},
        Year = {1996}}

@article{Rhee89,
        Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
        Date-Added = {2006-03-18 20:48:07 -0500},
        Date-Modified = {2006-07-18 14:33:26 -0400},
        Journal = {Phys. Rev. B},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
        Number = {1},
        Pages = {36-42},
        Title = {\uppercase{E}wald methods in molecular dynamics for systems of finite extent in one of three dimensions},
        Volume = {40},
        Year = {1989}}

@article{Hunenberger99a,
        Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
        Date-Added = {2006-03-18 20:14:24 -0500},
        Date-Modified = {2006-07-18 15:03:36 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
        Number = {4},
        Pages = {1856-1872},
        Title = {\uppercase{E}wald artifacts in computer simulations of ionic solvation and ion -- ion interaction: \uppercase{A} continuum electrostatics study},
        Volume = {110},
        Year = {1999}}

@article{Roberts95,
        Author = {J.~E. Roberts and J. Schnitker},
        Date-Added = {2006-03-18 20:12:23 -0500},
        Date-Modified = {2006-07-18 15:11:50 -0400},
        Journal = {J. Phys. Chem.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
        Pages = {1322-1331},
        Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: $\mbox{A}$ Systematic Study},
        Volume = {99},
        Year = {1995}}

@article{Roberts94,
        Author = {J.~E. Roberts and J. Schnitker},
        Date-Added = {2006-03-18 20:10:37 -0500},
        Date-Modified = {2006-03-18 20:12:19 -0500},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
        Number = {6},
        Pages = {5024-5031},
        Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
        Volume = {101},
        Year = {1994}}

@article{Yeh99,
        Author = {I.-C. Yeh and M.~L. Berkowitz},
        Date-Added = {2006-03-18 19:24:27 -0500},
        Date-Modified = {2006-07-18 14:34:09 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
        Number = {7},
        Pages = {3155-3162},
        Title = {\uppercase{E}wald summation for systems with slab geometry},
        Volume = {111},
        Year = {1999}}

@article{Parry76,
        Author = {D.~E. Parry},
        Date-Added = {2006-03-18 19:11:01 -0500},
        Date-Modified = {2006-07-18 15:09:52 -0400},
        Journal = {Surf. Sci.},
        Pages = {195},
        Title = {Errata: $\mbox{T}$he electrostatic potential in the surface region of an ionic crystal},
        Volume = {54},
        Year = {1976}}

@article{Parry75,
        Author = {D.~E. Parry},
        Date-Added = {2006-03-18 19:08:40 -0500},
        Date-Modified = {2006-03-18 19:16:14 -0500},
        Journal = {Surf. Sci.},
        Pages = {433-440},
        Title = {The electrostatic potential in the surface region of an ionic crystal},
        Volume = {49},
        Year = {1975}}

@article{deLeeuw79,
        Author = {S.~W. {de Leeuw} and J.~W. Perram},
        Date-Added = {2006-03-18 19:05:18 -0500},
        Date-Modified = {2006-03-18 19:07:48 -0500},
        Journal = {Mol. Phys.},
        Pages = {1313-1327},
        Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices},
        Volume = {37},
        Year = {1979}}

@article{Heyes77,
        Author = {D.~M. Heyes and M. Barber and J.~H.~R. Clarke},
        Date-Added = {2006-03-18 19:02:16 -0500},
        Date-Modified = {2006-03-18 19:04:48 -0500},
        Journal = {J. Chem. Soc., Faraday Trans. II},
        Number = {7},
        Pages = {1485-1496},
        Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride},
        Volume = {73},
        Year = {1977}}

@article{Spohr97,
        Author = {E. Spohr},
        Date-Added = {2006-03-18 18:51:02 -0500},
        Date-Modified = {2006-03-18 18:52:21 -0500},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
        Number = {16},
        Pages = {6342-6348},
        Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
        Volume = {107},
        Year = {1997}}

@article{York94,
        Author = {D. York and W. Yang},
        Date-Added = {2006-03-18 11:52:58 -0500},
        Date-Modified = {2006-07-18 14:34:21 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/York_FFPoissonEwald_94.pdf},
        Number = {4},
        Pages = {3298-3300},
        Title = {The fast Fourier Poisson method for calculating \uppercase{E}wald sums},
        Volume = {101},
        Year = {1994}}

@article{Shimada93,
        Author = {J. Shimada and H. Kaneko and T. Takada},
        Date-Added = {2006-03-18 11:10:38 -0500},
        Date-Modified = {2006-03-18 11:12:10 -0500},
        Journal = {J. Comp. Chem.},
        Pages = {867-78},
        Title = {Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions},
        Volume = {14},
        Year = {1993}}

@article{Luty94,
        Author = {B.~A. Luty and M.~E. Davis and I.~G. Tironi and W.~F. {van~Gunsteren}},
        Date-Added = {2006-03-18 10:37:17 -0500},
        Date-Modified = {2006-07-18 14:31:50 -0400},
        Journal = {Mol. Simul.},
        Pages = {11-20},
        Title = {A comparison of particle-particle particle-mesh and \uppercase{E}wald methods for calculating electrostatic interactions in periodic systems},
        Volume = {14},
        Year = {1994}}

@book{Hockney81,
        Address = {New York},
        Author = {R.~W. Hockney and J.~W. Eastwood},
        Date-Added = {2006-03-18 10:33:19 -0500},
        Date-Modified = {2006-03-18 10:35:04 -0500},
        Publisher = {McGraw-Hill},
        Title = {Computer Simulation Using Particles},
        Year = {1981}}

@article{Sagui99,
        Author = {C. Sagui and T.~A. Darden},
        Date-Added = {2006-03-17 18:27:01 -0500},
        Date-Modified = {2006-07-18 15:12:58 -0400},
        Journal = {Annu. Rev. Biophys. Biomol. Struct.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_electrostaticInBiomolecules_99.pdf},
        Pages = {155-179},
        Title = {Molecular Dynamics Simulations of Biomolecules: $\mbox{L}$ong-Range Electrostatic Effects},
        Volume = {28},
        Year = {1999}}

@article{Perram88,
        Author = {J.~W. Perram and H.~G. Petersen and S.~W. {de Leeuw}},
        Date-Added = {2006-03-17 13:42:04 -0500},
        Date-Modified = {2006-03-17 13:59:01 -0500},
        Journal = {Mol. Phys.},
        Pages = {875-893},
        Title = {An algorithm for the simulation of condensed matter that grows as the 3/2 power of the number of particles},
        Volume = {65},
        Year = {1988}}

@article{Woodcock71,
        Author = {L.~V. Woodcock and K. Singer},
        Date-Added = {2006-03-17 11:14:17 -0500},
        Date-Modified = {2006-07-18 14:46:33 -0400},
        Journal = {Trans. Faraday Soc.},
        Pages = {12-30},
        Title = {Thermodynamic and Structural Properties of Liquid Ionic Salts Obtained by $\mbox{Monte Carlo}$ Computation},
        Volume = {67},
        Year = {1971}}

@article{Smith81,
        Author = {E.~R. Smith},
        Date-Added = {2006-03-16 13:47:17 -0500},
        Date-Modified = {2006-03-16 13:48:34 -0500},
        Journal = {Proc. R. Soc. London Ser. A},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Smith_ElectrostaticEnergyInIonicCrystals_81.pdf},
        Pages = {475-505},
        Title = {Electrostatic Energy in Ionic Crystals},
        Volume = {375},
        Year = {1981}}

@article{Weber00,
        Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
        Date-Added = {2006-03-16 09:49:22 -0500},
        Date-Modified = {2006-07-18 15:18:48 -0400},
        Doi = {10.1021/jp9937757},
        Journal = {J. Phys. Chem. B},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
        Number = {15},
        Pages = {3668-3675},
        Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under \uppercase{E}wald Boundary Conditions: $\mbox{I}$nfluence of Artificial Periodicity on Peptide Conformation},
        Volume = {104},
        Year = {2000}}

@article{Hunenberger99b,
        Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
        Date-Added = {2006-03-16 09:45:10 -0500},
        Date-Modified = {2006-07-18 15:03:59 -0400},
        Journal = {Biophys. Chem.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
        Pages = {69-88},
        Title = {Effect of artificial periodicity in simulations of biomolecules under \uppercase{E}wald boundary conditions: \uppercase{A} continuum electrostatics study},
        Volume = {78},
        Year = {1999}}

@article{Petersen95,
        Author = {H.~G. Petersen},
        Date-Added = {2006-03-16 08:43:02 -0500},
        Date-Modified = {2006-07-18 14:33:13 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
        Month = {September},
        Number = {9},
        Pages = {3668-3679},
        Title = {Accuracy and efficiency of the particle mesh \uppercase{E}wald method},
        Volume = {103},
        Year = {1995}}

@article{Luty95,
        Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
        Date-Added = {2006-03-16 08:39:13 -0500},
        Date-Modified = {2006-03-16 08:41:15 -0500},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
        Number = {8},
        Pages = {3014-3021},
        Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
        Volume = {103},
        Year = {1995}}

@article{Barker73,
        Author = {J.~A. Barker and R.~O. Watts},
        Date-Added = {2006-03-15 18:58:17 -0500},
        Date-Modified = {2006-07-18 14:44:12 -0400},
        Journal = {Mol. Phys.},
        Pages = {789-792},
        Title = {$\mbox{Monte Carlo}$ studies of the dielectric properties of water-like models},
        Volume = {26},
        Year = {1973}}

@article{Adams79,
        Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills},
        Date-Added = {2006-03-15 17:46:36 -0500},
        Date-Modified = {2006-03-15 17:48:04 -0500},
        Journal = {Mol. Phys.},
        Number = {2},
        Pages = {387-400},
        Title = {The computer simulation of polar liquids},
        Volume = {38},
        Year = {1979}}

@article{Rahman71,
        Author = {A. Rahman and F.~H. Stillinger},
        Date-Added = {2006-03-15 17:04:53 -0500},
        Date-Modified = {2006-03-15 17:07:29 -0500},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
        Month = {October},
        Number = {7},
        Pages = {3336-3359},
        Title = {Molecular Dynamics Study of Liquid Water},
        Volume = {55},
        Year = {1971}}

@article{Andrea83,
        Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
        Date-Added = {2006-03-15 15:16:12 -0500},
        Date-Modified = {2006-03-15 15:18:10 -0500},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
        Number = {9},
        Pages = {4576-4584},
        Title = {The role of long ranged forces in determining the structure and properties of liquid water},
        Volume = {79},
        Year = {1983}}

@article{Brush66,
        Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
        Date-Added = {2006-03-13 16:55:39 -0500},
        Date-Modified = {2006-07-18 14:48:59 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
        Month = {September},
        Number = {6},
        Pages = {2102-2118},
        Title = {$\mbox{Monte Carlo}$ Study of a One-Component Plasma. \uppercase{I}},
        Volume = {45},
        Year = {1966}}

@article{Ewald21,
        Author = {P.~P. Ewald},
        Date-Added = {2006-03-13 13:32:04 -0500},
        Date-Modified = {2006-03-16 22:39:27 -0500},
        Journal = {Ann. Physik},
        Pages = {253-287},
        Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
        Volume = {64},
        Year = {1921}}

