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# 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{jmb = "J. Mol. Biol."}
18 +
19  
20   @Book{Berne90,
21    author =       {B.~J. Berne and R. Pecora},
# Line 1318 | Line 1320 | on Foundations of Computer Science},
1320   }
1321  
1322   @Article{Li2001,
1323 <  author =       {Z. Li and M. Lieberman and W. Hill},
1324 <  title =        {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine
1323 >  author =   {Z. Li and M. Lieberman and W. Hill},
1324 >  title =    {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine
1325                    Monolayers: umbrella vs. octopus design strategies
1326                    for formation of oriented {\sc sam}s},
1327 <  journal =      {Langmuir},
1328 <  year =         2001,
1327 >  journal =      {Langmuir},
1328 >  year =     2001,
1329    volume =       17,
1330    pages =        {4887-4894}
1331   }
# Line 1339 | Line 1341 | on Foundations of Computer Science},
1341  
1342  
1343   @Article{Dwyer1977,
1344 <  author =       {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
1345 <  title =        {},
1346 <  journal =      {Surf. Sci.},
1347 <  year =         1977,
1348 <  volume =       64,
1349 <  pages =        617
1344 >  author =   {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
1345 >  title =    {},
1346 >  journal =      {Surf. Sci.},
1347 >  year =     1977,
1348 >  volume =   64,
1349 >  pages =    617
1350   }
1351  
1352   @Article{Macritche1978,
1353 <  author =       {F. MacRitche},
1354 <  title =        {},
1355 <  journal =      {Adv. Protein Chem.},
1356 <  year =         1978,
1357 <  volume =       32,
1358 <  pages =        283
1353 >  author =   {F. MacRitche},
1354 >  title =    {},
1355 >  journal =      {Adv. Protein Chem.},
1356 >  year =     1978,
1357 >  volume =   32,
1358 >  pages =    283
1359   }
1360  
1361   @Article{Feder1980,
1362 <  author =       {J. Feder},
1363 <  title =        {},
1364 <  journal =      {J. Theor. Biol.},
1365 <  year =         1980,
1366 <  volume =       87,
1367 <  pages =        237
1362 >  author =   {J. Feder},
1363 >  title =    {},
1364 >  journal =      {J. Theor. Biol.},
1365 >  year =     1980,
1366 >  volume =   87,
1367 >  pages =    237
1368   }
1369  
1370   @Article{Ramsden1993,
1371 <  author =       {J.~J. Ramsden},
1372 <  title =        {},
1373 <  journal =      prl,
1374 <  year =         1993,
1375 <  volume =       71,
1376 <  pages =        295
1371 >  author =   {J.~J. Ramsden},
1372 >  title =    {},
1373 >  journal =      prl,
1374 >  year =     1993,
1375 >  volume =   71,
1376 >  pages =    295
1377   }
1378  
1379  
1380   @Article{Egelhoff1989,
1381 <  author =       {W.~F. Egelhoff and I. Jacob},
1382 <  title =        {},
1383 <  journal =      prl,
1384 <  year =         1989,
1385 <  volume =       62,
1386 <  pages =        921
1381 >  author =   {W.~F. Egelhoff and I. Jacob},
1382 >  title =    {},
1383 >  journal =      prl,
1384 >  year =     1989,
1385 >  volume =   62,
1386 >  pages =    921
1387   }
1388  
1389  
1390   @Article{Viot1992a,
1391 <  author =       {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1392 <  title =        {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC
1391 >  author =   {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1392 >  title =    {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC
1393                    PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
1394 <  journal =      jpc,
1395 <  year =         1992,
1396 <  volume =       97,
1397 <  pages =        {5212-5218}
1394 >  journal =      jpc,
1395 >  year =     1992,
1396 >  volume =   97,
1397 >  pages =    {5212-5218}
1398   }
1399  
1400   @Article{Viot1992b,
1401 <  author =       {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1402 <  title =        {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION
1401 >  author =   {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1402 >  title =    {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION
1403                    OF VERY ELONGATED PARTICLES},
1404 <  journal =      {Physica A},
1405 <  year =         1992,
1406 <  volume =       191,
1407 <  pages =        {248-252}
1404 >  journal =      {Physica A},
1405 >  year =     1992,
1406 >  volume =   191,
1407 >  pages =    {248-252}
1408   }
1409  
1410   @Article{Dobson1987,
# Line 1436 | Line 1438 | on Foundations of Computer Science},
1438  
1439   @Article{Ricci1994,
1440    author =       {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
1441 <  title =        {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND
1441 >  title =        {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND
1442                    EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
1443    journal =      jcp,
1444    year =         1994,
# Line 1445 | Line 1447 | on Foundations of Computer Science},
1447   }
1448  
1449   @Article{Semmler1998,
1450 <  author =       {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
1451 <  title =        {Diffusional Deposition of Charged Latex Particles on
1450 >  author =   {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
1451 >  title =    {Diffusional Deposition of Charged Latex Particles on
1452                    Water-Solid Interfaces at Low Ionic Strength},
1453 <  journal =      {Langmuir},
1454 <  year =         1998,
1455 <  volume =       14,
1456 <  pages =        {5127-5132}
1453 >  journal =      {Langmuir},
1454 >  year =     1998,
1455 >  volume =   14,
1456 >  pages =    {5127-5132}
1457   }
1458  
1459   @Article{Solomon1986,
1460 <  author =       {H. Solomon and H. Weiner},
1461 <  title =        {A REVIEW OF THE PACKING PROBLEM},
1462 <  journal =      {Comm. Statistics A},
1463 <  year =         1986,
1464 <  volume =       15,
1465 <  pages =        {2571-2607}
1460 >  author =   {H. Solomon and H. Weiner},
1461 >  title =    {A REVIEW OF THE PACKING PROBLEM},
1462 >  journal =      {Comm. Statistics A},
1463 >  year =     1986,
1464 >  volume =   15,
1465 >  pages =    {2571-2607}
1466   }
1467  
1468   @Article{Bonnier1993,
1469 <  author =       {B. Bonnier and M. Hontebeyrie and C. Meyers},
1470 <  title =        {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING
1469 >  author =   {B. Bonnier and M. Hontebeyrie and C. Meyers},
1470 >  title =    {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING
1471                    D-DIMENSIONAL CUBES},
1472 <  journal =      {Physica A},
1473 <  year =         1993,
1474 <  volume =       198,
1475 <  pages =        {1-10}
1472 >  journal =      {Physica A},
1473 >  year =     1993,
1474 >  volume =   198,
1475 >  pages =    {1-10}
1476   }
1477  
1478   @Book{Frenkel1996,
1479 <  author =       {D. Frenkel and B. Smit},
1480 <  title =        {Understanding Molecular Simulation : From Algorithms
1479 >  author =   {D. Frenkel and B. Smit},
1480 >  title =    {Understanding Molecular Simulation : From Algorithms
1481                    to Applications},
1482 <  publisher =    {Academic Press},
1483 <  year =         1996,
1484 <  address =      {New York}
1482 >  publisher =    {Academic Press},
1483 >  year =     1996,
1484 >  address =  {New York}
1485  
1486  
1487   }
1488  
1489   @Article{Dullweber1997,
1490 <  author =       {A. Dullweber and B. Leimkuhler and R. McLachlan},
1491 <  title =        {Symplectic splitting methods for rigid body molecular
1490 >  author =   {A. Dullweber and B. Leimkuhler and R. McLachlan},
1491 >  title =    {Symplectic splitting methods for rigid body molecular
1492                    dynamics},
1493 <  journal =      jcp,
1494 <  year =         1997,
1495 <  volume =       107,
1496 <  number =       15,
1497 <  pages =        {5840-5851}
1493 >  journal =      jcp,
1494 >  year =     1997,
1495 >  volume =   107,
1496 >  number =   15,
1497 >  pages =    {5840-5851}
1498   }
1499  
1500   @Article{Siepmann1998,
1501 <  author =       {M. Martin and J.~I. Siepmann},
1502 <  title =        {Transferable Potentials for Phase Equilibria. 1. United-Atom
1501 >  author =   {M. Martin and J.~I. Siepmann},
