mattDisertation/collections/disertation.bib

@string{jcp = "J. Chem. Phys."}
@string{cpl = "Chem. Phys. Lett."}
@string{jpc = "J. Phys. Chem."}
@string{jpcA = "J. Phys. Chem. A"}
@string{jpcB = "J. Phys. Chem. B"}
@string{cp  = "Chem. Phys."}
@string{acp = "Adv. Chem. Phys."}
@string{pra = "Phys. Rev. A"}
@string{prb = "Phys. Rev. B"}
@string{pre = "Phys. Rev. E"}
@string{prl = "Phys. Rev. Lett."}
@string{rmp = "Rev. Mod. Phys."}
@string{jml = "J. Mol. Liq."}
@string{mp = "Mol. Phys."}
@string{pnas = "Proc. Natl. Acad. Sci. USA"}
@string{jacs = "J. Am. Chem. Soc."}

@Book{Berne90,
  author =       {B.~J. Berne and R. Pecora},
  title =        {Dynamic Light Scattering},
  publisher =    {Robert E. Krieger Publishing Company, Inc.},
  year =         1990,
  address =      {Malabar, Florida}
}

@Article{Evans77,
  author =       {D.~J. Evans},
  title =        {On the representation of orientation space},
  journal =      {Mol. Phys.},
  year =         1977,
  volume =       34,
  pages =        {317-325}
}

@Article{Tuckerman92,
  author =       {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
  title =        {Reversible multiple time scale molecular dynamics},
  journal =      jcp,
  year =         1992,
  volume =       97,
  pages =        {1990-2001}
}

@Book{Hansen86,
  author =       {J.~P. Hansen and I.~R. McDonald},
  title =        {Theory of Simple Liquids},
  chapter =      7,
  publisher =    {Academic Press},
  year =         1986,
  address =      {London},
  pages =        {199-206}
}

@Article{Angelani98,
  author =       {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
  title =        {Connected Network of Minima as a Model Glass: Long
                  Time Dynamics},
  journal =      prl,
  year =         1998,
  volume =       81,
  number =       21,
  pages =        {4648-4651}
}

@Article{Stillinger82,
  author =       {F.~H. Stillinger and T.~A. Weber},
  title =        {Hidden structure in liquids},
  journal =      pra,
  year =         1982,
  volume =       25,
  number =       2,
  pages =        {978-989}
}

@Article{Stillinger83,
  author =       {F.~H. Stillinger and T.~A. Weber},
  title =        {Dynamics of structural transitions in liquids},
  journal =      pra,
  year =         1983,
  volume =       28,
  number =       4,
  pages =        {2408-2416}
}

@Article{Weber84,
  author =       {T.~A. Weber and F.~H. Stillinger},
  title =        {The effect of density on the inherent structure in
                  liquids},
  journal =      jcp,
  year =         1984,
  volume =       80,
  number =       6,
  pages =        {2742-2746}
}

@Article{Stillinger85,
  author =       {F.~H. Stillinger and T.~A. Weber},
  title =        {Inherent structure theory of liquids in the
                  hard-sphere limit},
  journal =      jcp,
  year =         1985,
  volume =       83,
  number =       9,
  pages =        {4767-4775}
}

@Article{Stillinger98,
  author =       {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
  title =        {Signatures of distinct dynamical regimes in the
                  energy landscape of a glass-forming liquid},
  journal =      {Nature},
  year =         1998,
  volume =       393,
  pages =        {554-557}
}


@Article{Parkhurst75a,
  author =       {H.~J. {Parkhurst, Jr.} and J. Jonas},
  title =        {Dense liquids. I. The effect of density and
                  temperature on viscosity of tetramethylsilane and
                  benzene-$\mbox{D}_6$},
  journal =      jcp,
  year =         1975,
  volume =       63,
  number =       6,
  pages =        {2698-2704}
}

@Article{Parkhurst75b,
  author =       {H.~J. {Parkhurst, Jr.} and J. Jonas},
  title =        {Dense liquids. II. The effect of density and
                  temperature on viscosity of tetramethylsilane and
                  benzene },
  journal =      jcp,
  year =         1975,
  volume =       63,
  number =       6,
  pages =        {2705-2709}
}

@Article{Forester97,
  author =       {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
  title =        {Antibiotic activity of valinomycin - Molecular
                  dynamics simulations involving the water/membrane
                  interface},
  journal =      {J. Chem. Soc. - Faraday Transactions},
  year =         1997,
  volume =       93,
  pages =        {613-619}
}

@Article{Tieleman98,
  author =       {D.~P. Tieleman and H.~J.~C. Berendsen},
  title =        {A molecular dynamics study of the pores formed by
                  Escherichia coli OmpF porin in a fully hydrated
                  palmitoyloleoylphosphatidylcholine bilayer},
  journal =      {Biophys. J.},
  year =         1998,
  volume =       74,
  pages =        {2786-2801}
}

@Article{Cascales98,
  author =       {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
  title =        {Anaesthetic mechanism on a model biological
                  membrane: A molecular dynamics simulation study},
  journal =      {J. Phys. Chem. B},
  year =         1998,
  volume =       102,
  pages =        {625-631}
}

@Article{Bassolino95,
  author =       {D. Bassolino and H.~E. Alper and T.~R. Stouch},
  title =        {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID
                  BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
  journal =      {J. Am. Chem. Soc.},
  year =         1995,
  volume =       117,
  pages =        {4118-4129}
}

@Article{Alper95,
  author =       {H.~E. Alper and T.~R. Stouch},
  title =        {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN
                  BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
  journal =      {J. Phys. Chem.},
  year =         1995,
  volume =       99,
  pages =        {5724-5731}
}

@Article{Sok92,
  author =       {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
  title =        {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF
                  SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
  journal =      {J. Chem. Phys.},
  year =         1992,
  volume =       96,
  pages =        {4699-4704}
}

@Article{Rabani99,
  author =       {E. Rabani and J.~D. Gezelter and B.~J. Berne},
  title =        {Direct Observation of Stretched-Exponential
                  Relaxation in Low-Temperature Lennard-Jones Systems
                  Using the Cage Correlation Function},
  journal =      prl,
  year =         {1999},
  volume =       82,
  pages =        {3649}
}

@Article{Rabani97,
  author =       {E. Rabani and J.~D. Gezelter and B.~J. Berne},
  title =        {Calculating the hopping rate for self-diffusion on
                  rough potential energy surfaces: Cage correlations},
  journal =      {J. Chem. Phys.},
  year =         1997,
  volume =       107,
  pages =        {6867-6876}
}

@Article{Gezelter99,
  author =       {J.~D. Gezelter and E. Rabani and B.~J. Berne},
  title =        {Methods for calculating the hopping rate for
                  orientational and spatial diffusion in a molecular
                  liquid: $\mbox{CS}_{2}$},
  journal =      jcp,
  year =         1999,
  volume =       110,
  pages =        3444
}

@Article{Gezelter98a,
  author =       {J.~D. Gezelter and E. Rabani and B.~J. Berne},
  title =        {Response to 'Comment on a Critique of the
                  Instantaneous Normal Mode (INM) Approach to
                  Diffusion'},
  journal =      jcp,
  year =         1998,
  volume =       109,
  pages =        4695
}