@article{Jones56,
        Author = {R.~E. Jones and D.~H. Templeton},
        Date-Added = {2006-03-13 13:25:58 -0500},
        Date-Modified = {2006-07-18 14:24:50 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
        Number = {5},
        Pages = {1062-1063},
        Title = {Optimum Atomic Shape for \uppercase{B}ertaut Series},
        Volume = {25},
        Year = {1956}}

@article{Heyes81,
        Author = {D.~M. Heyes},
        Date-Added = {2006-03-13 13:12:45 -0500},
        Date-Modified = {2006-03-13 13:14:27 -0500},
        Journal = {J. Chem. Phys.},
        Keywords = {Empty Keywords},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
        Number = {3},
        Pages = {1924-1929},
        Title = {Electrostatic potentials and fields in infinite point charge lattices},
        Volume = {74},
        Year = {1981}}

@article{Steinbach94,
        Author = {P.~J. Steinbach and B.~R. Brooks},
        Date-Added = {2006-03-12 19:26:45 -0500},
        Date-Modified = {2006-03-12 19:29:43 -0500},
        Doi = {10.1002/jcc.540150702},
        Journal = {J. Comput. Chem.},
        Number = {7},
        Pages = {667-683},
        Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
        Volume = {15},
        Year = {1994}}

@article{deLeeuw80,
        Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
        Date-Added = {2006-03-07 10:26:31 -0500},
        Date-Modified = {2006-07-18 14:52:02 -0400},
        Journal = {Proc. R. Soc. London Ser. A},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
        Number = {1752},
        Pages = {27-56},
        Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. \uppercase{I. L}attice Sums and Dielectric Constants},
        Volume = {373},
        Year = {1980}}

@article{Essmann95,
        Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
        Date-Added = {2006-03-05 12:25:25 -0500},
        Date-Modified = {2006-07-18 14:30:21 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf},
        Number = {19},
        Pages = {8577-8593},
        Title = {A smooth particle mesh \uppercase{E}wald method},
        Volume = {103},
        Year = {1995}}

@article{Kast03,
        Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
        Date-Added = {2006-02-18 16:47:26 -0500},
        Date-Modified = {2006-02-18 16:51:25 -0500},
        Journal = {Chem. Phys. Lett.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
        Pages = {398-404},
        Title = {Integral equation theory for correcting truncation errors in molecular simulations},
        Volume = {367},
        Year = {2003}}

@article{Tobias01,
        Author = {D.~J. Tobias},
        Date-Added = {2006-02-15 11:28:58 -0500},
        Date-Modified = {2006-07-18 15:21:08 -0400},
        Journal = {Curr. Opin. Struct. Biol.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
        Pages = {253-261},
        Title = {Electrostatics calculations: $\mbox{R}$ecent methodological advances and applications to membranes},
        Volume = {11},
        Year = {2001}}

@article{Zahn02,
        Author = {D. Zahn and B. Schilling and S.~M. Kast},
        Date-Added = {2006-02-15 09:21:27 -0500},
        Date-Modified = {2006-07-18 15:19:05 -0400},
        Journal = {J. Phys. Chem. B},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
        Number = {41},
        Pages = {10725-10732},
        Title = {Enhancement of the \uppercase{W}olf Damped Coulomb Potential: $\mbox{S}$tatic, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
        Volume = {106},
        Year = {2002}}

@article{Wolf99,
        Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
        Date-Added = {2006-02-15 09:09:39 -0500},
        Date-Modified = {2006-07-17 12:28:56 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
        Number = {17},
        Pages = {8255-8282},
        Rating = {0},
        Read = {No},
        Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise $r^{-1}$ summation},
        Volume = {110},
        Year = {1999}}

@book{Berne90,
        Address = {Malabar, Florida},
        Author = {B.~J. Berne and R. Pecora},
        Publisher = {Robert E. Krieger Publishing Company, Inc.},
        Title = {Dynamic Light Scattering},
        Year = 1990}

@article{Evans77,
        Author = {D.~J. Evans},
        Journal = {Mol. Phys.},
        Pages = {317-325},
        Title = {On the representation of orientation space},
        Volume = 34,
        Year = 1977}

@article{Tuckerman92,
        Author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
        Journal = jcp,
        Pages = {1990-2001},
        Title = {Reversible multiple time scale molecular dynamics},
        Volume = 97,
        Year = 1992}

@book{Hansen86,
        Address = {London},
        Author = {J.~P. Hansen and I.~R. McDonald},
        Chapter = 7,
        Pages = {199-206},
        Publisher = {Academic Press},
        Title = {Theory of Simple Liquids},
        Year = 1986}

@article{Angelani98,
        Author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
        Date-Modified = {2006-07-18 14:59:40 -0400},
        Journal = prl,
        Number = 21,
        Pages = {4648-4651},
        Title = {Connected Network of Minima as a Model Glass: \uppercase{L}ong Time Dynamics},
        Volume = 81,
        Year = 1998}

@article{Stillinger82,
        Author = {F.~H. Stillinger and T.~A. Weber},
        Journal = pra,
        Number = 2,
        Pages = {978-989},
        Title = {Hidden structure in liquids},
        Volume = 25,
        Year = 1982}

@article{Stillinger83,
        Author = {F.~H. Stillinger and T.~A. Weber},
        Journal = pra,
        Number = 4,
        Pages = {2408-2416},
        Title = {Dynamics of structural transitions in liquids},
        Volume = 28,
        Year = 1983}

@article{Weber84,
        Author = {T.~A. Weber and F.~H. Stillinger},
        Journal = jcp,
        Number = 6,
        Pages = {2742-2746},
        Title = {The effect of density on the inherent structure in liquids},
        Volume = 80,
        Year = 1984}

@article{Stillinger85,
        Author = {F.~H. Stillinger and T.~A. Weber},
        Journal = jcp,
        Number = 9,
        Pages = {4767-4775},
        Title = {Inherent structure theory of liquids in the hard-sphere limit},
        Volume = 83,
        Year = 1985}

@article{Stillinger98,
        Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
        Journal = {Nature},
        Pages = {554-557},
        Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
        Volume = 393,
        Year = 1998}

@article{Parkhurst75a,
        Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
        Date-Modified = {2006-07-18 14:50:48 -0400},
        Journal = jcp,
        Number = 6,
        Pages = {2698-2704},
        Title = {Dense liquids. \uppercase{I. T}he effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
        Volume = 63,
        Year = 1975}

@article{Parkhurst75b,
        Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
        Date-Modified = {2006-07-18 14:51:04 -0400},
        Journal = jcp,
        Number = 6,
        Pages = {2705-2709},
        Title = {Dense liquids. \uppercase{II. T}he effect of density and temperature on viscosity of tetramethylsilane and benzene},
        Volume = 63,
        Year = 1975}

@article{Forester97,
        Author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
        Journal = {J. Chem. Soc. - Faraday Transactions},
        Pages = {613-619},
        Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
        Volume = 93,
        Year = 1997}

@article{Tieleman98,
        Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
        Journal = {Biophys. J.},
        Pages = {2786-2801},
        Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
        Volume = 74,
        Year = 1998}

@article{Cascales98,
        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
        Date-Modified = {2006-07-18 15:01:21 -0400},
        Journal = {J. Phys. Chem. B},
        Pages = {625-631},
        Title = {Anaesthetic mechanism on a model biological membrane: \uppercase{A} molecular dynamics simulation study},
        Volume = 102,
        Year = 1998}

@article{Bassolino95,
        Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
        Journal = {J. Am. Chem. Soc.},
        Pages = {4118-4129},
        Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
        Volume = 117,
        Year = 1995}

@article{Alper95,
        Author = {H.~E. Alper and T.~R. Stouch},
        Journal = {J. Phys. Chem.},
        Pages = {5724-5731},
        Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
        Volume = 99,
        Year = 1995}

@article{Sok92,
        Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
        Journal = {J. Chem. Phys.},
        Pages = {4699-4704},
        Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
        Volume = 96,
        Year = 1992}

@article{Rabani99,
        Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
        Journal = prl,
        Pages = {3649},
        Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
        Volume = 82,
        Year = {1999}}

@article{Rabani97,
        Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
        Date-Modified = {2006-07-18 15:11:37 -0400},
        Journal = {J. Chem. Phys.},
        Pages = {6867-6876},
        Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: $\mbox{C}$age correlations},
        Volume = 107,
        Year = 1997}

@article{Gezelter99,
        Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
        Journal = jcp,
        Pages = 3444,
        Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
        Volume = 110,
        Year = 1999}

@article{Gezelter98,
        Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
        Date-Modified = {2006-02-15 10:18:42 -0500},
        Journal = jcp,
        Pages = 4695,
        Title = {Response to 'Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion'},
        Volume = 109,
        Year = 1998}

@article{Gezelter97,
        Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
        Journal = jcp,
        Pages = 4618,
        Title = {Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?},
        Volume = 107,
        Year = 1997}

@article{Zwanzig83,
        Author = {R. Zwanzig},
        Journal = jcp,
        Pages = {4507-4508},
        Title = {On the relation between self-diffusion and viscosity of liquids},
        Volume = 79,
        Year = 1983}

@article{Zwanzig88,
        Author = {R. Zwanzig},
        Journal = {Proc. Natl. Acad. Sci. USA},
        Pages = 2029,
        Title = {Diffusion in rough potential},
        Volume = 85,
        Year = 1988}

@article{Stillinger95,
        Author = {F.~H. Stillinger},
        Journal = {Science},
        Pages = {1935-1939},
        Title = {A Topographic View of Supercooled Liquids and Glass Formation},
        Volume = 267,
        Year = 1995}

@incollection{Angell85,
        Address = {Springfield, VA},
        Author = {C.~A. Angell},
        Booktitle = {Relaxations in Complex Systems},
        Editor = {K.~Ngai and G.~B. Wright},
        Pages = 1,
        Publisher = {National Technical Information Service, U.S. Department of Commerce},
        Title = {unknown},
        Year = 1985}

@article{Bembenek96,
        Author = {S.~D. Bembenek and B.~B. Laird},
        Journal = jcp,
        Pages = 5199,
        Title = {The role of localization in glasses and supercooled liquids},
        Volume = 104,
        Year = 1996}

@article{Sun97a,
        Author = {X. Sun and W.~H. Miller},
        Date-Modified = {2006-02-15 10:33:35 -0500},
        Journal = jcp,
        Pages = 6346,
        Title = {Semiclassical initial value representation for electronically nonadiabatic molecular dynamics},
        Volume = 106,
        Year = 1997}

@article{Spath96,
        Author = {B.~W. Spath and W.~H. Miller},
        Journal = jcp,
        Pages = 95,
        Title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION PROBABILITIES},
        Volume = 104,
        Year = 1996}

@book{Warshel91,
        Address = {New York},
        Author = {Arieh Warshel},
        Publisher = {Wiley},
        Title = {Computer modeling of chemical reactions in enzymes and solutions},
        Year = 1991}