1502 >  title =    {Transferable Potentials for Phase Equilibria. 1. United-Atom
1503                    Description of n-Alkanes},
1504 <  journal =      jpcB,
1505 <  year =         1998,
1506 <  volume =       102,
1507 <  pages =        {2569-2577}
1504 >  journal =      jpcB,
1505 >  year =     1998,
1506 >  volume =   102,
1507 >  pages =    {2569-2577}
1508   }
1509  
1510   @Article{Marrink01,
1511 <  author =       {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
1512 <  title =        {Simulations of the Spontaneous Aggregation of Phospholipids
1511 >  author =   {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
1512 >  title =    {Simulations of the Spontaneous Aggregation of Phospholipids
1513                    into Bilayers},
1514 <  journal =      jacs,
1515 <  year =         2001,
1516 <  volume =       123,
1517 <  pages =        {8638-8639}
1514 >  journal =      jacs,
1515 >  year =     2001,
1516 >  volume =   123,
1517 >  pages =    {8638-8639}
1518   }
1519  
1520   @Article{liu96:new_model,
1521 <  author =       {Y. Liu and T. Ichiye},
1522 <  title =        {Soft sticky dipole potential for liquid water: a new model},
1523 <  journal =      jpc,
1524 <  year =         1996,
1525 <  volume =       100,
1526 <  pages =        {2723-2730}
1521 >  author =   {Y. Liu and T. Ichiye},
1522 >  title =    {Soft sticky dipole potential for liquid water: a new model},
1523 >  journal =      jpc,
1524 >  year =     1996,
1525 >  volume =   100,
1526 >  pages =    {2723-2730}
1527   }
1528  
1529   @Article{liu96:monte_carlo,
1530 <  author =       {Y. Liu and T. Ichiye},
1531 <  title =        {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
1532 <  journal =      {Chemical Physics Letters},
1533 <  year =         1996,
1534 <  volume =       256,
1535 <  pages =        {334-340}
1530 >  author =   {Y. Liu and T. Ichiye},
1531 >  title =    {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
1532 >  journal =      {Chemical Physics Letters},
1533 >  year =     1996,
1534 >  volume =   256,
1535 >  pages =    {334-340}
1536   }
1537  
1538   @Article{chandra99:ssd_md,
1539 <  author =       {A. Chandra and T. Ichiye},
1540 <  title =        {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation},
1541 <  journal =      {Journal of Chemical Physics},
1542 <  year =         1999,
1543 <  volume =       111,
1544 <  number =       6,
1545 <  pages =        {2701-2709}
1539 >  author =   {A. Chandra and T. Ichiye},
1540 >  title =    {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation},
1541 >  journal =      {Journal of Chemical Physics},
1542 >  year =     1999,
1543 >  volume =   111,
1544 >  number =   6,
1545 >  pages =    {2701-2709}
1546   }
1547  
1548   @Book{allen87:csl,
1549 <  author =       {M.~P. Allen and D.~J. Tildesley},
1550 <  title =        {Computer Simulations of Liquids},
1551 <  publisher =    {Oxford University Press},
1552 <  year =         1987,
1553 <  address =      {New York}
1549 >  author =   {M.~P. Allen and D.~J. Tildesley},
1550 >  title =    {Computer Simulations of Liquids},
1551 >  publisher =    {Oxford University Press},
1552 >  year =     1987,
1553 >  address =  {New York}
1554   }
1555  
1556   @Book{leach01:mm,
1557 <  author =       {A. Leach},
1558 <  title =        {Molecular Modeling: Principles and Applications},
1559 <  publisher =    {Pearson Educated Limited},
1560 <  year =         2001,
1561 <  address =      {Harlow, England},
1562 <  edition =      {2nd}
1557 >  author =   {A. Leach},
1558 >  title =    {Molecular Modeling: Principles and Applications},
1559 >  publisher =    {Pearson Educated Limited},
1560 >  year =     2001,
1561 >  address =  {Harlow, England},
1562 >  edition =  {2nd}
1563   }
1564  
1565  
1566   @Article{katsaras00,
1567 <  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},
1568 <  title =        {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples},
1569 <  journal =      {Physical Review E},
1570 <  year =         2000,
1571 <  volume =       61,