@Article{Gezelter97,
  author =       {J.~D. Gezelter and E. Rabani and B.~J. Berne},
  title =        {Can imaginary instantaneous normal mode frequencies
                  predict barriers to self-diffusion?},
  journal =      jcp,
  year =         1997,
  volume =       107,
  pages =        4618
}

@Article{Zwanzig83,
  author =       {R. Zwanzig},
  title =        {On the relation between self-diffusion and viscosity
                  of liquids},
  journal =      jcp,
  year =         1983,
  volume =       79,
  pages =        {4507-4508}
}

@Article{Zwanzig88,
  author =       {R. Zwanzig},
  title =        {Diffusion in rough potential},
  journal =      {Proc. Natl. Acad. Sci. USA},
  year =         1988,
  volume =       85,
  pages =        2029
}

@Article{Stillinger95,
  author =       {F.~H. Stillinger},
  title =        {A Topographic View of Supercooled Liquids and Glass
                  Formation},
  journal =      {Science},
  year =         1995,
  volume =       267,
  pages =        {1935-1939}
}

@InCollection{Angell85,
  author =       {C.~A. Angell},
  title =        {unknown},
  booktitle =    {Relaxations in Complex Systems},
  publisher =    {National Technical Information Service,
                  U.S. Department of Commerce},
  year =         1985,
  editor =       {K.~Ngai and G.~B. Wright},
  address =      {Springfield, VA},
  pages =        1
}

@Article{Bembenek96,
  author =       {S.~D. Bembenek and B.~B. Laird},
  title =        {The role of localization in glasses and supercooled liquids},
  journal =      jcp,
  year =         1996,
  volume =       104,
  pages =        5199
}

@Article{Sun97,
  author =       {X. Sun and W.~H. Miller},
  title =        {Semiclassical initial value representation for
                  electronically nonadiabatic molecular dynamics},
  journal =      jcp,
  year =         1997,
  volume =       106,
  pages =        6346
}

@Article{Spath96,
  author =       {B.~W. Spath and W.~H. Miller},
  title =        {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION
                  PROBABILITIES},
  journal =      jcp,
  year =         1996,
  volume =       104,
  pages =        95
}

@Book{Warshel91,
  author =       {Arieh Warshel},
  title =        {Computer modeling of chemical reactions in enzymes
                  and solutions},
  publisher =    {Wiley},
  year =         1991,
  address =      {New York}
}

@Article{Vuilleumier97,
  author =       {Rodolphe Vuilleumier and Daniel Borgis},
  title =        {Molecular Dynamics of an excess proton in water
                  using a non-additive valence bond force field},
  journal =      jpc,
  year =         1997,
  volume =       {in press}
}

@Article{Kob95a,
  author =       {W. Kob and H.~C. Andersen},
  title =        {Testing mode-coupling theory for a supercooled
                  binary Lennard-Jones mixtures: The van Hove
                  corraltion function},
  journal =      pre,
  year =         1995,
  volume =       51,
  pages =        {4626-4641}
}

@Article{Kob95b,
  author =       {W. Kob and H.~C. Andersen},
  title =        {Testing mode-coupling theory for a supercooled
                  binary Lennard-Jones mixtures. II. Intermediate
                  scattering function and dynamic susceptibility},
  journal =      pre,
  year =         1995,
  volume =       52,
  pages =        {4134-4153}
}

@InProceedings{Gotze89,
  author =       "W. G{\"{o}}tze",
  title =        "Aspects of Structural Glass Transitions",
  editor =       "J.~P. Hansen and D. Levesque and J. Zinn-Justin",
  volume =       "I",
  pages =        "287-503",
  booktitle =    "Liquids, Freezing and Glass Transitions",
  year =         1989,
  publisher =    "North-Holland",
  address =      "Amsterdam"
}

@Article{Sun97a,
  author =       "X. Sun and W.~H. Miller",
  title =        {Mixed semiclassical-classical approaches to the
                  dynamics of complex molecular systems},
  journal =      jcp,
  year =         1997,
  pages =        916
}

@Article{Keshavamurthy94,
  author =       "S. Keshavamurthy and W.~H. Miller",
  title =        "ivr",
  journal =      cpl,
  year =         1994,
  volume =       218,
  pages =        189
}

@Article{Billing75,
  author =       "G.~D. Billing",
  title =        "ehrenfest",
  journal =      cpl,
  year =         1975,
  volume =       30,
  pages =        391
}

@Article{Chang90,
  author =       {Y.-T. Chang and W.~H. Miller},
  title =        {An Empirical Valence Bond Model for Constructing
                  Global Potential Energy Surfaces for Chemical
                  Reactions of Polyatomic Molecular Systems},
  journal =      jpc,
  year =         1990,
  volume =       94,
  pages =        {5884-5888}
}

@Article{Shor94,
  author =       {P.W. Shor},
  title =        {Algorithms for quantum computation: discrete
                  logarithms and factoring},
  journal =      {Proceedings of the 35th Annual Symposium
on Foundations of Computer Science},
  year =         1994,
  pages =        {124-134}
}

@Article{Feynman82,
  author =       {R.~P. Feynman},
  title =        {Simulating physics with computers},
  journal =      {Int. J. Theor. Phys.},
  year =         1982,
  volume =       21,
  pages =        {467-488}
}

@Article{Grover97,
  author =       {L.~K. Grover},
  title =        {Quantum computers can search arbitrarily large
                  databases by a single query},
  journal =      prl,
  year =         1997,
  volume =       79,
  pages =        {4709-4712}
}

@Article{Chuang98,
  author =       {I. Chuang and N. Gershenfeld and M. Kubinec},
  title =        {Experimental Implementation of Fast Quantum Searching},
  journal =      prl,
  year =         1998,
  volume =       80,
  pages =        {3408-3411}
}

@Article{Monroe95,
  author =       "C. Monroe and D.~M. Meekhof and B.~E. King and
                  W.~M. Itano and D.~J. Wineland",
  title =        {Demonstration of a fundamental quantum logic gate},
  journal =      prl,
  year =         1995,
  volume =       75,
  pages =        4714
}

@Article{Lent93,
  author =       "C.~S. Lent and P.~D. Tougaw and W.~Porod and
                  G.~H. Bernstein",
  title =        {Quantum Cellular Automata},
  journal =      {Nanotechnology},
  year =         1993,
  volume =       4,
  pages =        {49-57}
}

@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",
  title =        {elementary gates for quantum computation},
  journal =      {Phys. Rev. A},
  year =         1995,
  volume =       52,
  pages =        {3457-3467}
}

@Article{Small97,
  author =       {T. Reinot and J.~M. Hayes and G.~J. Small},
  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},
  journal =      jcp,
  year =         1997,
  volume =       106,
  pages =        {457-466}
}

@Article{Laflamme96,
  author =       {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
  title =        {A perfect quantum error correcting code: 5 bit code
                  correcting a general 1 qubit error to encode 1 qubit
                  of information},
  journal =      prl,
  year =         1996,
  volume =       98,
  pages =        77
}

