--- trunk/tengDissertation/dissertation.bib 2006/04/03 18:07:54 2685 +++ trunk/tengDissertation/dissertation.bib 2006/04/24 18:49:32 2730 @@ -14,6 +14,8 @@ @string{mp = "Mol. Phys."} @string{pnas = "Proc. Natl. Acad. Sci. USA"} @string{jacs = "J. Am. Chem. Soc."} +@string{jmb = "J. Mol. Biol."} + @Book{Berne90, author = {B.~J. Berne and R. Pecora}, @@ -1318,12 +1320,12 @@ on Foundations of Computer Science}, } @Article{Li2001, - author = {Z. Li and M. Lieberman and W. Hill}, - title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine + author = {Z. Li and M. Lieberman and W. Hill}, + title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine Monolayers: umbrella vs. octopus design strategies for formation of oriented {\sc sam}s}, - journal = {Langmuir}, - year = 2001, + journal = {Langmuir}, + year = 2001, volume = 17, pages = {4887-4894} } @@ -1339,70 +1341,70 @@ on Foundations of Computer Science}, @Article{Dwyer1977, - author = {D.~J. Dwyer and G.~W. 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Ramsden}, + title = {}, + journal = prl, + year = 1993, + volume = 71, + pages = 295 } @Article{Egelhoff1989, - author = {W.~F. Egelhoff and I. Jacob}, - title = {}, - journal = prl, - year = 1989, - volume = 62, - pages = 921 + author = {W.~F. Egelhoff and I. Jacob}, + title = {}, + journal = prl, + year = 1989, + volume = 62, + pages = 921 } @Article{Viot1992a, - author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot}, - title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC + author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot}, + title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR}, - journal = jpc, - year = 1992, - volume = 97, - pages = {5212-5218} + journal = jpc, + year = 1992, + volume = 97, + pages = {5212-5218} } @Article{Viot1992b, - author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot}, - title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION + author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot}, + title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION OF VERY ELONGATED PARTICLES}, - journal = {Physica A}, - year = 1992, - volume = 191, - pages = {248-252} + journal = {Physica A}, + year = 1992, + volume = 191, + pages = {248-252} } @Article{Dobson1987, @@ -1436,7 +1438,7 @@ on Foundations of Computer Science}, @Article{Ricci1994, author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot}, - title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND + title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS}, journal = jcp, year = 1994, @@ -1445,362 +1447,362 @@ on Foundations of Computer Science}, } @Article{Semmler1998, - author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec}, - title = {Diffusional Deposition of Charged Latex Particles on + author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec}, + title = {Diffusional Deposition of Charged Latex Particles on Water-Solid Interfaces at Low Ionic Strength}, - journal = {Langmuir}, - year = 1998, - volume = 14, - pages = {5127-5132} + journal = {Langmuir}, + year = 1998, + volume = 14, + pages = {5127-5132} } @Article{Solomon1986, - author = {H. Solomon and H. Weiner}, - title = {A REVIEW OF THE PACKING PROBLEM}, - journal = {Comm. Statistics A}, - year = 1986, - volume = 15, - pages = {2571-2607} + author = {H. Solomon and H. Weiner}, + title = {A REVIEW OF THE PACKING PROBLEM}, + journal = {Comm. Statistics A}, + year = 1986, + volume = 15, + pages = {2571-2607} } @Article{Bonnier1993, - author = {B. Bonnier and M. Hontebeyrie and C. Meyers}, - title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING + author = {B. Bonnier and M. Hontebeyrie and C. Meyers}, + title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING D-DIMENSIONAL CUBES}, - journal = {Physica A}, - year = 1993, - volume = 198, - pages = {1-10} + journal = {Physica A}, + year = 1993, + volume = 198, + pages = {1-10} } @Book{Frenkel1996, - author = {D. Frenkel and B. Smit}, - title = {Understanding Molecular Simulation : From Algorithms + author = {D. Frenkel and B. Smit}, + title = {Understanding Molecular Simulation : From Algorithms to Applications}, - publisher = {Academic Press}, - year = 1996, - address = {New York} + publisher = {Academic Press}, + year = 1996, + address = {New York} } @Article{Dullweber1997, - author = {A. Dullweber and B. Leimkuhler and R. McLachlan}, - title = {Symplectic splitting methods for rigid body molecular + author = {A. Dullweber and B. Leimkuhler and R. McLachlan}, + title = {Symplectic splitting methods for rigid body molecular dynamics}, - journal = jcp, - year = 1997, - volume = 107, - number = 15, - pages = {5840-5851} + journal = jcp, + year = 1997, + volume = 107, + number = 15, + pages = {5840-5851} } @Article{Siepmann1998, - author = {M. Martin and J.