1572 <  number =       5,
1573 <  pages =        {5668-5677}
1567 >  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},
1568 >  title =    {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples},
1569 >  journal =      {Physical Review E},
1570 >  year =     2000,
1571 >  volume =   61,
1572 >  number =   5,
1573 >  pages =    {5668-5677}
1574   }
1575  
1576   @Article{sengupta00,
1577 <  author =       {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
1578 <  title =        {Novel structural Features of the ripple phase of phospholipids},
1579 <  journal =      {Europhysics Letters},
1580 <  year =         2000,
1581 <  volume =       49,
1582 <  number =       6,
1583 <  pages =        {722-728}
1577 >  author =   {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
1578 >  title =    {Novel structural Features of the ripple phase of phospholipids},
1579 >  journal =      {Europhysics Letters},
1580 >  year =     2000,
1581 >  volume =   49,
1582 >  number =   6,
1583 >  pages =    {722-728}
1584   }
1585  
1586   @Article{venable00,
1587 <  author =       {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
1588 <  title =        {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
1589 <  journal =      jcp,
1590 <  year =         2000,
1591 <  volume =       112,
1592 <  number =       10,
1593 <  pages =        {4822-4832}
1587 >  author =   {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
1588 >  title =    {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
1589 >  journal =      jcp,
1590 >  year =     2000,
1591 >  volume =   112,
1592 >  number =   10,
1593 >  pages =    {4822-4832}
1594   }
1595  
1596   @Article{lindahl00,
1597 <  author =       {E. Lindahl and O. Edholm},
1598 <  title =        {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
1599 <  journal =      {Biophysical Journal},
1600 <  year =         2000,
1601 <  volume =       79,
1602 <  pages =        {426-433},
1603 <  month =        {July}
1597 >  author =   {E. Lindahl and O. Edholm},
1598 >  title =    {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
1599 >  journal =      {Biophysical Journal},
1600 >  year =     2000,
1601 >  volume =   79,
1602 >  pages =    {426-433},
1603 >  month =    {July}
1604   }
1605  
1606  
1607   @Article{saiz02,
1608 <  author =       {L. Saiz and M. Klein},
1609 <  title =        {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
1610 <  journal =      jcp,
1611 <  year =         2002,
1612 <  volume =       116,
1613 <  number =       7,
1614 <  pages =        {3052-3057}
1608 >  author =   {L. Saiz and M. Klein},
1609 >  title =    {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
1610 >  journal =      jcp,
1611 >  year =     2002,
1612 >  volume =   116,
1613 >  number =   7,
1614 >  pages =    {3052-3057}
1615   }
1616  
1617   @Article{stevens95,
1618 <  author =       {M.~J. Stevens and G.~S. Grest},
1619 <  title =        {Phase coexistence of a Stockmayer fluid in an aplied field},
1620 <  journal =      {Physical Review E},
1621 <  year =         1995,
1622 <  volume =       51,
1623 <  number =       6,
1624 <  pages =        {5976-5983}
1618 >  author =   {M.~J. Stevens and G.~S. Grest},
1619 >  title =    {Phase coexistence of a Stockmayer fluid in an aplied field},
1620 >  journal =      {Physical Review E},
1621 >  year =     1995,
1622 >  volume =   51,
1623 >  number =   6,
1624 >  pages =    {5976-5983}
1625   }
1626  
1627   @Article{darden93:pme,
1628 <  author =       {T. Darden and D. York and L. Pedersen},
1629 <  title =        {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
1630 <  journal =      {Journal of Chemical Physics},
1631 <  year =         1993,
1632 <  volume =       98,
1633 <  number =       12,
1634 <  pages =        {10089-10092}
1628 >  author =   {T. Darden and D. York and L. Pedersen},
1629 >  title =    {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
1630 >  journal =      {Journal of Chemical Physics},
1631 >  year =     1993,
1632 >  volume =   98,
1633 >  number =   12,
