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+%% This BibTeX bibliography file was created using BibDesk.
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+%% http://bibdesk.sourceforge.net/
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+%% Created for Dan Gezelter at 2008-01-08 17:00:16 -0500
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+%% Saved with string encoding Western (ASCII)
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->
->
+@article{hess:209,
->
+        Author = {Berk Hess},
->
+        Date-Added = {2008-01-08 16:41:06 -0500},
->
+        Date-Modified = {2008-01-08 16:41:06 -0500},
->
+        Doi = {10.1063/1.1421362},
->
+        Journal = {The Journal of Chemical Physics},
->
+        Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
->
+        Number = {1},
->
+        Pages = {209-217},
->
+        Publisher = {AIP},
->
+        Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
->
+        Url = {http://link.aip.org/link/?JCP/116/209/1},
->
+        Volume = {116},
->
+        Year = {2002}}
->
->
+@article{Garcia-de-la-Torre:1997qy,
->
+        Abstract = {Single-valued hydrodynamic coefficients of a rigid particle can be calculated from existing theories and computer programs for either bead models or ellipsoids. Starting from these coefficients, we review the procedures for the calculation of complex solution properties depending on rotational diffusion, such as the decays of electric birefringence and fluorescence anisotropy. We also describe the calculation of the scattering from factor of bead models. The hydrodynamic coefficients and solution properties can be combined to give universal, shape-dependent functions, which were initially intended for ellipsoidal particles, and are extended here for the most general case. We have implemented all three developments in a new computer program. SOLPRO, for calculation of SOLution PROperties, which can be linked to existing software for bead models or ellipsoids.},
->
+        Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es},
->
+        Au = {Garcia de la Torre, J and Carrasco, B and Harding, SE},
->
+        Author = {Garcia de la Torre, J and Carrasco, B and Harding, S E},
->
+        Da = {19970709},
->
+        Date-Added = {2008-01-08 15:45:31 -0500},
->
+        Date-Modified = {2008-01-08 15:46:57 -0500},
->
+        Dcom = {19970709},
->
+        Edat = {1997/01/01},
->
+        Issn = {0175-7571 (Print)},
->
+        Jid = {8409413},
->
+        Journal = {Eur Biophys J},
->
+        Jt = {European biophysics journal : EBJ},
->
+        Keywords = {Birefringence; Fluorescence Polarization; Humans; Immunoglobulin G/chemistry; Models, Structural; *Protein Conformation; Proteins/*chemistry; Scattering, Radiation; *Software; Ultracentrifugation/methods},
->
+        Language = {eng},
->
+        Lr = {20061115},
->
+        Mhda = {1997/01/01 00:01},
->
+        Number = {5-6},
->
+        Own = {NLM},
->
+        Pages = {361--372},
->
+        Pl = {GERMANY},
->
+        Pmid = {9213556},
->
+        Pst = {ppublish},
->
+        Pt = {Journal Article; Research Support, Non-U.S. Gov't},
->
+        Pubm = {Print},
->
+        Rn = {0 (Immunoglobulin G); 0 (Proteins)},
->
+        Sb = {IM},
->
+        So = {Eur Biophys J. 1997;25(5-6):361-72. },
->
+        Stat = {MEDLINE},
->
+        Title = {SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.},
->
+        Volume = {25},
->
+        Year = {1997}}
->
->
+@article{Ravichandran:1999fk,
->
+        Abstract = {Detailed molecular dynamics simulations of the rotational and the translational motions of Gay-Berne ellipsoids in a sea of Lennard-Jones spheres have been carried out. It is found that while the translational motion of an ellipsoid is isotropic at low density, it becomes increasingly anisotropic with density until the ratio of the parallel to the perpendicular diffusion coefficients becomes nearly equal to the value of the aspect ratio at high density. The latter is in agreement with the prediction of Navier-Stokes hydrodynamics with slip boundary condition. The product of the translational diffusion coefficient and the rotational correlation time also attains a hydrodynamic-like density independent behavior only at high density. The reorientational correlation function becomes nonexponential at high density and low temperature where it also develops a slow decay. The perpendicular component of the velocity time correlation function exhibits a clear double minimum, only at high density, which becomes more pronounced as the aspect ratio is increased. (C) 1999 American Institute of Physics. [S0021-9606(99)51440-2].},
->
+        Author = {Ravichandran, S and Bagchi, B},
->
+        Date-Added = {2008-01-08 15:24:48 -0500},
->
+        Date-Modified = {2008-01-08 15:25:41 -0500},
->
+        Journal = {Journal of Chemical Physics},
->
+        Pages = {7505-7511},
->
+        Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
->
+        Volume = {111},
->
+        Year = {1999}}
->
->
+@article{TANG:1993lr,
->
+        Abstract = {Translational friction coefficients of hard prolate ellipsoids (having aspect ratios of 1-10) have been calculated by solving the linearized Navier-Stokes equations of hydrodynamics, using the method of Faxen's theorem. When the stick boundary condition was used, the present results reproduce the famous work of Lamb. The new information derived from this study arises from the analysis of the friction under the influence of the slip hydrodynamic boundary condition. It was found that the slip friction perpendicular to the long axis of the prolate ellipsoid increases monotonically with aspect ratio, whereas the parallel component of the friction decreases monotonically to an apparent limiting value. The ratio f(perpendicular to)/f(parallel to) of friction coefficients perpendicular and parallel to the long axis of the particle, calculated using slip hydrodynamics, scales roughly as the aspect ratio of the ellipsoid, in accord with the findings from an Enskog (uncorrelated binary collision) kinetic theory of hard ellipsoids and from the estimate derived from molecular dynamics. In contrast, f(perpendicular to)/f(parallel to) derived by means of stick hydrodynamics shows a weak dependence on the aspect ratio and disagrees with kinetic theory and molecular dynamics findings.},
->
+        Author = {TANG, SA and EVANS, GT},
->
+        Date-Added = {2008-01-08 15:23:42 -0500},
->
+        Date-Modified = {2008-01-08 15:24:09 -0500},
->
+        Journal = {Molecular Physics},
->
+        Pages = {1443-1457},
->
+        Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
->
+        Volume = {80},
->
+        Year = {1993}}
->
->
+@article{Schmidt:2003kx,
->
+        Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a spherical solute in a dense fluid of spherical solvent particles. The size and mass of the solute particle are related in such a way that we can naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that as long as the solute radius is interpreted as an effective hydrodynamic radius, the Stokes-Einstein law with slip boundary conditions is satisfied as the Brownian limit is approached (specifically, when the solute is roughly 100 times more massive than the solvent particles). In contrast, the Stokes-Einstein law is not satisfied for a tagged particle of the neat solvent. We also find that in the Brownian limit the amplitude of the long-time tail of the solute's velocity autocorrelation function is in good agreement with theoretical hydrodynamic predictions. When the solvent density is substantially lower than the triple density, the Stokes-Einstein law is no longer satisfied, and the amplitude of the long-time tail is not in good agreement with theoretical predictions, signaling the breakdown of hydrodynamics. (C) 2003 American Institute of Physics.},
->
+        Author = {Schmidt, JR and Skinner, JL},
->
+        Date-Added = {2008-01-08 15:12:53 -0500},
->
+        Date-Modified = {2008-01-08 15:13:21 -0500},
->
+        Doi = {DOI 10.1063/1.1610442},
->
+        Journal = {Journal of Chemical Physics},
->
+        Pages = {8062-8068},
->
+        Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
->
+        Volume = {119},
->
+        Year = {2003}}
->
->
+@article{Schmidt:2004fj,
->
+        Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a variety of solutes in a dense fluid of spherical solvent particles. We explore the effects of surface roughness of the solute on the resulting hydrodynamic boundary condition as we naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that when the solute and solvent interact through a purely repulsive isotropic potential, in the Brownian limit the Stokes-Einstein law is satisfied with slip boundary conditions. However, when surface roughness is introduced through an anisotropic solute-solvent interaction potential, we find that the Stokes-Einstein law is satisfied with stick boundary conditions. In addition, when the attractive strength of a short-range isotropic solute-solvent potential is increased, the solute becomes dressed with solvent particles, making it effectively rough, and so stick boundary conditions are again recovered.},
->
+        Author = {Schmidt, JR and Skinner, JL},
->
+        Date-Added = {2008-01-08 15:12:53 -0500},
->
+        Date-Modified = {2008-01-08 15:13:20 -0500},
->
+        Doi = {DOI 10.1021/jp037185r},
->
+        Journal = {Journal of Physical Chemistry B},
->
+        Pages = {6767-6771},
->
+        Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
->
+        Volume = {108},
->
+        Year = {2004}}
->
->
+@article{Klein01,
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+        Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:56 -0500},
->
+        Journal = {J. Phys. Chem. B},
->
+        Pages = {4464-4470},
->
+        Title = {A Coarse Grain Model for Phospholipid Simulations},
->
+        Volume = 105,
->
+        Year = 2001}
->
->
+@article{Berardi98,
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+        Author = {R. Berardi and C. Fava and C. Zannoni},
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+        Date-Added = {2008-01-08 14:58:56 -0500},
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+        Date-Modified = {2008-01-08 14:58:56 -0500},
->
+        Journal = cpl,
->
+        Pages = {8-14},
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+        Title = {A Gay-Berne potential for dissimilar biaxial particles},
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+        Year = 1998}
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+        Journal = prl,
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+        Journal = {Proceedings of the 35th Annual Symposium on Foundations of Computer Science},
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+        Journal = pccp,
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+},
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+        Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}},
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+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:58 -0500},
->
+        Journal = prb,
->
+        Number = 12,
->
+        Pages = {6443-6453},
->
+        Title = {Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals},
->
+        Volume = 29,
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+        Year = 1984}
->
->
+@article{Foiles86,
->
+        Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:58 -0500},
->
+        Journal = prb,
->
+        Number = 12,
->
+        Pages = 7983,
->
+        Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
->
+        Volume = 33,
->
+        Year = 1986}
->
->
+@article{Zahn02,
->
+        Author = {D. Zahn and B. Schilling and S.~M. Kast},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:58 -0500},
->
+        Journal = {J. Phys. Chem. B},
->
+        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
->
+        Number = {41},
->
+        Pages = {10725-10732},
->
+        Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
->
+        Volume = {106},
->
+        Year = {2002}}
->
->
+@article{Metropolis53,
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+        Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
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+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:58 -0500},
->
+        Journal = {J. Chem. Phys.},
->
+        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Metropolis_MCCalculations_53.pdf},
->
+        Pages = {1087-1092},
->
+        Title = {Equation of State Calculations by Fast Computing Machines},
->
+        Volume = 21,
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+        Year = 1953}
->
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+@article{Parry76,
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+        Author = {D.~E. Parry},
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+        Date-Added = {2008-01-08 14:58:56 -0500},
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+        Date-Modified = {2008-01-08 14:58:58 -0500},
->
+        Journal = {Surf. Sci.},
->
+        Pages = {195},
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+        Title = {Errata: The electrostatic potential in the surface region of an ionic crystal},
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+        Volume = {54},
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+        Year = {1976}}
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->
+@article{Steane96,
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+        Author = {A.~M. Steane},
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+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:58 -0500},
->
+        Journal = prl,
->
+        Pages = {793-797},
->
+        Title = {Error correcting codes in quantum theory},
->
+        Volume = 77,
->
+        Year = 1996}
->
->
+@article{Todorova2004,
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+        Author = {L. Todorova and T. Angelov and Y. Marinov and A.~G. Petrov},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {J. Mat. Sci. Mat. Elect.},
->
+        Pages = {817-818},
->
+        Title = {Evidence of flexoelectricity in polymer-dispersed liquid crystals},
->
+        Volume = 14,
->
+        Year = 2004}
->
->
+@article{Hunenberger99a,
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+        Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {J. Chem. Phys.},
->
+        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
->
+        Number = {4},
->
+        Pages = {1856-1872},
->
+        Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study},
->
+        Volume = {110},
->
+        Year = {1999}}
->
->
+@article{Rhee89,
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+        Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {Phys. Rev. B},
->
+        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
->
+        Number = {1},
->
+        Pages = {36-42},
->
+        Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions},
->
+        Volume = {40},
->
+        Year = {1989}}
->
->
+@article{Yeh99,
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+        Author = {I.-C. Yeh and M.~L. Berkowitz},
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+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {J. Chem. Phys.},
->
+        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
->
+        Number = {7},
->
+        Pages = {3155-3162},
->
+        Title = {Ewald summation for systems with slab geometry},
->
+        Volume = {111},
->
+        Year = {1999}}
->
->
+@article{Brodka04,
->
+        Author = {A. Br\'{o}dka},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Doi = {10.1016/j.cplett.2004.10.086},
->
+        Journal = {Chem. Phys. Lett.},
->
+        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf},
->
+        Pages = {62-67},
->
+        Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
->
+        Volume = {400},
->
+        Year = {2004}}
->
->
+@article{Chuang98,
->
+        Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = prl,
->
+        Pages = {3408-3411},
->
+        Title = {Experimental Implementation of Fast Quantum Searching},
->
+        Volume = 80,
->
+        Year = 1998}
->
->
+@article{Banerjee02,
->
+        Author = {Srilekha Banerjee},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {Physica A},
->
+        Pages = {89-100},
->
+        Title = {Exploring the Ripple Phase of Biomembranes},
->
+        Volume = 308,
->
+        Year = 2002}
->
->
+@article{Bannerjee02,
->
+        Author = {S. Bannerjee},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {Physica A},
->
+        Pages = {89-100},
->
+        Title = {Exploring the ripple phase of biomembranes},
->
+        Volume = 308,
->
+        Year = 2002}
->
->
+@article{Cleaver96,
->
+        Author = {Douglas J. Cleaver and Christopher M. Care and Michael P. Allen and Maureen P. Neal},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = pre,
->
+        Number = 1,
->
+        Pages = {559-567},
->
+        Title = {Extension and generalization of the Gay-Berne potential},
->
+        Volume = 54,
->
+        Year = 1996}
->
->
+@article{Plimpton95,
->
+        Author = {S. Plimpton},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {J. Comp. Phys.},
->
+        Pages = {1-19},
->
+        Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
->
+        Volume = 117,
->
+        Year = 1995}
->
->
+@article{Ayton97,
->
+        Author = {G. Ayton and M. J. P. Gingras and G. N. Patey},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = pre,
->
+        Number = 1,
->
+        Pages = {562-570},
->
+        Title = {Ferroelectric and dipolar glass phases of noncrystalline systems},
->
+        Volume = 56,
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+        Year = 1997}
->
->
+@article{Benninger:2005qy,
->
+        Abstract = {The plasma membrane of cells is an ordered environment, giving rise to anisotropic orientation and restricted motion of molecules and proteins residing in the membrane. At the same time as being an organized matrix of defined structure, the cell membrane is heterogeneous and dynamic. Here we present a method where we use fluorescence imaging of linear dichroism to measure the orientation of molecules relative to the cell membrane. By detecting linear dichroism as well as fluorescence anisotropy, the orientation parameters are separated from dynamic properties such as rotational diffusion and homo energy transfer (energy migration). The sensitivity of the technique is enhanced by using two-photon excitation for higher photo-selection compared to single photon excitation. We show here that we can accurately image lipid organization in whole cell membranes and in delicate structures such as membrane nanotubes connecting two cells. The speed of our wide-field imaging system makes it possible to image changes in orientation and anisotropy occurring on a subsecond timescale. This is demonstrated by time-lapse studies showing that cholesterol depletion rapidly disrupts the orientation of a fluorophore located within the hydrophobic region of the cell membrane but not of a surface bound probe. This is consistent with cholesterol having an important role in stabilizing and ordering the lipid tails within the plasma membrane. },