@article{Vuilleumier97,
        Author = {Rodolphe Vuilleumier and Daniel Borgis},
        Journal = jpc,
        Title = {Molecular Dynamics of an excess proton in water using a non-additive valence bond force field},
        Volume = {in press},
        Year = 1997}

@article{Kob95a,
        Author = {W. Kob and H.~C. Andersen},
        Date-Modified = {2006-07-18 15:04:56 -0400},
        Journal = pre,
        Pages = {4626-4641},
        Title = {Testing mode-coupling theory for a supercooled binary $\mbox{Lennard-Jones} mixtures: \uppercase{T}he van \uppercase{H}ove corraltion function},
        Volume = 51,
        Year = 1995}

@article{Kob95b,
        Author = {W. Kob and H.~C. Andersen},
        Date-Modified = {2006-07-18 14:50:19 -0400},
        Journal = pre,
        Pages = {4134-4153},
        Title = {Testing mode-coupling theory for a supercooled binary $\mbox{Lennard-Jones}$ mixtures. \uppercase{II. I}ntermediate scattering function and dynamic susceptibility},
        Volume = 52,
        Year = 1995}

@inproceedings{Gotze89,
        Address = {Amsterdam},
        Author = {W. G{\"{o}}tze},
        Booktitle = {Liquids, Freezing and Glass Transitions},
        Editor = {J.~P. Hansen and D. Levesque and J. Zinn-Justin},
        Pages = {287-503},
        Publisher = {North-Holland},
        Title = {Aspects of Structural Glass Transitions},
        Volume = {I},
        Year = 1989}

@article{Sun97b,
        Author = {X. Sun and W.~H. Miller},
        Date-Modified = {2006-02-15 10:33:29 -0500},
        Journal = jcp,
        Pages = 916,
        Title = {Mixed semiclassical-classical approaches to the dynamics of complex molecular systems},
        Year = 1997}

@article{Keshavamurthy94,
        Author = {S. Keshavamurthy and W.~H. Miller},
        Journal = cpl,
        Pages = 189,
        Title = {ivr},
        Volume = 218,
        Year = 1994}

@article{Billing75,
        Author = {G.~D. Billing},
        Journal = cpl,
        Pages = 391,
        Title = {ehrenfest},
        Volume = 30,
        Year = 1975}

@article{Chang90,
        Author = {Y.-T. Chang and W.~H. Miller},
        Journal = jpc,
        Pages = {5884-5888},
        Title = {An Empirical Valence Bond Model for Constructing Global Potential Energy Surfaces for Chemical Reactions of Polyatomic Molecular Systems},
        Volume = 94,
        Year = 1990}

@article{Shor94,
        Author = {P.W. Shor},
        Date-Modified = {2006-07-18 15:13:14 -0400},
        Journal = {Proceedings of the 35th Annual Symposium on Foundations of Computer Science},
        Pages = {124-134},
        Title = {Algorithms for quantum computation: $\mbox{D}$iscrete logarithms and factoring},
        Year = 1994}

@article{Feynman82,
        Author = {R.~P. Feynman},
        Journal = {Int. J. Theor. Phys.},
        Pages = {467-488},
        Title = {Simulating physics with computers},
        Volume = 21,
        Year = 1982}

@article{Grover97,
        Author = {L.~K. Grover},
        Journal = prl,
        Pages = {4709-4712},
        Title = {Quantum computers can search arbitrarily large databases by a single query},
        Volume = 79,
        Year = 1997}

@article{Chuang98,
        Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
        Journal = prl,
        Pages = {3408-3411},
        Title = {Experimental Implementation of Fast Quantum Searching},
        Volume = 80,
        Year = 1998}

@article{Monroe95,
        Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
        Journal = prl,
        Pages = 4714,
        Title = {Demonstration of a fundamental quantum logic gate},
        Volume = 75,
        Year = 1995}

@article{Lent93,
        Author = {C.~S. Lent and P.~D. Tougaw and W.~Porod and G.~H. Bernstein},
        Journal = {Nanotechnology},
        Pages = {49-57},
        Title = {Quantum Cellular Automata},
        Volume = 4,
        Year = 1993}

@article{Barenco95,
        Author = {A. Barenco and C.~H. Bennett and R. Cleve and D.~P. DiVincenzo and N. Margolus and P. Shor and T. Sleator and J.~A. Smolin and H. Weinfurter},
        Journal = {Phys. Rev. A},
        Pages = {3457-3467},
        Title = {elementary gates for quantum computation},
        Volume = 52,
        Year = 1995}

@article{Reinot97,
        Author = {T. Reinot and J.~M. Hayes and G.~J. Small},
        Date-Modified = {2006-02-15 10:31:21 -0500},
        Journal = jcp,
        Pages = {457-466},
        Title = {Electronic dephasing and electron-phonon coupling of aluminum phthalocyanine tetrasulphonate in hyperquenched and annealed glassy films of ethanol and methanol over a broad temperature range},
        Volume = 106,
        Year = 1997}

@article{Laflamme96,
        Author = {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
        Journal = prl,
        Pages = 77,
        Title = {A perfect quantum error correcting code: 5 bit code correcting a general 1 qubit error to encode 1 qubit of information},
        Volume = 98,
        Year = 1996}

@article{Shor95,
        Author = {P.~W. Shor},
        Journal = {Phys. Rev. A},
        Pages = {2493-2496},
        Title = {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY},
        Volume = 52,
        Year = 1995}

@article{Calderbank96,
        Author = {A.~R. Calderbank and P.~W. Shor},
        Journal = {Phys. Rev. A},
        Pages = {1098-1105},
        Title = {Good quantum error-correcting codes exist},
        Volume = 54,
        Year = 1996}

@article{Steane96,
        Author = {A.~M. Steane},
        Journal = prl,
        Pages = {793-797},
        Title = {Error correcting codes in quantum theory},
        Volume = 77,
        Year = 1996}

@article{Gezelter95,
        Author = {J.~D. Gezelter and W.~H. Miller},
        Journal = jcp,
        Pages = {7868-7876},
        Title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE RATE OF KETENE ISOMERIZATION},
        Volume = 103,
        Year = 1995}

@article{Chakrabarti92,
        Author = {A.~C. Chakrabarti and D.~W. Deamer},
        Journal = {Biochimica et Biophysica Acta},
        Pages = {171-177},
        Title = {PERMEABILITY OF LIPID BILAYERS TO AMINO-ACIDS AND PHOSPHATE},
        Volume = 1111,
        Year = 1992}

@article{Paula96,
        Author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and T.~H. Haines and D.~W. Deamer},
        Journal = {Biophys. J.},
        Pages = {339-348},
        Title = {Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness},
        Volume = 70,
        Year = 1996}

@article{Little96,
        Author = {H.~J. Little},
        Journal = {Pharmacology \& Therapeutics},
        Pages = {37-58},
        Title = {How has molecular pharmacology contributed to our understanding of the mechanism(s) of general anesthesia?},
        Volume = 69,
        Year = 1996}

@article{McKinnon92,
        Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
        Journal = jpc,
        Pages = {10497-10506},
        Title = {Nonequilibrium Molecular Dynamics Simulation of Oxygen Diffusion through Hexadecane Monolayers with Varying Concentrations of Cholesterol},
        Volume = 96,
        Year = 1992}

@article{Venable93,
        Author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and R.~W. Pastor},
        Date-Modified = {2006-07-18 15:17:14 -0400},
        Journal = {Science},
        Pages = {223-226},
        Title = {Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: $\mbox{A}$n Investigation of Membrane Fluidity},
        Volume = 262,
        Year = 1993}

@article{Essmann99,
        Author = {U. Essmann and M.~L. Berkowitz},
        Journal = {Biophys. J.},
        Pages = {2081-2089},
        Title = {Dynamical properties of phospholipid bilayers from computer simulation},
        Volume = 76,
        Year = 1999}

@article{Tu98,
        Author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf},
        Date-Modified = {2006-07-18 15:16:12 -0400},
        Journal = {Biophys. J.},
        Pages = {2123-2134},
        Title = {Effects of anesthetics on the structure of a phospholipid bilayer: $\mbox{M}$olecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine},
        Volume = 75,
        Year = 1998}

@article{Pomes96,
        Author = {R. Pomes and B. Roux},
        Date-Modified = {2006-07-18 15:10:47 -0400},
        Journal = {Biophys. J.},
        Pages = {19-39},
        Title = {Structure and dynamics of a proton wire: $\mbox{A}$ theoretical study of H+ translocation along the single-file water chain in the gramicidin a channel},
        Volume = 71,
        Year = 1996}

@article{Duwez60,
        Author = {P. Duwez and R.~H. Willens and W. {Klement~Jr.}},
        Journal = {J. Appl. Phys.},
        Pages = {1136-1137},
        Title = {Continuous Series of Metastable Solid Solutions in Silver-Copper Alloys},
        Volume = 31,
        Year = 1960}

@article{Peker93,
        Author = {A. Peker and W.~L. Johnson},
        Journal = {Appl. Phys. Lett.},
        Pages = {2342-2344},
        Title = {A highly processable metallic-glass - $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
        Volume = 63,
        Year = 1993}

@article{ChoiYim97,
        Author = {H. Choi-Yim and W.~L. Johnson},
        Journal = {Appl. Phys. Lett.},
        Pages = {3808-3810},
        Title = {Bulk metallic glass matrix composites},
        Volume = 71,
        Year = 1997}

@article{Sun96,
        Author = {X. Sun and S. Schneider and U. Geyer and W.~L. Johnson and M.~A. Nicolet},
        Journal = {J. Mater. Res.},
        Pages = {2738-2743},
        Title = {Oxidation and crystallization of an amorphous $\mbox{Zr}_{60}\mbox{Al}_{15}\mbox{Ni}_{25}$ alloy},
        Volume = 11,
        Year = 1996}

@article{Heller93,
        Author = {H. Heller and M. Schaefer and K. Schulten},
        Journal = jpc,
        Pages = {8343-8360},
        Title = {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200 LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES},
        Volume = 97,
        Year = 1993}

@article{Kushick76,
        Author = {J. Kushick and B.~J. Berne},
        Journal = jcp,
        Pages = {1362-1367},
        Title = {Computer Simulation of anisotropic molecular fluids},
        Volume = 64,
        Year = 1976}

@article{Berardi96,
        Author = {R. Berardi and S. Orlandi and C Zannoni},
        Journal = cpl,
        Pages = {357-362},
        Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
        Volume = 261,
        Year = 1996}

@article{Berardi99,
        Author = {R. Berardi and S. Orlandi and C. Zannoni},
        Date-Modified = {2006-07-18 14:44:37 -0400},
        Journal = {Int. J. Mod. Phys. C},
        Pages = {477-484},
        Title = {$\mbox{Monte Carlo}$ simulations of rod-like $\mbox{Gay-Berne}$ mesogens with transverse dipoles},
        Volume = 10,
        Year = 1999}

@article{Pasterny00,
        Author = {K. Pasterny and E. Gwozdz and A. Brodka},
        Date-Modified = {2006-07-18 15:10:06 -0400},
        Journal = {J. Mol. Liq.},
        Pages = {173-184},
        Title = {Properties of a model liquid crystal: $\mbox{Polar Gay-Berne}$ particles},
        Volume = 85,
        Year = 2000}

