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

Comparing trunk/mattDisertation/disertation.bib (file contents):
Revision 1051 by mmeineke, Fri Feb 13 21:24:07 2004 UTC vs.
Revision 1089 by mmeineke, Mon Mar 8 22:15:54 2004 UTC

+@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{pearlman:1995,
-<
+  author =       {David~A. Pearlman and David~A. Case and James~W. Caldwell andWilson~S. Ross and Thomas~E. Cheatham~III, and Steve DeBolt and David Ferguson, and George Seibel and Peter Kollman},
->
+  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}
-+
+}
-+
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+@Book{Goldstein01,
-+
+  author =       {H. Goldstein and C. Poole and J. Safko},
-+
+  title =        {Classical Mechanics},
-+
+  publisher =    {Addison Wesley},
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+  year =         2001,
-+
+  address =      {San Francisco},
-+
+  edition =      {3rd}
-+
+}
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+@Article{Gezelter04,
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+  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 =        {?},
-+
+}
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+@Article{Bratko85,
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+  author =       {D. Bratko and L. Blum and A. Luzar},
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+  title =        {A simple model for the intermolecular potential of water},
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+  journal =      jcp,
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+  volume =       83,
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+  number =       12,
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+  pages =        {6367-6370}
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+}
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+@Article{Bratko95,
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+  author =       {L. Blum and F. Vericat and D. Bratko},
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+  title =        {Towards an analytical model of water: The octupolar model},
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+  journal =      jcp,
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+  volume =       102,
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+  number =       3,
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+  pages =        {1461-1462}
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+}
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+@Article{Ichiye03,
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+  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},
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+  journal =      cpl,
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+  year =         2003,
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+  volume =       376,
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+  pages =        {646-652},
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+}
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+@Article{Soper86,
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+  author =       {A.~K. Soper and M.~G. Phillips},
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+  title =        {A new determination of the structure of water at 298K},
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+  journal =      cp,
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+  year =         1986,
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+  volume =       107,
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+  number =       1,
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+  pages =        {47-60},
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+}
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+@Article{plimpton95,
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+  author =       {S. Plimpton},
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+  title =        {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
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+  journal =      jcompp,
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+  year =         1995,
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+  volume =       117,
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+  pages =        {1-19}
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+}
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+@Article{plimpton93,
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+  author =       {S.~J. Plimpton and B.~A. Hendrickson},
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+  title =        {Parallel Molecular Dynamics with the Embedded Atom Method},
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+  journal =      {MRS Proceedings},
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+  year =         1993,
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+  volume =       291,
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+  pages =        37
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+}
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+@Article{Ercolessi02,
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+  author =       {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
-+
+  title =        {Bending strain-driven modification of surface resconstructions: Au(111)},
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+  journal =      prb,
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+  year =         2002,
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+  volume =       65,
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+  pages =        241406
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+}
-+
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+@Article{Ercolessi88,
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+  author =       {F. Ercolessi  and M. Parrinello  and E. Tosatti},
-+
+  title =        {Simulation of Gold in the Glue Model.},
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+  journal =      {Philosophical Magazine A},
-+
+  year =         1988,
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+  volume =       58,
-+
+  pages =        {213-226}
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+}
-+
-+
+@Article{Finnis84,
-+
+  author =       {M.~W Finnis and J.~E. Sinclair },
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+  title =        {A Simple Empirical N-Body Potential for Transition-Metals},
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+  journal =      {Phil. Mag. A},
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+  year =         1984,
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+  volume =       50,
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+  pages =        {45-55}
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+}
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+@Article{FBD86,
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+  author =       {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
-+
+  title =        {Embedded-atom-method functions for the fcc metals
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+Cu, Ag, Au,Ni,Pd,Pt, and their alloys},
-+
+  journal =      prb,
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+  year =         1986,
-+
+  volume =       33,
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+  number =       12,
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+  pages =        7983
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+}
-+
-+
+@Article{johnson89,
-+
+  author =       {R.~A. Johnson},
-+
+  title =        {Alloy models with the embedded-atom method},
-+
+  journal =      prb,
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+  year =         1989,
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+  volume =       39,
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+  number =       17,
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+  pages =        12554
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+}
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+@Article{Laird97,
-+
+  author =       {A. Kol and B.~B. Laird and B.~J. Leimkuhler},
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+  title =        {A symplectic method for rigid-body molecular simulation},
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+  journal =      jcp,
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+  year =         1997,
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+  volume =       107,
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+  number =       7,
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+  pages =        {2580-2588}
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+}
-+
-+
-+
+@Article{hoover85,
-+
+  author =       {W.~G. Hoover},
-+
+  title =        {Canonical dynamics: Equilibrium phase-space distributions},
-+
+  journal =      pra,
-+
+  year =         1985,
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+  volume =       31,
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+  pages =        1695
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+}
-+
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+@Article{Roux91,
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+  author =       {B. Roux and M. Karplus},
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+  title =        {Ion transport in a Gramicidn-like channel: dynamics and mobility},
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+  journal =      jpc,