@Article{Shor95,
  author =       {P.~W. Shor},
  title =        {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY},
  journal =      {Phys. Rev. A},
  year =         1995,
  volume =       52,
  pages =        {2493-2496}
}

@Article{Calderbank96,
  author =       {A.~R. Calderbank and P.~W. Shor},
  title =        {Good quantum error-correcting codes exist},
  journal =      {Phys. Rev. A},
  year =         1996,
  volume =       54,
  pages =        {1098-1105}
}

@Article{Steane96,
  author =       {A.~M. Steane},
  title =        {Error correcting codes in quantum theory},
  journal =      prl,
  year =         1996,
  volume =       77,
  pages =        {793-797}
}

@Article{Gezelter95,
  author =       {J.~D. Gezelter and W.~H. Miller},
  title =        {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE
                  RATE OF KETENE ISOMERIZATION},
  journal =      jcp,
  year =         1995,
  volume =       103,
  pages =        {7868-7876}
}

@Article{Chakrabarti92,
  author =       {A.~C. Chakrabarti and D.~W. Deamer},
  title =        {PERMEABILITY OF LIPID BILAYERS TO AMINO-ACIDS AND PHOSPHATE},
  journal =      {Biochimica et Biophysica Acta},
  year =         1992,
  volume =       1111,
  pages =        {171-177}
}

@Article{Paula96,
  author =       {S. Paula and A.~G. Volkov and A.~N. VanHoek and
                  T.~H. Haines and D.~W. Deamer},
  title =        {Permeation of protons, potassium ions, and small
                  polar molecules through phospholipid bilayers as a
                  function of membrane thickness},
  journal =      {Biophys. J.},
  year =         1996,
  volume =       70,
  pages =        {339-348}
}

@Article{Little96,
  author =       {H.~J. Little},
  title =        {How has molecular pharmacology contributed to our
                  understanding of the mechanism(s) of general
                  anesthesia?},
  journal =      {Pharmacology \& Therapeutics},
  year =         1996,
  volume =       69,
  pages =        {37-58}
}

@Article{McKinnon92,
  author =       {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
  title =        {Nonequilibrium Molecular Dynamics Simulation of
                  Oxygen Diffusion through Hexadecane Monolayers with
                  Varying Concentrations of Cholesterol},
  journal =      jpc,
  year =         1992,
  volume =       96,
  pages =        {10497-10506}
}

@Article{Venable93,
  author =       {R.~M. Venable and Y. Zhang and B.~J. Hardy and
                  R.~W. Pastor},
  title =        {Molecular Dynamics Simulations of a Lipid Bilayer
                  and of Hexadecane: An Investigation of Membrane Fluidity},
  journal =      {Science},
  year =         1993,
  volume =       262,
  pages =        {223-226}
}

@Article{Essmann99,
  author =       {U. Essmann and M.~L. Berkowitz},
  title =        {Dynamical properties of phospholipid bilayers from
                  computer simulation},
  journal =      {Biophys. J.},
  year =         1999,
  volume =       76,
  pages =        {2081-2089}
}

@Article{Tu98,
  author =       {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf},
  title =        {Effects of anesthetics on the structure of a
                  phospholipid bilayer: Molecular dynamics
                  investigation of halothane in the hydrated liquid
                  crystal phase of dipalmitoylphosphatidylcholine},
  journal =      {Biophys. J.},
  year =         1998,
  volume =       75,
  pages =        {2123-2134}
}

@Article{Pomes96,
  author =       {R. Pomes and B. Roux},
  title =        {Structure and dynamics of a proton wire: A
                  theoretical study of H+ translocation along the
                  single-file water chain in the gramicidin a channel},
  journal =      {Biophys. J.},
  year =         1996,
  volume =       71,
  pages =        {19-39}
}

@Article{Duwez60,
  author =       {P. Duwez and R.~H. Willens and W. {Klement~Jr.}},
  title =        {Continuous Series of Metastable Solid Solutions in
                  Silver-Copper Alloys},
  journal =      {J. Appl. Phys.},
  year =         1960,
  volume =       31,
  pages =        {1136-1137}
}

@Article{Peker93,
  author =       {A. Peker and W.~L. Johnson},
  title =        {A highly processable metallic-glass -
                  $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
  journal =      {Appl. Phys. Lett.},
  year =         1993,
  volume =       63,
  pages =        {2342-2344}
}

@Article{ChoiYim97,
  author =       {H. Choi-Yim and W.~L. Johnson},
  title =        {Bulk metallic glass matrix composites},
  journal =      {Appl. Phys. Lett.},
  year =         1997,
  volume =       71,
  pages =        {3808-3810}
}

@Article{Sun96,
  author =       {X. Sun and S. Schneider and U. Geyer and
                  W.~L. Johnson and M.~A. Nicolet},
  title =        {Oxidation and crystallization of an amorphous
                  $\mbox{Zr}_{60}\mbox{Al}_{15}\mbox{Ni}_{25}$ alloy},
  journal =      {J. Mater. Res.},
  year =         1996,
  volume =       11,
  pages =        {2738-2743}
}

@Article{Heller93,
  author =       {H. Heller and M. Schaefer and K. Schulten},
  title =        {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200
                  LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES},
  journal =      jpc,
  year =         1993,
  volume =       97,
  pages =        {8343-8360}
}

@Article{Kushick76,
  author =       {J. Kushick and B.~J. Berne},
  title =        {Computer Simulation of anisotropic molecular fluids},
  journal =      jcp,
  year =         1976,
  volume =       64,
  pages =        {1362-1367}
}

@Article{Berardi96,
  author =       {R. Berardi and S. Orlandi and C Zannoni},
  title =        {Antiphase structures in polar smectic liquid
                  crystals and their molecular origin},
  journal =      cpl,
  year =         1996,
  volume =       261,
  pages =        {357-362}
}

@Article{Berardi99,
  author =       {R. Berardi and S. Orlandi and C. Zannoni},
  title =        {Monte Carlo simulations of rod-like Gay-Berne
                  mesogens with transverse dipoles},
  journal =      {Int. J. Mod. Phys. C},
  year =         1999,
  volume =       10,
  pages =        {477-484}
}

@Article{Pasterny2000,
  author =       {K. Pasterny and E. Gwozdz and A. Brodka},
  title =        {Properties of a model liquid crystal: Polar
                  Gay-Berne particles},
  journal =      {J. Mol. Liq.},
  year =         2000,
  volume =       85,
  pages =        {173-184}
}

@Article{Jorgensen83,
  author =       {W.~L. Jorgensen and J. Chandrasekhar and
                  J.~D. Madura and R.~W. Impey and M.~L. Klein},
  title =        {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR
                  SIMULATING LIQUID WATER},
  journal =      jcp,
  year =         1983,
  volume =       79,
  pages =        {926-935}
}

@Article{Berardi98,
  author =       {R. Berardi and C. Fava and C. Zannoni},
  title =        {A Gay-Berne potential for dissimilar biaxial particles},
  journal =      cpl,
  year =         1998,
  volume =       297,
  pages =        {8-14}
}