@article{Jorgensen83,
        Author = {W.~L. Jorgensen and J. Chandrasekhar and J.~D. Madura and R.~W. Impey and M.~L. Klein},
        Journal = jcp,
        Pages = {926-935},
        Title = {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER},
        Volume = 79,
        Year = 1983}

@article{Berardi98,
        Author = {R. Berardi and C. Fava and C. Zannoni},
        Journal = cpl,
        Pages = {8-14},
        Title = {A Gay-Berne potential for dissimilar biaxial particles},
        Volume = 297,
        Year = 1998}

@article{Luckhurst90,
        Author = {G.~R. Luckhurst and R.~A. Stephens and R.~W. Phippen},
        Date-Modified = {2006-07-18 14:54:27 -0400},
        Journal = {Liquid Crystals},
        Pages = {451-464},
        Title = {Computer simulation studies of anisotropic systems {XIX}. \uppercase{M}esophases formed by the $\mbox{Gay-Berne}$ model mesogen},
        Volume = 8,
        Year = 1990}

@article{Gay81,
        Author = {J.~G. Gay and B.~J. Berne},
        Journal = jcp,
        Pages = {3316-3319},
        Title = {MODIFICATION OF THE OVERLAP POTENTIAL TO MIMIC A LINEAR SITE-SITE POTENTIAL},
        Volume = 74,
        Year = 1981}

@article{Berne72,
        Author = {B.~J. Berne and P. Pechukas},
        Journal = jcp,
        Pages = {4213-4216},
        Title = {Gaussian Model Potentials for Molecular Interactions},
        Volume = 56,
        Year = 1972}

@article{Perram96,
        Author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and J.~L. Lebowitz},
        Date-Modified = {2006-07-18 15:10:36 -0400},
        Journal = pre,
        Pages = {6565-6572},
        Title = {Ellipsoid contact potential: $\mbox{T}$heory and relation to overlap potentials},
        Volume = 54,
        Year = 1996}

@article{Cornell95,
        Author = {W.~D. Cornell and P. Cieplak and C.~I. Bayly and I.~R. Gould and K.~M. {Merz, Jr.} and D.~M. Ferguson and D.~C. Spellmeyer and T. Fox and J.~W. Caldwell and P.~A. Kollman},
        Journal = jacs,
        Pages = {5179-5197},
        Title = {A second generation force field for the simulation of proteins and nucleic acids},
        Volume = 117,
        Year = 1995}

@article{Brooks83,
        Author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States and S. Swaminathan and M. Karplus},
        Date-Modified = {2006-07-18 15:00:32 -0400},
        Journal = {J. Comp. Chem.},
        Pages = {187-217},
        Title = {\uppercase{CHARMM: A} Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
        Volume = 4,
        Year = 1983}

@incollection{MacKerell98,
        Address = {New York},
        Author = {A.~D. {MacKerell, Jr.} and B. Brooks and C.~L. {Brooks III} and L. Nilsson and B. Roux and Y. Won and and M. Karplus},
        Booktitle = {The Encyclopedia of Computational Chemistry},
        Date-Modified = {2006-07-18 15:06:36 -0400},
        Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
        Pages = {271-277},
        Publisher = {John Wiley \& Sons},
        Title = {$\mbox{CHARMM: T}$he Energy Function and Its Parameterization with an Overview of the Program},
        Volume = 1,
        Year = 1998}

@incollection{Jorgensen98a,
        Address = {New York},
        Author = {W.~L. Jorgensen},
        Booktitle = {The Encyclopedia of Computational Chemistry},
        Date-Modified = {2006-02-15 10:21:45 -0500},
        Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
        Pages = {1986-1989},
        Publisher = {John Wiley \& Sons},
        Title = {OPLS Force Fields},
        Volume = 3,
        Year = 1998}

@article{Rabani00,
        Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
        Date-Modified = {2006-02-15 10:30:55 -0500},
        Journal = prl,
        Pages = 467,
        Title = {Reply to `Comment on ``Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using th eCage Correlation Function'' '},
        Volume = 85,
        Year = 2000}

@book{Cevc87,
        Address = {New York},
        Author = {G. Cevc and D. Marsh},
        Publisher = {John Wiley \& Sons},
        Title = {Phospholipid Bilayers},
        Year = 1987}

@article{Janiak79,
        Author = {M.~J. Janiak and D.~M. Small and G.~G. Shipley},
        Journal = {J. Biol. Chem.},
        Pages = {6068-6078},
        Title = {Temperature and Compositional Dependence of the Structure of Hydrated Dimyristoyl Lecithin},
        Volume = 254,
        Year = 1979}

@article{Mazur92,
        Author = {E. Mazur},
        Date-Modified = {2006-07-18 14:55:07 -0400},
        Journal = {Optics and Photonics News},
        Pages = 38,
        Title = {Qualitative vs. Quantititative Thinking: \uppercase{A}re we teaching the right thing?},
        Volume = 3,
        Year = 1992}

@book{Mazur97,
        Address = {New Jersey},
        Author = {Eric Mazur},
        Date-Modified = {2006-07-18 15:07:06 -0400},
        Publisher = {Prentice Hall},
        Title = {Peer Instruction: $\mbox{A}$ User's Manual},
        Year = 1997}

@article{Wigner55,
        Author = {E.~P. Wigner},
        Journal = {Annals of Mathematics},
        Pages = {548-564},
        Title = {Characteristic Vectors of Bordered Matrices with Infinite Dimensions},
        Volume = 62,
        Year = 1955}

@article{Gaukel98,
        Author = {C. Gaukel and H.~R. Schober},
        Journal = {Solid State Comm.},
        Pages = {1-5},
        Title = {Diffusion Mechanisms in under-cooled Binary Metal Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$},
        Volume = 107,
        Year = 1998}

@article{Qi99,
        Author = {Y. Qi and T. \c{C}a\v{g}in and Y. Kimura and W.~A. {Goddard III}},
        Journal = prb,
        Number = 5,
        Pages = {3527-3533},
        Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ and $\mbox{Cu-Ni}$},
        Volume = 59,
        Year = 1999}

@article{Khorunzhy97,
        Author = {A. Khorunzhy and G.~J. Rodgers},
        Journal = {J. Math. Phys.},
        Pages = {3300-3320},
        Title = {Eigenvalue distribution of large dilute random matrices},
        Volume = 38,
        Year = 1997}

@article{Rodgers88,
        Author = {G.~J. Rodgers and A. Bray},
        Journal = {Phys. Rev. B},
        Pages = 355703562,
        Title = {Density of States of a Sparse Random Matrix},
        Volume = 37,
        Year = 1988}

@article{Rodgers90,
        Author = {G.~J. Rodgers and C. {De Dominicis}},
        Journal = {J. Phys. A: Math. Gen.},
        Pages = {1567-1573},
        Title = {Density of states of sparse random matrices},
        Volume = 23,
        Year = 1990}

@inproceedings{Barker80,
        Author = {J.~A. Barker},
        Booktitle = {The problem of long-range forces in the computer simulation of condensed matter},
        Editor = {D. Ceperley},
        Pages = {45-6},
        Series = {NRCC Workshop Proceedings},
        Title = {Reaction field method for polar fluids},
        Volume = 9,
        Year = 1980}

@article{Smith82,
        Author = {W. Smith},
        Date-Modified = {2006-07-18 14:33:49 -0400},
        Journal = {CCP5 Quarterly},
        Pages = {13-25},
        Title = {Point multipoles in the \uppercase{E}wald summation},
        Volume = 4,
        Year = 1982}

@article{Daw84,
        Author = {M.~S. Daw and M.~I. Baskes},
        Date-Modified = {2006-07-18 15:01:56 -0400},
        Journal = prb,
        Number = 12,
        Pages = {6443-6453},
        Title = {Embedded-atom method: \uppercase{D}erivation and application to impurities, surfaces, and other defects in metals},
        Volume = 29,
        Year = 1984}

@article{Sutton90,
        Author = {A.~P. Sutton and J. Chen},
        Date-Modified = {2006-02-15 10:33:48 -0500},
        Journal = {Phil. Mag. Lett.},
        Pages = {139-146},
        Title = {Long-Range $\mbox{Finnis Sinclair}$ Potentials},
        Volume = 61,
        Year = 1990}

@article{Lu97,
        Author = {J. Lu and J.~A. Szpunar},
        Journal = {Phil. Mag. A},
        Pages = {1057-1066},
        Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
        Volume = {75},
        Year = {1997}}

@article{Shlesinger99,
        Author = {M.~F. Shlesinger and J. Klafter and G. Zumofen},
        Journal = {Am. J. Phys.},
        Pages = {1253-1259},
        Title = {Above, below, and beyond Brownian motion},
        Volume = 67,
        Year = 1999}

@article{Klafter96,
        Author = {J. Klafter and M. Shlesinger and G. Zumofen},
        Journal = {Physics Today},
        Pages = {33-39},
        Title = {Beyond Brownian Motion},
        Volume = 49,
        Year = 1996}

@article{Blumen83,
        Author = {A. Blumen and J. Klafter and G. Zumofen},
        Journal = {Phys. Rev. B},
        Pages = {3429-3435},
        Title = {Recombination in amorphous materials as a continuous-time random-walk problem},
        Volume = 27,
        Year = 1983}

@article{Klafter94,
        Author = {J. Klafter and G. Zumofen},
        Journal = jpc,
        Pages = {7366-7370},
        Title = {Probability Distributions for Continuous-Time Random Walks with Long Tails},
        Volume = 98,
        Year = 1994}

@article{Dzugutov92,
        Author = {M. Dzugutov},
        Journal = pra,
        Pages = {R2984-R2987},
        Title = {Glass formation in a simple monatomic liquid with icosahedral inherent local order},
        Volume = 46,
        Year = 1992}

@article{Moore94,
        Author = {P. Moore and T. Keyes},
        Date-Modified = {2006-07-18 15:07:46 -0400},
        Journal = jcp,
        Pages = 6709,
        Title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: $\mbox{V}$elocity Correlation Functions and Self-Diffusion Constants},
        Volume = 100,
        Year = 1994}

@article{Seeley89,
        Author = {G. Seeley and T. Keyes},
        Journal = jcp,
        Pages = {5581-5586},
        Title = {Normal-mode analysis of liquid-state dynamics},
        Volume = 91,
        Year = 1989}

@article{Madan90,
        Author = {B. Madan and T. Keyes and G. Seeley},
        Journal = jcp,
        Pages = {7565-7569},
        Title = {Diffusion in supercooled liquids via normal mode analysis},
        Volume = 92,
        Year = 1990}

@article{Madan91,
        Author = {B. Madan and T. Keyes and G. Seeley},
        Journal = jcp,
        Pages = {6762-6769},
        Title = {Normal mode analysis of the velocity correlation function in supercooled liquids},
        Volume = 94,
        Year = 1991}

