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# Line 795 | Line 795 | on Foundations of Computer Science},
795   @Article{Brooks83,
796    author =       {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson
797                    and D.~J. States and S. Swaminathan and M. Karplus},
798 <  title =        {CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
798 >  title =        {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
799    journal =      {J. Comp. Chem.},
800    year =         1983,
801    volume =       4,
# Line 806 | Line 806 | on Foundations of Computer Science},
806    author =       {A.~D. {MacKerell, Jr.} and B. Brooks and
807                    C.~L. {Brooks III} and L. Nilsson and B. Roux and
808                    Y. Won and and M. Karplus},
809 <  title =        {CHARMM: The Energy Function and Its Parameterization
809 >  title =        {{\sc charmm}: The Energy Function and Its Parameterization
810                    with an Overview of the Program},
811    booktitle =    {The Encyclopedia of Computational Chemistry},
812    pages =        {271-277},
# Line 910 | Line 910 | on Foundations of Computer Science},
910    author =       {Y. Qi and T. \c{C}a\v{g}in and Y.
911                    Kimura and W.~A. {Goddard III}},
912    title =        {Molecular-dynamics simulations of glass formation
913 <                  and crystallization in binary liquid metals: Cu-Ag
914 <                  and Cu-Ni},
913 >                  and crystallization in binary liquid metals: $\mbox{Cu-Ag}$
914 >                  and $\mbox{Cu-Ni}$},
915    journal =      prb,
916    year =         1999,
917    volume =    59,
# Line 981 | Line 981 | on Foundations of Computer Science},
981  
982   @Article{Chen90,
983    author =       {A.~P. Sutton and J. Chen},
984 <  title =        {Long-Range Finnis Sinclair Potentials},
984 >  title =        {Long-Range $\mbox{Finnis Sinclair}$ Potentials},
985    journal =      {Phil. Mag. Lett.},
986    year =         1990,
987    volume =    61,
# Line 1319 | Line 1319 | on Foundations of Computer Science},
1319  
1320   @Article{Li2001,
1321    author =       {Z. Li and M. Lieberman and W. Hill},
1322 <  title =        {XPS and SERS Study of Silicon Phthalocyanine
1322 >  title =        {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine
1323                    Monolayers: umbrella vs. octopus design strategies
1324 <                  for formation of oriented SAMs},
1324 >                  for formation of oriented {\sc sam}s},
1325    journal =      {Langmuir},
1326    year =         2001,
1327 <  note =         {submitted}
1327 >  volume =       17,
1328 >  pages =        {4887-4894}
1329   }
1330  
1331   @Article{Evans1993,
# Line 1339 | Line 1340 | on Foundations of Computer Science},
1340  
1341   @Article{Dwyer1977,
1342    author =       {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
1343 <  title =        {unknown},
1343 >  title =        {},
1344    journal =      {Surf. Sci.},
1345    year =         1977,
1346    volume =       64,
# Line 1348 | Line 1349 | on Foundations of Computer Science},
1349  
1350   @Article{Macritche1978,
1351    author =       {F. MacRitche},
1352 <  title =        {unknown},
1352 >  title =        {},
1353    journal =      {Adv. Protein Chem.},
1354    year =         1978,
1355    volume =       32,
# Line 1357 | Line 1358 | on Foundations of Computer Science},
1358  
1359   @Article{Feder1980,
1360    author =       {J. Feder},
1361 <  title =        {unknown},
1361 >  title =        {},
1362    journal =      {J. Theor. Biol.},
1363    year =         1980,
1364    volume =       87,
# Line 1366 | Line 1367 | on Foundations of Computer Science},
1367  
1368   @Article{Ramsden1993,
1369    author =       {J.~J. Ramsden},
1370 <  title =        {unknown},
1370 >  title =        {},
1371    journal =      prl,
1372    year =         1993,
1373    volume =       71,
# Line 1376 | Line 1377 | on Foundations of Computer Science},
1377  
1378   @Article{Egelhoff1989,
1379    author =       {W.~F. Egelhoff and I. Jacob},
1380 <  title =        {unknown},
1380 >  title =        {},
1381    journal =      prl,
1382    year =         1989,
1383    volume =       62,
# Line 1406 | Line 1407 | on Foundations of Computer Science},
1407  
1408   @Article{Dobson1987,