@Article{Luckhurst90,
  author =       {G.~R. Luckhurst and R.~A. Stephens and R.~W. Phippen},
  title =        {Computer simulation studies of anisotropic systems
                  {XIX}. Mesophases formed by the Gay-Berne model mesogen},
  journal =      {Liquid Crystals},
  year =         1990,
  volume =       8,
  pages =        {451-464}
}

@Article{Gay81,
  author =       {J.~G. Gay and B.~J. Berne},
  title =        {MODIFICATION OF THE OVERLAP POTENTIAL TO MIMIC A
                  LINEAR SITE-SITE POTENTIAL},
  journal =      jcp,
  year =         1981,
  volume =       74,
  pages =        {3316-3319}
}

@Article{Berne72,
  author =       {B.~J. Berne and P. Pechukas},
  title =        {Gaussian Model Potentials for Molecular Interactions},
  journal =      jcp,
  year =         1972,
  volume =       56,
  pages =        {4213-4216}
}

@Article{Perram96,
  author =       {J.~W. Perram and J. Rasmussen and E. Praestgaard and
                  J.~L. Lebowitz},
  title =        {Ellipsoid contact potential: Theory and relation to
                  overlap potentials},
  journal =      pre,
  year =         1996,
  volume =       54,
  pages =        {6565-6572}
}

@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},
  title =        {A second generation force field for the simulation
                  of proteins and nucleic acids},
  journal =      jacs,
  year =         1995,
  volume =       117,
  pages =        {5179-5197}
}

@Article{Brooks83,
  author =       {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson
                  and D.~J. States and S. Swaminathan and M. Karplus},
  title =        {CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
  journal =      {J. Comp. Chem.},
  year =         1983,
  volume =       4,
  pages =        {187-217}
}

@InCollection{MacKerell98,
  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},
  title =        {CHARMM: The Energy Function and Its Parameterization
                  with an Overview of the Program},
  booktitle =    {The Encyclopedia of Computational Chemistry},
  pages =        {271-277},
  publisher =    {John Wiley \& Sons},
  year =         1998,
  editor =       {P.~v.~R. {Schleyer, {\it et al.}}},
  volume =       1,
  address =      {New York}
}

@InCollection{Jorgensen98,
  author =       {W.~L. Jorgensen},
  title =        {OPLS Force Fields},
  booktitle =    {The Encyclopedia of Computational Chemistry},
  pages =        {1986-1989},
  publisher =    {John Wiley \& Sons},
  year =         1998,
  editor =       {P.~v.~R. {Schleyer, {\it et al.}}},
  volume =       3,
  address =      {New York}
}

@Article{Rabani2000,
  author =       {E. Rabani and J.~D. Gezelter and B.~J. Berne},
  title =        {Reply to `Comment on ``Direct Observation of
                  Stretched-Exponential Relaxation in Low-Temperature
                  Lennard-Jones Systems Using th eCage Correlation
                  Function'' '},
  journal =      prl,
  year =         2000,
  volume =       85,
  pages =        467
}

@Book{Cevc87,
  author =       {G. Cevc and D. Marsh},
  title =        {Phospholipid Bilayers},
  publisher =    {John Wiley \& Sons},
  year =         1987,
  address =      {New York}
}

@Article{Janiak79,
  author =       {M.~J. Janiak and D.~M. Small and G.~G. Shipley},
  title =        {Temperature and Compositional Dependence of the
                  Structure of Hydrated Dimyristoyl Lecithin},
  journal =      {J. Biol. Chem.},
  year =         1979,
  volume =       254,
  pages =        {6068-6078}
}

@Book{Tobias90,
  author =       {Sheila Tobias},
  title =        {They're not Dumb. They're Different: Stalking the
                  Second Tier},
  publisher =    {Research Corp.},
  year =         1990,
  address =      {Tucson}
}

@Article{Mazur92,
  author =       {E. Mazur},
  title =        {Qualitative vs. Quantititative Thinking: Are we
                  teaching the right thing? },
  journal =      {Optics and Photonics News},
  year =         1992,
  volume =       3,
  pages =        38
}

@Book{Mazur97,
  author =       {Eric Mazur},
  title =        {Peer Instruction: A User's Manual},
  publisher =    {Prentice Hall},
  year =         1997,
  address =      {New Jersey}
}

@Article{Wigner55,
  author =       {E.~P. Wigner},
  title =        {Characteristic Vectors of Bordered Matrices with
                  Infinite Dimensions},
  journal =      {Annals of Mathematics},
  year =         1955,
  volume =       62,
  pages =        {548-564}
}

@Article{Gaukel98,
  author =       {C. Gaukel and H.~R. Schober},
  title =        {Diffusion Mechanisms in under-cooled Binary Metal
                  Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$},
  journal =      {Solid State Comm.},
  year =         1998,
  volume =       107,
  pages =        {1-5}
}

@Article{Qi99,
  author =       {Y. Qi and T. \c{C}a\v{g}in and Y.
                  Kimura and W.~A. {Goddard III}},
  title =        {Molecular-dynamics simulations of glass formation
                  and crystallization in binary liquid metals: Cu-Ag
                  and Cu-Ni},
  journal =      prb,
  year =         1999,
  volume =    59,
  number =    5,
  pages =     {3527-3533}
}

@Article{Khorunzhy97,
  author =       {A. Khorunzhy and G.~J. Rodgers},
  title =        {Eigenvalue distribution of large dilute random matrices},
  journal =      {J. Math. Phys.},
  year =         1997,
  volume =       38,
  pages =        {3300-3320}
}

@Article{Rodgers88,
  author =       {G.~J. Rodgers and A. Bray},
  title =        {Density of States of a Sparse Random Matrix},
  journal =      {Phys. Rev. B},
  year =         1988,
  volume =       37,
  pages =        355703562
}

@Article{Rodgers90,
  author =       {G.~J. Rodgers and C. {De Dominicis}},
  title =        {Density of states of sparse random matrices},
  journal =      {J. Phys. A: Math. Gen.},
  year =         1990,
  volume =       23,
  pages =        {1567-1573}
}

@InProceedings{Barker80,
  author =       {J.~A. Barker},
  title =        {Reaction field method for polar fluids},
  booktitle =    {The problem of long-range forces in the computer
                  simulation of condensed matter},
  pages =        {45-6},
  year =         1980,
  editor =       {D. Ceperley},
  volume =       9,
  series =       {NRCC Workshop Proceedings}
}

@Article{Smith82,
  author =       {W. Smith},
  title =        {Point multipoles in the Ewald summation},
  journal =      {CCP5 Quarterly},
  year =         1982,
  volume =       4,
  pages =        {13-25}
}

@Article{Daw84,
  author =       {M.~S. Daw and M.~I. Baskes},
  title =        {Embedded-atom method: Derivation and application to
                  impurities, surfaces, and other defects in metals},
  journal =      prb,
  year =         1984,
  volume =    29,
  number =    12,
  pages =     {6443-6453}
}


@Article{Chen90,
  author =       {A.~P. Sutton and J. Chen},
  title =        {Long-Range Finnis Sinclair Potentials},
  journal =      {Phil. Mag. Lett.},
  year =         1990,
  volume =    61,
  pages =     {139-146}
}