->
+        Annote = {10.1529/biophysj.104.050096},
->
+        Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {Biophysical Journal},
->
+        Journal1 = {Biophys. J.},
->
+        Number = {1},
->
+        Pages = {609--622},
->
+        Title = {Fluorescence Imaging of Two-Photon Linear Dichroism: Cholesterol Depletion Disrupts Molecular Orientation in Cell Membranes},
->
+        Ty = {JOUR},
->
+        Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
->
+        Volume = {88},
->
+        Year = {2005}}
->
->
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+        Address = {Amsterdam},
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+        Chapter = {Reactions in Disordered Media Modelled by Fractals},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Editor = {Luciano Peitronero and E. Tosatti},
->
+        Pages = 399,
->
+        Publisher = {North-Holland},
->
+        Series = {International Symposium on Fractals in Physics},
->
+        Title = {Fractals in Physics},
->
+        Year = 1986}
->
->
+@article{Marland1979,
->
+        Author = {L.~G. Marland and D.~D. Betts},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = prl,
->
+        Number = 21,
->
+        Pages = {1618-1621},
->
+        Title = {Frustration Effect in Quantum Spin Systems},
->
+        Volume = 43,
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+        Year = 1979}
->
->
+@article{Berne72,
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+        Author = {B.~J. Berne and P. Pechukas},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = jcp,
->
+        Pages = {4213-4216},
->
+        Title = {Gaussian Model Potentials for Molecular Interactions},
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+        Volume = 56,
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+        Year = 1972}
->
->
+@article{Golubkov06,
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+        Author = {Pavel A. Golubkov and Rengyu Ren},
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+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = jcp,
->
+        Pages = 064103,
->
+        Title = {Generalized coarse-grained model based on point multipole and Gay-Berne potentials},
->
+        Volume = 125,
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+        Year = 2006}
->
->
+@article{Harden2006,
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+        Author = {J. Harden and B. Mbanga and N. Eber and K. Fodor-Csorba and S. Sprunt and J. T. Gleeson and A. Jakli},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Eid = 157802,
->
+        Journal = {Physical Review Letters},
->
+        Number = 15,
->
+        Numpages = 4,
->
+        Pages = 157802,
->
+        Publisher = {APS},
->
+        Title = {Giant Flexoelectricity of Bent-Core Nematic Liquid Crystals},
->
+        Volume = 97,
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+        Year = 2006}
->
->
+@article{Dzugutov92,
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+        Author = {M. Dzugutov},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
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+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = pra,
->
+        Pages = {R2984-R2987},
->
+        Title = {Glass formation in a simple monatomic liquid with icosahedral inherent local order},
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+        Volume = 46,
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+        Year = 1992}
->
->
+@article{Calderbank96,
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+        Author = {A.~R. Calderbank and P.~W. Shor},
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+        Date-Added = {2008-01-08 14:58:56 -0500},
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+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {Phys. Rev. A},
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+        Pages = {1098-1105},
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+        Title = {Good quantum error-correcting codes exist},
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+        Volume = 54,
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+        Year = 1996}
->
->
+@article{Carraro1993,
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+        Author = {Carlo Carraro and David R. Nelson},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
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+        Date-Modified = {2008-01-08 14:58:59 -0500},
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+        Journal = pre,
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+        Number = 4,
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+        Pages = {3082-3090},
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+        Title = {Grain-boundary buckling and spin-glass models of disorder in membranes},
->
+        Volume = 48,
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+        Year = 1993}
->
->
+@article{Stillinger82,
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+        Author = {F.~H. Stillinger and T.~A. Weber},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = pra,
->
+        Number = 2,
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+        Pages = {978-989},
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+        Title = {Hidden structure in liquids},
->
+        Volume = 25,
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+        Year = 1982}
->
->
+@article{Little96,
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+        Author = {H.~J. Little},
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+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {Pharmacology \& Therapeutics},
->
+        Pages = {37-58},
->
+        Title = {How has molecular pharmacology contributed to our understanding of the mechanism(s) of general anesthesia?},
->
+        Volume = 69,
->
+        Year = 1996}
->
->
+@article{Roberts94,
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+        Author = {J.~E. Roberts and J. Schnitker},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {J. Chem. Phys.},
->
+        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
->
+        Number = {6},
->
+        Pages = {5024-5031},
->
+        Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
->
+        Volume = {101},
->
+        Year = {1994}}
->
->
+@article{Stillinger85,
->
+        Author = {F.~H. Stillinger and T.~A. Weber},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = jcp,
->
+        Number = 9,
->
+        Pages = {4767-4775},
->
+        Title = {Inherent structure theory of liquids in the hard-sphere limit},
->
+        Volume = 83,
->
+        Year = 1985}
->
->
+@article{Kast03,
->
+        Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {Chem. Phys. Lett.},
->
+        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
->
+        Pages = {398-404},
->
+        Title = {Integral equation theory for correcting truncation errors in molecular simulations},
->
+        Volume = {367},
->
+        Year = {2003}}
->
->
+@article{Ayton01,
->
+        Author = {Gary Ayton and Scott G. Bardenhagen and Patrick McMurty and Deborah Sulsky and Gregory A. Voth},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = jcp,
->
+        Number = 15,
->
+        Pages = {6913-6924},
->
+        Title = {Interfacing continuum and molecular dynamics: An application to lipid bilayers},
->
+        Volume = 114,
->
+        Year = 2001}
->
->
+@inbook{Voter95b,
->
+        Author = {A.~F. Voter},
->
+        Chapter = 4,
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Editor = {J.~H. Westbrook and R.~L. Fleischer},
->
+        Pages = 77,
->
+        Publisher = {John Wiley and Sons Ltd},
->
+        Title = {Intermetallic Compounds: Principles and Practice},
->
+        Volume = 1,
->
+        Year = 1995}
->
->
+@article{Truhlar78,
->
+        Author = {Donald G. Truhlar},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:58:59 -0500},
->
+        Journal = {J. Chem. Ed.},
->
+        Pages = 309,
->
+        Title = {Interpretation of the Activation Energy},
->
+        Volume = 55,
->
+        Year = 1978}
->
->
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+        Abstract = {Quantitative structures of the fully hydrated fluid phases of dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) were obtained at 30{degrees}C. Data for the relative form factors F(qz) for DMPC were obtained using a combination of four methods. 1), Volumetric data provided F(0). 2), Diffuse x-ray scattering from oriented stacks of bilayers provided relative form factors |F(qz)| for high qz, 0.22 < qz < 0.8 A-1. 3), X-ray scattering from extruded unilamellar vesicles with diameter 600 A provided |F(qz)| for low qz, 0.1 < qz < 0.3 A-1. 4), Previous measurements using a liquid crystallographic x-ray method provided |F(2{pi}h/D)| for h = 1 and 2 for a range of nearly fully hydrated D-spacings. The data from method 4 overlap and validate the new unilamellar vesicles data for DMPC, so method 4 is not required for DLPC or future studies. We used hybrid electron density models to obtain structural results from these form factors. Comparison of the model electron density profiles with that of gel phase DMPC provides areas per lipid A, 60.6 {+/-} 0.5 A2 for DMPC and 63.2 {+/-} 0.5 A2 for DLPC. Constraints on the model provided by volume measurements and component volumes obtained from simulations put the electron density profiles {rho}(z) and the corresponding form factors F(qz) on absolute scales. Various thicknesses, such as the hydrophobic thickness and the steric thickness, are obtained and compared to literature values.
->
+},
->
+        Author = {Kucerka, Norbert and Liu, Yufeng and Chu, Nanjun and Petrache, Horia I. and Tristram-Nagle, Stephanie and Nagle, John F.},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:59:02 -0500},
->
+        Doi = {10.1529/biophysj.104.056606},
->
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->
+        Journal = {Biophys. J.},
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+        Number = {4},
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+        Pages = {2626-2637},
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+        Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}},
->
+        Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
->
+        Volume = {88},
->
+        Year = {2005}}
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+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:59:03 -0500},
->
+        Journal = prl,
->
+        Pages = 295,
->
+        Volume = 71,
->
+        Year = 1993}
->
->
+@article{Egelhoff89,
->
+        Author = {W.~F. Egelhoff and I. Jacob},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:59:03 -0500},
->
+        Journal = prl,
->
+        Pages = 921,
->
+        Volume = 62,
->
+        Year = 1989}
-<
+@ARTICLE{Torre2003,
-<
+  author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez
-<
+    and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez},
-<
+  title = {Calculation of the solution properties of flexible macromolecules:
-<
+    methods and applications},
-<
+  journal = {European Biophysics Journal with Biophysics Letters},
-<
+  year = {2003},
-<
+  volume = {32},
-<
+  pages = {477-486},
-<
+  number = {5},
-<
+  month = {Aug},
-<
+  abstract = {While the prediction of hydrodynamic properties of rigid particles
->
+@article{Dobson1987,
->
+        Author = {B.~W. Dobson},
->
+        Date-Added = {2008-01-08 14:58:56 -0500},
->
+        Date-Modified = {2008-01-08 14:59:03 -0500},
->
+        Journal = prb,
->
+        Pages = 1068,
->
+        Volume = 36,
->
+        Year = 1987}
->
->
+@article{Davis:1969uq,
->
+        Abstract = { Exact solutions of the Stokes equations are derived for the case of two unequal spheres slowly rotating or translating perpendicular to their line of centers in a quiescent, unbounded viscous fluid, following Wakiya[16]. Numerical results are presented for the force and torque coefficients for size ratios from 1[middle dot]0 to 10[middle dot]0, and separations down to 0[middle dot]001 times the radius of the smaller.},
->
+        Author = {Davis, M. H.},
->
+        Date-Added = {2008-01-08 14:57:14 -0500},
->
+        Date-Modified = {2008-01-08 14:57:14 -0500},
->
+        Journal = {Chemical Engineering Science},
->
+        Number = {12},
->
+        Pages = {1769--1776},
->
+        Title = {The slow translation and rotation of two unequal spheres in a viscous fluid},
->
+        Ty = {JOUR},
->
+        Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
->
+        Volume = {24},
->
+        Year = {1969}}
->
->
+@article{Stimson:1926qy,
->
+        Author = {Stimson, M and Jeffery, GB},
->
+        Date-Added = {2008-01-08 14:51:23 -0500},
->
+        Date-Modified = {2008-01-08 14:51:35 -0500},
->
+        Journal = {Proceedings of the Royal Society of London Series A-Containing Papers of a Mathematical and Physical Character},
->
+        Pages = {110-116},
->
+        Title = {The motion of two spheres in a viscous fluid},
->
+        Volume = {111},
->
+        Year = {1926}}
->
->
+@article{Orlandi:2006fk,
->
+        Abstract = {Liquid crystal phases formed by bent-shaped (or {\tt{}"{}}banana{\tt{}"{}}) molecules are currently of great interest. Here we investigate by Monte Carlo computer simulations the phases formed by rigid banana molecules modeled combining three Gay-Berne sites and containing either one central or two lateral and transversal dipoles. We show that changing the dipole position and orientation has a profound effect on the mesophase stability and molecular organization. In particular, we find a uniaxial nematic phase only for off-center dipolar models and tilted phases only for the one with terminal dipoles.},
->
+        Address = {Dipartimento di Chimica Fisica e Inorganica, and INSTM, Universita di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.},
->
+        Au = {Orlandi, S and Berardi, R and Steltzer, J and Zannoni, C},
->
+        Author = {Orlandi, Silvia and Berardi, Roberto and Steltzer, Joachim and Zannoni, Claudio},
->
+        Da = {20060407},
->
+        Date-Added = {2008-01-08 14:47:56 -0500},
->
+        Date-Modified = {2008-01-08 14:48:06 -0500},
->
+        Dcom = {20070727},
->
+        Doi = {10.1063/1.2176622},
->
+        Edat = {2006/04/08 09:00},
->
+        Issn = {0021-9606 (Print)},
->
+        Jid = {0375360},
->
+        Journal = {J Chem Phys},
->
+        Jt = {The Journal of chemical physics},
->
+        Language = {eng},
->
+        Mhda = {2006/04/08 09:01},
->
+        Number = {12},
->
+        Own = {NLM},
->
+        Pages = {124907},
->
+        Pl = {United States},
->
+        Pmid = {16599725},
->
+        Pst = {ppublish},
->
+        Pt = {Journal Article},
->
+        Pubm = {Print},
->
+        So = {J Chem Phys. 2006 Mar 28;124(12):124907.},
->
+        Stat = {PubMed-not-MEDLINE},
->
+        Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.},
->
+        Volume = {124},
->
+        Year = {2006}}
->
->
+@article{sun:031602,
->
+        Author = {Xiuquan Sun and J. Daniel Gezelter},
->
+        Date-Added = {2008-01-08 14:42:33 -0500},
->
+        Date-Modified = {2008-01-08 14:42:33 -0500},
->
+        Doi = {10.1103/PhysRevE.75.031602},
->
+        Eid = {031602},
->
+        Journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)},
->
+        Keywords = {lattice theory; membranes},
->
+        Number = {3},
->
+        Numpages = {7},
->
+        Pages = {031602},
->
+        Publisher = {APS},
->
+        Title = {Spontaneous corrugation of dipolar membranes},
->
+        Url = {http://link.aps.org/abstract/PRE/v75/e031602},
->
+        Volume = {75},
->
+        Year = {2007}}
->
->
+@article{Ortega:2007lr,
->
+        Abstract = {The equivalent radius for any solution property is the radius of a spherical particle having the same value of solution property as that of the macromolecule under consideration. Equivalent radii for different properties present a dependence on size and shape that are more similar than the values of the properties themselves. Furthermore, the ratios of equivalent radii of two properties depend on the conformation (shape or flexibility), but not on the absolute sizes. We define equivalent radii and their ratios, and describe their evaluation for some common models of rigid and flexible macromolecules. Using radii and ratios, we have devised procedures to fit macromolecular models to experimental properties, allowing the determination of the model parameters. Using these quantities, we can construct target functions for an equilibrated, unbiased optimization. The procedures, which have been implemented in public-domain computer programs, are illustrated for rigid, globular proteins, and the rodlike tobacco mosaic virus, and for semiflexible, wormlike heparin molecules.},
->
+        Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.},
->
+        Au = {Ortega, A and Garcia de la Torre, J},
->
+        Author = {Ortega, A and Garcia de la Torre, J},
->
+        Da = {20070813},
->
+        Date-Added = {2008-01-08 14:38:03 -0500},
->
+        Date-Modified = {2008-01-08 14:38:49 -0500},
->
+        Dcom = {20071017},
->
+        Dep = {20070724},
->
+        Doi = {10.1021/bm700473f},
->
+        Edat = {2007/07/25 09:00},
->
+        Issn = {1525-7797 (Print)},
->
+        Jid = {100892849},
->
+        Journal = {Biomacromolecules},
->
+        Jt = {Biomacromolecules},
->
+        Keywords = {Computer Simulation; Heparin/chemistry; Macromolecular Substances/*chemistry; *Models, Chemical; *Models, Molecular; Molecular Conformation; Particle Size; Protein Conformation; Proteins/chemistry; Software; Solutions},
->
+        Language = {eng},
->
+        Mhda = {2007/10/18 09:00},
->
+        Number = {8},
->
+        Own = {NLM},
->
+        Pages = {2464--2475},
->
+        Phst = {2007/07/24 {$[$}aheadofprint{$]$}},
->
+        Pl = {United States},
->
+        Pmid = {17645309},
->
+        Pst = {ppublish},
->
+        Pt = {Journal Article; Research Support, Non-U.S. Gov't},
->
+        Pubm = {Print-Electronic},
->
+        Rn = {0 (Macromolecular Substances); 0 (Proteins); 0 (Solutions); 9005-49-6 (Heparin)},
->
+        Sb = {IM},
->
+        So = {Biomacromolecules. 2007 Aug;8(8):2464-75. Epub 2007 Jul 24.},
->
+        Stat = {MEDLINE},
->
+        Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.},
->
+        Volume = {8},
->
+        Year = {2007}}
->
->
+@article{Torre2003,
->
+        Abstract = {While the prediction of hydrodynamic properties of rigid particles
+    is nowadays feasible using simple and efficient computer programs,
+    the calculation of such properties and, in general, the dynamic
+    behavior of flexible macromolecules has not reached a similar situation.