1409    author =       {B.~W. Dobson},
1410 <  title =        {unknown},
1410 >  title =        {},
1411    journal =      prb,
1412    year =         1987,
1413    volume =       36,
# Line 1415 | Line 1416 | on Foundations of Computer Science},
1416  
1417   @Article{Boyer1995,
1418    author =       {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
1419 <  title =        {PERCUS-YEVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL
1419 >  title =        {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL
1420                    ADSORPTION},
1421    journal =      jcp,
1422    year =         1995,
# Line 1525 | Line 1526 | on Foundations of Computer Science},
1526  
1527   @Article{liu96:monte_carlo,
1528    author =       {Y. Liu and T. Ichiye},
1529 <  title =        {The static dielectric constant of the soft sticky dipole model of liquid water: MOnte Carlo simulation},
1529 >  title =        {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
1530    journal =      {Chemical Physics Letters},
1531    year =         1996,
1532    volume =       256,
# Line 1582 | Line 1583 | on Foundations of Computer Science},
1583  
1584   @Article{venable00,
1585    author =       {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
1586 <  title =        {MOlecular dynamics simulations of gel ($L_{\betaI}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
1586 >  title =        {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
1587    journal =      jcp,
1588    year =         2000,
1589    volume =       112,
# Line 1592 | Line 1593 | on Foundations of Computer Science},
1593  
1594   @Article{lindahl00,
1595    author =       {E. Lindahl and O. Edholm},
1596 <  title =        {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamicxs simulations},
1596 >  title =        {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
1597    journal =      {Biophysical Journal},
1598    year =         2000,
1599    volume =       79,
# Line 1663 | Line 1664 | on Foundations of Computer Science},
1664  
1665   @Article{metropolis:1949,
1666    author =       {N. Metropolis and S. Ulam},
1667 <  title =        {The Monte Carlo Method},
1667 >  title =        {The $\mbox{Monte Carlo}$ Method},
1668    journal =      {J. Am. Stat. Ass.},
1669    year =         1949,
1670    volume =       44,
# Line 1697 | Line 1698 | on Foundations of Computer Science},
1698  
1699  
1700   @Article{pearlman:1995,
1701 <  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},
1701 >  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},
1702    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},
1703    journal =      {Computer Physics Communications},
1704    year =         1995,
1705    volume =       91,
1706    pages =        {1-41}
1707 + }
1708 +
1709 + @Book{Goldstein01,
1710 +  author =       {H. Goldstein and C. Poole and J. Safko},
1711 +  title =        {Classical Mechanics},
1712 +  publisher =    {Addison Wesley},
1713 +  year =         2001,
1714 +  address =      {San Francisco},
1715 +  edition =      {3rd}
1716 + }
1717 +
1718 + @Article{Bratko85,
1719 +  author =       {D. Bratko and L. Blum and A. Luzar},
1720 +  title =        {A simple model for the intermolecular potential of water},
1721 +  journal =      jcp,
1722 +  year =         1985,
1723 +  volume =       83,
1724 +  number =       12,
1725 +  pages =        {6367-6370}
1726 + }
1727 +
1728 + @Article{Bratko95,
1729 +  author =       {L. Blum and F. Vericat and D. Bratko},
1730 +  title =        {Towards an analytical model of water: The octupolar model},
1731 +  journal =      jcp,
1732 +  year =         1995,
1733 +  volume =       102,
1734 +  number =       3,
1735 +  pages =        {1461-1462}
1736 + }
1737 +
1738 + @Article{Ichiye03,
1739 +  author =       {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks
1740 +                  and T. Ichiye},
1741 +  title =        {A temperature of maximum density in soft sticky dipole
1742 +                  water},
1743 +  journal =      cpl,
1744 +  year =         2003,
1745 +  volume =       376,
1746 +  pages =        {646-652},
1747 + }
1748 +
1749 +
1750 + @Article{Soper86,
1751 +  author =       {A.~K. Soper and M.~G. Phillips},
1752 +  title =        {A new determination of the structure of water at 298K},
1753 +  journal =      cp,