@Article{Lu97,
  author =       {J. Lu and J.~A. Szpunar},
  title =        {Applications of the embedded-atom method to glass
                  formation and crystallization of liquid and glass
                  transition-metal nickel},
  journal =      {Phil. Mag. A},
  year =         {1997},
  volume =    {75},
  pages =        {1057-1066},
}

@Article{Shlesinger99,
  author =       {M.~F. Shlesinger and J. Klafter and G. Zumofen},
  title =        {Above, below, and beyond Brownian motion},
  journal =      {Am. J. Phys.},
  year =         1999,
  volume =       67,
  pages =        {1253-1259}
}

@Article{Klafter96,
  author =       {J. Klafter and M. Shlesinger and G. Zumofen},
  title =        {Beyond Brownian Motion},
  journal =      {Physics Today},
  year =         1996,
  volume =       49,
  pages =        {33-39}
}

@Article{Blumen83,
  author =       {A. Blumen and J. Klafter and G. Zumofen},
  title =        {Recombination in amorphous materials as a
                  continuous-time random-walk problem},
  journal =      {Phys. Rev. B},
  year =         1983,
  volume =       27,
  pages =        {3429-3435}
}

@Article{Klafter94,
  author =       {J. Klafter and G. Zumofen},
  title =        {Probability Distributions for Continuous-Time Random
                  Walks with Long Tails},
  journal =      jpc,
  year =         1994,
  volume =       98,
  pages =        {7366-7370}
}


@Article{Dzugutov92,
  author =       {M. Dzugutov},
  title =        {Glass formation in a simple monatomic liquid with
                  icosahedral inherent local order},
  journal =      pra,
  year =         1992,
  volume =       46,
  pages =        {R2984-R2987}
}

@Article{Moore94,
  author =       {P. Moore and T. Keyes},
  title =        {Normal Mode Analysis of Liquid $\mbox{CS}_2$: Velocity
                  Correlation Functions and Self-Diffusion Constants},
  journal =      jcp,
  year =         1994,
  volume =       100,
  pages =        6709
}

@Article{Seeley89,
  author =       {G. Seeley and T. Keyes},
  title =        {Normal-mode analysis of liquid-state dynamics},
  journal =      jcp,
  year =         1989,
  volume =       91,
  pages =        {5581-5586}
}

@Article{Madan90,
  author =       {B. Madan and T. Keyes and G. Seeley},
  title =        {Diffusion in supercooled liquids via normal mode
                  analysis},
  journal =      jcp,
  year =         1990,
  volume =       92,
  pages =        {7565-7569}
}

@Article{Madan91,
  author =       {B. Madan and T. Keyes and G. Seeley},
  title =        {Normal mode analysis of the velocity correlation
                  function in supercooled liquids},
  journal =      jcp,
  year =         1991,
  volume =       94,
  pages =        {6762-6769}
}

@Article{Buchner92,
  author =       {M. Buchner, B.~M. Ladanyi and R.~M. Stratt},
  title =        {The short-time dynamics of molecular
                  liquids. Instantaneous-normal-mode theory},
  journal =      jcp,
  year =         1992,
  volume =       97,
  pages =        {8522-8535}
}

@Article{Wan94,
  author =       {Yi. Wan and R.~M. Stratt},
  title =        {Liquid theory for the instantaneous normal modes of
                  a liquid},
  journal =      jcp,
  year =         1994,
  volume =       100,
  pages =        {5123-5138}
}

@article{Stratt95,
  author =       {R.~M. Stratt},
  title =        {The instantaneous normal modes of liquids},
  journal =      {Acc. Chem. Res.},
  year =         1995,
  volume =       28,
  pages =        {201-207}
}

@Article{Nitzan95,
  author =       {G.~V. Vijayadamodar and A. Nitzan},
  title =        {On the application of instantaneous normal mode
                  analysis to long time dynamics of liquids},
  journal =      jcp,
  year =         1995,
  volume =       103,
  pages =        {2169-2177}
}

@Article{Ribeiro98,
  author =       "M.~C.~C. Ribeiro and P.~A. Madden",
  title =        "Unstable Modes in Ionic Melts",
  journal =      jcp,
  year =         1998,
  volume =       108,
  pages =        {3256-3263}
}

@Article{Keyes98a,
  author =       {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher},
  title =        {Comment on a critique of the instantaneous normal
                  mode (INM) approach to diffusion
                  (J. Chem. Phys. {\bf 107}, 4618 (1997))},
  journal =      jcp,
  year =         1998,
  volume =       109,
  pages =        {4693-4694}
}

@Article{Alemany98,
  author =       {M.~M.~G. Alemany and C. Rey and L.~J. Gallego},
  title =        {Transport coefficients of liquid transition metals:
                  A computer simulation study using the embedded atom
                  model},
  journal =      jcp,
  year =         1998,
  volume =       109,
  pages =        {5175-5176}
}

@Article{Belonoshko00,
  author =       {A.~B. Belonoshko and R. Ahuja and O. Eriksson and
                  B. Johansson},
  title =        {Quasi ab initio molecular dynamic study of Cu melting},
  journal =      prb,
  year =         2000,
  volume =       61,
  pages =        {3838-3844}
}

@Article{Banhart92,
  author =       {J. Banhart and H. Ebert and R. Kuentzler and
                  J. Voitl\"{a}nder},
  title =        {Electronic properties of single-phased metastable
                  Ag-Cu alloys},
  journal =      prb,
  year =         1992,
  volume =       46,
  pages =        {9968-9975}
}

@Article{Wendt78,
  author =       {H. Wendt and F.~F. Abraham},
  title =        {},
  journal =      prl,
  year =         1978,
  volume =       41,
  pages =        1244
}

@Article{Lewis91,
  author =       {L.~J. Lewis},
  title =        {Atomic dynamics through the glass transition},
  journal =      prb,
  year =         1991,
  volume =       44,
  pages =        {4245-4254}
}

@Article{Liu92,
  author =       {R.~S. Liu and D.~W. Qi and S. Wang},
  title =        {Subpeaks of structure factors for rapidly quenched metals},
  journal =      prb,
  year =         1992,
  volume =       45,
  pages =        {451-453}
}

@Book{pliny,
  author =       {Pliny},
  title =        {Hist. Nat.},
  publisher =    { },
  year =         { },
  volume =       {XXXVI}
}

@Article{Anheuser94,
  author =       {K. Anheuser and J.P. Northover},
  title =        {Silver plating of Roman and Celtic coins from Britan - a technical study},
  journal =      {Brit. Num. J.},
  year =         1994,
  volume =       64,
  pages =        22
}

@Article{Pense92,
  author =       {A. W. Pense},
  title =        {The Decline and Fall of the Roman Denarius},
  journal =      {Mat. Char.},
  year =         1992,
  volume =       29,
  pages =        213
}

@Article{Ngai81,
  author =       {K.~L. Ngai and F.-S. Liu},
  title =        {Dispersive diffusion transport and noise,
                  time-dependent diffusion coefficient, generalized
                  Einstein-Nernst relation, and dispersive
                  diffusion-controlled unimolecular and bimolecular
                  reactions},
  journal =      prb,
  year =         1981,
  volume =       24,
  pages =        {1049-1065}
}