+    such as bending, internal rotation, excluded volume effects, etc.
+    We provide an example of the application of this methodology to
+    the dynamics of a semiflexible, wormlike DNA.},
-<
+  annote = {724XK Times Cited:6 Cited References Count:64},
-<
+  issn = {0175-7571},
-<
+  uri = {<Go to ISI>://000185513400011},
-<
+}
->
+        Annote = {724XK Times Cited:6 Cited References Count:64},
->
+        Author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez},
->
+        Issn = {0175-7571},
->
+        Journal = {European Biophysics Journal with Biophysics Letters},
->
+        Month = {Aug},
->
+        Number = {5},
->
+        Pages = {477-486},
->
+        Title = {Calculation of the solution properties of flexible macromolecules: methods and applications},
->
+        Uri = {<Go to ISI>://000185513400011},
->
+        Volume = {32},
->
+        Year = {2003}}
-<
+@ARTICLE{Alakent2005,
-<
+  author = {B. Alakent and M. C. Camurdan and P. Doruker},
-<
+  title = {Hierarchical structure of the energy landscape of proteins revisited
-<
+    by time series analysis. II. Investigation of explicit solvent effects},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2005},
-<
+  volume = {123},
-<
+  pages = {-},
-<
+  number = {14},
-<
+  month = {Oct 8},
-<
+  abstract = {Time series analysis tools are employed on the principal modes obtained
->
+@article{Alakent2005,
->
+        Abstract = {Time series analysis tools are employed on the principal modes obtained
+    from the C-alpha trajectories from two independent molecular-dynamics
+    simulations of alpha-amylase inhibitor (tendamistat). Fluctuations
+    inside an energy minimum (intraminimum motions), transitions between
+    approximately 200 ps (about five times of that in vacuum) in the
+    low-indexed modes, showing the lowering of energy barriers between
+    the higher-level minima.},
-<
+  annote = {973OH Times Cited:1 Cited References Count:33},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000232532000064},
-<
+}
->
+        Annote = {973OH Times Cited:1 Cited References Count:33},
->
+        Author = {B. Alakent and M. C. Camurdan and P. Doruker},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Oct 8},
->
+        Number = {14},
->
+        Pages = {-},
->
+        Title = {Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects},
->
+        Uri = {<Go to ISI>://000232532000064},
->
+        Volume = {123},
->
+        Year = {2005}}
-<
+@BOOK{Alexander1987,
-<
+  title = {A Pattern Language: Towns, Buildings, Construction},
-<
+  publisher = {Oxford University Press},
-<
+  year = {1987},
-<
+  author = {C. Alexander},
-<
+  address = {New York},
-<
+}
->
+@book{Alexander1987,
->
+        Address = {New York},
->
+        Author = {C. Alexander},
->
+        Publisher = {Oxford University Press},
->
+        Title = {A Pattern Language: Towns, Buildings, Construction},
->
+        Year = {1987}}
-<
+@BOOK{Allen1987,
-<
+  title = {Computer Simulations of Liquids},
-<
+  publisher = {Oxford University Press},
-<
+  year = {1987},
-<
+  author = {M.~P. Allen and D.~J. Tildesley},
-<
+  address = {New York},
-<
+}
->
+@book{Allen1987,
->
+        Address = {New York},
->
+        Author = {M.~P. Allen and D.~J. Tildesley},
->
+        Publisher = {Oxford University Press},
->
+        Title = {Computer Simulations of Liquids},
->
+        Year = {1987}}
-<
+@ARTICLE{Allison1991,
-<
+  author = {S. A. Allison},
-<
+  title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application
-<
+    to Polarized Dynamic Light-Scattering},
-<
+  journal = {Macromolecules},
-<
+  year = {1991},
-<
+  volume = {24},
-<
+  pages = {530-536},
-<
+  number = {2},
-<
+  month = {Jan 21},
-<
+  abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
->
+@article{Allison1991,
->
+        Abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
+    of rigid macromolecules. It is applied to polarized dynamic light
+    scattering from rodlike sturctures and from a model of a DNA fragment
+    (762 base pairs). A number of rod cases are examined in which the
+    of this fragment, it is shown directly that flexing contributes
+    to the faster decay processes probed by light scattering and that
+    the flexible model studies are in good agreement with experiment.},
-<
+  annote = {Eu814 Times Cited:8 Cited References Count:32},
-<
+  issn = {0024-9297},
-<
+  uri = {<Go to ISI>://A1991EU81400029},
-<
+}
->
+        Annote = {Eu814 Times Cited:8 Cited References Count:32},
->
+        Author = {S. A. Allison},
->
+        Issn = {0024-9297},
->
+        Journal = {Macromolecules},
->
+        Month = {Jan 21},
->
+        Number = {2},
->
+        Pages = {530-536},
->
+        Title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application to Polarized Dynamic Light-Scattering},
->
+        Uri = {<Go to ISI>://A1991EU81400029},
->
+        Volume = {24},
->
+        Year = {1991}}
-<
+@ARTICLE{Andersen1983,
-<
+  author = {H. C. Andersen},
-<
+  title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics
-<
+    Calculations},
-<
+  journal = {Journal of Computational Physics},
-<
+  year = {1983},
-<
+  volume = {52},
-<
+  pages = {24-34},
-<
+  number = {1},
-<
+  annote = {Rq238 Times Cited:559 Cited References Count:14},
-<
+  issn = {0021-9991},
-<
+  uri = {<Go to ISI>://A1983RQ23800002},
-<
+}
->
+@article{Andersen1983,
->
+        Annote = {Rq238 Times Cited:559 Cited References Count:14},
->
+        Author = {H. C. Andersen},
->
+        Issn = {0021-9991},
->
+        Journal = {Journal of Computational Physics},
->
+        Number = {1},
->
+        Pages = {24-34},
->
+        Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
->
+        Uri = {<Go to ISI>://A1983RQ23800002},
->
+        Volume = {52},
->
+        Year = {1983}}
-<
+@ARTICLE{Auerbach2005,
-<
+  author = {A. Auerbach},
-<
+  title = {Gating of acetylcholine receptor channels: Brownian motion across
-<
+    a broad transition state},
-<
+  journal = {Proceedings of the National Academy of Sciences of the United States
-<
+    of America},
-<
+  year = {2005},
-<
+  volume = {102},
-<
+  pages = {1408-1412},
-<
+  number = {5},
-<
+  month = {Feb 1},
-<
+  abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
->
+@article{Auerbach2005,
->
+        Abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
+    stable #closed# and #open# conformations. In patch clamp recordings,
+    diliganded AChR gating appears to be a simple, two-state reaction.
+    However, mutagenesis studies indicate that during gating dozens
+    coarse-grained AChR gating conformational change propagates through
+    the protein with dynamics that are governed by the Brownian motion
+    of individual gating blocks.},
-<
+  annote = {895QF Times Cited:9 Cited References Count:33},
-<
+  issn = {0027-8424},
-<
+  uri = {<Go to ISI>://000226877300030},
-<
+}
->
+        Annote = {895QF Times Cited:9 Cited References Count:33},
->
+        Author = {A. Auerbach},
->
+        Issn = {0027-8424},
->
+        Journal = {Proceedings of the National Academy of Sciences of the United States of America},
->
+        Month = {Feb 1},
->
+        Number = {5},
->
+        Pages = {1408-1412},
->
+        Title = {Gating of acetylcholine receptor channels: Brownian motion across a broad transition state},
->
+        Uri = {<Go to ISI>://000226877300030},
->
+        Volume = {102},
->
+        Year = {2005}}
-<
+@ARTICLE{Baber1995,
-<
+  author = {J. Baber and J. F. Ellena and D. S. Cafiso},
-<
+  title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined
-<
+    Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
-<
+  journal = {Biochemistry},
-<
+  year = {1995},
-<
+  volume = {34},
-<
+  pages = {6533-6539},
-<
+  number = {19},
-<
+  month = {May 16},
-<
+  abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
->
+@article{Baber1995,
->
+        Abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
+    on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine
+    membranes in the liquid crystalline phase was investigated using
+    H-2 NMR. Upon the addition of the anesthetics, the first five methylene
+    the NOE data indicate that anesthetics prefer the interfacial and
+    hydrocarbon regions of the membrane and are not found in high concentrations
+    in the phospholipid headgroup.},
-<
+  annote = {Qz716 Times Cited:38 Cited References Count:37},
-<
+  issn = {0006-2960},
-<
+  uri = {<Go to ISI>://A1995QZ71600035},
-<
+}
->
+        Annote = {Qz716 Times Cited:38 Cited References Count:37},
->
+        Author = {J. Baber and J. F. Ellena and D. S. Cafiso},
->
+        Issn = {0006-2960},
->
+        Journal = {Biochemistry},
->
+        Month = {May 16},
->
+        Number = {19},
->
+        Pages = {6533-6539},
->
+        Title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
->
+        Uri = {<Go to ISI>://A1995QZ71600035},
->
+        Volume = {34},
->
+        Year = {1995}}
-<
+@ARTICLE{Banerjee2004,
-<
+  author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
-<
+  title = {Solution of quantum Langevin equation: Approximations, theoretical
-<
+    and numerical aspects},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2004},
-<
+  volume = {120},
-<
+  pages = {8960-8972},
-<
+  number = {19},
-<
+  month = {May 15},
-<
+  abstract = {Based on a coherent state representation of noise operator and an
->
+@article{Banerjee2004,
->
+        Abstract = {Based on a coherent state representation of noise operator and an
+    ensemble averaging procedure using Wigner canonical thermal distribution
+    for harmonic oscillators, a generalized quantum Langevin equation
+    has been recently developed [Phys. Rev. E 65, 021109 (2002); 66,
+    calculation of barrier crossing, in a cubic potential to demonstrate
+    the quantum Kramers' turnover and the quantum Arrhenius plot. (C)
+American Institute of Physics.},
-<
+  annote = {816YY Times Cited:8 Cited References Count:35},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000221146400009},
-<
+}
->
+        Annote = {816YY Times Cited:8 Cited References Count:35},
->
+        Author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {May 15},
->
+        Number = {19},
->
+        Pages = {8960-8972},
->
+        Title = {Solution of quantum Langevin equation: Approximations, theoretical and numerical aspects},
->
+        Uri = {<Go to ISI>://000221146400009},
->
+        Volume = {120},
->
+        Year = {2004}}
-<
+@ARTICLE{Barojas1973,
-<
+  author = {J. Barojas and D. Levesque},
-<
+  title = {Simulation of Diatomic Homonuclear Liquids},
-<
+  journal = {Phys. Rev. A},
-<
+  year = {1973},
-<
+  volume = {7},
-<
+  pages = {1092-1105},
-<
+}
->
+@article{Barojas1973,
->
+        Author = {J. Barojas and D. Levesque},
->
+        Journal = {Phys. Rev. A},
->
+        Pages = {1092-1105},
->
+        Title = {Simulation of Diatomic Homonuclear Liquids},
->
+        Volume = {7},
->
+        Year = {1973}}
-<
+@ARTICLE{Barth1998,
-<
+  author = {E. Barth and T. Schlick},
-<
+  title = {Overcoming stability limitations in biomolecular dynamics. I. Combining
-<
+    force splitting via extrapolation with Langevin dynamics in LN},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {1998},
-<
+  volume = {109},
-<
+  pages = {1617-1632},
-<
+  number = {5},
-<
+  month = {Aug 1},
-<
+  abstract = {We present an efficient new method termed LN for propagating biomolecular
->
+@article{Barth1998,
->
+        Abstract = {We present an efficient new method termed LN for propagating biomolecular
+    dynamics according to the Langevin equation that arose fortuitously
+    upon analysis of the range of harmonic validity of our normal-mode
+    scheme LIN. LN combines force linearization with force splitting
+    of LN to biomolecular dynamics is well suited for configurational
+    sampling, thermodynamic, and structural questions. (C) 1998 American
+    Institute of Physics.},
-<
+  annote = {105HH Times Cited:29 Cited References Count:49},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000075066300006},
-<
+}
->
+        Annote = {105HH Times Cited:29 Cited References Count:49},
->
+        Author = {E. Barth and T. Schlick},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Aug 1},
->
+        Number = {5},
->
+        Pages = {1617-1632},
->
+        Title = {Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN},
->
+        Uri = {<Go to ISI>://000075066300006},
->
+        Volume = {109},
->
+        Year = {1998}}
-<
+@ARTICLE{Batcho2001,
-<
+  author = {P. F. Batcho and T. Schlick},
-<
+  title = {Special stability advantages of position-Verlet over velocity-Verlet
-<
+    in multiple-time step integration},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2001},
-<
+  volume = {115},
-<
+  pages = {4019-4029},
-<
+  number = {9},
-<
+  month = {Sep 1},
-<
+  abstract = {We present an analysis for a simple two-component harmonic oscillator
->
+@article{Batcho2001,
->
+        Abstract = {We present an analysis for a simple two-component harmonic oscillator
+    that compares the use of position-Verlet to velocity-Verlet for
+    multiple-time step integration. The numerical stability analysis
+    based on the impulse-Verlet splitting shows that position-Verlet
+    to a biomolecule. a solvated protein, for both Newtonian and Langevin
+    dynamics echo these trends over large outer time-step regimes. (C)
+American Institute of Physics.},
-<
+  annote = {469KV Times Cited:6 Cited References Count:30},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000170813800005},
-<
+}
->
+        Annote = {469KV Times Cited:6 Cited References Count:30},
->
+        Author = {P. F. Batcho and T. Schlick},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Sep 1},
->
+        Number = {9},
->
+        Pages = {4019-4029},
->
+        Title = {Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration},
->
+        Uri = {<Go to ISI>://000170813800005},
->
+        Volume = {115},
->
+        Year = {2001}}
-<
+@ARTICLE{Bates2005,
-<
+  author = {M. A. Bates and G. R. Luckhurst},
-<
+  title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation
-<
+    study},
-<
+  journal = {Physical Review E},
-<
+  year = {2005},
-<
+  volume = {72},
-<
+  pages = {-},
-<
+  number = {5},
-<
+  month = {Nov},
-<
+  abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
->
+@article{Bates2005,
->
+        Abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
+    can exhibit the elusive biaxial nematic phase, we have developed
+    a generic simulation model for such systems. This contains the features
+    of the molecule that are essential to its liquid crystal behavior,
+    determination of this. The simulation results show that, whereas
+    some positions are extremely sensitive to the phase biaxiality,
+    others are totally blind to this.},
-<
+  annote = {Part 1 988LQ Times Cited:0 Cited References Count:38},
-<
+  issn = {1539-3755},
-<
+  uri = {<Go to ISI>://000233603100030},
-<
+}
->
+        Annote = {Part 1 988LQ Times Cited:0 Cited References Count:38},
->
+        Author = {M. A. Bates and G. R. Luckhurst},
->
+        Issn = {1539-3755},
->
+        Journal = {Physical Review E},
->
+        Month = {Nov},
->
+        Number = {5},
->
+        Pages = {-},
->
+        Title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation study},
->
+        Uri = {<Go to ISI>://000233603100030},
->
+        Volume = {72},
->
+        Year = {2005}}
-<
+@ARTICLE{Beard2003,
-<
+  author = {D. A. Beard and T. Schlick},
-<
+  title = {Unbiased rotational moves for rigid-body dynamics},
-<
+  journal = {Biophysical Journal},
-<
+  year = {2003},
-<
+  volume = {85},
-<
+  pages = {2973-2976},
-<
+  number = {5},
-<
+  month = {Nov 1},
-<
+  abstract = {We introduce an unbiased protocol for performing rotational moves
->
+@article{Beard2003,
->
+        Abstract = {We introduce an unbiased protocol for performing rotational moves
+    in rigid-body dynamics simulations. This approach - based on the
+    analytic solution for the rotational equations of motion for an
+    orthogonal coordinate system at constant angular velocity - removes
+    applying the noncommuting rotational matrices in an arbitrary order.