@article{Buchner92,
        Author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt},
        Date-Modified = {2006-07-18 14:49:51 -0400},
        Journal = jcp,
        Pages = {8522-8535},
        Title = {The short-time dynamics of molecular liquids. \uppercase{I}nstantaneous-normal-mode theory},
        Volume = 97,
        Year = 1992}

@article{Wan94,
        Author = {Yi. Wan and R.~M. Stratt},
        Journal = jcp,
        Pages = {5123-5138},
        Title = {Liquid theory for the instantaneous normal modes of a liquid},
        Volume = 100,
        Year = 1994}

@article{Stratt95,
        Author = {R.~M. Stratt},
        Journal = {Acc. Chem. Res.},
        Pages = {201-207},
        Title = {The instantaneous normal modes of liquids},
        Volume = 28,
        Year = 1995}

@article{Nitzan95,
        Author = {G.~V. Vijayadamodar and A. Nitzan},
        Journal = jcp,
        Pages = {2169-2177},
        Title = {On the application of instantaneous normal mode analysis to long time dynamics of liquids},
        Volume = 103,
        Year = 1995}

@article{Ribeiro98,
        Author = {M.~C.~C. Ribeiro and P.~A. Madden},
        Journal = jcp,
        Pages = {3256-3263},
        Title = {Unstable Modes in Ionic Melts},
        Volume = 108,
        Year = 1998}

@article{Keyes98,
        Author = {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher},
        Date-Modified = {2006-07-18 14:53:08 -0400},
        Journal = jcp,
        Pages = {4693-4694},
        Title = {Comment on a critique of the instantaneous normal mode (\uppercase{INM}) approach to diffusion},
        Volume = 109,
        Year = 1998}

@article{Alemany98,
        Author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego},
        Date-Modified = {2006-07-18 14:58:53 -0400},
        Journal = jcp,
        Pages = {5175-5176},
        Title = {Transport coefficients of liquid transition metals: \uppercase{A} computer simulation study using the embedded atom model},
        Volume = 109,
        Year = 1998}

@article{Belonoshko00,
        Author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and B. Johansson},
        Journal = prb,
        Pages = {3838-3844},
        Title = {Quasi ab initio molecular dynamic study of Cu melting},
        Volume = 61,
        Year = 2000}

@article{Banhart92,
        Author = {J. Banhart and H. Ebert and R. Kuentzler and J. Voitl\"{a}nder},
        Journal = prb,
        Pages = {9968-9975},
        Title = {Electronic properties of single-phased metastable Ag-Cu alloys},
        Volume = 46,
        Year = 1992}

@article{Wendt78,
        Author = {H. Wendt and F.~F. Abraham},
        Journal = prl,
        Pages = 1244,
        Volume = 41,
        Year = 1978}

@article{Lewis91,
        Author = {L.~J. Lewis},
        Journal = prb,
        Pages = {4245-4254},
        Title = {Atomic dynamics through the glass transition},
        Volume = 44,
        Year = 1991}

@article{Liu92,
        Author = {R.~S. Liu and D.~W. Qi and S. Wang},
        Journal = prb,
        Pages = {451-453},
        Title = {Subpeaks of structure factors for rapidly quenched metals},
        Volume = 45,
        Year = 1992}

@article{Anheuser94,
        Author = {K. Anheuser and J.P. Northover},
        Journal = {Brit. Num. J.},
        Pages = 22,
        Title = {Silver plating of Roman and Celtic coins from Britan - a technical study},
        Volume = 64,
        Year = 1994}

@article{Pense92,
        Author = {A. W. Pense},
        Journal = {Mat. Char.},
        Pages = 213,
        Title = {The Decline and Fall of the Roman Denarius},
        Volume = 29,
        Year = 1992}

@article{Ngai81,
        Author = {K.~L. Ngai and F.-S. Liu},
        Journal = prb,
        Pages = {1049-1065},
        Title = {Dispersive diffusion transport and noise, time-dependent diffusion coefficient, generalized Einstein-Nernst relation, and dispersive diffusion-controlled unimolecular and bimolecular reactions},
        Volume = 24,
        Year = 1981}

@unpublished{Truhlar00,
        Author = {D.~G. Truhlar and A. Kohen},
        Date-Modified = {2006-02-15 16:35:52 -0500},
        Note = {private correspondence},
        Year = {2000}}

@article{Truhlar78,
        Author = {Donald G. Truhlar},
        Journal = {J. Chem. Ed.},
        Pages = 309,
        Title = {Interpretation of the Activation Energy},
        Volume = 55,
        Year = 1978}

@book{Tolman27,
        Address = {New York},
        Author = {R. C. Tolman},
        Pages = {260-270},
        Publisher = {Chemical Catalog Co.},
        Title = {Statistical Mechanics with Applications to Physics and Chemistry},
        Year = 1927}

@article{Tolman20,
        Author = {R. C. Tolman},
        Journal = jacs,
        Pages = 2506,
        Title = {Statistical Mechanics Applied to Chemical Kinetics},
        Volume = 42,
        Year = 1920}

@article{Ediger96,
        Author = {M.D. Ediger and C.A. Angell and Sidney R. Nagel},
        Date-Modified = {2006-02-15 10:16:35 -0500},
        Journal = jpc,
        Pages = 13200,
        Title = {Supercooled Liquids and Glasses},
        Volume = 100,
        Year = 1996}

@inbook{Blumen86,
        Address = {Amsterdam},
        Author = {A. Blumen and J. Klafter and G. Zumofen},
        Chapter = {Reactions in Disordered Media Modelled by Fractals},
        Editor = {Luciano Peitronero and E. Tosatti},
        Pages = 399,
        Publisher = {North-Holland},
        Series = {International Symposium on Fractals in Physics},
        Title = {Fractals in Physics},
        Year = 1986}

@article{Shlesinger84,
        Author = {M.~F. Shlesinger and E.~W. Montroll},
        Journal = {Proc. Natl. Acad. Sci. USA},
        Pages = {1280-1283},
        Title = {On the Williams-Watts function of dielectric relaxation},
        Volume = 81,
        Year = 1984}

@article{Klafter86,
        Author = {J. Klafter and M.~F. Shlesinger},
        Journal = {Proc. Natl. Acad. Sci. USA},
        Pages = {848-851},
        Title = {On the relationship among three theories of relaxation in disordered systems},
        Volume = 83,
        Year = 1986}

@article{Li01,
        Author = {Z. Li and M. Lieberman and W. Hill},
        Date-Modified = {2006-07-18 15:05:41 -0400},
        Journal = {Langmuir},
        Pages = {4887-4894},
        Title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine Monolayers: \uppercase{U}mbrella vs. octopus design strategies for formation of oriented {\sc sam}s},
        Volume = 17,
        Year = 2001}

@article{Evans93,
        Author = {J.~W. Evans},
        Date-Modified = {2006-02-15 10:17:03 -0500},
        Journal = rmp,
        Pages = {1281-1329},
        Title = {Random and Cooperative Sequential Adsorption},
        Volume = 65,
        Year = 1993}

@article{Dwyer1977,
        Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
        Journal = {Surf. Sci.},
        Pages = 617,
        Volume = 64,
        Year = 1977}

@article{Macritche78,
        Author = {F. MacRitche},
        Date-Modified = {2006-02-15 10:27:37 -0500},
        Journal = {Adv. Protein Chem.},
        Pages = 283,
        Volume = 32,
        Year = 1978}

@article{Feder80,
        Author = {J. Feder},
        Date-Modified = {2006-02-15 10:17:21 -0500},
        Journal = {J. Theor. Biol.},
        Pages = 237,
        Volume = 87,
        Year = 1980}

@article{Ramsden93,
        Author = {J.~J. Ramsden},
        Date-Modified = {2006-02-15 10:31:03 -0500},
        Journal = prl,
        Pages = 295,
        Volume = 71,
        Year = 1993}

@article{Egelhoff89,
        Author = {W.~F. Egelhoff and I. Jacob},
        Date-Modified = {2006-02-15 10:16:54 -0500},
        Journal = prl,
        Pages = 921,
        Volume = 62,
        Year = 1989}

@article{Viot92a,
        Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
        Date-Modified = {2006-07-18 14:57:12 -0400},
        Journal = jpc,
        Pages = {5212-5218},
        Title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC PARTICLES 1. \uppercase{J}AMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
        Volume = 97,
        Year = 1992}

@article{Viot92b,
        Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
        Date-Modified = {2006-02-15 10:12:57 -0500},
        Journal = {Physica A},
        Pages = {248-252},
        Title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION OF VERY ELONGATED PARTICLES},
        Volume = 191,
        Year = 1992}

@article{Dobson1987,
        Author = {B.~W. Dobson},
        Journal = prb,
        Pages = 1068,
        Volume = 36,
        Year = 1987}

@article{Boyer95,
        Author = {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
        Date-Modified = {2006-02-15 10:15:52 -0500},
        Journal = jcp,
        Pages = 1607,
        Title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL ADSORPTION},
        Volume = 103,
        Year = 1995}

@article{Viot92c,
        Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
        Date-Modified = {2006-02-15 10:13:03 -0500},
        Journal = {Physica A},
        Pages = {248-252},
        Title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC PARTICLES},
        Volume = 191,
        Year = 1992}

@article{Ricci94,
        Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
        Date-Modified = {2006-02-15 10:31:32 -0500},
        Journal = jcp,
        Pages = 9164,
        Title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
        Volume = 101,
        Year = 1994}

@article{Semmler98,
        Author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
        Date-Modified = {2006-02-15 10:14:46 -0500},
        Journal = {Langmuir},
        Pages = {5127-5132},
        Title = {Diffusional Deposition of Charged Latex Particles on Water-Solid Interfaces at Low Ionic Strength},
        Volume = 14,
        Year = 1998}

@article{Solomon86,
        Author = {H. Solomon and H. Weiner},
        Date-Modified = {2006-02-15 10:10:38 -0500},
        Journal = {Comm. Statistics A},
        Pages = {2571-2607},
        Title = {A REVIEW OF THE PACKING PROBLEM},
        Volume = 15,
        Year = 1986}

@article{Bonnier93,
        Author = {B. Bonnier and M. Hontebeyrie and C. Meyers},
        Date-Modified = {2006-02-15 10:08:35 -0500},
        Journal = {Physica A},
        Pages = {1-10},
        Title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING D-DIMENSIONAL CUBES},
        Volume = 198,
        Year = 1993}

@book{Frenkel96,
        Address = {New York},
        Author = {D. Frenkel and B. Smit},
        Date-Modified = {2006-07-18 15:02:21 -0400},
        Publisher = {Academic Press},
        Title = {Understanding Molecular Simulation: \uppercase{F}rom Algorithms to Applications},
        Year = 1996}

@article{Dullweber1997,
        Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
        Journal = jcp,
        Number = 15,
        Pages = {5840-5851},
        Title = {Symplectic splitting methods for rigid body molecular dynamics},
        Volume = 107,
        Year = 1997}

@article{Martin98,
        Author = {M. Martin and J.~I. Siepmann},
        Date-Modified = {2006-07-18 14:54:51 -0400},
        Journal = jpcB,
        Pages = {2569-2577},
        Title = {Transferable Potentials for Phase Equilibria. 1. \uppercase{U}nited-Atom Description of n-Alkanes},
        Volume = 102,
        Year = 1998}