1634 >  pages =    {10089-10092}
1635   }
1636  
1637  
1638  
1639   @Article{goetz98,
1640 <  author =       {R. Goetz and R. Lipowsky},
1641 <  title =        {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
1642 <  journal =      {Journal of Chemical Physics},
1643 <  year =         1998,
1644 <  volume =       108,
1645 <  number =       17,
1646 <  pages =        7397
1640 >  author =   {R. Goetz and R. Lipowsky},
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1939 <  title =        {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
1940 <  journal =      {Biophysical Journal},
1941 <  year =         2000,
1942 <  volume =       79,
1943 <  pages =        {1537-1553}
1938 >  author =   {J. Norberg and L. Nilsson},
1939 >  title =    {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
1940 >  journal =      {Biophysical Journal},
1941 >  year =     2000,
1942 >  volume =   79,
1943 >  pages =    {1537-1553}
1944   }
1945  
1946   @Article{patra:2003,
1947 <  author =       {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
1948 <  title =        {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
1949 <  journal =      {Biophysical Journal},
1950 <  year =         2003,
1951 <  volume =       84,
1952 <  pages =        {3636-3645}
1947 >  author =   {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
1948 >  title =    {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
1949 >  journal =      {Biophysical Journal},
1950 >  year =     2003,
1951 >  volume =   84,
1952 >  pages =    {3636-3645}
1953   }
1954  
1955   @Article{marrink04,
1956 <  author =       {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
1957 <  title =        {Coarse Grained Model for Semiquantitative Lipid Simulations},
1958 <  journal =      {J. Phys. Chem. B},
1959 <  year =         2004,
1960 <  volume =       108,
1961 <  pages =        {750-760}
1956 >  author =   {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
1957 >  title =    {Coarse Grained Model for Semiquantitative Lipid Simulations},
1958 >  journal =      {J. Phys. Chem. B},
1959 >  year =     2004,
1960 >  volume =   108,
1961 >  pages =    {750-760}
1962   }
1963  
1964   @Article{andersen83,
1965 <  author =       {H.~C. Andersen},
1966 <  title =        {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
1967 <  journal =      {Journal of Computational Physics},
1968 <  year =         1983,
1969 <  volume =       52,
1970 <  pages =        {24-34}
1965 >  author =   {H.~C. Andersen},
1966 >  title =    {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
1967 >  journal =      {Journal of Computational Physics},
1968 >  year =     1983,
1969 >  volume =   52,
1970 >  pages =    {24-34}
1971   }
1972  
1973   @Article{hura00,
1974 <  author =       {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
1975 <  title =        {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
1976 <  journal =      {J. Chem. Phys.},
1977 <  year =         2000,
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1979 <  pages =        {9140-9148}
1974 >  author =   {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
1975 >  title =    {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
1976 >  journal =      {J. Chem. Phys.},
1977 >  year =     2000,
1978 >  volume =   113,
1979 >  pages =    {9140-9148}
1980   }
1981  
1982  
1983   @Article{ryckaert77,
1984 <  author =       {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
1985 <  title =        {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
1986 <  journal =      {Journal of Computational Physics},
1987 <  year =         1977,
1988 <  volume =       23,
1989 <  pages =        {327-341}
1984 >  author =   {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
1985 >  title =    {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
1986 >  journal =      {Journal of Computational Physics},
1987 >  year =     1977,
1988 >  volume =   23,
1989 >  pages =    {327-341}
1990   }
1991  
1992  
1993   @InBook{fowles99:lagrange,
1994 <  author =       {G.~R. Fowles and G.~L. Cassiday},