+    Our algorithm should thus replace standard approaches to rotate
+    local coordinate frames in Langevin and Brownian dynamics simulations.},
-<
+  annote = {736UA Times Cited:0 Cited References Count:11},
-<
+  issn = {0006-3495},
-<
+  uri = {<Go to ISI>://000186190500018},
-<
+}
->
+        Annote = {736UA Times Cited:0 Cited References Count:11},
->
+        Author = {D. A. Beard and T. Schlick},
->
+        Issn = {0006-3495},
->
+        Journal = {Biophysical Journal},
->
+        Month = {Nov 1},
->
+        Number = {5},
->
+        Pages = {2973-2976},
->
+        Title = {Unbiased rotational moves for rigid-body dynamics},
->
+        Uri = {<Go to ISI>://000186190500018},
->
+        Volume = {85},
->
+        Year = {2003}}
-<
+@ARTICLE{Beloborodov1998,
-<
+  author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev},
-<
+  title = {Effect of coupling between rotational and translational Brownian
-<
+    motions on NMR spin relaxation: Consideration using green function
-<
+    of rigid body diffusion},
-<
+  journal = {Journal of Magnetic Resonance},
-<
+  year = {1998},
-<
+  volume = {132},
-<
+  pages = {328-329},
-<
+  number = {2},
-<
+  month = {Jun},
-<
+  abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
->
+@article{Beloborodov1998,
->
+        Abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
+    Biopolymers 33, 409-436, 1993), it was analytically shown that coupling
+    between translation and rotation diffusion degrees of freedom does
+    not affect the correlation functions relevant to the NMR intramolecular
+-654, 1962) can be regarded as exact in respect to the rotation-translation
+    coupling for the spin system connected with a rigid body. (C) 1998
+    Academic Press.},
-<
+  annote = {Zu605 Times Cited:2 Cited References Count:6},
-<
+  issn = {1090-7807},
-<
+  uri = {<Go to ISI>://000074214800017},
-<
+}
->
+        Annote = {Zu605 Times Cited:2 Cited References Count:6},
->
+        Author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev},
->
+        Issn = {1090-7807},
->
+        Journal = {Journal of Magnetic Resonance},
->
+        Month = {Jun},
->
+        Number = {2},
->
+        Pages = {328-329},
->
+        Title = {Effect of coupling between rotational and translational Brownian motions on NMR spin relaxation: Consideration using green function of rigid body diffusion},
->
+        Uri = {<Go to ISI>://000074214800017},
->
+        Volume = {132},
->
+        Year = {1998}}
-<
+@ARTICLE{Berardi1996,
-<
+  author = {R. Berardi and S. Orlandi and C. Zannoni},
-<
+  title = {Antiphase structures in polar smectic liquid crystals and their molecular
-<
+    origin},
-<
+  journal = {Chemical Physics Letters},
-<
+  year = {1996},
-<
+  volume = {261},
-<
+  pages = {357-362},
-<
+  number = {3},
-<
+  month = {Oct 18},
-<
+  abstract = {We demonstrate that the overall molecular dipole organization in a
->
+@article{Berardi1996,
->
+        Abstract = {We demonstrate that the overall molecular dipole organization in a
+    smectic liquid crystal formed of polar molecules can be strongly
+    influenced by the position of the dipole in the molecule. We study
+    by large scale Monte Carlo simulations systems of attractive-repulsive
+    liquid crystals and modulated antiferroelectric bilayer stripe domains
+    similar to the experimentally observed ''antiphase'' structures
+    are obtained in the two cases.},
-<
+  annote = {Vn637 Times Cited:49 Cited References Count:26},
-<
+  issn = {0009-2614},
-<
+  uri = {<Go to ISI>://A1996VN63700023},
-<
+}
->
+        Annote = {Vn637 Times Cited:49 Cited References Count:26},
->
+        Author = {R. Berardi and S. Orlandi and C. Zannoni},
->
+        Issn = {0009-2614},
->
+        Journal = {Chemical Physics Letters},
->
+        Month = {Oct 18},
->
+        Number = {3},
->
+        Pages = {357-362},
->
+        Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
->
+        Uri = {<Go to ISI>://A1996VN63700023},
->
+        Volume = {261},
->
+        Year = {1996}}
-<
+@ARTICLE{Berkov2005,
-<
+  author = {D. V. Berkov and N. L. Gorn},
-<
+  title = {Magnetization precession due to a spin-polarized current in a thin
-<
+    nanoelement: Numerical simulation study},
-<
+  journal = {Physical Review B},
-<
+  year = {2005},
-<
+  volume = {72},
-<
+  pages = {-},
-<
+  number = {9},
-<
+  month = {Sep},
-<
+  abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
->
+@article{Berkov2005,
->
+        Abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
+    formalism) of magnetization oscillations driven by a spin-polarized
+    current through a thin elliptical nanoelement is presented. We show
+    that a sophisticated micromagnetic model, where a polycrystalline
+    of reasonable parameter values, indicating that further model refinement
+    is necessary for a complete understanding of the spin-driven magnetization
+    precession even in this relatively simple experimental situation.},
-<
+  annote = {969IT Times Cited:2 Cited References Count:55},
-<
+  issn = {1098-0121},
-<
+  uri = {<Go to ISI>://000232228500058},
-<
+}
->
+        Annote = {969IT Times Cited:2 Cited References Count:55},
->
+        Author = {D. V. Berkov and N. L. Gorn},
->
+        Issn = {1098-0121},
->
+        Journal = {Physical Review B},
->
+        Month = {Sep},
->
+        Number = {9},
->
+        Pages = {-},
->
+        Title = {Magnetization precession due to a spin-polarized current in a thin nanoelement: Numerical simulation study},
->
+        Uri = {<Go to ISI>://000232228500058},
->
+        Volume = {72},
->
+        Year = {2005}}
-<
+@ARTICLE{Berkov2005a,
-<
+  author = {D. V. Berkov and N. L. Gorn},
-<
+  title = {Stochastic dynamic simulations of fast remagnetization processes:
-<
+    recent advances and applications},
-<
+  journal = {Journal of Magnetism and Magnetic Materials},
-<
+  year = {2005},
-<
+  volume = {290},
-<
+  pages = {442-448},
-<
+  month = {Apr},
-<
+  abstract = {Numerical simulations of fast remagnetization processes using stochastic
->
+@article{Berkov2005a,
->
+        Abstract = {Numerical simulations of fast remagnetization processes using stochastic
+    dynamics are widely used to study various magnetic systems. In this
+    paper, we first address several crucial methodological problems
+    of such simulations: (i) the influence of finite-element discretization
+    in pulsed fields and show some results for a remagnetization dynamics
+    induced by a spin-polarized current. (c) 2004 Elsevier B.V. All
+    rights reserved.},
-<
+  annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
-<
+  issn = {0304-8853},
-<
+  uri = {<Go to ISI>://000228837600109},
-<
+}
->
+        Annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
->
+        Author = {D. V. Berkov and N. L. Gorn},
->
+        Issn = {0304-8853},
->
+        Journal = {Journal of Magnetism and Magnetic Materials},
->
+        Month = {Apr},
->
+        Pages = {442-448},
->
+        Title = {Stochastic dynamic simulations of fast remagnetization processes: recent advances and applications},
->
+        Uri = {<Go to ISI>://000228837600109},
->
+        Volume = {290},
->
+        Year = {2005}}
-<
+@ARTICLE{Berkov2002,
-<
+  author = {D. V. Berkov and N. L. Gorn and P. Gornert},
-<
+  title = {Magnetization dynamics in nanoparticle systems: Numerical simulation
-<
+    using Langevin dynamics},
-<
+  journal = {Physica Status Solidi a-Applied Research},
-<
+  year = {2002},
-<
+  volume = {189},
-<
+  pages = {409-421},
-<
+  number = {2},
-<
+  month = {Feb 16},
-<
+  abstract = {We report on recent progress achieved by the development of numerical
->
+@article{Berkov2002,
->
+        Abstract = {We report on recent progress achieved by the development of numerical
+    methods based on the stochastic (Langevin) dynamics applied to systems
+    of interacting magnetic nanoparticles. The method enables direct
+    simulations of the trajectories of magnetic moments taking into
+    For the second system the complex ac susceptibility chi(omega, T)
+    for various particle concentrations and particle anisotropies were
+    computed and compared with numerous experimental results.},
-<
+  annote = {526TF Times Cited:4 Cited References Count:37},
-<
+  issn = {0031-8965},
-<
+  uri = {<Go to ISI>://000174145200026},
-<
+}
->
+        Annote = {526TF Times Cited:4 Cited References Count:37},
->
+        Author = {D. V. Berkov and N. L. Gorn and P. Gornert},
->
+        Issn = {0031-8965},
->
+        Journal = {Physica Status Solidi a-Applied Research},
->
+        Month = {Feb 16},
->
+        Number = {2},
->
+        Pages = {409-421},
->
+        Title = {Magnetization dynamics in nanoparticle systems: Numerical simulation using Langevin dynamics},
->
+        Uri = {<Go to ISI>://000174145200026},
->
+        Volume = {189},
->
+        Year = {2002}}
-<
+@ARTICLE{Bernal1980,
-<
+  author = {J.M. Bernal and J. G. {de la Torre}},
-<
+  title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules
-<
+    with Arbitrary Shape},
-<
+  journal = {Biopolymers},
-<
+  year = {1980},
-<
+  volume = {19},
-<
+  pages = {751-766},
-<
+}
->
+@article{Bernal1980,
->
+        Author = {J.M. Bernal and J. G. {de la Torre}},
->
+        Journal = {Biopolymers},
->
+        Pages = {751-766},
->
+        Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape},
->
+        Volume = {19},
->
+        Year = {1980}}
-<
+@ARTICLE{Brenner1967,
-<
+  author = {H. Brenner },
-<
+  title = {Coupling between the Translational and Rotational Brownian Motions
-<
+    of Rigid Particles of Arbitrary shape},
-<
+  journal = {J. Collid. Int. Sci.},
-<
+  year = {1967},
-<
+  volume = {23},
-<
+  pages = {407-436},
-<
+}
->
+@article{Brenner1967,
->
+        Author = {H. Brenner},
->
+        Journal = {J. Collid. Int. Sci.},
->
+        Pages = {407-436},
->
+        Title = {Coupling between the Translational and Rotational Brownian Motions of Rigid Particles of Arbitrary shape},
->
+        Volume = {23},
->
+        Year = {1967}}
-<
+@ARTICLE{Brooks1983,
-<
+  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},
-<
+  journal = {Journal of Computational Chemistry},
-<
+  year = {1983},
-<
+  volume = {4},
-<
+  pages = {187-217},
-<
+  number = {2},
-<
+  annote = {Qp423 Times Cited:6414 Cited References Count:96},
-<
+  issn = {0192-8651},
-<
+  uri = {<Go to ISI>://A1983QP42300010},
-<
+}
->
+@article{Brooks1983,
->
+        Annote = {Qp423 Times Cited:6414 Cited References Count:96},
->
+        Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus},
->
+        Issn = {0192-8651},
->
+        Journal = {Journal of Computational Chemistry},
->
+        Number = {2},
->
+        Pages = {187-217},
->
+        Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
->
+        Uri = {<Go to ISI>://A1983QP42300010},
->
+        Volume = {4},
->
+        Year = {1983}}
-<
+@ARTICLE{Brunger1984,
-<
+  author = {A. Brunger and C. L. Brooks and M. Karplus},
-<
+  title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations
-<
+    of St2 Water},
-<
+  journal = {Chemical Physics Letters},
-<
+  year = {1984},
-<
+  volume = {105},
-<
+  pages = {495-500},
-<
+  number = {5},
-<
+  annote = {Sm173 Times Cited:143 Cited References Count:22},
-<
+  issn = {0009-2614},
-<
+  uri = {<Go to ISI>://A1984SM17300007},
-<
+}
->
+@article{Brunger1984,
->
+        Annote = {Sm173 Times Cited:143 Cited References Count:22},
->
+        Author = {A. Brunger and C. L. Brooks and M. Karplus},
->
+        Issn = {0009-2614},
->
+        Journal = {Chemical Physics Letters},
->
+        Number = {5},
->
+        Pages = {495-500},
->
+        Title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations of St2 Water},
->
+        Uri = {<Go to ISI>://A1984SM17300007},
->
+        Volume = {105},
->
+        Year = {1984}}
-<
+@ARTICLE{Budd1999,
-<
+  author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell},
-<
+  title = {Self-similar numerical solutions of the porous-medium equation using
-<
+    moving mesh methods},
-<
+  journal = {Philosophical Transactions of the Royal Society of London Series
-<
+    a-Mathematical Physical and Engineering Sciences},
-<
+  year = {1999},
-<
+  volume = {357},
-<
+  pages = {1047-1077},
-<
+  number = {1754},
-<
+  month = {Apr 15},
-<
+  abstract = {This paper examines a synthesis of adaptive mesh methods with the
->
+@article{Budd1999,
->
+        Abstract = {This paper examines a synthesis of adaptive mesh methods with the
+    use of symmetry to study a partial differential equation. In particular,
+    it considers methods which admit discrete self-similar solutions,
+    examining the convergence of these to the true self-similar solution
+    as well as their stability. Special attention is given to the nonlinear
+    diffusion equation describing flow in a porous medium.},
-<
+  annote = {199EE Times Cited:4 Cited References Count:14},
-<
+  issn = {1364-503X},
-<
+  uri = {<Go to ISI>://000080466800005},
-<
+}
->
+        Annote = {199EE Times Cited:4 Cited References Count:14},
->
+        Author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell},
->
+        Issn = {1364-503X},
->
+        Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
->
+        Month = {Apr 15},
->
+        Number = {1754},
->
+        Pages = {1047-1077},
->
+        Title = {Self-similar numerical solutions of the porous-medium equation using moving mesh methods},
->
+        Uri = {<Go to ISI>://000080466800005},
->
+        Volume = {357},
->
+        Year = {1999}}
-<
+@ARTICLE{Camp1999,
-<
+  author = {P. J. Camp and M. P. Allen and A. J. Masters},
-<
+  title = {Theory and computer simulation of bent-core molecules},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {1999},
-<
+  volume = {111},
-<
+  pages = {9871-9881},
-<
+  number = {21},
-<
+  month = {Dec 1},
-<
+  abstract = {Fluids of hard bent-core molecules have been studied using theory
->
+@article{Camp1999,
->
+        Abstract = {Fluids of hard bent-core molecules have been studied using theory
+    and computer simulation. The molecules are composed of two hard
+    spherocylinders, with length-to-breadth ratio L/D, joined by their
+    ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20
+    bond angle-a feature that is also reflected in the lack of variation
+    with angle of the calculated second and third virial coefficients.
