[ViewVC] Diff of: group/trunk/mattDisertation/disertation.bib

Comparing trunk/mattDisertation/disertation.bib (file contents):
Revision 974 by mmeineke, Wed Jan 21 20:31:32 2004 UTC vs.
Revision 1115 by mmeineke, Thu Apr 15 19:19:06 2004 UTC

+@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},
->
+  title =        {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
+  journal =      {J. Comp. Chem.},
+  year =         1983,
+  volume =       4,
+  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
->
+  title =        {{\sc charmm}: The Energy Function and Its Parameterization
+                  with an Overview of the Program},
+  booktitle =    {The Encyclopedia of Computational Chemistry},
+  pages =        {271-277},
+  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},
->
+                  and crystallization in binary liquid metals: $\mbox{Cu-Ag}$
->
+                  and $\mbox{Cu-Ni}$},
+  journal =      prb,
+  year =         1999,
+  volume =    59,
+@Article{Chen90,
+  author =       {A.~P. Sutton and J. Chen},
-<
+  title =        {Long-Range Finnis Sinclair Potentials},
->
+  title =        {Long-Range $\mbox{Finnis Sinclair}$ Potentials},
+  journal =      {Phil. Mag. Lett.},
+  year =         1990,
+  volume =    61,
+@Article{Li2001,
+  author =       {Z. Li and M. Lieberman and W. Hill},
-<
+  title =        {XPS and SERS Study of Silicon Phthalocyanine
->
+  title =        {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine
+                  Monolayers: umbrella vs. octopus design strategies
-<
+                  for formation of oriented SAMs},
->
+                  for formation of oriented {\sc sam}s},
+  journal =      {Langmuir},
+  year =         2001,
-<
+  note =         {submitted}
->
+  volume =       17,
->
+  pages =        {4887-4894}
+@Article{Evans1993,
+@Article{Dwyer1977,
+  author =       {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
-<
+  title =        {unknown},
->
+  title =        {},
+  journal =      {Surf. Sci.},
+  year =         1977,
+  volume =       64,
+@Article{Macritche1978,
+  author =       {F. MacRitche},
-<
+  title =        {unknown},
->
+  title =        {},
+  journal =      {Adv. Protein Chem.},
+  year =         1978,
+  volume =       32,
+@Article{Feder1980,
+  author =       {J. Feder},
-<
+  title =        {unknown},
->
+  title =        {},
+  journal =      {J. Theor. Biol.},
+  year =         1980,
+  volume =       87,
+@Article{Ramsden1993,
+  author =       {J.~J. Ramsden},
-<
+  title =        {unknown},
->
+  title =        {},
+  journal =      prl,
+  year =         1993,
+  volume =       71,
+@Article{Egelhoff1989,
+  author =       {W.~F. Egelhoff and I. Jacob},
-<
+  title =        {unknown},
->
+  title =        {},
+  journal =      prl,
+  year =         1989,
+  volume =       62,
+@Article{Dobson1987,
+  author =       {B.~W. Dobson},
-<
+  title =        {unknown},
->
+  title =        {},
+  journal =      prb,
+  year =         1987,
+  volume =       36,
+@Article{Boyer1995,
+  author =       {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
-<
+  title =        {PERCUS-YEVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL
->
+  title =        {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL
+                  ADSORPTION},
+  journal =      jcp,
+  year =         1995,
+@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},
->
+  title =        {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
+  journal =      {Chemical Physics Letters},
+  year =         1996,
+  volume =       256,
+@Article{venable00,
+  author =       {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
-<
+  title =        {MOlecular dynamics simulations of gel ($L_{\betaI}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
->
+  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,
+@Article{lindahl00,
+  author =       {E. Lindahl and O. Edholm},
-<
+  title =        {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamicxs simulations},
->
+  title =        {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
+  journal =      {Biophysical Journal},
+  year =         2000,
+  volume =       79,
+@Article{metropolis:1949,
+  author =       {N. Metropolis and S. Ulam},
-<
+  title =        {The Monte Carlo Method},
->
+  title =        {The $\mbox{Monte Carlo}$ Method},
+  journal =      {J. Am. Stat. Ass.},
+  year =         1949,
+  volume =       44,
+  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{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 =      {J. Comp. Phys.},
-+
+  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
-+
+$\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, 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 Gramicidin-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 {\sc dppc} Bilayer in {\sc 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 of Long-Range Electrostatic Interactions in {\sc 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 =        {{\sc 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 $^2\text{H}$ {\sc 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 $^1${\sc h} {\sc nmr pfg} measurements},
-+
+  journal =      {Phys. Chem. Chem. Phys.},
-+
+  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 {\sc 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}
-+
+}
-+
-+
+@Article{klein01,
-+
+  author =       {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
-+
+  title =        {A coarse Grain Model for Phospholipid Simulations},
-+
+  journal =      {J. Phys. Chem. B},
-+
+  year =         2001,
-+
+  volume =       105,
-+
+  pages =        {4464-4470}
-+
+}
-+
-+
-+
+@Article{marrink03:vesicles,
-+
+  author =       {S.~J. Marrink and A.~E. Mark},
-+
+  title =        {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
-+
+  journal =      {J. Am. Chem. Soc.},
-+
+  year =         2003,
-+
+  volume =       125,
-+
+  pages =        {15233-15242}
-+
+}
-+

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/mattDisertation/disertation.bib (file contents): Revision 974 by mmeineke, Wed Jan 21 20:31:32 2004 UTC vs. Revision 1115 by mmeineke, Thu Apr 15 19:19:06 2004 UTC

Diff Legend

Comparing trunk/mattDisertation/disertation.bib (file contents):
Revision 974 by mmeineke, Wed Jan 21 20:31:32 2004 UTC vs.
Revision 1115 by mmeineke, Thu Apr 15 19:19:06 2004 UTC