1995 <  title =        {Analytical Mechanics},
1996 <  chapter =      10,
1997 <  publisher =    {Saunders College Publishing},
1998 <  year =         1999,
1999 <  edition =      {6th}
1994 >  author =   {G.~R. Fowles and G.~L. Cassiday},
1995 >  title =    {Analytical Mechanics},
1996 >  chapter =      10,
1997 >  publisher =    {Saunders College Publishing},
1998 >  year =     1999,
1999 >  edition =  {6th}
2000   }
2001  
2002   @Article{petrache00,
2003 <  author =       {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
2004 <  title =        {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
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2006 <  year =         2000,
2007 <  volume =       79,
2008 <  pages =        {3172-3192}
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2004 >  title =    {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
2005 >  journal =      {Biophysical Journal},
2006 >  year =     2000,
2007 >  volume =   79,
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2009   }
2010  
2011   @Article{egberts88,
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2013 >  title =    {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
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2023 <                  water and six selected molecular liquids for calibration
2024 <                  in accurate $^1${\sc h} {\sc nmr pfg} measurements},
2025 <  journal =      {Phys. Chem. Chem. Phys.},
2026 <  year =         2000,
2027 <  volume =       2,
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2022 >  title =        {Temperature-dependent self-diffusion coefficients of
2023 >                  water and six selected molecular liquids for calibration
2024 >                  in accurate $^1${\sc h} {\sc nmr pfg} measurements},
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2027 >  volume =       2,
2028    pages =        {4740-4742},
2029   }
2030  
2031   @InCollection{zannoni94,
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2033 <  title =        {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
2034 <  booktitle =    {The Molecular Dynamics of Liquid Crstals},
2035 <  pages =        {139-169},
2036 <  publisher =    {Kluwer Academic Publishers},
2037 <  year =         1994,
2038 <  editor =       {G.~R. Luckhurst and C.~A. Veracini},
2039 <  chapter =      6
2032 >  author =   {C. Zannoni},
2033 >  title =    {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
2034 >  booktitle =    {The Molecular Dynamics of Liquid Crstals},
2035 >  pages =    {139-169},
2036 >  publisher =    {Kluwer Academic Publishers},
2037 >  year =     1994,
2038 >  editor =   {G.~R. Luckhurst and C.~A. Veracini},
2039 >  chapter =  6
2040   }
2041  
2042  
2043   @Article{melchionna93,
2044 <  author =       {S. Melchionna and G. Ciccotti and B.~L. Holian},
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2047 <  year =         1993,
2048 <  volume =       78,
2049 <  pages =        {533-544}
2044 >  author =   {S. Melchionna and G. Ciccotti and B.~L. Holian},
2045 >  title =    {Hoover {\sc npt} dynamics for systems varying in shape and size},
2046 >  journal =      {Molecular Physics},
2047 >  year =     1993,
2048 >  volume =   78,
2049 >  pages =    {533-544}
2050   }
2051  
2052   @Article{fennell04,
2053 <  author =       {C.~J. Fennell and J.~D. Gezelter},
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2055 <  journal =      {J. Chem. Phys},
2056 <  year =         {in press 2004}
2053 >  author =   {C.~J. Fennell and J.~D. Gezelter},
2054 >  title =    {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models},
2055 >  journal =      {J. Chem. Phys},
2056 >  year =     {in press 2004}
2057   }
2058  
2059   @Article{klein01,
2060 <  author =       {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
2061 <  title =        {A coarse Grain Model for Phospholipid Simulations},
2062 <  journal =      {J. Phys. Chem. B},
2063 <  year =         2001,
2064 <  volume =       105,
2065 <  pages =        {4464-4470}