+    (C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].},
-<
+  annote = {255TC Times Cited:24 Cited References Count:38},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000083685400056},
-<
+}
->
+        Annote = {255TC Times Cited:24 Cited References Count:38},
->
+        Author = {P. J. Camp and M. P. Allen and A. J. Masters},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Dec 1},
->
+        Number = {21},
->
+        Pages = {9871-9881},
->
+        Title = {Theory and computer simulation of bent-core molecules},
->
+        Uri = {<Go to ISI>://000083685400056},
->
+        Volume = {111},
->
+        Year = {1999}}
-<
+@ARTICLE{Care2005,
-<
+  author = {C. M. Care and D. J. Cleaver},
-<
+  title = {Computer simulation of liquid crystals},
-<
+  journal = {Reports on Progress in Physics},
-<
+  year = {2005},
-<
+  volume = {68},
-<
+  pages = {2665-2700},
-<
+  number = {11},
-<
+  month = {Nov},
-<
+  abstract = {A review is presented of molecular and mesoscopic computer simulations
->
+@article{Care2005,
->
+        Abstract = {A review is presented of molecular and mesoscopic computer simulations
+    of liquid crystalline systems. Molecular simulation approaches applied
+    to such systems are described, and the key findings for bulk phase
+    behaviour are reported. Following this, recently developed lattice
+    Boltzmann approaches to the mesoscale modelling of nemato-dynanics
+    are reviewed. This paper concludes with a discussion of possible
+    areas for future development in this field.},
-<
+  annote = {989TU Times Cited:2 Cited References Count:258},
-<
+  issn = {0034-4885},
-<
+  uri = {<Go to ISI>://000233697600004},
-<
+}
->
+        Annote = {989TU Times Cited:2 Cited References Count:258},
->
+        Author = {C. M. Care and D. J. Cleaver},
->
+        Issn = {0034-4885},
->
+        Journal = {Reports on Progress in Physics},
->
+        Month = {Nov},
->
+        Number = {11},
->
+        Pages = {2665-2700},
->
+        Title = {Computer simulation of liquid crystals},
->
+        Uri = {<Go to ISI>://000233697600004},
->
+        Volume = {68},
->
+        Year = {2005}}
-<
+@ARTICLE{Carrasco1999,
-<
+  author = {B. Carrasco and J. G. {de la Torre}},
-<
+  title = {Hydrodynamic properties of rigid particles: Comparison of different
-<
+    modeling and computational procedures},
-<
+  journal = {Biophysical Journal},
-<
+  year = {1999},
-<
+  volume = {76},
-<
+  pages = {3044-3057},
-<
+  number = {6},
-<
+  month = {Jun},
-<
+  abstract = {The hydrodynamic properties of rigid particles are calculated from
->
+@article{Carrasco1999,
->
+        Abstract = {The hydrodynamic properties of rigid particles are calculated from
+    models composed of spherical elements (beads) using theories developed
+    by Kirkwood, Bloomfield, and their coworkers. Bead models have usually
+    been built in such a way that the beads fill the volume occupied
+    comparison of the performance of the various strategies by applying
+    them to some test cases, for which the properties are known a priori.
+    We provide guidelines and computational tools for bead modeling.},
-<
+  annote = {200TT Times Cited:46 Cited References Count:57},
-<
+  issn = {0006-3495},
-<
+  uri = {<Go to ISI>://000080556700016},
-<
+}
->
+        Annote = {200TT Times Cited:46 Cited References Count:57},
->
+        Author = {B. Carrasco and J. G. {de la Torre}},
->
+        Issn = {0006-3495},
->
+        Journal = {Biophysical Journal},
->
+        Month = {Jun},
->
+        Number = {6},
->
+        Pages = {3044-3057},
->
+        Title = {Hydrodynamic properties of rigid particles: Comparison of different modeling and computational procedures},
->
+        Uri = {<Go to ISI>://000080556700016},
->
+        Volume = {76},
->
+        Year = {1999}}
-<
+@ARTICLE{Chandra1999,
-<
+  author = {A. Chandra and T. Ichiye},
-<
+  title = {Dynamical properties of the soft sticky dipole model of water: Molecular
-<
+    dynamics simulations},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {1999},
-<
+  volume = {111},
-<
+  pages = {2701-2709},
-<
+  number = {6},
-<
+  month = {Aug 8},
-<
+  abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
->
+@article{Chandra1999,
->
+        Abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
+    are calculated by means of molecular dynamics simulations. Since
+    this is not a simple point model, the forces and torques arising
+    from the SSD potential are derived here. Simulations are carried
+    dynamics simulations of the SSD model are found to run much faster
+    than TIP3P, SPC/E, and other multisite models. (C) 1999 American
+    Institute of Physics. [S0021-9606(99)51430-X].},
-<
+  annote = {221EN Times Cited:14 Cited References Count:66},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000081711200038},
-<
+}
->
+        Annote = {221EN Times Cited:14 Cited References Count:66},
->
+        Author = {A. Chandra and T. Ichiye},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Aug 8},
->
+        Number = {6},
->
+        Pages = {2701-2709},
->
+        Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations},
->
+        Uri = {<Go to ISI>://000081711200038},
->
+        Volume = {111},
->
+        Year = {1999}}
-<
+@ARTICLE{Channell1990,
-<
+  author = {P. J. Channell and C. Scovel},
-<
+  title = {Symplectic Integration of Hamiltonian-Systems},
-<
+  journal = {Nonlinearity},
-<
+  year = {1990},
-<
+  volume = {3},
-<
+  pages = {231-259},
-<
+  number = {2},
-<
+  month = {may},
-<
+  annote = {Dk631 Times Cited:152 Cited References Count:34},
-<
+  issn = {0951-7715},
-<
+  uri = {<Go to ISI>://A1990DK63100001},
-<
+}
->
+@article{Channell1990,
->
+        Annote = {Dk631 Times Cited:152 Cited References Count:34},
->
+        Author = {P. J. Channell and C. Scovel},
->
+        Issn = {0951-7715},
->
+        Journal = {Nonlinearity},
->
+        Month = {may},
->
+        Number = {2},
->
+        Pages = {231-259},
->
+        Title = {Symplectic Integration of Hamiltonian-Systems},
->
+        Uri = {<Go to ISI>://A1990DK63100001},
->
+        Volume = {3},
->
+        Year = {1990}}
-<
+@ARTICLE{Chen2003,
-<
+  author = {B. Chen and F. Solis},
-<
+  title = {Explicit mixed finite order Runge-Kutta methods},
-<
+  journal = {Applied Numerical Mathematics},
-<
+  year = {2003},
-<
+  volume = {44},
-<
+  pages = {21-30},
-<
+  number = {1-2},
-<
+  month = {Jan},
-<
+  abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
->
+@article{Chen2003,
->
+        Abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
+    equations and introduce a family of mixed methods from combinations
+    of explicit Runge-Kutta methods. These methods have better stability
+    behavior than traditional Runge-Kutta methods and generally extend
+    or spurious. Emphasis is put on examples coming from mathematical
+    models in ecology. (C) 2002 IMACS. Published by Elsevier Science
+    B.V. All rights reserved.},
-<
+  annote = {633ZD Times Cited:0 Cited References Count:9},
-<
+  issn = {0168-9274},
-<
+  uri = {<Go to ISI>://000180314200002},
-<
+}
->
+        Annote = {633ZD Times Cited:0 Cited References Count:9},
->
+        Author = {B. Chen and F. Solis},
->
+        Issn = {0168-9274},
->
+        Journal = {Applied Numerical Mathematics},
->
+        Month = {Jan},
->
+        Number = {1-2},
->
+        Pages = {21-30},
->
+        Title = {Explicit mixed finite order Runge-Kutta methods},
->
+        Uri = {<Go to ISI>://000180314200002},
->
+        Volume = {44},
->
+        Year = {2003}}
-<
+@ARTICLE{Cheung2004,
-<
+  author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
-<
+  title = {Calculation of flexoelectric coefficients for a nematic liquid crystal
-<
+    by atomistic simulation},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2004},
-<
+  volume = {121},
-<
+  pages = {9131-9139},
-<
+  number = {18},
-<
+  month = {Nov 8},
-<
+  abstract = {Equilibrium molecular dynamics calculations have been performed for
->
+@article{Cheung2004,
->
+        Abstract = {Equilibrium molecular dynamics calculations have been performed for
+    the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile
+    (PCH5) using a fully atomistic model. Simulation data have been
+    obtained for a series of temperatures in the nematic phase. The
+    different intermolecular interactions. Values of e(s) and e(b) calculated
+    from simulation are consistent with those found from experiment.
+    (C) 2004 American Institute of Physics.},
-<
+  annote = {866UM Times Cited:4 Cited References Count:61},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000224798900053},
-<
+}
->
+        Annote = {866UM Times Cited:4 Cited References Count:61},
->
+        Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Nov 8},
->
+        Number = {18},
->
+        Pages = {9131-9139},
->
+        Title = {Calculation of flexoelectric coefficients for a nematic liquid crystal by atomistic simulation},
->
+        Uri = {<Go to ISI>://000224798900053},
->
+        Volume = {121},
->
+        Year = {2004}}
-<
+@ARTICLE{Cheung2002,
-<
+  author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
-<
+  title = {Calculation of the rotational viscosity of a nematic liquid crystal},
-<
+  journal = {Chemical Physics Letters},
-<
+  year = {2002},
-<
+  volume = {356},
-<
+  pages = {140-146},
-<
+  number = {1-2},
-<
+  month = {Apr 15},
-<
+  abstract = {Equilibrium molecular dynamics calculations have been performed for
->
+@article{Cheung2002,
->
+        Abstract = {Equilibrium molecular dynamics calculations have been performed for
+    the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile
+    (PCH5) using a fully atomistic model. Simulation data has been obtained
+    for a series of temperatures in the nematic phase. The rotational
+    on the rotational diffusion co-efficient. We find good agreement
+    between the first two methods and experimental values. (C) 2002
+    Published by Elsevier Science B.V.},
-<
+  annote = {547KF Times Cited:8 Cited References Count:31},
-<
+  issn = {0009-2614},
-<
+  uri = {<Go to ISI>://000175331000020},
-<
+}
->
+        Annote = {547KF Times Cited:8 Cited References Count:31},
->
+        Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
->
+        Issn = {0009-2614},
->
+        Journal = {Chemical Physics Letters},
->
+        Month = {Apr 15},
->
+        Number = {1-2},
->
+        Pages = {140-146},
->
+        Title = {Calculation of the rotational viscosity of a nematic liquid crystal},
->
+        Uri = {<Go to ISI>://000175331000020},
->
+        Volume = {356},
->
+        Year = {2002}}
-<
+@ARTICLE{Chin2004,
-<
+  author = {S. A. Chin},
-<
+  title = {Dynamical multiple-time stepping methods for overcoming resonance
-<
+    instabilities},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2004},
-<
+  volume = {120},
-<
+  pages = {8-13},
-<
+  number = {1},
-<
+  month = {Jan 1},
-<
+  abstract = {Current molecular dynamics simulations of biomolecules using multiple
->
+@article{Chin2004,
->
+        Abstract = {Current molecular dynamics simulations of biomolecules using multiple
+    time steps to update the slowly changing force are hampered by instabilities
+    beginning at time steps near the half period of the fastest vibrating
+    mode. These #resonance# instabilities have became a critical barrier
+    changing force, one must also update the position with a modified
+    mass. Thus multiple-time stepping must be done dynamically. (C)
+American Institute of Physics.},
-<
+  annote = {757TK Times Cited:1 Cited References Count:22},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000187577400003},
-<
+}
->
+        Annote = {757TK Times Cited:1 Cited References Count:22},
->
+        Author = {S. A. Chin},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Jan 1},
->
+        Number = {1},
->
+        Pages = {8-13},
->
+        Title = {Dynamical multiple-time stepping methods for overcoming resonance instabilities},
->
+        Uri = {<Go to ISI>://000187577400003},
->
+        Volume = {120},
->
+        Year = {2004}}
-<
+@ARTICLE{Cook2000,
-<
+  author = {M. J. Cook and M. R. Wilson},
-<
+  title = {Simulation studies of dipole correlation in the isotropic liquid
-<
+    phase},
-<
+  journal = {Liquid Crystals},
-<
+  year = {2000},
-<
+  volume = {27},
-<
+  pages = {1573-1583},
-<
+  number = {12},
-<
+  month = {Dec},
-<
+  abstract = {The Kirkwood correlation factor g(1) determines the preference for
->
+@article{Cook2000,
->
+        Abstract = {The Kirkwood correlation factor g(1) determines the preference for
+    local parallel or antiparallel dipole association in the isotropic
+    phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood
+    factors greater than 1 have an enhanced effective dipole moment
+    experimental dielectric measurements. Analysis of the molecular
+    dynamics trajectories allows an assessment of why these molecules
+    behave differently.},
-<
+  annote = {376BF Times Cited:10 Cited References Count:16},
-<
+  issn = {0267-8292},
-<
+  uri = {<Go to ISI>://000165437800002},
-<
+}
->
+        Annote = {376BF Times Cited:10 Cited References Count:16},
->
+        Author = {M. J. Cook and M. R. Wilson},
->
+        Issn = {0267-8292},
->
+        Journal = {Liquid Crystals},
->
+        Month = {Dec},
->
+        Number = {12},
->
+        Pages = {1573-1583},
->
+        Title = {Simulation studies of dipole correlation in the isotropic liquid phase},
->
+        Uri = {<Go to ISI>://000165437800002},
->
+        Volume = {27},
->
+        Year = {2000}}
-<
+@ARTICLE{Cui2003,
-<
+  author = {B. X. Cui and M. Y. Shen and K. F. Freed},
-<
+  title = {Folding and misfolding of the papillomavirus E6 interacting peptide
-<
+    E6ap},
-<
+  journal = {Proceedings of the National Academy of Sciences of the United States
-<
+    of America},
-<
+  year = {2003},
-<
+  volume = {100},
-<
+  pages = {7087-7092},
-<
+  number = {12},
-<
+  month = {Jun 10},
-<
+  abstract = {All-atom Langevin dynamics simulations have been performed to study
->
+@article{Cui2003,
->
+        Abstract = {All-atom Langevin dynamics simulations have been performed to study
+    the folding pathways of the 18-residue binding domain fragment E6ap
+    of the human papillomavirus E6 interacting peptide. Six independent
+    folding trajectories, with a total duration of nearly 2 mus, all
+    reveals a significant barrier between the basins separating the
+    native and misfolded states. We also discuss the various underlying
+    forces that drive the peptide into its native state.},
-<
+  annote = {689LC Times Cited:3 Cited References Count:48},
-<
+  issn = {0027-8424},
-<
+  uri = {<Go to ISI>://000183493500037},
-<
+}
->
+        Annote = {689LC Times Cited:3 Cited References Count:48},
->
+        Author = {B. X. Cui and M. Y. Shen and K. F. Freed},
->
+        Issn = {0027-8424},
->
+        Journal = {Proceedings of the National Academy of Sciences of the United States of America},
->
+        Month = {Jun 10},
->
+        Number = {12},
->
+        Pages = {7087-7092},
->
+        Title = {Folding and misfolding of the papillomavirus E6 interacting peptide E6ap},
->
+        Uri = {<Go to ISI>://000183493500037},
->
+        Volume = {100},
->
+        Year = {2003}}
-<
+@ARTICLE{Denisov2003,
-<
+  author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou},
-<
+  title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
-<
+  journal = {Physical Review B},
-<
+  year = {2003},
-<
+  volume = {67},
-<
+  pages = {-},
-<
+  number = {1},
-<
+  month = {Jan 1},
-<
+  abstract = {We study the slow phase of thermally activated magnetic relaxation
->
+@article{Denisov2003,
->
+        Abstract = {We study the slow phase of thermally activated magnetic relaxation
+    in finite two-dimensional ensembles of dipolar interacting ferromagnetic
+    nanoparticles whose easy axes of magnetization are perpendicular
+    to the distribution plane. We develop a method to numerically simulate
+    Within this framework, we analyze in detail the role that the correlations
+    of the nanoparticle magnetic moments and the finite size of the
+    nanoparticle ensemble play in magnetic relaxation.},
-<
+  annote = {642XH Times Cited:11 Cited References Count:31},
-<
+  issn = {1098-0121},
-<
+  uri = {<Go to ISI>://000180830400056},
-<
+}
->
+        Annote = {642XH Times Cited:11 Cited References Count:31},
->
+        Author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou},
->
+        Issn = {1098-0121},
->
+        Journal = {Physical Review B},
->
+        Month = {Jan 1},
->
+        Number = {1},
->
+        Pages = {-},
->
+        Title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
->
+        Uri = {<Go to ISI>://000180830400056},
->
+        Volume = {67},
->
+        Year = {2003}}
-<
+@ARTICLE{Derreumaux1998,
-<
+  author = {P. Derreumaux and T. Schlick},
-<
+  title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
-<
+  journal = {Biophysical Journal},
-<
+  year = {1998},
-<
+  volume = {74},
-<
+  pages = {72-81},
-<
+  number = {1},
-<
+  month = {Jan},
-<
+  abstract = {To explore the origin of the large-scale motion of triosephosphate
->
+@article{Derreumaux1998,
->
+        Abstract = {To explore the origin of the large-scale motion of triosephosphate
+    isomerase's flexible loop (residues 166 to 176) at the active site,
+    several simulation protocols are employed both for the free enzyme
+    in vacuo and for the free enzyme with some solvent modeling: high-temperature
+    is of rigid-body type and that the specific interaction between
+    residues Ala(176) and Tyr(208) plays a crucial role in the loop
+    opening/closing mechanism.},
-<
+  annote = {Zl046 Times Cited:30 Cited References Count:29},
-<
+  issn = {0006-3495},
-<
+  uri = {<Go to ISI>://000073393400009},
-<
+}
->
+        Annote = {Zl046 Times Cited:30 Cited References Count:29},
->
+        Author = {P. Derreumaux and T. Schlick},
->
+        Issn = {0006-3495},
->
+        Journal = {Biophysical Journal},
->
+        Month = {Jan},
->
+        Number = {1},
->
+        Pages = {72-81},
->
+        Title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
->
+        Uri = {<Go to ISI>://000073393400009},
->
+        Volume = {74},
->
+        Year = {1998}}
-<
+@ARTICLE{Dullweber1997,
-<
+  author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
-<
+  title = {Symplectic splitting methods for rigid body molecular dynamics},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {1997},
-<
+  volume = {107},
-<
+  pages = {5840-5851},
-<
+  number = {15},
-<
+  month = {Oct 15},
-<
+  abstract = {Rigid body molecular models possess symplectic structure and time-reversal
->
+@article{Dullweber1997,
->
+        Abstract = {Rigid body molecular models possess symplectic structure and time-reversal
+    symmetry. Standard numerical integration methods destroy both properties,
+    introducing nonphysical dynamical behavior such as numerically induced
+    dissipative states and drift in the energy during long term simulations.