@article{Marrink01a,
        Author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
        Date-Modified = {2006-02-15 10:28:09 -0500},
        Journal = jacs,
        Pages = {8638-8639},
        Title = {Simulations of the Spontaneous Aggregation of Phospholipids into Bilayers},
        Volume = 123,
        Year = 2001}

@article{Liu96b,
        Author = {Y. Liu and T. Ichiye},
        Date-Modified = {2006-07-18 15:06:06 -0400},
        Journal = jpc,
        Pages = {2723-2730},
        Title = {Soft sticky dipole potential for liquid water: \uppercase{a} new model},
        Volume = 100,
        Year = 1996}

@article{Liu96a,
        Author = {Y. Liu and T. Ichiye},
        Date-Modified = {2006-02-15 10:27:01 -0500},
        Journal = {Chem. Phys. Lett.},
        Pages = {334-340},
        Title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
        Volume = 256,
        Year = 1996}

@article{Chandra99,
        Author = {A. Chandra and T. Ichiye},
        Date-Modified = {2006-07-18 15:01:30 -0400},
        Journal = {J. Chem. Phys.},
        Number = 6,
        Pages = {2701-2709},
        Title = {Dynamical properties of the soft sticky dipole model of water: \uppercase{M}olecular dynamics simulation},
        Volume = 111,
        Year = 1999}

@book{Allen87,
        Address = {New York},
        Author = {M.~P. Allen and D.~J. Tildesley},
        Date-Modified = {2006-02-15 10:08:08 -0500},
        Publisher = {Oxford University Press},
        Title = {Computer Simulations of Liquids},
        Year = 1987}

@book{Leach01,
        Address = {Harlow, England},
        Author = {A.~R. Leach},
        Date-Modified = {2006-07-18 15:19:59 -0400},
        Edition = {2nd},
        Publisher = {Pearson Educated Limited},
        Title = {Molecular Modeling: Principles and Applications},
        Year = 2001}

@article{Katsaras00,
        Author = {J. Katsaras and S. Tristram-Nagle and Y. Liu and R.~L. Headrick and E. Fontes and P.~C. Mason and J.~F. Nagle},
        Date-Modified = {2006-02-15 10:21:52 -0500},
        Journal = {Physical Review E},
        Number = 5,
        Pages = {5668-5677},
        Title = {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples},
        Volume = 61,
        Year = 2000}

@article{Sengupta00,
        Author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
        Date-Modified = {2006-02-15 10:32:00 -0500},
        Journal = {Europhysics Letters},
        Number = 6,
        Pages = {722-728},
        Title = {Novel structural Features of the ripple phase of phospholipids},
        Volume = 49,
        Year = 2000}

@article{Venable00,
        Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
        Date-Modified = {2006-02-15 10:11:19 -0500},
        Journal = jcp,
        Number = 10,
        Pages = {4822-4832},
        Title = {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
        Volume = 112,
        Year = 2000}

@article{Lindahl00,
        Author = {E. Lindahl and O. Edholm},
        Date-Modified = {2006-02-15 10:26:05 -0500},
        Journal = {Biophysical Journal},
        Month = {July},
        Pages = {426-433},
        Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
        Volume = 79,
        Year = 2000}

@article{Saiz02,
        Author = {L. Saiz and M. Klein},
        Date-Modified = {2006-02-15 10:31:50 -0500},
        Journal = jcp,
        Number = 7,
        Pages = {3052-3057},
        Title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
        Volume = 116,
        Year = 2002}

@article{Stevens95,
        Author = {M.~J. Stevens and G.~S. Grest},
        Date-Modified = {2006-02-15 10:10:47 -0500},
        Journal = {Physical Review E},
        Number = 6,
        Pages = {5976-5983},
        Title = {Phase coexistence of a Stockmayer fluid in an aplied field},
        Volume = 51,
        Year = 1995}

@article{Darden93,
        Author = {T. Darden and D. York and L. Pedersen},
        Date-Modified = {2006-07-18 15:01:45 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_ParticleMeshEwald_93.pdf},
        Number = 12,
        Pages = {10089-10092},
        Title = {Particle mesh \uppercase{E}wald: \uppercase{A}n $\uppercase{N} \log \uppercase{N}$ method for \uppercase{E}wald sums in large systems},
        Volume = 98,
        Year = 1993}

@article{Goetz98,
        Author = {R. Goetz and R. Lipowsky},
        Date-Modified = {2006-07-18 15:03:05 -0400},
        Journal = {J. Chem. Phys.},
        Number = 17,
        Pages = 7397,
        Title = {Computer simulations of bilayer membranes: \uppercase{S}elf-assembly and interfacial tension},
        Volume = 108,
        Year = 1998}

@article{Marrink01b,
        Author = {S.~J. Marrink and A.~E. Mark},
        Date-Modified = {2006-02-15 10:28:01 -0500},
        Journal = {Journal of Physical Chemistry B},
        Pages = {6122-6127},
        Title = {Effect of undulations on surface tension in simulated bilayers},
        Volume = 105,
        Year = 2001}

@article{Metropolis49,
        Author = {N. Metropolis and S. Ulam},
        Date-Modified = {2006-02-15 10:29:03 -0500},
        Journal = {J. Am. Stat. Ass.},
        Pages = {335-341},
        Title = {The $\mbox{Monte Carlo}$ Method},
        Volume = 44,
        Year = 1949}

@article{Metropolis53,
        Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
        Date-Modified = {2006-03-09 10:44:24 -0500},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Metropolis_MCCalculations_53.pdf},
        Pages = {1087-1092},
        Title = {Equation of State Calculations by Fast Computing Machines},
        Volume = 21,
        Year = 1953}

@article{Born12,
        Author = {M. Born and Th. Von~Karman},
        Date-Modified = {2006-02-15 10:08:50 -0500},
        Journal = {Physik Z.},
        Number = {297-309},
        Title = {Uber Schwingungen in Raumgittern},
        Volume = 13,
        Year = 1912}

@book{Chandler87,
        Author = {David Chandler},
        Date-Modified = {2006-02-15 10:09:20 -0500},
        Publisher = {Oxford University Press},
        Title = {Introduction to Modern Statistical Mechanics},
        Year = 1987}

@article{Pearlman95,
        Author = {David~A. Pearlman and David~A. Case and James~W. Caldwell and Wilson~S. Ross and Thomas~E. Cheatham~III and Steve DeBolt and David Ferguson and George Seibel and Peter Kollman},
        Date-Modified = {2006-07-18 14:56:08 -0400},
        Journal = {Computer Physics Communications},
        Pages = {1-41},
        Title = {\uppercase{AMBER}, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics, and free energy calculations to simulate the structural and energetic properties of molecules},
        Volume = 91,
        Year = 1995}

@book{Goldstein01,
        Address = {San Francisco},
        Author = {H. Goldstein and C. Poole and J. Safko},
        Edition = {3rd},
        Publisher = {Addison Wesley},
        Title = {Classical Mechanics},
        Year = 2001}

@article{Bratko85,
        Author = {D. Bratko and L. Blum and A. Luzar},
        Journal = jcp,
        Number = 12,
        Pages = {6367-6370},
        Title = {A simple model for the intermolecular potential of water},
        Volume = 83,
        Year = 1985}

@article{Bratko95,
        Author = {L. Blum and F. Vericat and D. Bratko},
        Date-Modified = {2006-07-18 15:00:02 -0400},
        Journal = jcp,
        Number = 3,
        Pages = {1461-1462},
        Title = {Towards an analytical model of water: \uppercase{T}he octupolar model},
        Volume = 102,
        Year = 1995}

@article{Tan03,
        Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks and T. Ichiye},
        Journal = cpl,
        Pages = {646-652},
        Title = {A temperature of maximum density in soft sticky dipole water},
        Volume = 376,
        Year = 2003}

@article{Soper86,
        Author = {A.~K. Soper and M.~G. Phillips},
        Journal = cp,
        Number = 1,
        Pages = {47-60},
        Title = {A new determination of the structure of water at 298K},
        Volume = 107,
        Year = 1986}

@article{Plimpton95,
        Author = {S. Plimpton},
        Date-Modified = {2006-02-15 10:30:31 -0500},
        Journal = {J. Comp. Phys.},
        Pages = {1-19},
        Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
        Volume = 117,
        Year = 1995}

@article{Tartaglino02,
        Author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
        Date-Modified = {2006-07-18 15:14:01 -0400},
        Journal = prb,
        Pages = 241406,
        Title = {Bending strain-driven modification of surface resconstructions: $\mbox{Au}$(111)},
        Volume = 65,
        Year = 2002}

@article{Ercolessi88,
        Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
        Date-Modified = {2006-07-18 14:52:08 -0400},
        Journal = {Philosophical Magazine A},
        Pages = {213-226},
        Title = {Simulation of Gold in the Glue Model},
        Volume = 58,
        Year = 1988}

@article{Finnis84,
        Author = {M.~W Finnis and J.~E. Sinclair},
        Journal = {Phil. Mag. A},
        Pages = {45-55},
        Title = {A Simple Empirical N-Body Potential for Transition-Metals},
        Volume = 50,
        Year = 1984}

@article{Foiles86,
        Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
        Date-Modified = {2006-02-15 10:17:44 -0500},
        Journal = prb,
        Number = 12,
        Pages = 7983,
        Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
        Volume = 33,
        Year = 1986}

@article{Daw93,
        Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes},
        Date-Modified = {2006-02-15 10:16:13 -0500},
        Journal = {Mat. Sci. Rep.},
        Pages = {251-310},
        Title = {The embededd-atom method},
        Volume = 9,
        Year = 1993}

@article{Johnson89,
        Author = {R.~A. Johnson},
        Date-Modified = {2006-02-15 10:21:36 -0500},
        Journal = prb,
        Number = 17,
        Pages = 12554,
        Title = {Alloy models with the embedded-atom method},
        Volume = 39,
        Year = 1989}

@article{Kol97,
        Author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler},
        Date-Modified = {2006-02-15 10:24:53 -0500},
        Journal = jcp,
        Number = 7,
        Pages = {2580-2588},
        Title = {A symplectic method for rigid-body molecular simulation},
        Volume = 107,
        Year = 1997}

@article{Hoover85,
        Author = {W.~G. Hoover},
        Date-Modified = {2006-07-18 15:03:15 -0400},
        Journal = pra,
        Pages = 1695,
        Title = {Canonical dynamics: \uppercase{E}quilibrium phase-space distributions},
        Volume = 31,
        Year = 1985}

@article{Roux91,
        Author = {B. Roux and M. Karplus},
        Date-Modified = {2006-07-18 15:12:04 -0400},
        Journal = jpc,
        Number = 15,
        Pages = {4856-4868},
        Title = {Ion transport in a Gramicidin-like channel: $\mbox{D}$ynamics and mobility},
        Volume = 95,
        Year = 1991}