1754 +  year =         1986,
1755 +  volume =       107,
1756 +  number =       1,
1757 +  pages =        {47-60},
1758 + }
1759 +
1760 + @Article{plimpton95,
1761 +  author =       {S. Plimpton},
1762 +  title =        {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
1763 +  journal =      {J. Comp. Phys.},
1764 +  year =         1995,
1765 +  volume =       117,
1766 +  pages =        {1-19},
1767 + }
1768 +
1769 + @Article{plimpton93,
1770 +  author =       {S.~J. Plimpton and B.~A. Hendrickson},
1771 +  title =        {Parallel Molecular Dynamics with the Embedded Atom Method},
1772 +  journal =      {MRS Proceedings},
1773 +  year =         1993,
1774 +  volume =       291,
1775 +  pages =        37
1776 + }
1777 +
1778 +
1779 + @Article{Ercolessi02,
1780 +  author =       {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
1781 +  title =        {Bending strain-driven modification of surface resconstructions: Au(111)},
1782 +  journal =      prb,
1783 +  year =         2002,
1784 +  volume =       65,
1785 +  pages =        241406
1786 + }
1787 +
1788 + @Article{Ercolessi88,
1789 +  author =       {F. Ercolessi  and M. Parrinello  and E. Tosatti},
1790 +  title =        {Simulation of Gold in the Glue Model.},
1791 +  journal =      {Philosophical Magazine A},
1792 +  year =         1988,
1793 +  volume =       58,
1794 +  pages =        {213-226}
1795 + }
1796 +
1797 + @Article{Finnis84,
1798 +  author =       {M.~W Finnis and J.~E. Sinclair },
1799 +  title =        {A Simple Empirical N-Body Potential for Transition-Metals},
1800 +  journal =      {Phil. Mag. A},
1801 +  year =         1984,
1802 +  volume =       50,
1803 +  pages =        {45-55}
1804 + }
1805 +
1806 + @Article{FBD86,
1807 +  author =       {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
1808 +  title =        {Embedded-atom-method functions for the fcc metals
1809 + $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1810 +  journal =      prb,
1811 +  year =         1986,
1812 +  volume =       33,
1813 +  number =       12,
1814 +  pages =        7983
1815 + }
1816 +
1817 + @Article{johnson89,
1818 +  author =       {R.~A. Johnson},
1819 +  title =        {Alloy models with the embedded-atom method},
1820 +  journal =      prb,
1821 +  year =         1989,
1822 +  volume =       39,
1823 +  number =       17,
1824 +  pages =        12554
1825 + }
1826 +
1827 + @Article{Laird97,
1828 +  author =       {A. Kol and B.~B. Laird and B.~J. Leimkuhler},
1829 +  title =        {A symplectic method for rigid-body molecular simulation},
1830 +  journal =      jcp,
1831 +  year =         1997,
1832 +  volume =       107,
1833 +  number =       7,
1834 +  pages =        {2580-2588}
1835 + }
1836 +
1837 +
1838 + @Article{hoover85,
1839 +  author =       {W.~G. Hoover},
1840 +  title =        {Canonical dynamics: Equilibrium phase-space distributions},
1841 +  journal =      pra,
1842 +  year =         1985,
1843 +  volume =       31,
1844 +  pages =        1695
1845 + }
1846 +
1847 + @Article{Roux91,
1848 +  author =       {B. Roux and M. Karplus},
1849 +  title =        {Ion transport in a Gramicidin-like channel: dynamics and mobility},
1850 +  journal =      jpc,
1851 +  year =         1991,
1852 +  volume =       95,
1853 +  number =       15,
1854 +  pages =        {4856-4868}
1855 + }
1856 +
1857 +
1858 + @Article{Marrink94,
1859 +  author =       {S.~J Marrink and H.~J.~C. Berendsen},
1860 +  title =        {Simulation of water transport through a lipid membrane},
1861 +  journal =      jpc,
1862 +  year =         1994,
1863 +  volume =       98,
1864 +  number =       15,
1865 +  pages =        {4155-4168}
1866 + }
1867 +
1868 +
1869 + @Article{Daw89,
1870 +  author =       {Murray~S. Daw},
1871 +  title =        {Model of metallic cohesion: The embedded-atom method},
1872 +  journal =      {Physical Review B},
1873 +  year =         1989,
1874 +  volume =       39,
1875 +  pages =        {7441-7452}
1876   }
1877  
1878 + @InBook{voter,
1879 +  author =       {A.~F. Voter},
1880 +  editor =       {J.~H. Westbrook and R.~L. Fleischer},
1881 +  title =        {Intermetallic Compounds: Principles and Practice},
1882 +  chapter =      4,
1883 +  publisher =    {John Wiley and Sons Ltd},
1884 +  year =         1995,
1885 +  volume =       1,
1886 +  pages =        77