+    model of water. Our experiments show that the symplectic-reversible
+    scheme is far superior to the more traditional quaternion method.
+    (C) 1997 American Institute of Physics.},
-<
+  annote = {Ya587 Times Cited:35 Cited References Count:32},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://A1997YA58700024},
-<
+}
->
+        Annote = {Ya587 Times Cited:35 Cited References Count:32},
->
+        Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Oct 15},
->
+        Number = {15},
->
+        Pages = {5840-5851},
->
+        Title = {Symplectic splitting methods for rigid body molecular dynamics},
->
+        Uri = {<Go to ISI>://A1997YA58700024},
->
+        Volume = {107},
->
+        Year = {1997}}
-<
+@BOOK{Gamma1994,
-<
+  title = {Design Patterns: Elements of Reusable Object-Oriented Software},
-<
+  publisher = {Perason Education},
-<
+  year = {1994},
-<
+  author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
-<
+  address = {London},
-<
+  chapter = {7},
-<
+}
->
+@book{Gamma1994,
->
+        Address = {London},
->
+        Author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
->
+        Chapter = {7},
->
+        Publisher = {Perason Education},
->
+        Title = {Design Patterns: Elements of Reusable Object-Oriented Software},
->
+        Year = {1994}}
-<
+@ARTICLE{Edwards2005,
-<
+  author = {S. A. Edwards and D. R. M. Williams},
-<
+  title = {Stretching a single diblock copolymer in a selective solvent: Langevin
-<
+    dynamics simulations},
-<
+  journal = {Macromolecules},
-<
+  year = {2005},
-<
+  volume = {38},
-<
+  pages = {10590-10595},
-<
+  number = {25},
-<
+  month = {Dec 13},
-<
+  abstract = {Using the Langevin dynamics technique, we have carried out simulations
->
+@article{Edwards2005,
->
+        Abstract = {Using the Langevin dynamics technique, we have carried out simulations
+    of a single-chain flexible diblock copolymer. The polymer consists
+    of two blocks of equal length, one very poorly solvated and the
+    other close to theta-conditions. We study what happens when such
+    not increase monotonically, in disagreement with earlier predictions,
+    and that at high speeds there is a strong dependence on which end
+    of the polymer is pulled, as well as a high level of hysteresis.},
-<
+  annote = {992EC Times Cited:0 Cited References Count:13},
-<
+  issn = {0024-9297},
-<
+  uri = {<Go to ISI>://000233866200035},
-<
+}
->
+        Annote = {992EC Times Cited:0 Cited References Count:13},
->
+        Author = {S. A. Edwards and D. R. M. Williams},
->
+        Issn = {0024-9297},
->
+        Journal = {Macromolecules},
->
+        Month = {Dec 13},
->
+        Number = {25},
->
+        Pages = {10590-10595},
->
+        Title = {Stretching a single diblock copolymer in a selective solvent: Langevin dynamics simulations},
->
+        Uri = {<Go to ISI>://000233866200035},
->
+        Volume = {38},
->
+        Year = {2005}}
-<
+@ARTICLE{Egberts1988,
-<
+  author = {E. Egberts and H. J. C. Berendsen},
-<
+  title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic
-<
+    Detail},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {1988},
-<
+  volume = {89},
-<
+  pages = {3718-3732},
-<
+  number = {6},
-<
+  month = {Sep 15},
-<
+  annote = {Q0188 Times Cited:219 Cited References Count:43},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://A1988Q018800036},
-<
+}
->
+@article{Egberts1988,
->
+        Annote = {Q0188 Times Cited:219 Cited References Count:43},
->
+        Author = {E. Egberts and H. J. C. Berendsen},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Sep 15},
->
+        Number = {6},
->
+        Pages = {3718-3732},
->
+        Title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic Detail},
->
+        Uri = {<Go to ISI>://A1988Q018800036},
->
+        Volume = {89},
->
+        Year = {1988}}
-<
+@ARTICLE{Ermak1978,
-<
+  author = {D. L. Ermak and J. A. Mccammon},
-<
+  title = {Brownian Dynamics with Hydrodynamic Interactions},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {1978},
-<
+  volume = {69},
-<
+  pages = {1352-1360},
-<
+  number = {4},
-<
+  annote = {Fp216 Times Cited:785 Cited References Count:42},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://A1978FP21600004},
-<
+}
->
+@article{Ermak1978,
->
+        Annote = {Fp216 Times Cited:785 Cited References Count:42},
->
+        Author = {D. L. Ermak and J. A. Mccammon},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Number = {4},
->
+        Pages = {1352-1360},
->
+        Title = {Brownian Dynamics with Hydrodynamic Interactions},
->
+        Uri = {<Go to ISI>://A1978FP21600004},
->
+        Volume = {69},
->
+        Year = {1978}}
-<
+@ARTICLE{Evans1977,
-<
+  author = {D. J. Evans},
-<
+  title = {Representation of Orientation Space},
-<
+  journal = {Molecular Physics},
-<
+  year = {1977},
-<
+  volume = {34},
-<
+  pages = {317-325},
-<
+  number = {2},
-<
+  annote = {Ds757 Times Cited:271 Cited References Count:18},
-<
+  issn = {0026-8976},
-<
+  uri = {<Go to ISI>://A1977DS75700002},
-<
+}
->
+@article{Evans1977,
->
+        Annote = {Ds757 Times Cited:271 Cited References Count:18},
->
+        Author = {D. J. Evans},
->
+        Issn = {0026-8976},
->
+        Journal = {Molecular Physics},
->
+        Number = {2},
->
+        Pages = {317-325},
->
+        Title = {Representation of Orientation Space},
->
+        Uri = {<Go to ISI>://A1977DS75700002},
->
+        Volume = {34},
->
+        Year = {1977}}
-<
+@ARTICLE{Fennell2004,
-<
+  author = {C. J. Fennell and J. D. Gezelter},
-<
+  title = {On the structural and transport properties of the soft sticky dipole
-<
+    and related single-point water models},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2004},
-<
+  volume = {120},
-<
+  pages = {9175-9184},
-<
+  number = {19},
-<
+  month = {May 15},
-<
+  abstract = {The density maximum and temperature dependence of the self-diffusion
->
+@article{Fennell2004,
->
+        Abstract = {The density maximum and temperature dependence of the self-diffusion
+    constant were investigated for the soft sticky dipole (SSD) water
+    model and two related reparametrizations of this single-point model.
+    A combination of microcanonical and isobaric-isothermal molecular
+    ice structure is presented which appears to be the most stable ice
+    structure for the entire SSD family. (C) 2004 American Institute
+    of Physics.},
-<
+  annote = {816YY Times Cited:5 Cited References Count:39},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000221146400032},
-<
+}
->
+        Annote = {816YY Times Cited:5 Cited References Count:39},
->
+        Author = {C. J. Fennell and J. D. Gezelter},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {May 15},
->
+        Number = {19},
->
+        Pages = {9175-9184},
->
+        Title = {On the structural and transport properties of the soft sticky dipole and related single-point water models},
->
+        Uri = {<Go to ISI>://000221146400032},
->
+        Volume = {120},
->
+        Year = {2004}}
-<
+@ARTICLE{Fernandes2002,
-<
+  author = {M. X. Fernandes and J. G. {de la Torre}},
-<
+  title = {Brownian dynamics simulation of rigid particles of arbitrary shape
-<
+    in external fields},
-<
+  journal = {Biophysical Journal},
-<
+  year = {2002},
-<
+  volume = {83},
-<
+  pages = {3039-3048},
-<
+  number = {6},
-<
+  month = {Dec},
-<
+  abstract = {We have developed a Brownian dynamics simulation algorithm to generate
->
+@article{Fernandes2002,
->
+        Abstract = {We have developed a Brownian dynamics simulation algorithm to generate
+    Brownian trajectories of an isolated, rigid particle of arbitrary
+    shape in the presence of electric fields or any other external agents.
+    Starting from the generalized diffusion tensor, which can be calculated
+    method, which serve as tests of its performance, and also illustrate
+    its applicability. Examples include free diffusion, transport in
+    an electric field, and diffusion in a restricting environment.},
-<
+  annote = {633AD Times Cited:2 Cited References Count:43},
-<
+  issn = {0006-3495},
-<
+  uri = {<Go to ISI>://000180256300012},
-<
+}
->
+        Annote = {633AD Times Cited:2 Cited References Count:43},
->
+        Author = {M. X. Fernandes and J. G. {de la Torre}},
->
+        Issn = {0006-3495},
->
+        Journal = {Biophysical Journal},
->
+        Month = {Dec},
->
+        Number = {6},
->
+        Pages = {3039-3048},
->
+        Title = {Brownian dynamics simulation of rigid particles of arbitrary shape in external fields},
->
+        Uri = {<Go to ISI>://000180256300012},
->
+        Volume = {83},
->
+        Year = {2002}}
-<
+@BOOK{Frenkel1996,
-<
+  title = {Understanding Molecular Simulation : From Algorithms to Applications},
-<
+  publisher = {Academic Press},
-<
+  year = {1996},
-<
+  author = {D. Frenkel and B. Smit},
-<
+  address = {New York},
-<
+}
->
+@book{Frenkel1996,
->
+        Address = {New York},
->
+        Author = {D. Frenkel and B. Smit},
->
+        Publisher = {Academic Press},
->
+        Title = {Understanding Molecular Simulation : From Algorithms to Applications},
->
+        Year = {1996}}
-<
+@ARTICLE{Gay1981,
-<
+  author = {J. G. Gay and B. J. Berne},
-<
+  title = {Modification of the Overlap Potential to Mimic a Linear Site-Site
-<
+    Potential},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {1981},
-<
+  volume = {74},
-<
+  pages = {3316-3319},
-<
+  number = {6},
-<
+  annote = {Lj347 Times Cited:482 Cited References Count:13},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://A1981LJ34700029},
-<
+}
->
+@article{Gay1981,
->
+        Annote = {Lj347 Times Cited:482 Cited References Count:13},
->
+        Author = {J. G. Gay and B. J. Berne},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Number = {6},
->
+        Pages = {3316-3319},
->
+        Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
->
+        Uri = {<Go to ISI>://A1981LJ34700029},
->
+        Volume = {74},
->
+        Year = {1981}}
-<
+@ARTICLE{Gelin1999,
-<
+  author = {M. F. Gelin},
-<
+  title = {Inertial effects in the Brownian dynamics with rigid constraints},
-<
+  journal = {Macromolecular Theory and Simulations},
-<
+  year = {1999},
-<
+  volume = {8},
-<
+  pages = {529-543},
-<
+  number = {6},
-<
+  month = {Nov},
-<
+  abstract = {To investigate the influence of inertial effects on the dynamics of
->
+@article{Gelin1999,
->
+        Abstract = {To investigate the influence of inertial effects on the dynamics of
+    an assembly of beads subjected to rigid constraints and placed in
+    a buffer medium, a convenient method to introduce suitable generalized
+    coordinates is presented. Without any restriction on the nature
+    behavior, which is irreproducible within the standard diffusion
+    equation. Several methods are considered for the approximate solution
+    of the DEM, and their application to three dimensional DEMs is discussed.},
-<
+  annote = {257MM Times Cited:2 Cited References Count:82},
-<
+  issn = {1022-1344},
-<
+  uri = {<Go to ISI>://000083785700002},
-<
+}
->
+        Annote = {257MM Times Cited:2 Cited References Count:82},
->
+        Author = {M. F. Gelin},
->
+        Issn = {1022-1344},
->
+        Journal = {Macromolecular Theory and Simulations},
->
+        Month = {Nov},
->
+        Number = {6},
->
+        Pages = {529-543},
->
+        Title = {Inertial effects in the Brownian dynamics with rigid constraints},
->
+        Uri = {<Go to ISI>://000083785700002},
->
+        Volume = {8},
->
+        Year = {1999}}
-<
+@ARTICLE{Goetz1998,
-<
+  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},
-<
+  pages = {7397},
-<
+  number = {17},
-<
+}
->
+@article{Goetz1998,
->
+        Author = {R. Goetz and R. Lipowsky},
->
+        Journal = {Journal of Chemical Physics},
->
+        Number = {17},
->
+        Pages = {7397},
->
+        Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
->
+        Volume = {108},
->
+        Year = {1998}}
-<
+@BOOK{Goldstein2001,
-<
+  title = {Classical Mechanics},
-<
+  publisher = {Addison Wesley},
-<
+  year = {2001},
-<
+  author = {H. Goldstein and C. Poole and J. Safko},
-<
+  address = {San Francisco},
-<
+  edition = {3rd},
-<
+}
->
+@book{Goldstein2001,
->
+        Address = {San Francisco},
->
+        Author = {H. Goldstein and C. Poole and J. Safko},
->
+        Edition = {3rd},
->
+        Publisher = {Addison Wesley},
->
+        Title = {Classical Mechanics},
->
+        Year = {2001}}
-<
+@ARTICLE{Gray2003,
-<
+  author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and
-<
+    B. Kuhlman and C. A. Rohl and D. Baker},
-<
+  title = {Protein-protein docking with simultaneous optimization of rigid-body
-<
+    displacement and side-chain conformations},
-<
+  journal = {Journal of Molecular Biology},
-<
+  year = {2003},
-<
+  volume = {331},
-<
+  pages = {281-299},
-<
+  number = {1},
-<
+  month = {Aug 1},
-<
+  abstract = {Protein-protein docking algorithms provide a means to elucidate structural
->
+@article{Gray2003,
->
+        Abstract = {Protein-protein docking algorithms provide a means to elucidate structural
+    details for presently unknown complexes. Here, we present and evaluate
+    a new method to predict protein-protein complexes from the coordinates
+    of the unbound monomer components. The method employs a low-resolution,
+    but they also highlight the challenges that must be met to achieve
+    consistent and accurate prediction of protein-protein interactions.