~I. Siepmann}, - title = {Transferable Potentials for Phase Equilibria. 1. United-Atom + author = {M. Martin and J.~I. Siepmann}, + title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes}, - journal = jpcB, - year = 1998, - volume = 102, - pages = {2569-2577} + journal = jpcB, + year = 1998, + volume = 102, + pages = {2569-2577} } @Article{Marrink01, - author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark}, - title = {Simulations of the Spontaneous Aggregation of Phospholipids + author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark}, + title = {Simulations of the Spontaneous Aggregation of Phospholipids into Bilayers}, - journal = jacs, - year = 2001, - volume = 123, - pages = {8638-8639} + journal = jacs, + year = 2001, + volume = 123, + pages = {8638-8639} } @Article{liu96:new_model, - author = {Y. Liu and T. Ichiye}, - title = {Soft sticky dipole potential for liquid water: a new model}, - journal = jpc, - year = 1996, - volume = 100, - pages = {2723-2730} + author = {Y. Liu and T. Ichiye}, + title = {Soft sticky dipole potential for liquid water: a new model}, + journal = jpc, + year = 1996, + volume = 100, + pages = {2723-2730} } @Article{liu96:monte_carlo, - author = {Y. Liu and T. Ichiye}, - title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation}, - journal = {Chemical Physics Letters}, - year = 1996, - volume = 256, - pages = {334-340} + author = {Y. Liu and T. Ichiye}, + title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation}, + journal = {Chemical Physics Letters}, + year = 1996, + volume = 256, + pages = {334-340} } @Article{chandra99:ssd_md, - author = {A. Chandra and T. Ichiye}, - title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation}, - journal = {Journal of Chemical Physics}, - year = 1999, - volume = 111, - number = 6, - pages = {2701-2709} + author = {A. Chandra and T. Ichiye}, + title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation}, + journal = {Journal of Chemical Physics}, + year = 1999, + volume = 111, + number = 6, + pages = {2701-2709} } @Book{allen87:csl, - author = {M.~P. Allen and D.~J. Tildesley}, - title = {Computer Simulations of Liquids}, - publisher = {Oxford University Press}, - year = 1987, - address = {New York} + author = {M.~P. Allen and D.~J. Tildesley}, + title = {Computer Simulations of Liquids}, + publisher = {Oxford University Press}, + year = 1987, + address = {New York} } @Book{leach01:mm, - author = {A. Leach}, - title = {Molecular Modeling: Principles and Applications}, - publisher = {Pearson Educated Limited}, - year = 2001, - address = {Harlow, England}, - edition = {2nd} + author = {A. Leach}, + title = {Molecular Modeling: Principles and Applications}, + publisher = {Pearson Educated Limited}, + year = 2001, + address = {Harlow, England}, + edition = {2nd} } @Article{katsaras00, - 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}, - title = {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples}, - journal = {Physical Review E}, - year = 2000, - volume = 61, - number = 5, - pages = {5668-5677} + 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}, + title = {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples}, + journal = {Physical Review E}, + year = 2000, + volume = 61, + number = 5, + pages = {5668-5677} } @Article{sengupta00, - author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras}, - title = {Novel structural Features of the ripple phase of phospholipids}, - journal = {Europhysics Letters}, - year = 2000, - volume = 49, - number = 6, - pages = {722-728} + author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras}, + title = {Novel structural Features of the ripple phase of phospholipids}, + journal = {Europhysics Letters}, + year = 2000, + volume = 49, + number = 6, + pages = {722-728} } @Article{venable00, - author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor}, - 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, - number = 10, - pages = {4822-4832} + author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor}, + 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, + number = 10, + pages = {4822-4832} } @Article{lindahl00, - author = {E. Lindahl and O. Edholm}, - title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations}, - journal = {Biophysical Journal}, - year = 2000, - volume = 79, - pages = {426-433}, - month = {July} + author = {E. Lindahl and O. Edholm}, + title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations}, + journal = {Biophysical Journal}, + year = 2000, + volume = 79, + pages = {426-433}, + month = {July} } @Article{saiz02, - author = {L. Saiz and M. Klein}, - title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations}, - journal = jcp, - year = 2002, - volume = 116, - number = 7, - pages = {3052-3057} + author = {L. Saiz and M. Klein}, + title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations}, + journal = jcp, + year = 2002, + volume = 116, + number = 7, + pages = {3052-3057} } @Article{stevens95, - author = {M.