ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/oopsePaper/oopsePaper.bib
(Generate patch)

Comparing trunk/oopsePaper/oopsePaper.bib (file contents):
Revision 1434 by chrisfen, Thu Jul 29 18:01:05 2004 UTC vs.
Revision 1439 by gezelter, Thu Jul 29 20:06:07 2004 UTC

# Line 14 | Line 14
14   @string{mp = "Mol. Phys."}
15   @string{pnas = "Proc. Natl. Acad. Sci. USA"}
16   @string{jacs = "J. Am. Chem. Soc."}
17 + @string{jcc = "J. Comp. Chem."}
18 + @string{cpc = "Comp. Phys. Comm."}
19 + @string{bj = "Biophys. J."}
20  
21   @Book{Berne90,
22    author =       {B.~J. Berne and R. Pecora},
# Line 155 | Line 158
158    title =        {A molecular dynamics study of the pores formed by
159                    Escherichia coli OmpF porin in a fully hydrated
160                    palmitoyloleoylphosphatidylcholine bilayer},
161 <  journal =      {Biophys. J.},
161 >  journal =      bj,
162    year =         1998,
163    volume =       74,
164    pages =        {2786-2801}
# Line 192 | Line 195
195   }
196  
197   @Article{Sok92,
198 <  author =       {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
198 >  author =       {R.~M. Sok and H.~J.~C. Berendsen and W.~F. {van~Gunsteren}},
199    title =        {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF
200                    SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
201    journal =      {J. Chem. Phys.},
# Line 558 | Line 561 | on Foundations of Computer Science},
561    title =        {Permeation of protons, potassium ions, and small
562                    polar molecules through phospholipid bilayers as a
563                    function of membrane thickness},
564 <  journal =      {Biophys. J.},
564 >  journal =      bj,
565    year =         1996,
566    volume =       70,
567    pages =        {339-348}
# Line 601 | Line 604 | on Foundations of Computer Science},
604    author =       {U. Essmann and M.~L. Berkowitz},
605    title =        {Dynamical properties of phospholipid bilayers from
606                    computer simulation},
607 <  journal =      {Biophys. J.},
607 >  journal =      bj,
608    year =         1999,
609    volume =       76,
610    pages =        {2081-2089}
# Line 613 | Line 616 | on Foundations of Computer Science},
616                    phospholipid bilayer: Molecular dynamics
617                    investigation of halothane in the hydrated liquid
618                    crystal phase of dipalmitoylphosphatidylcholine},
619 <  journal =      {Biophys. J.},
619 >  journal =      bj,
620    year =         1998,
621    volume =       75,
622    pages =        {2123-2134}
# Line 624 | Line 627 | on Foundations of Computer Science},
627    title =        {Structure and dynamics of a proton wire: A
628                    theoretical study of H+ translocation along the
629                    single-file water chain in the gramicidin a channel},
630 <  journal =      {Biophys. J.},
630 >  journal =      bj,
631    year =         1996,
632    volume =       71,
633    pages =        {19-39}
# Line 796 | Line 799 | on Foundations of Computer Science},
799    author =       {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson
800                    and D.~J. States and S. Swaminathan and M. Karplus},
801    title =        {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
802 <  journal =      {J. Comp. Chem.},
802 >  journal =      jcc,
803    year =         1983,
804    volume =       4,
805    pages =        {187-217}
# Line 805 | Line 808 | on Foundations of Computer Science},
808   @InCollection{MacKerell98,
809    author =       {A.~D. {MacKerell, Jr.} and B. Brooks and
810                    C.~L. {Brooks III} and L. Nilsson and B. Roux and
811 <                  Y. Won and and M. Karplus},
811 >                  Y. Won and M. Karplus},
812    title =        {{\sc charmm}: The Energy Function and Its Parameterization
813                    with an Overview of the Program},
814    booktitle =    {The Encyclopedia of Computational Chemistry},
# Line 1527 | Line 1530 | on Foundations of Computer Science},
1530   @Article{liu96:monte_carlo,
1531    author =       {Y. Liu and T. Ichiye},
1532    title =        {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
1533 <  journal =      {Chemical Physics Letters},
1533 >  journal =      cpl,
1534    year =         1996,
1535    volume =       256,
1536    pages =        {334-340}
# Line 1536 | Line 1539 | on Foundations of Computer Science},
1539   @Article{chandra99:ssd_md,
1540    author =       {A. Chandra and T. Ichiye},
1541    title =        {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation},
1542 <  journal =      {Journal of Chemical Physics},
1542 >  journal =      jcp,
1543    year =         1999,
1544    volume =       111,
1545    number =       6,
# Line 1564 | Line 1567 | on Foundations of Computer Science},
1567   @Article{katsaras00,
1568    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},
1569    title =        {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples},