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+  year =         1991,
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+  volume =       95,
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+  number =       15,
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+  pages =        {4856-4868}
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+}
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-+
+@Article{Marrink94,
-+
+  author =       {S.~J Marrink and H.~J.~C. Berendsen},
-+
+  title =        {Simulation of water transport through a lipid membrane},
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+  journal =      jpc,
-+
+  year =         1994,
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+  volume =       98,
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+  number =       15,
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+  pages =        {4155-4168}
-+
+}
-+
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+@Article{Daw89,
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+  author =       {Murray~S. Daw},
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+  title =        {Model of metallic cohesion: The embedded-atom method},
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+  journal =      {Physical Review B},
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+  year =         1989,
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+  volume =       39,
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+  pages =        {7441-7452}
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+@InBook{voter,
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+  author =       {A.~F. Voter},
-+
+  editor =       {J.~H. Westbrook and R.~L. Fleischer},
-+
+  title =        {Intermetallic Compounds: Principles and Practice},
-+
+  chapter =      4,
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+  publisher =    {John Wiley and Sons Ltd},
-+
+  year =         1995,
-+
+  volume =       1,
-+
+  pages =        77
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+}
-+
-+
+@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},
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+  year =         2002,
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+  volume =       83,
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+  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,
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+  volume =       85,
-+
+  pages =        {3636-3645}
-+
+}
-+
-+
+@Article{gomez:2003,
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+  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,
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+  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,
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+  volume =       106,
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+  pages =        {3696-3705}
-+
+}
-+
-+
+@Article{norberg:2000,
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+  author =       {J. Norberg and L. Nilsson},
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+  title =        {On the truncation od Long-Range Electrostatic Interactions in DNA},
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+  journal =      {Biophysical Journal},
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+  year =         2000,
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+  volume =       79,
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+  pages =        {1537-1553}
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+}
-+
-+
+@Article{patra:2003,
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+  author =       {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
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+  title =        {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
-+
+  journal =      {Biophysical Journal},
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+  year =         2003,
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+  volume =       84,
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+  pages =        {3636-3645}
-+
+}
-+
-+
+@Article{marrink04,
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+  author =       {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
-+
+  title =        {Coarse Grained Model for Semiquantitative Lipid Simulations},
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+  journal =      {J. Phys. Chem. B},
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+  year =         2004,
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+  volume =       108,
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+  pages =        {750-760}
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+}
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+@Article{andersen83,
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+  author =       {H.~C. Andersen},
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+  title =        {Rattle: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
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+  journal =      {Journal of Computational Physics},
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+  year =         1983,
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+  volume =       52,
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+  pages =        {24-34}
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+}
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+@Article{hura00,
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+  author =       {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
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+  title =        {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
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+  journal =      {J. Chem. Phys.},
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+  year =         2000,
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+  volume =       113,
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+  pages =        {9140-9148}
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+}
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+@Article{ryckaert77,
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+  author =       {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
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+  title =        {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
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+  journal =      {Journal of Computational Physics},
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+  year =         1977,
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+  volume =       23,
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+  pages =        {327-341}
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+}
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+@InBook{fowles99:lagrange,
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+  author =       {G.~R. Fowles and G.~L. Cassiday},
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+  title =        {Analytical Mechanics},
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+  chapter =      10,
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+  publisher =    {Saunders College Publishing},
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+  year =         1999,
-+
+  edition =      {6th}
-+
+}
-+
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+@Article{petrache00,
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+  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},
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+  journal =      {Biophysical Journal},
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+  year =         2000,
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+  volume =       79,
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+  pages =        {3172-3192}
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+}
-+
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+@Article{egberts88,
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+  author =       {E. Egberts and H.~J.~C. Berendsen},
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+  title =        {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
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+  volume =       89,
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+  pages =        {3718-3732}
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+}
-+
-+
+@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},
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+  journal =      pccp,
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+  year =         2000,
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+  volume =       2,
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+  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},
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+  pages =        {139-169},
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+  publisher =    {Kluwer Academic Publishers},
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+  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}
-+
+}
-+

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Comparing trunk/mattDisertation/disertation.bib (file contents): Revision 1051 by mmeineke, Fri Feb 13 21:24:07 2004 UTC vs. Revision 1089 by mmeineke, Mon Mar 8 22:15:54 2004 UTC

Diff Legend

Comparing trunk/mattDisertation/disertation.bib (file contents):
Revision 1051 by mmeineke, Fri Feb 13 21:24:07 2004 UTC vs.
Revision 1089 by mmeineke, Mon Mar 8 22:15:54 2004 UTC