+    (C) 2003 Elsevier Ltd. All rights reserved.},
-<
+  annote = {704QL Times Cited:48 Cited References Count:60},
-<
+  issn = {0022-2836},
-<
+  uri = {<Go to ISI>://000184351300022},
-<
+}
->
+        Annote = {704QL Times Cited:48 Cited References Count:60},
->
+        Author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and B. Kuhlman and C. A. Rohl and D. Baker},
->
+        Issn = {0022-2836},
->
+        Journal = {Journal of Molecular Biology},
->
+        Month = {Aug 1},
->
+        Number = {1},
->
+        Pages = {281-299},
->
+        Title = {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations},
->
+        Uri = {<Go to ISI>://000184351300022},
->
+        Volume = {331},
->
+        Year = {2003}}
-<
+@ARTICLE{Greengard1994,
-<
+  author = {L. Greengard},
-<
+  title = {Fast Algorithms for Classical Physics},
-<
+  journal = {Science},
-<
+  year = {1994},
-<
+  volume = {265},
-<
+  pages = {909-914},
-<
+  number = {5174},
-<
+  month = {Aug 12},
-<
+  abstract = {Some of the recently developed fast summation methods that have arisen
->
+@article{Greengard1994,
->
+        Abstract = {Some of the recently developed fast summation methods that have arisen
+    in scientific computing are described. These methods require an
+    amount of work proportional to N or N log N to evaluate all pairwise
+    interactions in an ensemble of N particles. Traditional methods,
+    computer resources. In combination with supercomputers, it is possible
+    to address questions that were previously out of reach. Problems
+    from diffusion, gravitation, and wave propagation are considered.},
-<
+  annote = {Pb499 Times Cited:99 Cited References Count:44},
-<
+  issn = {0036-8075},
-<
+  uri = {<Go to ISI>://A1994PB49900031},
-<
+}
->
+        Annote = {Pb499 Times Cited:99 Cited References Count:44},
->
+        Author = {L. Greengard},
->
+        Issn = {0036-8075},
->
+        Journal = {Science},
->
+        Month = {Aug 12},
->
+        Number = {5174},
->
+        Pages = {909-914},
->
+        Title = {Fast Algorithms for Classical Physics},
->
+        Uri = {<Go to ISI>://A1994PB49900031},
->
+        Volume = {265},
->
+        Year = {1994}}
-<
+@ARTICLE{Greengard1987,
-<
+  author = {L. Greengard and V. Rokhlin},
-<
+  title = {A Fast Algorithm for Particle Simulations},
-<
+  journal = {Journal of Computational Physics},
-<
+  year = {1987},
-<
+  volume = {73},
-<
+  pages = {325-348},
-<
+  number = {2},
-<
+  month = {Dec},
-<
+  annote = {L0498 Times Cited:899 Cited References Count:7},
-<
+  issn = {0021-9991},
-<
+  uri = {<Go to ISI>://A1987L049800006},
-<
+}
->
+@article{Greengard1987,
->
+        Annote = {L0498 Times Cited:899 Cited References Count:7},
->
+        Author = {L. Greengard and V. Rokhlin},
->
+        Issn = {0021-9991},
->
+        Journal = {Journal of Computational Physics},
->
+        Month = {Dec},
->
+        Number = {2},
->
+        Pages = {325-348},
->
+        Title = {A Fast Algorithm for Particle Simulations},
->
+        Uri = {<Go to ISI>://A1987L049800006},
->
+        Volume = {73},
->
+        Year = {1987}}
-<
+@ARTICLE{Hairer1997,
-<
+  author = {E. Hairer and C. Lubich},
-<
+  title = {The life-span of backward error analysis for numerical integrators},
-<
+  journal = {Numerische Mathematik},
-<
+  year = {1997},
-<
+  volume = {76},
-<
+  pages = {441-462},
-<
+  number = {4},
-<
+  month = {Jun},
-<
+  abstract = {Backward error analysis is a useful tool for the study of numerical
->
+@article{Hairer1997,
->
+        Abstract = {Backward error analysis is a useful tool for the study of numerical
+    approximations to ordinary differential equations. The numerical
+    solution is formally interpreted as the exact solution of a perturbed
+    differential equation, given as a formal and usually divergent series
+    near hyperbolic equilibrium points, to asymptotically stable periodic
+    orbits and Hopf bifurcation, and to energy conservation and approximation
+    of invariant tori in Hamiltonian systems.},
-<
+  annote = {Xj488 Times Cited:50 Cited References Count:19},
-<
+  issn = {0029-599X},
-<
+  uri = {<Go to ISI>://A1997XJ48800002},
-<
+}
->
+        Annote = {Xj488 Times Cited:50 Cited References Count:19},
->
+        Author = {E. Hairer and C. Lubich},
->
+        Issn = {0029-599X},
->
+        Journal = {Numerische Mathematik},
->
+        Month = {Jun},
->
+        Number = {4},
->
+        Pages = {441-462},
->
+        Title = {The life-span of backward error analysis for numerical integrators},
->
+        Uri = {<Go to ISI>://A1997XJ48800002},
->
+        Volume = {76},
->
+        Year = {1997}}
-<
+@ARTICLE{Hao1993,
-<
+  author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga},
-<
+  title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic
-<
+    Trypsin-Inhibitor Studied by Computer-Simulations},
-<
+  journal = {Biochemistry},
-<
+  year = {1993},
-<
+  volume = {32},
-<
+  pages = {9614-9631},
-<
+  number = {37},
-<
+  month = {Sep 21},
-<
+  abstract = {A new procedure for studying the folding and unfolding of proteins,
->
+@article{Hao1993,
->
+        Abstract = {A new procedure for studying the folding and unfolding of proteins,
+    with an application to bovine pancreatic trypsin inhibitor (BPTI),
+    is reported. The unfolding and refolding of the native structure
+    of the protein are characterized by the dimensions of the protein,
+    progressive formation of partially folded structural units, followed
+    by collapse to the compact native structure. The general applicability
+    of the procedure is also discussed.},
-<
+  annote = {Ly294 Times Cited:27 Cited References Count:57},
-<
+  issn = {0006-2960},
-<
+  uri = {<Go to ISI>://A1993LY29400014},
-<
+}
->
+        Annote = {Ly294 Times Cited:27 Cited References Count:57},
->
+        Author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga},
->
+        Issn = {0006-2960},
->
+        Journal = {Biochemistry},
->
+        Month = {Sep 21},
->
+        Number = {37},
->
+        Pages = {9614-9631},
->
+        Title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic Trypsin-Inhibitor Studied by Computer-Simulations},
->
+        Uri = {<Go to ISI>://A1993LY29400014},
->
+        Volume = {32},
->
+        Year = {1993}}
-<
+@ARTICLE{Hinsen2000,
-<
+  author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel
-<
+    and G. R. Kneller},
-<
+  title = {Harmonicity in slow protein dynamics},
-<
+  journal = {Chemical Physics},
-<
+  year = {2000},
-<
+  volume = {261},
-<
+  pages = {25-37},
-<
+  number = {1-2},
-<
+  month = {Nov 1},
-<
+  abstract = {The slow dynamics of proteins around its native folded state is usually
->
+@article{Hinsen2000,
->
+        Abstract = {The slow dynamics of proteins around its native folded state is usually
+    described by diffusion in a strongly anharmonic potential. In this
+    paper, we try to understand the form and origin of the anharmonicities,
+    with the principal aim of gaining a better understanding of the
+    MD simulations, which are best suited for detailed studies on smaller
+    systems or for shorter time scales. (C) 2000 Elsevier Science B.V.
+    All rights reserved.},
-<
+  annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31},
-<
+  issn = {0301-0104},
-<
+  uri = {<Go to ISI>://000090121700003},
-<
+}
->
+        Annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31},
->
+        Author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel and G. R. Kneller},
->
+        Issn = {0301-0104},
->
+        Journal = {Chemical Physics},
->
+        Month = {Nov 1},
->
+        Number = {1-2},
->
+        Pages = {25-37},
->
+        Title = {Harmonicity in slow protein dynamics},
->
+        Uri = {<Go to ISI>://000090121700003},
->
+        Volume = {261},
->
+        Year = {2000}}
-<
+@ARTICLE{Ho1992,
-<
+  author = {C. Ho and C. D. Stubbs},
-<
+  title = {Hydration at the Membrane Protein-Lipid Interface},
-<
+  journal = {Biophysical Journal},
-<
+  year = {1992},
-<
+  volume = {63},
-<
+  pages = {897-902},
-<
+  number = {4},
-<
+  month = {Oct},
-<
+  abstract = {Evidence has been found for the existence water at the protein-lipid
->
+@article{Ho1992,
->
+        Abstract = {Evidence has been found for the existence water at the protein-lipid
+    hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome
+    C, using two related fluorescence spectroscopic approaches. The
+    first approach exploited the fact that the presence of water in
+    hydration at the protein-lipid interface could affect conformation,
+    thereby offering a new route by which membrane protein functioning
+    may be modified.},
-<
+  annote = {Ju251 Times Cited:55 Cited References Count:44},
-<
+  issn = {0006-3495},
-<
+  uri = {<Go to ISI>://A1992JU25100002},
-<
+}
->
+        Annote = {Ju251 Times Cited:55 Cited References Count:44},
->
+        Author = {C. Ho and C. D. Stubbs},
->
+        Issn = {0006-3495},
->
+        Journal = {Biophysical Journal},
->
+        Month = {Oct},
->
+        Number = {4},
->
+        Pages = {897-902},
->
+        Title = {Hydration at the Membrane Protein-Lipid Interface},
->
+        Uri = {<Go to ISI>://A1992JU25100002},
->
+        Volume = {63},
->
+        Year = {1992}}
-<
+@BOOK{Hockney1981,
-<
+  title = {Computer Simulation Using Particles},
-<
+  publisher = {McGraw-Hill},
-<
+  year = {1981},
-<
+  author = {R.W. Hockney and J.W. Eastwood},
-<
+  address = {New York},
-<
+}
->
+@book{Hockney1981,
->
+        Address = {New York},
->
+        Author = {R.W. Hockney and J.W. Eastwood},
->
+        Publisher = {McGraw-Hill},
->
+        Title = {Computer Simulation Using Particles},
->
+        Year = {1981}}
-<
+@ARTICLE{Hoover1985,
-<
+  author = {W. G. Hoover},
-<
+  title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
-<
+  journal = {Physical Review A},
-<
+  year = {1985},
-<
+  volume = {31},
-<
+  pages = {1695-1697},
-<
+  number = {3},
-<
+  annote = {Acr30 Times Cited:1809 Cited References Count:11},
-<
+  issn = {1050-2947},
-<
+  uri = {<Go to ISI>://A1985ACR3000056},
-<
+}
->
+@article{Hoover1985,
->
+        Annote = {Acr30 Times Cited:1809 Cited References Count:11},
->
+        Author = {W. G. Hoover},
->
+        Issn = {1050-2947},
->
+        Journal = {Physical Review A},
->
+        Number = {3},
->
+        Pages = {1695-1697},
->
+        Title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
->
+        Uri = {<Go to ISI>://A1985ACR3000056},
->
+        Volume = {31},
->
+        Year = {1985}}
-<
+@ARTICLE{Huh2004,
-<
+  author = {Y. Huh and N. M. Cann},
-<
+  title = {Discrimination in isotropic, nematic, and smectic phases of chiral
-<
+    calamitic molecules: A computer simulation study},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2004},
-<
+  volume = {121},
-<
+  pages = {10299-10308},
-<
+  number = {20},
-<
+  month = {Nov 22},
-<
+  abstract = {Racemic fluids of chiral calamitic molecules are investigated with
->
+@article{Huh2004,
->
+        Abstract = {Racemic fluids of chiral calamitic molecules are investigated with
+    molecular dynamics simulations. In particular, the phase behavior
+    as a function of density is examined for eight racemates. The relationship
+    between chiral discrimination and orientational order in the phase
+    Among ordered phases, discrimination is largest for smectic phases
+    with a significant preference for heterochiral contact within the
+    layers. (C) 2004 American Institute of Physics.},
-<
+  annote = {870FJ Times Cited:0 Cited References Count:63},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000225042700059},
-<
+}
->
+        Annote = {870FJ Times Cited:0 Cited References Count:63},
->
+        Author = {Y. Huh and N. M. Cann},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Nov 22},
->
+        Number = {20},
->
+        Pages = {10299-10308},
->
+        Title = {Discrimination in isotropic, nematic, and smectic phases of chiral calamitic molecules: A computer simulation study},
->
+        Uri = {<Go to ISI>://000225042700059},
->
+        Volume = {121},
->
+        Year = {2004}}
-<
+@ARTICLE{Humphrey1996,
-<
+  author = {W. Humphrey and A. Dalke and K. Schulten},
-<
+  title = {VMD: Visual molecular dynamics},
-<
+  journal = {Journal of Molecular Graphics},
-<
+  year = {1996},
-<
+  volume = {14},
-<
+  pages = {33-\&},
-<
+  number = {1},
-<
+  month = {Feb},
-<
+  abstract = {VMD is a molecular graphics program designed for the display and analysis
->
+@article{Humphrey1996,
->
+        Abstract = {VMD is a molecular graphics program designed for the display and analysis
+    of molecular assemblies, in particular biopolymers such as proteins
+    and nucleic acids. VMD can simultaneously display any number of
+    structures using a wide variety of rendering styles and coloring
+    using an object-oriented design; the program, including source code
+    and extensive documentation, is freely available via anonymous ftp
+    and through the World Wide Web.},
-<
+  annote = {Uh515 Times Cited:1418 Cited References Count:19},
-<
+  issn = {0263-7855},
-<
+  uri = {<Go to ISI>://A1996UH51500005},
-<
+}
->
+        Annote = {Uh515 Times Cited:1418 Cited References Count:19},
->
+        Author = {W. Humphrey and A. Dalke and K. Schulten},
->
+        Issn = {0263-7855},
->
+        Journal = {Journal of Molecular Graphics},
->
+        Month = {Feb},
->
+        Number = {1},
->
+        Pages = {33-\&},
->
+        Title = {VMD: Visual molecular dynamics},
->
+        Uri = {<Go to ISI>://A1996UH51500005},
->
+        Volume = {14},
->
+        Year = {1996}}
-<
+@ARTICLE{Izaguirre2001,
-<
+  author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
-<
+  title = {Langevin stabilization of molecular dynamics},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2001},
-<
+  volume = {114},
-<
+  pages = {2090-2098},
-<
+  number = {5},
-<
+  month = {Feb 1},
-<
+  abstract = {In this paper we show the possibility of using very mild stochastic
->
+@article{Izaguirre2001,
->
+        Abstract = {In this paper we show the possibility of using very mild stochastic
+    damping to stabilize long time step integrators for Newtonian molecular
+    dynamics. More specifically, stable and accurate integrations are
+    obtained for damping coefficients that are only a few percent of
+    of diffusion coefficients for flexible water and ER/ERE shows that
+    when mild damping of up to 0.2 ps-1 is used the dynamics are not
+    significantly distorted. (C) 2001 American Institute of Physics.},
-<
+  annote = {397CQ Times Cited:14 Cited References Count:36},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000166676100020},
-<
+}
->
+        Annote = {397CQ Times Cited:14 Cited References Count:36},
->
+        Author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Feb 1},
->
+        Number = {5},
->
+        Pages = {2090-2098},
->
+        Title = {Langevin stabilization of molecular dynamics},
->
+        Uri = {<Go to ISI>://000166676100020},
->
+        Volume = {114},
->
+        Year = {2001}}
-<
+@ARTICLE{Torre1977,
-<
+  author = {Jose Garcia De La Torre, V.A. Bloomfield},
-<
+  title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
-<
+  journal = {Biopolymers},
-<
+  year = {1977},
-<
+  volume = {16},
-<
+  pages = {1747-1763},
-<
+}
->
+@article{Torre1977,
->
+        Author = {Jose Garcia De La Torre, V.A. Bloomfield},
->
+        Journal = {Biopolymers},
->
+        Pages = {1747-1763},
->
+        Title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
->
+        Volume = {16},
->
+        Year = {1977}}
-<
+@ARTICLE{Kale1999,
-<
+  author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy
-<
+    and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan
-<
+    and K. Schulten},
-<
+  title = {NAMD2: Greater scalability for parallel molecular dynamics},
-<
+  journal = {Journal of Computational Physics},
-<
+  year = {1999},
-<
+  volume = {151},
-<
+  pages = {283-312},
-<
+  number = {1},
-<
+  month = {May 1},
-<
+  abstract = {Molecular dynamics programs simulate the behavior of biomolecular
->
+@article{Kale1999,
->
+        Abstract = {Molecular dynamics programs simulate the behavior of biomolecular
+    systems, leading to understanding of their functions. However, the
+    computational complexity of such simulations is enormous. Parallel
+    machines provide the potential to meet this computational challenge.