@Unpublished{Truhlar00,
  author =       {D.~G. Truhlar and A. Kohen},
  note =         {private correspondence}
}

@Article{Truhlar78,
  author =       {Donald G. Truhlar},
  title =        {Interpretation of the Activation Energy},
  journal =      {J. Chem. Ed.},
  year =         1978,
  volume =       55,
  pages =        309
}

@Book{Tolman27,
  author =       {R. C. Tolman},
  title =        {Statistical Mechanics with Applications to Physics and Chemistry},
  chapter =      {},
  publisher =    {Chemical Catalog Co.},
  address =      {New York},
  year =         1927,
  pages =        {260-270}
}

@Article{Tolman20,
  author =       {R. C. Tolman},
  title =        {Statistical Mechanics Applied to Chemical Kinetics},
  journal =      jacs,
  year =         1920,
  volume =       42,
  pages =        2506
}

@Article{Nagel96,
  author =       {M.D. Ediger and  C.A. Angell and Sidney R. Nagel},
  title =        {Supercooled Liquids and Glasses},
  journal =      jpc,
  year =         1996,
  volume =       100,
  pages =        13200
}

@InBook{Blumen86,
  author =       {A. Blumen and J. Klafter and G. Zumofen},
  editor =       {Luciano Peitronero and E. Tosatti},
  title =        {Fractals in Physics},
  chapter =      {Reactions in Disordered Media Modelled by Fractals},
  publisher =    {North-Holland},
  year =         1986,
  series =       {International Symposium on Fractals in Physics},
  address =      {Amsterdam},
  pages =        399
}

@Article{Shlesinger84,
  author =       {M.~F. Shlesinger and E.~W. Montroll},
  title =        {On the Williams-Watts function of dielectric relaxation},
  journal =      {Proc. Natl. Acad. Sci. USA},
  year =         1984,
  volume =       81,
  pages =        {1280-1283}
}

@Article{Klafter86,
  author =       {J. Klafter and M.~F. Shlesinger},
  title =        {On the relationship among three theories of
                  relaxation in disordered systems},
  journal =      {Proc. Natl. Acad. Sci. USA},
  year =         1986,
  volume =       83,
  pages =        {848-851}
}

@Article{Li2001,
  author =       {Z. Li and M. Lieberman and W. Hill},
  title =        {XPS and SERS Study of Silicon Phthalocyanine
                  Monolayers: umbrella vs. octopus design strategies
                  for formation of oriented SAMs},
  journal =      {Langmuir},
  year =         2001,
  note =         {submitted}
}

@Article{Evans1993,
  author =       {J.~W. Evans},
  title =        {Random and Cooperative Sequential Adsorption},
  journal =      rmp,
  year =         1993,
  volume =       65,
  pages =        {1281-1329}
}


@Article{Dwyer1977,
  author =       {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
  title =        {unknown},
  journal =      {Surf. Sci.},
  year =         1977,
  volume =       64,
  pages =        617
}

@Article{Macritche1978,
  author =       {F. MacRitche},
  title =        {unknown},
  journal =      {Adv. Protein Chem.},
  year =         1978,
  volume =       32,
  pages =        283
}

@Article{Feder1980,
  author =       {J. Feder},
  title =        {unknown},
  journal =      {J. Theor. Biol.},
  year =         1980,
  volume =       87,
  pages =        237
}

@Article{Ramsden1993,
  author =       {J.~J. Ramsden},
  title =        {unknown},
  journal =      prl,
  year =         1993,
  volume =       71,
  pages =        295
}


@Article{Egelhoff1989,
  author =       {W.~F. Egelhoff and I. Jacob},
  title =        {unknown},
  journal =      prl,
  year =         1989,
  volume =       62,
  pages =        921
}


@Article{Viot1992a,
  author =       {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
  title =        {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC
                  PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
  journal =      jpc,
  year =         1992,
  volume =       97,
  pages =        {5212-5218}
}

@Article{Viot1992b,
  author =       {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
  title =        {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION
                  OF VERY ELONGATED PARTICLES},
  journal =      {Physica A},
  year =         1992,
  volume =       191,
  pages =        {248-252}
}

@Article{Dobson1987,
  author =       {B.~W. Dobson},
  title =        {unknown},
  journal =      prb,
  year =         1987,
  volume =       36,
  pages =        1068
}

@Article{Boyer1995,
  author =       {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
  title =        {PERCUS-YEVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL
                  ADSORPTION},
  journal =      jcp,
  year =         1995,
  volume =       103,
  pages =        1607
}

@Article{Viot1992c,
  author =       {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
  title =        {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC
                  PARTICLES},
  journal =      {Physica A},
  year =         1992,
  volume =       191,
  pages =        {248-252}
}

@Article{Ricci1994,
  author =       {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
  title =        {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND 
                  EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
  journal =      jcp,
  year =         1994,
  volume =       101,
  pages =        9164
}

@Article{Semmler1998,
  author =       {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
  title =        {Diffusional Deposition of Charged Latex Particles on
                  Water-Solid Interfaces at Low Ionic Strength},
  journal =      {Langmuir},
  year =         1998,
  volume =       14,
  pages =        {5127-5132}
}

@Article{Solomon1986,
  author =       {H. Solomon and H. Weiner},
  title =        {A REVIEW OF THE PACKING PROBLEM},
  journal =      {Comm. Statistics A},
  year =         1986,
  volume =       15,
  pages =        {2571-2607}
}

@Article{Bonnier1993,
  author =       {B. Bonnier and M. Hontebeyrie and C. Meyers},
  title =        {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING
                  D-DIMENSIONAL CUBES},
  journal =      {Physica A},
  year =         1993,
  volume =       198,
  pages =        {1-10}
}

@Book{Frenkel1996,
  author =       {D. Frenkel and B. Smit},
  title =        {Understanding Molecular Simulation : From Algorithms
                  to Applications},
  publisher =    {Academic Press},
  year =         1996,
  address =      {New York}


}

@Article{Dullweber1997,
  author =       {A. Dullweber and B. Leimkuhler and R. McLachlan},
  title =        {Symplectic splitting methods for rigid body molecular 
                  dynamics},
  journal =      jcp,
  year =         1997,
  volume =       107,
  number =       15,
  pages =        {5840-5851}
}

@Article{Siepmann1998,
  author =       {M. Martin and J.~I. Siepmann},
  title =        {Transferable Potentials for Phase Equilibria. 1. United-Atom
                  Description of n-Alkanes},
  journal =      jpcB,
  year =         1998,
  volume =       102,
  pages =        {2569-2577}
}

@Article{Marrink01,
  author =       {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
  title =        {Simulations of the Spontaneous Aggregation of Phospholipids 
                  into Bilayers},
  journal =      jacs,
  year =         2001,
  volume =       123,
  pages =        {8638-8639}
}

@Article{liu96:new_model,
  author =       {Y. Liu and T. Ichiye},
  title =        {Soft sticky dipole potential for liquid water: a new model},
  journal =      jpc,
  year =         1996,
  volume =       100,
  pages =        {2723-2730}
}