1887 + }
1888 +
1889 + @Article{marrink:2002,
1890 +  author =       {S.~J. Marrink and D.~P. Teileman},
1891 +  title =        {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1892 +  journal =      {Biophysical Journal},
1893 +  year =         2002,
1894 +  volume =       83,
1895 +  pages =        {2386-2392}
1896 + }
1897 +
1898 + @Article{sum:2003,
1899 +  author =       {A.~K. Sum and J.~J. de~Pablo},
1900 +  title =        {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
1901 +  journal =      {Biophysical Journal},
1902 +  year =         2003,
1903 +  volume =       85,
1904 +  pages =        {3636-3645}
1905 + }
1906 +
1907 + @Article{gomez:2003,
1908 +  author =       {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom},
1909 +  title =        {Setting up and optimization of membrane protein simulations},
1910 +  journal =      {Eur. Biophys. J.},
1911 +  year =         2002,
1912 +  volume =       31,
1913 +  pages =        {217-227}
1914 + }
1915 +
1916 +
1917 + @Article{smondyrev:1999,
1918 +  author =       {A.~M. Smondyrev and M.~L. Berkowitz},
1919 +  title =        {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1920 +  journal =      {Biophysical Journal},
1921 +  year =         1999,
1922 +  volume =       76,
1923 +  pages =        {2472-2478}
1924 + }
1925 +
1926 + @Article{nina:2002,
1927 +  author =       {M. Nina and T. Simonson},
1928 +  title =        {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments},
1929 +  journal =      {J. Phys. Chem. B},
1930 +  year =         2002,
1931 +  volume =       106,
1932 +  pages =        {3696-3705}
1933 + }
1934 +
1935 + @Article{norberg:2000,
1936 +  author =       {J. Norberg and L. Nilsson},
1937 +  title =        {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
1938 +  journal =      {Biophysical Journal},
1939 +  year =         2000,
1940 +  volume =       79,
1941 +  pages =        {1537-1553}
1942 + }
1943 +
1944 + @Article{patra:2003,
1945 +  author =       {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
1946 +  title =        {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
1947 +  journal =      {Biophysical Journal},
1948 +  year =         2003,
1949 +  volume =       84,
1950 +  pages =        {3636-3645}
1951 + }
1952 +
1953 + @Article{marrink04,
1954 +  author =       {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
1955 +  title =        {Coarse Grained Model for Semiquantitative Lipid Simulations},
1956 +  journal =      {J. Phys. Chem. B},
1957 +  year =         2004,
1958 +  volume =       108,
1959 +  pages =        {750-760}
1960 + }
1961 +
1962 + @Article{andersen83,
1963 +  author =       {H.~C. Andersen},
1964 +  title =        {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
1965 +  journal =      {Journal of Computational Physics},
1966 +  year =         1983,
1967 +  volume =       52,
1968 +  pages =        {24-34}
1969 + }
1970 +
1971 + @Article{hura00,
1972 +  author =       {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
1973 +  title =        {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
1974 +  journal =      {J. Chem. Phys.},
1975 +  year =         2000,
1976 +  volume =       113,
1977 +  pages =        {9140-9148}
1978 + }
1979 +
1980 +
1981 + @Article{ryckaert77,
1982 +  author =       {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
1983 +  title =        {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
1984 +  journal =      {Journal of Computational Physics},
1985 +  year =         1977,
1986 +  volume =       23,
1987 +  pages =        {327-341}
1988 + }
1989 +
1990 +
1991 + @InBook{fowles99:lagrange,
1992 +  author =       {G.~R. Fowles and G.~L. Cassiday},
1993 +  title =        {Analytical Mechanics},
1994 +  chapter =      10,
1995 +  publisher =    {Saunders College Publishing},
1996 +  year =         1999,
1997 +  edition =      {6th}
1998 + }
1999 +
2000 + @Article{petrache00,
2001 +  author =       {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
2002 +  title =        {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
2003 +  journal =      {Biophysical Journal},
2004 +  year =         2000,
2005 +  volume =       79,
2006 +  pages =        {3172-3192}
2007 + }
2008 +
2009 + @Article{egberts88,
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