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2061 >  title =    {A coarse Grain Model for Phospholipid Simulations},
2062 >  journal =      {J. Phys. Chem. B},
2063 >  year =     2001,
2064 >  volume =   105,
2065 >  pages =    {4464-4470}
2066   }
2067  
2068  
2069   @Article{marrink03:vesicles,
2070 <  author =       {S.~J. Marrink and A.~E. Mark},
2071 <  title =        {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
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2073 <  year =         2003,
2074 <  volume =       125,
2075 <  pages =        {15233-15242}
2070 >  author =   {S.~J. Marrink and A.~E. Mark},
2071 >  title =    {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
2072 >  journal =      {J. Am. Chem. Soc.},
2073 >  year =     2003,
2074 >  volume =   125,
2075 >  pages =    {15233-15242}
2076   }
2077  
2078 + @Book{gamma94,
2079 +  author =       {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
2080 +  title =        {Design Patterns: Elements of Reusable Object-Oriented Software},
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2082 +  publisher =    {Perason Education},
2083 +  year =         1994,
2084 +  address =      {London},
2085 + }
2086 +
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2092 +  address =      {New York}
2093 + }
2094 +
2095 + @Article{wilson,
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2101 + }
2102 +
2103 + @article{Meineke05,
2104 +        Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
2105 +        Date-Modified = {2006-03-05 12:37:31 -0500},
2106 +        Journal = {J. Comp. Chem.},
2107 +        Pages = {252-271},
2108 +        Title = {OOPSE: An Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
2109 +        Volume = 26,
2110 +        Year = 2005
2111 + }
2112 +
2113 + @article{Matthey05,
2114 +        Author = {T. Matthey, T. Cickovski and \textit{et al}},
2115 +        Date-Modified = {2006-03-05 12:37:31 -0500},
2116 +        Journal = {ACM Transactions on Mathematical Software},
2117 +        Pages = {237-265},
2118 +        Title = {ProtoMol, an Object-Oriented Framework for Prototyping Novel Algorithms for Molecular Dynamics},
2119 +        Volume = 20,
2120 +        Year = 2004
2121 + }
2122 +
2123 + @Book{tolman79,
2124 +  author =       {R.~C. Tolman},
2125 +  title =        {The Principles of Statistical Mechanics},
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2128 +  year =         1979,
2129 +  address =      {New York},
2130 +  pages =        {19-22}
2131 + }
2132 +
2133 + @Book{Marion90,
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2138 +  address =  {New York},
2139 +  edition =  {2rd}
2140 + }
2141 +
2142 + @Book{Leimkuhler04,
2143 +  author =   {B. Leimkuhler and S. Reich},
2144 +  title =    {Simulating Hamiltonian Dynamics},
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2148 + }
2149 +
2150 + @Article{Gray03,
2151 +  author =       {J.~J Gray,S. Moughon, C. Wang },
2152 +  title =        {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations},
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2157 + }
2158 +
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2161 +  title =        {Explicit Lie-Poisson integration and the Euler equations},
2162 +  journal =      {prl},
2163 +  year =         1993,
2164 +  volume =       71,
2165 +  pages =        {3043-3046}
2166 + }
2167 + @ARTICLE{Wegener79,
2168 +  AUTHOR =       {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
2169 +  TITLE =        {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
2170 +  JOURNAL =      {Proc. Natl. Acad. Sci.},
2171 +  YEAR =         {1979},
2172 +  volume =       {76},
2173 +  number =       {12},
2174 +  pages =        {6356-6360}
2175 + }
2176 +
2177 + @ARTICLE{Powles73,
2178 +  AUTHOR =       {J.~G. Powles},
2179 +  TITLE =        {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
2180 +  JOURNAL =      {Advan. Phys.},
2181 +  YEAR =         {1973},
2182 +  volume =       {22},
2183 +  pages =        {1-56}
2184 + }

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