1570 <  journal =      {Physical Review E},
1570 >  journal =      pre,
1571    year =         2000,
1572    volume =       61,
1573    number =       5,
# Line 1594 | Line 1597 | on Foundations of Computer Science},
1597   @Article{lindahl00,
1598    author =       {E. Lindahl and O. Edholm},
1599    title =        {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
1600 <  journal =      {Biophysical Journal},
1600 >  journal =      bj,
1601    year =         2000,
1602    volume =       79,
1603    pages =        {426-433},
# Line 1615 | Line 1618 | on Foundations of Computer Science},
1618   @Article{stevens95,
1619    author =       {M.~J. Stevens and G.~S. Grest},
1620    title =        {Phase coexistence of a Stockmayer fluid in an aplied field},
1621 <  journal =      {Physical Review E},
1621 >  journal =      pre,
1622    year =         1995,
1623    volume =       51,
1624    number =       6,
# Line 1625 | Line 1628 | on Foundations of Computer Science},
1628   @Article{darden93:pme,
1629    author =       {T. Darden and D. York and L. Pedersen},
1630    title =        {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
1631 <  journal =      {Journal of Chemical Physics},
1631 >  journal =      jcp,
1632    year =         1993,
1633    volume =       98,
1634    number =       12,
# Line 1637 | Line 1640 | on Foundations of Computer Science},
1640   @Article{goetz98,
1641    author =       {R. Goetz and R. Lipowsky},
1642    title =        {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
1643 <  journal =      {Journal of Chemical Physics},
1643 >  journal =      jcp,
1644    year =         1998,
1645    volume =       108,
1646    number =       17,
# Line 1647 | Line 1650 | on Foundations of Computer Science},
1650   @Article{marrink01:undulation,
1651    author =       {S.~J. Marrink and A.~E. Mark},
1652    title =        {Effect of undulations on surface tension in simulated bilayers},
1653 <  journal =      {Journal of Physical Chemistry B},
1653 >  journal =      jpcB,
1654    year =         2001,
1655    volume =       105,
1656    pages =        {6122-6127}
# Line 1656 | Line 1659 | on Foundations of Computer Science},
1659   @Article{lindahl00:undulation,
1660    author =       {E. Lindahl and O. Edholm},
1661    title =        {Mesoscopic undulation and thickness fluctuations in lipid bilayers from molecular dynamics simulation},
1662 <  journal =      {Biophysical Journal},
1662 >  journal =      bj,
1663    year =         2000,
1664    volume =       79,
1665    pages =        {426-433}
# Line 1674 | Line 1677 | on Foundations of Computer Science},
1677   @Article{metropolis:1953,
1678    author =       {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
1679    title =        {Equation of State Calculations by Fast Computing Machines},
1680 <  journal =      {J. Chem. Phys.},
1680 >  journal =      jcp,
1681    year =         1953,
1682    volume =       21,
1683    pages =        {1087-1092}
# Line 1698 | Line 1701 | on Foundations of Computer Science},
1701  
1702  
1703   @Article{pearlman:1995,
1704 <  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},
1704 >  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},
1705    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},
1706 <  journal =      {Computer Physics Communications},
1706 >  journal =      cpc,
1707    year =         1995,
1708    volume =       91,
1709    pages =        {1-41}
# Line 1779 | Line 1782 | on Foundations of Computer Science},
1782   @Article{Ercolessi88,
1783    author =       {F. Ercolessi  and M. Parrinello  and E. Tosatti},
1784    title =        {Simulation of Gold in the Glue Model.},
1785 <  journal =      {Philosophical Magazine A},
1785 >  journal =      {Phil. Mag. A},
1786    year =         1988,
1787    volume =       58,
1788    pages =        {213-226}
# Line 1869 | Line 1872 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1872   @Article{Daw89,
1873    author =       {Murray~S. Daw},
1874    title =        {Model of metallic cohesion: The embedded-atom method},
1875 <  journal =      {Physical Review B},
1875 >  journal =      prb,
1876    year =         1989,
1877    volume =       39,
1878    pages =        {7441-7452}
# Line 1891 | Line 1894 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1894   @Article{marrink:2002,
1895    author =       {S.~J. Marrink and D.~P. Teileman},
1896    title =        {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1897 <  journal =      {Biophysical Journal},
1897 >  journal =      bj,
1898    year =         2002,
1899    volume =       83,
1900    pages =        {2386-2392}
# Line 1900 | Line 1903 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1903   @Article{sum:2003,
1904    author =       {A.~K. Sum and J.~J. de~Pablo},
1905    title =        {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
1906 <  journal =      {Biophysical Journal},
1906 >  journal =      bj,
1907    year =         2003,
1908    volume =       85,
1909    pages =        {3636-3645}