@article{Marrink94,
        Author = {S.~J Marrink and H.~J.~C. Berendsen},
        Journal = jpc,
        Number = 15,
        Pages = {4155-4168},
        Title = {Simulation of water transport through a lipid membrane},
        Volume = 98,
        Year = 1994}

@article{Daw89,
        Author = {Murray~S. Daw},
        Date-Modified = {2006-07-18 15:02:06 -0400},
        Journal = {Physical Review B},
        Pages = {7441-7452},
        Title = {Model of metallic cohesion: \uppercase{T}he embedded-atom method},
        Volume = 39,
        Year = 1989}

@inbook{Voter95b,
        Author = {A.~F. Voter},
        Chapter = 4,
        Date-Modified = {2006-02-15 10:35:07 -0500},
        Editor = {J.~H. Westbrook and R.~L. Fleischer},
        Pages = 77,
        Publisher = {John Wiley and Sons Ltd},
        Title = {Intermetallic Compounds: Principles and Practice},
        Volume = 1,
        Year = 1995}

@article{Marrink02,
        Author = {S.~J. Marrink and D.~P. Teileman},
        Date-Modified = {2006-02-15 10:28:20 -0500},
        Journal = {Biophysical Journal},
        Pages = {2386-2392},
        Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
        Volume = 83,
        Year = 2002}

@article{Sum03,
        Author = {A.~K. Sum and J.~J. de~Pablo},
        Date-Modified = {2006-02-15 10:11:01 -0500},
        Journal = {Biophysical Journal},
        Pages = {3636-3645},
        Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
        Volume = 85,
        Year = 2003}

@article{Gomez03,
        Author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom},
        Date-Modified = {2006-02-15 10:17:14 -0500},
        Journal = {Eur. Biophys. J.},
        Pages = {217-227},
        Title = {Setting up and optimization of membrane protein simulations},
        Volume = 31,
        Year = 2002}

@article{Smondyrev99,
        Author = {A.~M. Smondyrev and M.~L. Berkowitz},
        Date-Modified = {2006-02-15 10:10:29 -0500},
        Journal = {Biophysical Journal},
        Pages = {2472-2478},
        Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
        Volume = 76,
        Year = 1999}

@article{Nina02,
        Author = {M. Nina and T. Simonson},
        Date-Modified = {2006-07-18 15:08:00 -0400},
        Journal = {J. Phys. Chem. B},
        Pages = {3696-3705},
        Title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: $\mbox{C}$omparison between Continuum Reaction Field and Particle-Mesh \uppercase{E}wald Electrostatic Treatments},
        Volume = 106,
        Year = 2002}

@article{Norberg00,
        Author = {J. Norberg and L. Nilsson},
        Date-Modified = {2006-02-15 10:29:36 -0500},
        Journal = {Biophysical Journal},
        Pages = {1537-1553},
        Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
        Volume = 79,
        Year = 2000}

@article{Patra03,
        Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
        Date-Modified = {2006-07-18 15:10:24 -0400},
        Journal = {Biophysical Journal},
        Pages = {3636-3645},
        Title = {Molecular Dynamics Simulations of Lipid Bilayers: $\mbox{M}$ajor Artifacts Due to Truncating Electrostatic Interactions},
        Volume = 84,
        Year = 2003}

@article{Marrink04,
        Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
        Date-Modified = {2006-02-15 10:28:28 -0500},
        Journal = {J. Phys. Chem. B},
        Pages = {750-760},
        Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
        Volume = 108,
        Year = 2004}

@article{Andersen83,
        Author = {H.~C. Andersen},
        Date-Modified = {2006-07-18 14:59:26 -0400},
        Journal = {Journal of Computational Physics},
        Pages = {24-34},
        Title = {\uppercase{RATTLE: A} Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
        Volume = 52,
        Year = 1983}

@article{Hura00,
        Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
        Date-Modified = {2006-07-21 11:45:15 -0400},
        Journal = {J. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/THGord_X-RayH2O_2000.pdf},
        Pages = {9140-9148},
        Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
        Volume = 113,
        Year = 2000}

@inbook{Fowles99,
        Author = {G.~R. Fowles and G.~L. Cassiday},
        Chapter = 10,
        Date-Modified = {2006-02-15 10:18:00 -0500},
        Edition = {6th},
        Publisher = {Saunders College Publishing},
        Title = {Analytical Mechanics},
        Year = 1999}

@article{Petrache00,
        Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
        Date-Modified = {2006-02-15 10:30:24 -0500},
        Journal = {Biophysical Journal},
        Pages = {3172-3192},
        Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
        Volume = 79,
        Year = 2000}

@article{Egberts88,
        Author = {E. Egberts and H.~J.~C. Berendsen},
        Date-Modified = {2006-02-15 10:16:43 -0500},
        Journal = {J. Chem. Phys.},
        Pages = {3718-3732},
        Title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
        Volume = 89,
        Year = 1988}

@article{Holz00,
        Author = {M. Holz and S.~R. Heil and A. Sacco},
        Date-Modified = {2006-08-06 14:07:16 -0400},
        Journal = {Phys. Chem. Chem. Phys.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Holz_SelfDiffusionOfWaterFromNMR_00.pdf},
        Pages = {4740-4742},
        Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1$\uppercase{h nmr pfg} measurements},
        Volume = 2,
        Year = 2000}

@incollection{Zannoni94,
        Author = {C. Zannoni},
        Booktitle = {The Molecular Dynamics of Liquid Crstals},
        Chapter = 6,
        Date-Modified = {2006-02-15 10:12:36 -0500},
        Editor = {G.~R. Luckhurst and C.~A. Veracini},
        Pages = {139-169},
        Publisher = {Kluwer Academic Publishers},
        Title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
        Year = 1994}

@article{Melchionna93,
        Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
        Date-Modified = {2006-07-20 08:41:04 -0400},
        Journal = {Molecular Physics},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Melchionna_HooverNVTandNPT_93.pdf},
        Pages = {533-544},
        Title = {Hoover \uppercase{$NPT$} dynamics for systems varying in shape and size},
        Volume = 78,
        Year = 1993}

@article{Fennell04,
        Author = {C.~J. Fennell and J.~D. Gezelter},
        Date-Modified = {2006-07-18 14:20:59 -0400},
        Journal = jcp,
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_TempSSDs_04.pdf},
        Number = 19,
        Pages = {9175-9184},
        Title = {On the structural and transport properties of the soft sticky dipole (\uppercase{SSD}) and related single point water models},
        Volume = 120,
        Year = 2004}

@article{Klein01,
        Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
        Date-Modified = {2006-02-15 10:27:22 -0500},
        Journal = {J. Phys. Chem. B},
        Pages = {4464-4470},
        Title = {A Coarse Grain Model for Phospholipid Simulations},
        Volume = 105,
        Year = 2001}

@article{Marrink03,
        Author = {S.~J. Marrink and A.~E. Mark},
        Date-Modified = {2006-03-16 09:54:52 -0500},
        Journal = {J. Am. Chem. Soc.},
        Pages = {15233-15242},
        Title = {Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
        Volume = 125,
        Year = 2003}

@article{Fletcher64,
        Author = {R. Fletcher and C.~M. Reeves},
        Date-Modified = {2006-02-15 10:17:34 -0500},
        Journal = {Comput. J.},
        Number = 2,
        Pages = {149-154},
        Title = {Function minimization by conjugate gradients},
        Volume = 7,
        Year = 1964}

@article{Polak69,
        Author = {E. Polak and G. Ribiere},
        Date-Modified = {2006-02-15 10:14:00 -0500},
        Journal = {Rev. Fr. Inform. Rech. Oper.},
        Pages = {35-43},
        Title = {Note sur la convergence de methodes de directions conjugees},
        Volume = {16-R1},
        Year = 1969}

@article{Voter87,
        Author = {A.~F. Voter and S.~P. Chen},
        Date-Modified = {2006-02-15 10:35:19 -0500},
        Journal = {Mat. Res. Soc. Symp. Proc.},
        Pages = {175},
        Title = {Accurate Interatomic Potentials for Ni, Al, and Ni3Al},
        Volume = {82},
        Year = {1987}}

@article{Hendrickson95,
        Author = {Bruce Hendrickson and Steve Plimpton},
        Date-Modified = {2006-02-15 10:19:11 -0500},
        Journal = {Journal of Parallel and Distributed Computing},
        Pages = {15-25},
        Title = {Parallel Many-body Simulations without All-to-All Communication},
        Volume = {27},
        Year = {1995}}

@inproceedings{Paradyn93,
        Address = {Pittsburgh, PA},
        Author = {S.~J. Plimpton and B.~A. Hendrickson},
        Booktitle = {Materials Theory and Modelling},
        Date-Modified = {2006-02-15 10:30:42 -0500},
        Editor = {J. Broughton and P. Bristowe and J. Newsam},
        Pages = 37,
        Publisher = {Materials Research Society},
        Series = {MRS Proceedings},
        Title = {Parallel Molecular Dynamics With the Embedded Atom Method},
        Volume = 291,
        Year = 1993}

@article{Voter95a,
        Author = {A.~F. Voter},
        Date-Modified = {2006-02-15 10:35:27 -0500},
        Journal = {Intermetallic Compounds: Principles and Practice},
        Pages = {77},
        Title = {The Embedded-Atom Method},
        Volume = {1},
        Year = {1995}}

@article{Heller90,
        Author = {H. Heller and H. Grubmuller and K. Schulten},
        Date-Modified = {2006-02-15 10:19:02 -0500},
        Journal = {Molecular Simulation},
        Pages = {133},
        Title = {Molecular dynamics simulation on a parallel computer},
        Volume = {5},
        Year = {1990}}

@book{Fox88,
        Address = {Englewood Cliffs, NJ},
        Author = {G.~C. Fox and M.~A. Johnson and G.~A Lyzenga and S.~W. Otto and J.~K. Salmon and D.~W. Walker},
        Publisher = {Prentice-Hall},
        Title = {Solving Promblems on Concurrent Processors},
        Volume = {I},
        Year = 1988}

@article{Berendsen95,
        Author = {H.~J.~C. Berendsen and D. van~der~Spoel and R. van~Drunen},
        Date-Modified = {2006-07-18 14:59:51 -0400},
        Journal = {Comp. Phys. Comm.},
        Pages = {43-56},
        Title = {\uppercase{GROMACS: A} message-passing parallel molecular dynamics implementation},
        Volume = 91,
        Year = 1995}

@article{Lindahl01,
        Author = {E. Lindahl and B. Hess and D. van~der~Spoel},
        Date-Modified = {2006-07-18 14:53:59 -0400},
        Journal = {J. Mol. Mod.},
        Pages = {306-317},
        Title = {\uppercase{GROMACS 3.0: A} package for molecular simulation and trajectory analysis},
        Volume = 7,
        Year = 2001}

@article{Smith96,
        Author = {W. Smith and T. Forester},
        Date-Modified = {2006-07-18 14:56:36 -0400},
        Journal = {J. Molec. Graphics.},
        Number = 3,
        Pages = {136-141},
        Title = {\uppercase{DL_POLY_2.0: A} general-purpose parallel molecular dynamics simulation package},
        Volume = 14,
        Year = 1996}

