--- trunk/mattDisertation/disertation.bib 2004/02/25 21:48:44 1068 +++ trunk/mattDisertation/disertation.bib 2004/04/15 19:19:06 1115 @@ -795,7 +795,7 @@ on Foundations of Computer Science}, @Article{Brooks83, author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States and S. Swaminathan and M. Karplus}, - title = {CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations}, + title = {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations}, journal = {J. Comp. Chem.}, year = 1983, volume = 4, @@ -806,7 +806,7 @@ on Foundations of Computer Science}, author = {A.~D. {MacKerell, Jr.} and B. Brooks and C.~L. {Brooks III} and L. Nilsson and B. Roux and Y. Won and and M. Karplus}, - title = {CHARMM: The Energy Function and Its Parameterization + title = {{\sc charmm}: The Energy Function and Its Parameterization with an Overview of the Program}, booktitle = {The Encyclopedia of Computational Chemistry}, pages = {271-277}, @@ -910,8 +910,8 @@ on Foundations of Computer Science}, author = {Y. Qi and T. \c{C}a\v{g}in and Y. Kimura and W.~A. {Goddard III}}, title = {Molecular-dynamics simulations of glass formation - and crystallization in binary liquid metals: Cu-Ag - and Cu-Ni}, + and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ + and $\mbox{Cu-Ni}$}, journal = prb, year = 1999, volume = 59, @@ -981,7 +981,7 @@ on Foundations of Computer Science}, @Article{Chen90, author = {A.~P. Sutton and J. Chen}, - title = {Long-Range Finnis Sinclair Potentials}, + title = {Long-Range $\mbox{Finnis Sinclair}$ Potentials}, journal = {Phil. Mag. 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Daw}, title = {Embedded-atom-method functions for the fcc metals -Cu, Ag, Au,Ni,Pd,Pt, and their alloys}, +$\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys}, journal = prb, year = 1986, volume = 33, @@ -1855,7 +1846,7 @@ Cu, Ag, Au,Ni,Pd,Pt, and their alloys}, @Article{Roux91, author = {B. Roux and M. Karplus}, - title = {Ion transport in a Gramicidn-like channel: dynamics and mobility}, + title = {Ion transport in a Gramicidin-like channel: dynamics and mobility}, journal = jpc, year = 1991, volume = 95, @@ -1925,7 +1916,7 @@ Cu, Ag, Au,Ni,Pd,Pt, and their alloys}, @Article{smondyrev:1999, author = {A.~M. Smondyrev and M.~L. Berkowitz}, - title = {Molecular Dynamics Simulation of DPPC Bilayer in DMSO}, + title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}}, journal = {Biophysical Journal}, year = 1999, volume = 76, @@ -1943,7 +1934,7 @@ Cu, Ag, Au,Ni,Pd,Pt, and their alloys}, @Article{norberg:2000, author = {J. Norberg and L. Nilsson}, - title = {On the truncation od Long-Range Electrostatic Interactions in DNA}, + title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}}, journal = {Biophysical Journal}, year = 2000, volume = 79, @@ -1970,7 +1961,7 @@ Cu, Ag, Au,Ni,Pd,Pt, and their alloys}, @Article{andersen83, author = {H.~C. Andersen}, - title = {Rattle: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations}, + title = {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations}, journal = {Journal of Computational Physics}, year = 1983, volume = 52, @@ -1986,3 +1977,99 @@ Cu, Ag, Au,Ni,Pd,Pt, and their alloys}, pages = {9140-9148} } + +@Article{ryckaert77, + author = {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. 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Holian}, + title = {Hoover {\sc npt} dynamics for systems varying in shape and size}, + journal = {Molecular Physics}, + year = 1993, + volume = 78, + pages = {533-544} +} + +@Article{fennell04, + author = {C.~J. Fennell and J.~D. Gezelter}, + title = {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models}, + journal = {J. Chem. Phys}, + year = {in press 2004} +} + +@Article{klein01, + author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein}, + title = {A coarse Grain Model for Phospholipid Simulations}, + journal = {J. Phys. Chem. B}, + year = 2001, + volume = 105, + pages = {4464-4470} +} + + +@Article{marrink03:vesicles, + author = {S.~J. Marrink and A.~E. Mark}, + title = {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles}, + journal = {J. Am. Chem. Soc.}, + year = 2003, + volume = 125, + pages = {15233-15242} +} +