# Line 1919 | Line 1922 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1922   @Article{smondyrev:1999,
1923    author =       {A.~M. Smondyrev and M.~L. Berkowitz},
1924    title =        {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1925 <  journal =      {Biophysical Journal},
1925 >  journal =      bj,
1926    year =         1999,
1927    volume =       76,
1928    pages =        {2472-2478}
# Line 1928 | Line 1931 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1931   @Article{nina:2002,
1932    author =       {M. Nina and T. Simonson},
1933    title =        {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments},
1934 <  journal =      {J. Phys. Chem. B},
1934 >  journal =      jpcB,
1935    year =         2002,
1936    volume =       106,
1937    pages =        {3696-3705}
# Line 1937 | Line 1940 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1940   @Article{norberg:2000,
1941    author =       {J. Norberg and L. Nilsson},
1942    title =        {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
1943 <  journal =      {Biophysical Journal},
1943 >  journal =      bj,
1944    year =         2000,
1945    volume =       79,
1946    pages =        {1537-1553}
# Line 1946 | Line 1949 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1949   @Article{patra:2003,
1950    author =       {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
1951    title =        {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
1952 <  journal =      {Biophysical Journal},
1952 >  journal =      bj,
1953    year =         2003,
1954    volume =       84,
1955    pages =        {3636-3645}
1956   }
1957  
1958   @Article{marrink04,
1959 <  author =       {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
1959 >  author =       {S.~J. Marrink and A.~H. {de~Vries} and A.~E. Mark},
1960    title =        {Coarse Grained Model for Semiquantitative Lipid Simulations},
1961 <  journal =      {J. Phys. Chem. B},
1961 >  journal =      jpcB,
1962    year =         2004,
1963    volume =       108,
1964    pages =        {750-760}
# Line 1964 | Line 1967 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1967   @Article{andersen83,
1968    author =       {H.~C. Andersen},
1969    title =        {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
1970 <  journal =      {Journal of Computational Physics},
1970 >  journal =      {J. Comp. Phys.},
1971    year =         1983,
1972    volume =       52,
1973    pages =        {24-34}
# Line 1973 | Line 1976 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1976   @Article{hura00,
1977    author =       {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
1978    title =        {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
1979 <  journal =      {J. Chem. Phys.},
1979 >  journal =      jcp,
1980    year =         2000,
1981    volume =       113,
1982    pages =        {9140-9148}
# Line 1983 | Line 1986 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1986   @Article{ryckaert77,
1987    author =       {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
1988    title =        {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
1989 <  journal =      {Journal of Computational Physics},
1989 >  journal =      {J. Comp. Phys.},
1990    year =         1977,
1991    volume =       23,
1992    pages =        {327-341}
# Line 2003 | Line 2006 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2006   @Article{petrache00,
2007    author =       {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
2008    title =        {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
2009 <  journal =      {Biophysical Journal},
2009 >  journal =      bj,
2010    year =         2000,
2011    volume =       79,
2012    pages =        {3172-3192}
# Line 2012 | Line 2015 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2015   @Article{egberts88,
2016    author =       {E. Egberts and H.~J.~C. Berendsen},
2017    title =        {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
2018 <  journal =      {J. Chem. Phys.},
2018 >  journal =      jcp,
2019    year =         1988,
2020    volume =       89,
2021    pages =        {3718-3732}
# Line 2044 | Line 2047 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2047   @Article{melchionna93,
2048    author =       {S. Melchionna and G. Ciccotti and B.~L. Holian},
2049    title =        {Hoover {\sc npt} dynamics for systems varying in shape and size},
2050 <  journal =      {Molecular Physics},
2050 >  journal =      {Mol. Phys.},
2051    year =         1993,
2052    volume =       78,
2053    pages =        {533-544}
# Line 2065 | Line 2068 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2068   @Article{klein01,
2069    author =       {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
2070    title =        {A coarse Grain Model for Phospholipid Simulations},
2071 <  journal =      {J. Phys. Chem. B},
2071 >  journal =      jpcB,
2072    year =         2001,
2073    volume =       105,
2074    pages =        {4464-4470}