~J. Stevens and G.~S. Grest}, - title = {Phase coexistence of a Stockmayer fluid in an aplied field}, - journal = {Physical Review E}, - year = 1995, - volume = 51, - number = 6, - pages = {5976-5983} + author = {M.~J. Stevens and G.~S. Grest}, + title = {Phase coexistence of a Stockmayer fluid in an aplied field}, + journal = {Physical Review E}, + year = 1995, + volume = 51, + number = 6, + pages = {5976-5983} } @Article{darden93:pme, - author = {T. Darden and D. York and L. Pedersen}, - title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems}, - journal = {Journal of Chemical Physics}, - year = 1993, - volume = 98, - number = 12, - pages = {10089-10092} + author = {T. Darden and D. York and L. Pedersen}, + title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems}, + journal = {Journal of Chemical Physics}, + year = 1993, + volume = 98, + number = 12, + pages = {10089-10092} } @Article{goetz98, - author = {R. Goetz and R. Lipowsky}, - title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension}, - journal = {Journal of Chemical Physics}, - year = 1998, - volume = 108, - number = 17, - pages = 7397 + author = {R. Goetz and R. Lipowsky}, + title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension}, + journal = {Journal of Chemical Physics}, + year = 1998, + volume = 108, + number = 17, + pages = 7397 } @Article{marrink01:undulation, - author = {S.~J. Marrink and A.~E. Mark}, - title = {Effect of undulations on surface tension in simulated bilayers}, - journal = {Journal of Physical Chemistry B}, - year = 2001, - volume = 105, - pages = {6122-6127} + author = {S.~J. Marrink and A.~E. Mark}, + title = {Effect of undulations on surface tension in simulated bilayers}, + journal = {Journal of Physical Chemistry B}, + year = 2001, + volume = 105, + pages = {6122-6127} } @Article{lindahl00:undulation, - author = {E. Lindahl and O. Edholm}, - title = {Mesoscopic undulation and thickness fluctuations in lipid bilayers from molecular dynamics simulation}, - journal = {Biophysical Journal}, - year = 2000, - volume = 79, - pages = {426-433} + author = {E. Lindahl and O. Edholm}, + title = {Mesoscopic undulation and thickness fluctuations in lipid bilayers from molecular dynamics simulation}, + journal = {Biophysical Journal}, + year = 2000, + volume = 79, + pages = {426-433} } @Article{metropolis:1949, - author = {N. Metropolis and S. Ulam}, - title = {The $\mbox{Monte Carlo}$ Method}, - journal = {J. Am. Stat. Ass.}, - year = 1949, - volume = 44, - pages = {335-341} + author = {N. Metropolis and S. Ulam}, + title = {The $\mbox{Monte Carlo}$ Method}, + journal = {J. Am. Stat. Ass.}, + year = 1949, + volume = 44, + pages = {335-341} } @Article{metropolis:1953, - author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller}, - title = {Equation of State Calculations by Fast Computing Machines}, - journal = {J. Chem. Phys.}, - year = 1953, - volume = 21, - pages = {1087-1092} + author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller}, + title = {Equation of State Calculations by Fast Computing Machines}, + journal = {J. Chem. Phys.}, + year = 1953, + volume = 21, + pages = {1087-1092} } @Article{born:1912, - author = {M. Born and Th. Von~Karman}, - title = {Uber Schwingungen in Raumgittern}, - journal = {Physik Z.}, - year = 1912, - volume = 13, - number = {297-309} + author = {M. Born and Th. Von~Karman}, + title = {Uber Schwingungen in Raumgittern}, + journal = {Physik Z.}, + year = 1912, + volume = 13, + number = {297-309} } @Book{chandler:1987, - author = {David Chandler}, - title = {Introduction to Modern Statistical Mechanics}, - publisher = {Oxford University Press}, - year = 1987 + author = {David Chandler}, + title = {Introduction to Modern Statistical Mechanics}, + publisher = {Oxford University Press}, + year = 1987 } @Article{pearlman:1995, - author = {David~A. Pearlman and David~A. Case and James~W. Caldwell and Wilson~S. Ross and Thomas~E. Cheatham~III and Steve DeBolt and David Ferguson and George Seibel and Peter Kollman}, - title = {{\sc amber}, a package of computer programs for applying molecular mechanics. normal mode analysis, molecular dynamics, and free energy calculations to simulate the structural and energetic properties of molecules}, - journal = {Computer Physics Communications}, - year = 1995, - volume = 91, - pages = {1-41} + author = {David~A. Pearlman and David~A. Case and James~W. Caldwell and Wilson~S. Ross and Thomas~E. Cheatham~III and Steve DeBolt and David Ferguson and George Seibel and Peter Kollman}, + title = {{\sc amber}, a package of computer programs for applying molecular mechanics. normal mode analysis, molecular dynamics, and free energy calculations to simulate the structural and energetic properties of molecules}, + journal = {Computer Physics Communications}, + year = 1995, + volume = 91, + pages = {1-41} } @Book{Goldstein01, - author = {H. Goldstein and C. Poole and J. Safko}, - title = {Classical Mechanics}, - publisher = {Addison Wesley}, - year = 2001, - address = {San Francisco}, - edition = {3rd} + author = {H. Goldstein and C. Poole and J. Safko}, + title = {Classical Mechanics}, + publisher = {Addison Wesley}, + year = 2001, + address = {San Francisco}, + edition = {3rd} } @Article{Bratko85, - author = {D. Bratko and L. Blum and A. Luzar}, - title = {A simple model for the intermolecular potential of water}, - journal = jcp, - year = 1985, - volume = 83, - number = 12, - pages = {6367-6370} + author = {D. Bratko and L. Blum and A. Luzar}, + title = {A simple model for the intermolecular potential of water}, + journal = jcp, + year = 1985, + volume = 83, + number = 12, + pages = {6367-6370} } @Article{Bratko95, - author = {L. Blum and F. Vericat and D. Bratko}, - title = {Towards an analytical model of water: The octupolar model}, - journal = jcp, - year = 1995, - volume = 102, - number = 3, - pages = {1461-1462} + author = {L. Blum and F. Vericat and D. Bratko}, + title = {Towards an analytical model of water: The octupolar model}, + journal = jcp, + year = 1995, + volume = 102, + number = 3, + pages = {1461-1462} } @Article{Ichiye03, - author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks + 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 + title = {A temperature of maximum density in soft sticky dipole water}, - journal = cpl, - year = 2003, - volume = 376, - pages = {646-652}, + journal = cpl, + year = 2003, + volume = 376, + pages = {646-652}, } @Article{Soper86, - author = {A.~K. Soper and M.~G. Phillips}, - title = {A new determination of the structure of water at 298K}, - journal = cp, - year = 1986, - volume = 107, - number = 1, - pages = {47-60}, + author = {A.~K. Soper and M.~G. Phillips}, + title = {A new determination of the structure of water at 298K}, + journal = cp, + year = 1986, + volume = 107, + number = 1, + pages = {47-60}, } @Article{plimpton95, - author = {S. Plimpton}, - title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics}, - journal = {J. Comp. Phys.}, - year = 1995, - volume = 117, - pages = {1-19}, + author = {S. Plimpton}, + title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics}, + journal = {J. Comp. Phys.}, + year = 1995, + volume = 117, + pages = {1-19}, } @Article{plimpton93, - author = {S.~J. Plimpton and B.~A. Hendrickson}, - title = {Parallel Molecular Dynamics with the Embedded Atom Method}, - journal = {MRS Proceedings}, - year = 1993, - volume = 291, - pages = 37 + author = {S.~J. Plimpton and B.~A. Hendrickson}, + title = {Parallel Molecular Dynamics with the Embedded Atom Method}, + journal = {MRS Proceedings}, + year = 1993, + volume = 291, + pages = 37 } @Article{Ercolessi02, - author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi}, - title = {Bending strain-driven modification of surface resconstructions: Au(111)}, - journal = prb, - year = 2002, - volume = 65, - pages = 241406 + author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi}, + title = {Bending strain-driven modification of surface resconstructions: Au(111)}, + journal = prb, + year = 2002, + volume = 65, + pages = 241406 } @Article{Ercolessi88, - author = {F. Ercolessi and M. Parrinello and E. Tosatti}, - title = {Simulation of Gold in the Glue Model.}, - journal = {Philosophical Magazine A}, - year = 1988, - volume = 58, - pages = {213-226} + author = {F. Ercolessi and M. Parrinello and E. Tosatti}, + title = {Simulation of Gold in the Glue Model.}, + journal = {Philosophical Magazine A}, + year = 1988, + volume = 58, + pages = {213-226} } @Article{Finnis84, - author = {M.~W Finnis and J.~E. Sinclair }, - title = {A Simple Empirical N-Body Potential for Transition-Metals}, - journal = {Phil. Mag. A}, - year = 1984, - volume = 50, - pages = {45-55} + author = {M.~W Finnis and J.~E. Sinclair }, + title = {A Simple Empirical N-Body Potential for Transition-Metals}, + journal = {Phil. Mag. A}, + year = 1984, + volume = 50, + pages = {45-55} } @Article{FBD86, @@ -1815,261 +1817,368 @@ $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys}, } @Article{johnson89, - author = {R.