@Article{liu96:monte_carlo,
  author =       {Y. Liu and T. Ichiye},
  title =        {The static dielectric constant of the soft sticky dipole model of liquid water: MOnte Carlo simulation},
  journal =      {Chemical Physics Letters},
  year =         1996,
  volume =       256,
  pages =        {334-340}
}

@Article{chandra99:ssd_md,
  author =       {A. Chandra and T. Ichiye},
  title =        {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation},
  journal =      {Journal of Chemical Physics},
  year =         1999,
  volume =       111,
  number =       6,
  pages =        {2701-2709}
}

@Book{allen87:csl,
  author =       {M.~P. Allen and D.~J. Tildesley},
  title =        {Computer Simulations of Liquids},
  publisher =    {Oxford University Press},
  year =         1987,
  address =      {New York}
}

@Book{leach01:mm,
  author =       {A. Leach},
  title =        {Molecular Modeling: Principles and Applications},
  publisher =    {Pearson Educated Limited},
  year =         2001,
  address =      {Harlow, England},
  edition =      {2nd}
}


@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},
  title =        {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples},
  journal =      {Physical Review E},
  year =         2000,
  volume =       61,
  number =       5,
  pages =        {5668-5677}
}

@Article{sengupta00,
  author =       {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
  title =        {Novel structural Features of the ripple phase of phospholipids},
  journal =      {Europhysics Letters},
  year =         2000,
  volume =       49,
  number =       6,
  pages =        {722-728}
}

@Article{venable00,
  author =       {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
  title =        {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
  journal =      jcp,
  year =         2000,
  volume =       112,
  number =       10,
  pages =        {4822-4832}
}

@Article{lindahl00,
  author =       {E. Lindahl and O. Edholm},
  title =        {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
  journal =      {Biophysical Journal},
  year =         2000,
  volume =       79,
  pages =        {426-433},
  month =        {July}
}


@Article{saiz02,
  author =       {L. Saiz and M. Klein},
  title =        {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
  journal =      jcp,
  year =         2002,
  volume =       116,
  number =       7,
  pages =        {3052-3057}
}

@Article{stevens95,
  author =       {M.~J. Stevens and G.~S. Grest},
  title =        {Phase coexistence of a Stockmayer fluid in an aplied field},
  journal =      {Physical Review E},
  year =         1995,
  volume =       51,
  number =       6,
  pages =        {5976-5983}
}

@Article{darden93:pme,
  author =       {T. Darden and D. York and L. Pedersen},
  title =        {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
  journal =      {Journal of Chemical Physics},
  year =         1993,
  volume =       98,
  number =       12,
  pages =        {10089-10092}
}


@Article{goetz98,
  author =       {R. Goetz and R. Lipowsky},
  title =        {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
  journal =      {Journal of Chemical Physics},
  year =         1998,
  volume =       108,
  number =       17,
  pages =        7397
}

@Article{marrink01:undulation,
  author =       {S.~J. Marrink and A.~E. Mark},
  title =        {Effect of undulations on surface tension in simulated bilayers},
  journal =      {Journal of Physical Chemistry B},
  year =         2001,
  volume =       105,
  pages =        {6122-6127}
}

@Article{lindahl00:undulation,
  author =       {E. Lindahl and O. Edholm},
  title =        {Mesoscopic undulation and thickness fluctuations in lipid bilayers from molecular dynamics simulation},
  journal =      {Biophysical Journal},
  year =         2000,
  volume =       79,
  pages =        {426-433}
}

@Article{metropolis:1949,
  author =       {N. Metropolis and S. Ulam},
  title =        {The Monte Carlo Method},
  journal =      {J. Am. Stat. Ass.},
  year =         1949,
  volume =       44,
  pages =        {335-341}
}

@Article{metropolis:1953,
  author =       {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
  title =        {Equation of State Calculations by Fast Computing Machines},
  journal =      {J. Chem. Phys.},
  year =         1953,
  volume =       21,
  pages =        {1087-1092}
}

@Article{born:1912,
  author =       {M. Born and Th. Von~Karman},
  title =        {Uber Schwingungen in Raumgittern},
  journal =      {Physik Z.},
  year =         1912,
  volume =       13,
  number =       {297-309}
}

@Book{chandler:1987,
  author =       {David Chandler},
  title =        {Introduction to Modern Statistical Mechanics},
  publisher =    {Oxford University Press},
  year =         1987
}


@Article{pearlman:1995,
  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},
  title =        {{\sc 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},
  journal =      {Computer Physics Communications},
  year =         1995,
  volume =       91,
  pages =        {1-41}
}

@Book{Goldstein01,
  author =       {H. Goldstein and C. Poole and J. Safko},
  title =        {Classical Mechanics},
  publisher =    {Addison Wesley},
  year =         2001,
  address =      {San Francisco},
  edition =      {3rd}
}

@Article{Gezelter04,
  author =       {C.~J. Fennell and J.~D. Gezelter},
  title =        {On the temperature dependent properties of the soft sticky 
                  dipole (SSD) and related single point water models},
  journal =      {Submitted for Publication},
  year =         2004,
  volume =       ?,
  pages =        {?},
}

@Article{Bratko85,
  author =       {D. Bratko and L. Blum and A. Luzar},
  title =        {A simple model for the intermolecular potential of water},
  journal =      jcp,
  year =         1985,
  volume =       83,
  number =       12,
  pages =        {6367-6370}
}

@Article{Bratko95,
  author =       {L. Blum and F. Vericat and D. Bratko},
  title =        {Towards an analytical model of water: The octupolar model},
  journal =      jcp,
  year =         1995,
  volume =       102,
  number =       3,
  pages =        {1461-1462}
}

@Article{Ichiye03,
  author =       {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks 
                  and T. Ichiye},
  title =        {A temperature of maximum density in soft sticky dipole 
                  water},
  journal =      cpl,
  year =         2003,
  volume =       376,
  pages =        {646-652},
}


@Article{Soper86,
  author =       {A.~K. Soper and M.~G. Phillips},
  title =        {A new determination of the structure of water at 298K},
  journal =      cp,
  year =         1986,
  volume =       107,
  number =       1,
  pages =        {47-60},
}

@Article{plimpton95,
  author =       {S. Plimpton},
  title =        {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
  journal =      jcompp,
  year =         1995,
  volume =       117,
  pages =        {1-19}
}

@Article{plimpton93,
  author =       {S.~J. Plimpton and B.~A. Hendrickson},
  title =        {Parallel Molecular Dynamics with the Embedded Atom Method},
  journal =      {MRS Proceedings},
  year =         1993,
  volume =       291,
  pages =        37
}


@Article{Ercolessi02,
  author =       {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
  title =        {Bending strain-driven modification of surface resconstructions: Au(111)},
  journal =      prb,
  year =         2002,
  volume =       65,
  pages =        241406
}

@Article{Ercolessi88,
  author =       {F. Ercolessi  and M. Parrinello  and E. Tosatti},
  title =        {Simulation of Gold in the Glue Model.},
  journal =      {Philosophical Magazine A},
  year =         1988,
  volume =       58,
  pages =        {213-226}
}