# Line 2075 | Line 2078 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2078   @Article{marrink03:vesicles,
2079    author =       {S.~J. Marrink and A.~E. Mark},
2080    title =        {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
2081 <  journal =      {J. Am. Chem. Soc.},
2081 >  journal =      jacs,
2082    year =         2003,
2083    volume =       125,
2084    pages =        {15233-15242}
# Line 2141 | Line 2144 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2144  
2145   @article{Heller:90,
2146          Author = {H. Heller and H. Grubmuller and K. Schulten},
2147 <        Journal = {Molecular Simulation},
2147 >        Journal = {Mol. Sim.},
2148          Pages = {133},
2149          Title = {Molecular dynamics simulation on a parallel computer},
2150          Volume = {5},
2151          Year = {1990}}
2152  
2153 + @Article{smd,
2154 +  author =       {H. Grubmuller and B. Heymann and P. Tavan},
2155 +  title =        {Ligand Binding: Molecular Mechanics Calculation of The Streptavidin-Biotin Rupture Force},
2156 +  journal =      {Science},
2157 +  year =         1996,
2158 +  volume =       271,
2159 +  pages =        {997-999}
2160 + }
2161 +
2162   @Book{Fox88,
2163    author =       {G.~C. Fox and M.~A. Johnson and G.~A Lyzenga and S.~W. Otto and J.~K. Salmon and D.~W. Walker},
2164    title =        {Solving Promblems on Concurrent Processors},
# Line 2157 | Line 2169 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2169   }
2170  
2171   @Article{Gromacs,
2172 <  author =       {H.~J.~C. Berendsen, D. van~der~Spoel and R. van~Drunen},
2172 >  author =       {H.~J.~C. Berendsen and D. {van~der~Spoel} and R. {van~Drunen}},
2173    title =        {GROMACS: A message-passing parallel molecular dynamics implementation},
2174 <  journal =      {Comp. Phys. Comm.},
2174 >  journal =      cpc,
2175    year =         1995,
2176    volume =       91,
2177    pages =        {43-56}
2178   }
2179  
2180   @Article{Gromacs3,
2181 <  author =       {E. Lindahl and B. Hess and D. van~der~Spoel},
2181 >  author =       {E. Lindahl and B. Hess and D. {van~der~Spoel}},
2182    title =        {GROMACS 3.0: A package for molecular simulation and trajectory analysis},
2183 <  journal =      {J. Mol. Mod.},
2183 >  journal =      {J. Mol. Modelling},
2184    year =         2001,
2185    volume =       7,
2186    pages =        {306-317}
# Line 2177 | Line 2189 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2189   @Article{DL_POLY,
2190    author =       {W. Smith and T. Forester},
2191    title =        {DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package },
2192 <  journal =      {J. Molec. Graphics.},
2192 >  journal =      {J. Mol. Graphics},
2193    year =         1996,
2194    volume =       14,
2195    number =       3,
# Line 2187 | Line 2199 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2199   @Article{Tinker,
2200    author =       {J.~W. Ponder and F.~M. Richards},
2201    title =        {AN EFFICIENT NEWTON-LIKE METHOD FOR MOLECULAR MECHANICS ENERGY MINIMIZATION OF LARGE MOLECULES},
2202 <  journal =      {J. Comp. Chem.},
2202 >  journal =      jcc,
2203    year =         1987,
2204    volume =       8,
2205    number =       7,
2206    pages =        {1016-1024}
2207   }
2208  
2209 + @Article{namd,
2210 +  author =       {Laxmikant Kal\'{e} and Robert Skeel and Milind Bhandarkar and Robert Brunner and Attila Gursoy and Neal Krawetz and James Phillips and Aritomo Shinozaki and Krishnan Varadarajan and Klaus Schulten},
2211 +  title =        {NAMD2: Greater scalability for parallel molecular dynamics},
2212 +  journal =      {J. Comp. Phys.},
2213 +  year =         1999,
2214 +  volume =       151,
2215 +  pages =        {283-312}
2216 + }
2217 +
2218 + @Article{macromodel,
2219 +  author =       {F. Mohamadi and N.~G.~J. Richards and W.~C. Guida and R. Liskamp and M. Lipton and C. Caufield and G. Chang and T. Hendrickson and W.~C. Still},
2220 +  title =        {MacroModel-An Integrated Software System for Modeling Organic and Bioorganic Molecules using Molecular Mechanics},
2221 +  journal =      jcc,
2222 +  year =         1990,
2223 +  volume =       11,
2224 +  pages =        440
2225 + }
2226 +
2227   @Article{Berendsen87,
2228    author =       {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
2229    title =        {The Missing Term in Effective Pair Potentials},
# Line 2225 | Line 2255 | $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2255    pages =        {8910-8922}
2256   }
2257  
2258 + @inproceedings{Alsing:00,
2259 +        Address = {Boston},
2260 +        Author = {Paul M. Alsing and Evangelos Coutsias and John McIver},
2261 +        Booktitle = {High Performance Computing in Engineering VI},
2262 +        Editor = {M. Ingber and H. Power and C.A. Brebbia},
2263 +        Pages = {81-90},
2264 +        Publisher = {WIT},
2265 +        Title = {The interfacial behavior of liquid water near hydrophobic surfaces: a parallel force decomposition molecular dynamics code},
2266 +        Year = {2000}}

Diff Legend

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