@article{Ponder87,
        Author = {J.~W. Ponder and F.~M. Richards},
        Date-Modified = {2006-02-15 10:13:45 -0500},
        Journal = {J. Comp. Chem.},
        Number = 7,
        Pages = {1016-1024},
        Title = {AN EFFICIENT NEWTON-LIKE METHOD FOR MOLECULAR MECHANICS ENERGY MINIMIZATION OF LARGE MOLECULES},
        Volume = 8,
        Year = 1987}

@article{Berendsen87,
        Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
        Journal = jpc,
        Pages = {6269-6271},
        Title = {The Missing Term in Effective Pair Potentials},
        Volume = 91,
        Year = 1987}

@incollection{Berendsen81,
        Address = {Dordrecht},
        Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
        Booktitle = {Intermolecular Forces},
        Date-Modified = {2006-08-02 13:23:53 -0400},
        Editor = {B. Pullman},
        Pages = {331-342},
        Publisher = {Reidel},
        Title = {Simple Point Charge Water},
        Year = 1981}

@article{Mahoney00,
        Author = {M.~W. Mahoney and W.~L. Jorgensen},
        Journal = jcp,
        Number = 20,
        Pages = {8910-8922},
        Title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
        Volume = 112,
        Year = 2000}

@article{Meineke05,
        Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
        Date-Modified = {2006-07-18 15:22:51 -0400},
        Journal = {J. Comp. Chem.},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Meineke_OOPSE_05.pdf},
        Pages = {252-271},
        Title = {$\mbox{OOPSE: A}$n Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
        Volume = 26,
        Year = 2005}

@article{Baez95a,
        Author = {L.~A. B\`{a}ez and P. Clancy},
        Journal = mp,
        Number = 3,
        Pages = {385-396},
        Title = {Calculation of free energy for molecular crystals by thermodynamic integration},
        Volume = 86,
        Year = 1995}

@article{Baez95b,
        Author = {L.~A. B\`{a}ez and P. Clancy},
        Journal = jcp,
        Number = 22,
        Pages = {9744-9755},
        Title = {Phase equilibria in extended simple point charge ice-water systems},
        Volume = 103,
        Year = 1995}

@article{Davidson84,
        Author = {E.~R. Davidson and K. Morokuma},
        Journal = jcp,
        Number = 8,
        Pages = {3741-3742},
        Title = {A proposed antiferroelectric structure for proton ordered ice Ih},
        Volume = 81,
        Year = 1984}

@article{Sanz04,
        Author = {E. Sanz and C. Vega and J.~L.~F. Abascal and L.~G. MacDowell},
        Journal = prl,
        Number = 25,
        Pages = 255701,
        Title = {Phase Diagram of Water from Computer Simulation},
        Volume = 92,
        Year = 2004}

@article{Onsager36,
        Author = {L. Onsager},
        Date-Modified = {2006-08-02 10:49:57 -0400},
        Journal = jacs,
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Onsager_electMoments_36.pdf},
        Pages = {1486-1493},
        Title = {Electric Moments of Molecules in Liquids},
        Volume = 58,
        Year = 1936}

@article{Matsumoto02,
        Author = {M. Matsumoto and S. Saito and I. Ohimine},
        Journal = {Nature (London)},
        Pages = {409-413},
        Title = {Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing},
        Volume = 416,
        Year = 2002}

@article{Yamada02,
        Author = {M. Yamada and S. Mossa and H.~E. Stanley and F. Sciortino},
        Journal = prl,
        Number = 19,
        Pages = 195701,
        Title = {Interplay between Time-Temperature Transformation and the Liquid-Liquid Phase Transition in Water},
        Volume = 88,
        Year = 2002}

@article{Wallqvist95,
        Author = {A. Wallqvist and B.~J. Berne},
        Journal = jpc,
        Pages = {2885-2892},
        Title = {Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area},
        Volume = 99,
        Year = 1995}

@article{Vlot99,
        Author = {M.~J. Vlot and J. Huinink and J.~P. van~der~Eerden},
        Date-Modified = {2006-07-18 15:18:07 -0400},
        Journal = jcp,
        Number = 1,
        Pages = {55-61},
        Title = {Free energy calculations on systems of rigid molecules: $\mbox{A}$n application to the $\mbox{TIP4P}$ model of $\mbox{H}_2$\mbox{O}$},
        Volume = 110,
        Year = 1999}

@article{Gao00,
        Author = {G.~T. Gao and X.~C. Zeng and H. Tanaka},
        Date-Modified = {2006-07-18 15:02:44 -0400},
        Journal = jcp,
        Number = 19,
        Pages = {8534-8538},
        Title = {The melting temperature of proton-disordered hexagonal ice: \uppercase{A} computer simulation of 4-site transferable intermolecular potential model of water},
        Volume = 112,
        Year = 2000}

@article{Bizid87,
        Author = {A. Bizid and L. Bosio and A. Defrain and M. Oumezzine},
        Date-Modified = {2006-07-18 14:51:30 -0400},
        Journal = jcp,
        Number = 4,
        Pages = {2225-2230},
        Title = {Structure of high-density amorphous water. \uppercase{I. X}-ray diffraction study},
        Volume = 87,
        Year = 1987}

@article{Quintana92,
        Author = {J. Quintana and A.~D.~J. Haymet},
        Date-Modified = {2006-07-18 15:11:19 -0400},
        Journal = cpl,
        Number = 3,
        Pages = {273-277},
        Title = {The chemical potential of water: $\mbox{m}$olecular dynamics computer simulation of the $\mbox{CF and SPC}$ models},
        Volume = 189,
        Year = 1992}

@article{Mezei92,
        Author = {M. Mezei},
        Journal = {J. Comput. Chem.},
        Pages = 651,
        Title = {Don't Remember},
        Volume = 13,
        Year = 1992}

@article{Widom63,
        Author = {B. Widom},
        Journal = jcp,
        Pages = 2808,
        Title = {Particle insertion},
        Volume = 39,
        Year = 1963}

@article{Clancy94,
        Author = {L.~A. B\'{a}ez and P. Clancy},
        Journal = jcp,
        Number = 11,
        Pages = {9837-9840},
        Title = {Existence of a density maximum in extended simple point charge water},
        Volume = 101,
        Year = 1994}

@article{Jorgensen98b,
        Author = {W.~L. Jorgensen and C. Jenson},
        Date-Modified = {2006-07-18 15:04:13 -0400},
        Journal = jcc,
        Number = 10,
        Pages = {1179-1186},
        Title = {Temperature Dependence of $\mbox{TIP3P, SPC, and TIP4P}$ Water from $\mbox{NPT Monte Carlo}$ Simulations: \uppercase{S}eeking Temperatures of Maximum Density},
        Volume = 19,
        Year = 1998}

@article{Mahoney01,
        Author = {M.~W. Mahoney and W.~L. Jorgensen},
        Journal = jcp,
        Number = 1,
        Pages = {363-366},
        Title = {Diffusion constant of the TIP5P model of liquid water},
        Volume = 114,
        Year = 2001}

@article{Rahman75,
        Author = {A. Rahman and F.~H. Stillinger and H.~L. Lemberg},
        Journal = jcp,
        Number = 12,
        Pages = {5223-5230},
        Title = {Study of a central force model for liquid water by molecular dynamics},
        Volume = 63,
        Year = 1975}

@article{vanderSpoel98,
        Author = {D. {van der Spoel} and P.~J. {van Maaren} and H.~J.~C. Berendsen},
        Date-Modified = {2006-07-18 15:14:10 -0400},
        Journal = jcp,
        Number = 24,
        Pages = {10220-10230},
        Title = {A systematic study of water models for molecular simulation: $\mbox{D}$erivation of water models optimized for use with a reaction field},
        Volume = 108,
        Year = 1998}

@article{Gallagher03,
        Author = {K.~R. Gallagher and K.~A. Sharp},
        Journal = jacs,
        Pages = 9853,
        Title = {A New Angle on Heat Capacity Changes in Hydrophobic Solvation},
        Volume = 125,
        Year = 2003}

@article{Frenkel84,
        Author = {D. Frenkel and A.~J.~C. Ladd},
        Date-Modified = {2006-07-18 14:52:23 -0400},
        Journal = jcp,
        Number = 7,
        Pages = {3188-3193},
        Title = {New $\mbox{Monte Carlo}$ method to compute the free energy of arbitrary solids. \uppercase{A}pplication to the fcc and hcp phases of hard spheres},
        Volume = 81,
        Year = 1984}

@article{Hermens88,
        Author = {J. Hermans and A. Pathiaseril and A. Anderson},
        Date-Modified = {2006-07-18 14:52:38 -0400},
        Journal = jacs,
        Pages = {5982-5986},
        Title = {Excess Free Energy of Liquids from Molecular Dynamics Simulations. \uppercase{A}pplication to Water Models},
        Volume = 110,
        Year = 1988}

@article{Meijer90,
        Author = {E.~J. Meijer and D. Frenkel and R.~A. LeSar and A.~J.~C. Ladd},
        Date-Modified = {2006-07-18 14:46:17 -0400},
        Journal = jcp,
        Number = 12,
        Pages = {7570-7575},
        Title = {Location of melting point at 300 \uppercase{K} of nitrogen by $\mbox{Monte Carlo}$ simulation},
        Volume = 92,
        Year = 1990}

@article{Li96,
        Author = {H. Li and R. Helling and C. Tang and N. Wingreen},
        Journal = {Science},
        Pages = {666-669},
        Title = {Emergence of Preferred Structures in a Simple Model of Protein Folding},
        Volume = 273,
        Year = 1996}

@article{Stillinger74,
        Author = {F.~H. Stillinger and A. Rahman},
        Journal = jcp,
        Number = 4,
        Pages = {1545-1557},
        Title = {Improved simulation of liquid water by molecular dynamics},
        Volume = 60,
        Year = 1974}

@article{Caldwell95,
        Author = {J.~W. Caldwell and P.~A. Kollman},
        Journal = jpc,
        Number = 16,
        Pages = {6208-6219},
        Title = {Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and $N$-Methylacetamide},
        Volume = 99,
        Year = 1995}

@article{Urbic00,
        Author = {T. Urbi\v{c} and V. Vlachy and Y.~V. Kalyuzhnyi and N.~T. Southall and K.~A. Dill},
        Date-Modified = {2006-07-18 15:16:53 -0400},
        Journal = jcp,
        Number = 6,
        Pages = {2843-2848},
        Title = {A two-dimensional model of water: $\mbox{T}$heory and computer simulations},
        Volume = 112,
        Year = 2000}

@article{Yang04,
        Author = {Jianjun Yang and Sheng Meng and L.~F. Xu and E.~G. Wang},
        Journal = prl,
        Number = 14,
        Pages = 146102,
        Title = {Ice Tessellation on a Hydroxylated Silica Surface},
        Volume = 92,
        Year = 2004}
Revision:	2971
Committed:	Sun Aug 6 22:29:27 2006 UTC (18 years, 1 month ago) by chrisfen
File size:	95540 byte(s)
Log Message:	added text and figures in the tip5p-e application section