~A. Johnson}, - title = {Alloy models with the embedded-atom method}, - journal = prb, - year = 1989, - volume = 39, - number = 17, - pages = 12554 + author = {R.~A. Johnson}, + title = {Alloy models with the embedded-atom method}, + journal = prb, + year = 1989, + volume = 39, + number = 17, + pages = 12554 } @Article{Laird97, - author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler}, - title = {A symplectic method for rigid-body molecular simulation}, - journal = jcp, - year = 1997, - volume = 107, - number = 7, - pages = {2580-2588} + author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler}, + title = {A symplectic method for rigid-body molecular simulation}, + journal = jcp, + year = 1997, + volume = 107, + number = 7, + pages = {2580-2588} } @Article{hoover85, - author = {W.~G. Hoover}, - title = {Canonical dynamics: Equilibrium phase-space distributions}, - journal = pra, - year = 1985, - volume = 31, - pages = 1695 + author = {W.~G. Hoover}, + title = {Canonical dynamics: Equilibrium phase-space distributions}, + journal = pra, + year = 1985, + volume = 31, + pages = 1695 } @Article{Roux91, - author = {B. Roux and M. Karplus}, - title = {Ion transport in a Gramicidin-like channel: dynamics and mobility}, - journal = jpc, - year = 1991, - volume = 95, - number = 15, - pages = {4856-4868} + author = {B. Roux and M. Karplus}, + title = {Ion transport in a Gramicidin-like channel: dynamics and mobility}, + journal = jpc, + year = 1991, + volume = 95, + number = 15, + pages = {4856-4868} } @Article{Marrink94, - author = {S.~J Marrink and H.~J.~C. Berendsen}, - title = {Simulation of water transport through a lipid membrane}, - journal = jpc, - year = 1994, - volume = 98, - number = 15, - pages = {4155-4168} + author = {S.~J Marrink and H.~J.~C. Berendsen}, + title = {Simulation of water transport through a lipid membrane}, + journal = jpc, + year = 1994, + volume = 98, + number = 15, + pages = {4155-4168} } @Article{Daw89, - author = {Murray~S. Daw}, - title = {Model of metallic cohesion: The embedded-atom method}, - journal = {Physical Review B}, - year = 1989, - volume = 39, - pages = {7441-7452} + author = {Murray~S. Daw}, + title = {Model of metallic cohesion: The embedded-atom method}, + journal = {Physical Review B}, + year = 1989, + volume = 39, + pages = {7441-7452} } @InBook{voter, - author = {A.~F. Voter}, - editor = {J.~H. Westbrook and R.~L. Fleischer}, - title = {Intermetallic Compounds: Principles and Practice}, - chapter = 4, - publisher = {John Wiley and Sons Ltd}, - year = 1995, - volume = 1, - pages = 77 + author = {A.~F. Voter}, + editor = {J.~H. Westbrook and R.~L. Fleischer}, + title = {Intermetallic Compounds: Principles and Practice}, + chapter = 4, + publisher = {John Wiley and Sons Ltd}, + year = 1995, + volume = 1, + pages = 77 } @Article{marrink:2002, - author = {S.~J. Marrink and D.~P. Teileman}, - title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition}, - journal = {Biophysical Journal}, - year = 2002, - volume = 83, - pages = {2386-2392} + author = {S.~J. Marrink and D.~P. Teileman}, + title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition}, + journal = {Biophysical Journal}, + year = 2002, + volume = 83, + pages = {2386-2392} } @Article{sum:2003, - author = {A.~K. Sum and J.~J. de~Pablo}, - title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers}, - journal = {Biophysical Journal}, - year = 2003, - volume = 85, - pages = {3636-3645} + author = {A.~K. Sum and J.~J. de~Pablo}, + title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers}, + journal = {Biophysical Journal}, + year = 2003, + volume = 85, + pages = {3636-3645} } @Article{gomez:2003, - author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom}, - title = {Setting up and optimization of membrane protein simulations}, - journal = {Eur. Biophys. J.}, - year = 2002, - volume = 31, - pages = {217-227} + author = {J.~D. 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Nina and T. Simonson}, + title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments}, + journal = {J. Phys. Chem. B}, + year = 2002, + volume = 106, + pages = {3696-3705} } @Article{norberg:2000, - author = {J. Norberg and L. Nilsson}, - title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}}, - journal = {Biophysical Journal}, - year = 2000, - volume = 79, - pages = {1537-1553} + author = {J. Norberg and L. Nilsson}, + title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}}, + journal = {Biophysical Journal}, + year = 2000, + volume = 79, + pages = {1537-1553} } @Article{patra:2003, - author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. 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