@Article{Finnis84,
  author =       {M.~W Finnis and J.~E. Sinclair },
  title =        {A Simple Empirical N-Body Potential for Transition-Metals},
  journal =      {Phil. Mag. A},
  year =         1984,
  volume =       50,
  pages =        {45-55}
}

@Article{FBD86,
  author =       {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
  title =        {Embedded-atom-method functions for the fcc metals
Cu, Ag, Au,Ni,Pd,Pt, and their alloys},
  journal =      prb,
  year =         1986,
  volume =       33,
  number =       12,
  pages =        7983
}

@Article{johnson89,
  author =       {R.~A. Johnson},
  title =        {Alloy models with the embedded-atom method},
  journal =      prb,
  year =         1989,
  volume =       39,
  number =       17,
  pages =        12554
}

@Article{Laird97,
  author =       {A. Kol and B.~B. Laird and B.~J. Leimkuhler},
  title =        {A symplectic method for rigid-body molecular simulation},
  journal =      jcp,
  year =         1997,
  volume =       107,
  number =       7,
  pages =        {2580-2588}
}


@Article{hoover85,
  author =       {W.~G. Hoover},
  title =        {Canonical dynamics: Equilibrium phase-space distributions},
  journal =      pra,
  year =         1985,
  volume =       31,
  pages =        1695
}

@Article{Roux91,
  author =       {B. Roux and M. Karplus},
  title =        {Ion transport in a Gramicidn-like channel: dynamics and mobility},
  journal =      jpc,
  year =         1991,
  volume =       95,
  number =       15,
  pages =        {4856-4868}
}


@Article{Marrink94,
  author =       {S.~J Marrink and H.~J.~C. Berendsen},
  title =        {Simulation of water transport through a lipid membrane},
  journal =      jpc,
  year =         1994,
  volume =       98,
  number =       15,
  pages =        {4155-4168}
}


@Article{Daw89,
  author =       {Murray~S. Daw},
  title =        {Model of metallic cohesion: The embedded-atom method},
  journal =      {Physical Review B},
  year =         1989,
  volume =       39,
  pages =        {7441-7452}
}

@InBook{voter,
  author =       {A.~F. Voter},
  editor =       {J.~H. Westbrook and R.~L. Fleischer},
  title =        {Intermetallic Compounds: Principles and Practice},
  chapter =      4,
  publisher =    {John Wiley and Sons Ltd},
  year =         1995,
  volume =       1,
  pages =        77
}

@Article{marrink:2002,
  author =       {S.~J. Marrink and D.~P. Teileman},
  title =        {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
  journal =      {Biophysical Journal},
  year =         2002,
  volume =       83,
  pages =        {2386-2392}
}

@Article{sum:2003,
  author =       {A.~K. Sum and J.~J. de~Pablo},
  title =        {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
  journal =      {Biophysical Journal},
  year =         2003,
  volume =       85,
  pages =        {3636-3645}
}

@Article{gomez:2003,
  author =       {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom},
  title =        {Setting up and optimization of membrane protein simulations},
  journal =      {Eur. Biophys. J.},
  year =         2002,
  volume =       31,
  pages =        {217-227}
}


@Article{smondyrev:1999,
  author =       {A.~M. Smondyrev and M.~L. Berkowitz},
  title =        {Molecular Dynamics Simulation of DPPC Bilayer in DMSO},
  journal =      {Biophysical Journal},
  year =         1999,
  volume =       76,
  pages =        {2472-2478}
}

@Article{nina:2002,
  author =       {M. Nina and T. Simonson},
  title =        {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments},
  journal =      {J. Phys. Chem. B},
  year =         2002,
  volume =       106,
  pages =        {3696-3705}
}

@Article{norberg:2000,
  author =       {J. Norberg and L. Nilsson},
  title =        {On the truncation od Long-Range Electrostatic Interactions in DNA},
  journal =      {Biophysical Journal},
  year =         2000,
  volume =       79,
  pages =        {1537-1553}
}

@Article{patra:2003,
  author =       {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
  title =        {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
  journal =      {Biophysical Journal},
  year =         2003,
  volume =       84,
  pages =        {3636-3645}
}

@Article{marrink04,
  author =       {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
  title =        {Coarse Grained Model for Semiquantitative Lipid Simulations},
  journal =      {J. Phys. Chem. B},
  year =         2004,
  volume =       108,
  pages =        {750-760}
}

@Article{andersen83,
  author =       {H.~C. Andersen},
  title =        {Rattle: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
  journal =      {Journal of Computational Physics},
  year =         1983,
  volume =       52,
  pages =        {24-34}
}

@Article{hura00,
  author =       {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
  title =        {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
  journal =      {J. Chem. Phys.},
  year =         2000,
  volume =       113,
  pages =        {9140-9148}
}


@Article{ryckaert77,
  author =       {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
  title =        {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
  journal =      {Journal of Computational Physics},
  year =         1977,
  volume =       23,
  pages =        {327-341}
}


@InBook{fowles99:lagrange,
  author =       {G.~R. Fowles and G.~L. Cassiday},
  title =        {Analytical Mechanics},
  chapter =      10,
  publisher =    {Saunders College Publishing},
  year =         1999,
  edition =      {6th}
}

@Article{petrache00,
  author =       {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
  title =        {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ NMR Spectroscopy},
  journal =      {Biophysical Journal},
  year =         2000,
  volume =       79,
  pages =        {3172-3192}
}

@Article{egberts88,
  author =       {E. Egberts and H.~J.~C. Berendsen},
  title =        {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
  journal =      {J. Chem. Phys.},
  year =         1988,
  volume =       89,
  pages =        {3718-3732}
}

@Article{Holz00, 
  author =       {M. Holz and S.~R. Heil and A. Sacco}, 
  title =        {Temperature-dependent self-diffusion coefficients of 
                  water and six selected molecular liquids for calibration 
                  in accurate $^1$H NMR PFG measurements}, 
  journal =      pccp, 
  year =         2000, 
  volume =       2, 
  pages =        {4740-4742},
}

@InCollection{zannoni94,
  author =       {C. Zannoni},
  title =        {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
  booktitle =    {The Molecular Dynamics of Liquid Crstals},
  pages =        {139-169},
  publisher =    {Kluwer Academic Publishers},
  year =         1994,
  editor =       {G.~R. Luckhurst and C.~A. Veracini},
  chapter =      6
}


@Article{melchionna93,
  author =       {S. Melchionna and G. Ciccotti and B.~L. Holian},
  title =        {Hoover NPT dynamics for systems varying in shape and size},
  journal =      {Molecular Physics},
  year =         1993,
  volume =       78,
  pages =        {533-544}
}

@Article{fennell04,
  author =       {C.~J. Fennell and J.~D. Gezelter},
  title =        {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models},
  journal =      {J. Chem. Phys},
  year =         {in press 2004}
}

Revision:	1090
Committed:	Tue Mar 9 14:45:01 2004 UTC (21 years, 7 months ago) by mmeineke
File size:	58914 byte(s)
Log Message:	final draft submitted to the readers.