+    and has yielded speedups in excess of 180 on 220 processors. This
+    paper also describes the performance obtained on some benchmark
+    applications. (C) 1999 Academic Press.},
-<
+  annote = {194FM Times Cited:373 Cited References Count:51},
-<
+  issn = {0021-9991},
-<
+  uri = {<Go to ISI>://000080181500013},
-<
+}
->
+        Annote = {194FM Times Cited:373 Cited References Count:51},
->
+        Author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan and K. Schulten},
->
+        Issn = {0021-9991},
->
+        Journal = {Journal of Computational Physics},
->
+        Month = {May 1},
->
+        Number = {1},
->
+        Pages = {283-312},
->
+        Title = {NAMD2: Greater scalability for parallel molecular dynamics},
->
+        Uri = {<Go to ISI>://000080181500013},
->
+        Volume = {151},
->
+        Year = {1999}}
-<
+@ARTICLE{Kane2000,
-<
+  author = {C. Kane and J. E. Marsden and M. Ortiz and M. West},
-<
+  title = {Variational integrators and the Newmark algorithm for conservative
-<
+    and dissipative mechanical systems},
-<
+  journal = {International Journal for Numerical Methods in Engineering},
-<
+  year = {2000},
-<
+  volume = {49},
-<
+  pages = {1295-1325},
-<
+  number = {10},
-<
+  month = {Dec 10},
-<
+  abstract = {The purpose of this work is twofold. First, we demonstrate analytically
->
+@article{Kane2000,
->
+        Abstract = {The purpose of this work is twofold. First, we demonstrate analytically
+    that the classical Newmark family as well as related integration
+    algorithms are variational in the sense of the Veselov formulation
+    of discrete mechanics. Such variational algorithms are well known
+    in terms of obtaining the correct amounts by which the energy changes
+    over the integration run. Copyright (C) 2000 John Wiley & Sons,
+    Ltd.},
-<
+  annote = {373CJ Times Cited:30 Cited References Count:41},
-<
+  issn = {0029-5981},
-<
+  uri = {<Go to ISI>://000165270600004},
-<
+}
->
+        Annote = {373CJ Times Cited:30 Cited References Count:41},
->
+        Author = {C. Kane and J. E. Marsden and M. Ortiz and M. West},
->
+        Issn = {0029-5981},
->
+        Journal = {International Journal for Numerical Methods in Engineering},
->
+        Month = {Dec 10},
->
+        Number = {10},
->
+        Pages = {1295-1325},
->
+        Title = {Variational integrators and the Newmark algorithm for conservative and dissipative mechanical systems},
->
+        Uri = {<Go to ISI>://000165270600004},
->
+        Volume = {49},
->
+        Year = {2000}}
-<
+@ARTICLE{Klimov1997,
-<
+  author = {D. K. Klimov and D. Thirumalai},
-<
+  title = {Viscosity dependence of the folding rates of proteins},
-<
+  journal = {Physical Review Letters},
-<
+  year = {1997},
-<
+  volume = {79},
-<
+  pages = {317-320},
-<
+  number = {2},
-<
+  month = {Jul 14},
-<
+  abstract = {The viscosity (eta) dependence of the folding rates for four sequences
->
+@article{Klimov1997,
->
+        Abstract = {The viscosity (eta) dependence of the folding rates for four sequences
+    (the native state of three sequences is a beta sheet, while the
+    fourth forms an alpha helix) is calculated for off-lattice models
+    of proteins. Assuming that the dynamics is given by the Langevin
+    the simulation results to real proteins we estimate that for optimized
+    sequences the time scale for forming a four turn alpha-helix topology
+    is about 500 ns, whereas for beta sheet it is about 10 mu s.},
-<
+  annote = {Xk293 Times Cited:77 Cited References Count:17},
-<
+  issn = {0031-9007},
-<
+  uri = {<Go to ISI>://A1997XK29300035},
-<
+}
->
+        Annote = {Xk293 Times Cited:77 Cited References Count:17},
->
+        Author = {D. K. Klimov and D. Thirumalai},
->
+        Issn = {0031-9007},
->
+        Journal = {Physical Review Letters},
->
+        Month = {Jul 14},
->
+        Number = {2},
->
+        Pages = {317-320},
->
+        Title = {Viscosity dependence of the folding rates of proteins},
->
+        Uri = {<Go to ISI>://A1997XK29300035},
->
+        Volume = {79},
->
+        Year = {1997}}
-<
+@ARTICLE{Kol1997,
-<
+  author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
-<
+  title = {A symplectic method for rigid-body molecular simulation},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {1997},
-<
+  volume = {107},
-<
+  pages = {2580-2588},
-<
+  number = {7},
-<
+  month = {Aug 15},
-<
+  abstract = {Rigid-body molecular dynamics simulations typically are performed
->
+@article{Kol1997,
->
+        Abstract = {Rigid-body molecular dynamics simulations typically are performed
+    in a quaternion representation. The nonseparable form of the Hamiltonian
+    in quaternions prevents the use of a standard leapfrog (Verlet)
+    integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation
+    tolerance can be achieved by using a larger time step, The superiority
+    of RSHAKE increases with system size. (C) 1997 American Institute
+    of Physics.},
-<
+  annote = {Xq332 Times Cited:11 Cited References Count:18},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://A1997XQ33200046},
-<
+}
->
+        Annote = {Xq332 Times Cited:11 Cited References Count:18},
->
+        Author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Aug 15},
->
+        Number = {7},
->
+        Pages = {2580-2588},
->
+        Title = {A symplectic method for rigid-body molecular simulation},
->
+        Uri = {<Go to ISI>://A1997XQ33200046},
->
+        Volume = {107},
->
+        Year = {1997}}
-<
+@ARTICLE{Lansac2001,
-<
+  author = {Y. Lansac and M. A. Glaser and N. A. Clark},
-<
+  title = {Microscopic structure and dynamics of a partial bilayer smectic liquid
-<
+    crystal},
-<
+  journal = {Physical Review E},
-<
+  year = {2001},
-<
+  volume = {6405},
-<
+  pages = {-},
-<
+  number = {5},
-<
+  month = {Nov},
-<
+  abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
->
+@article{Lansac2001,
->
+        Abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
+    class of mesogens. Many of the peculiar properties of nCB's (e.g.,
+    the occurence of the partial bilayer smectic-A(d) phase) are thought
+    to be a manifestation of short-range antiparallel association of
+    antiparallel association of molecules arising from dipole-dipole
+    interactions plays a dominant role in determining the molecular-scale
+    structure of 8CB.},
-<
+  annote = {Part 1 496QF Times Cited:10 Cited References Count:60},
-<
+  issn = {1063-651X},
-<
+  uri = {<Go to ISI>://000172406900063},
-<
+}
->
+        Annote = {Part 1 496QF Times Cited:10 Cited References Count:60},
->
+        Author = {Y. Lansac and M. A. Glaser and N. A. Clark},
->
+        Issn = {1063-651X},
->
+        Journal = {Physical Review E},
->
+        Month = {Nov},
->
+        Number = {5},
->
+        Pages = {-},
->
+        Title = {Microscopic structure and dynamics of a partial bilayer smectic liquid crystal},
->
+        Uri = {<Go to ISI>://000172406900063},
->
+        Volume = {6405},
->
+        Year = {2001}}
-<
+@ARTICLE{Lansac2003,
-<
+  author = {Y. Lansac and P. K. Maiti and N. A. Clark and M. A. Glaser},
-<
+  title = {Phase behavior of bent-core molecules},
-<
+  journal = {Physical Review E},
-<
+  year = {2003},
-<
+  volume = {67},
-<
+  pages = {-},
-<
+  number = {1},
-<
+  month = {Jan},
-<
+  abstract = {Recently, a new class of smectic liquid crystal phases characterized
->
+@article{Lansac2003,
->
+        Abstract = {Recently, a new class of smectic liquid crystal phases characterized
+    by the spontaneous formation of macroscopic chiral domains from
+    achiral bent-core molecules has been discovered. We have carried
+    out Monte Carlo simulations of a minimal hard spherocylinder dimer
+    Free energy calculations indicate that the antipolar smectic A (SmAP(A))
+    phase is more stable than the polar smectic A phase (SmAP(F)). No
+    chiral smectic or biaxial nematic phases were found.},
-<
+  annote = {Part 1 646CM Times Cited:15 Cited References Count:38},
-<
+  issn = {1063-651X},
-<
+  uri = {<Go to ISI>://000181017300042},
-<
+}
->
+        Annote = {Part 1 646CM Times Cited:15 Cited References Count:38},
->
+        Author = {Y. Lansac and P. K. Maiti and N. A. Clark and M. A. Glaser},
->
+        Issn = {1063-651X},
->
+        Journal = {Physical Review E},
->
+        Month = {Jan},
->
+        Number = {1},
->
+        Pages = {-},
->
+        Title = {Phase behavior of bent-core molecules},
->
+        Uri = {<Go to ISI>://000181017300042},
->
+        Volume = {67},
->
+        Year = {2003}}
->
->
+@book{Leach2001,
->
+        Address = {Harlow, England},
->
+        Author = {A. Leach},
->
+        Edition = {2nd},
->
+        Publisher = {Pearson Educated Limited},
->
+        Title = {Molecular Modeling: Principles and Applications},
->
+        Year = {2001}}
->
->
+@article{Leimkuhler1999,
->
+        Abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
->
+    regularization and modified Sundman transformations are applied
->
+    to simulate general perturbed Kepler motion and to compute classical
->
+    trajectories of atomic systems (e.g. Rydberg atoms). The new family
->
+    of reversible adaptive regularization methods also conserves angular
->
+    momentum and exhibits superior energy conservation and numerical
->
+    stability in long-time integrations. The schemes are appropriate
->
+    for scattering, for astronomical calculations of escape time and
->
+    long-term stability, and for classical and semiclassical studies
->
+    of atomic dynamics. The components of an algorithm for trajectory
->
+    calculations are described. Numerical experiments illustrate the
->
+    effectiveness of the reversible approach.},
->
+        Annote = {199EE Times Cited:11 Cited References Count:48},
->
+        Author = {B. Leimkuhler},
->
+        Issn = {1364-503X},
->
+        Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
->
+        Month = {Apr 15},
->
+        Number = {1754},
->
+        Pages = {1101-1133},
->
+        Title = {Reversible adaptive regularization: perturbed Kepler motion and classical atomic trajectories},
->
+        Uri = {<Go to ISI>://000080466800007},
->
+        Volume = {357},
->
+        Year = {1999}}
->
->
+@book{Leimkuhler2004,
->
+        Address = {Cambridge},
->
+        Author = {B. Leimkuhler and S. Reich},
->
+        Publisher = {Cambridge University Press},
->
+        Title = {Simulating Hamiltonian Dynamics},
->
+        Year = {2004}}
->
->
+@article{Levelut1981,
->
+        Annote = {Ml751 Times Cited:96 Cited References Count:16},
->
+        Author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard and G. Sigaud},
->
+        Issn = {1050-2947},
->
+        Journal = {Physical Review A},
->
+        Number = {4},
->
+        Pages = {2180-2186},
->
+        Title = {Number of Sa Phases},
->
+        Uri = {<Go to ISI>://A1981ML75100057},
->
+        Volume = {24},
->
+        Year = {1981}}
->
->
+@article{Lieb1982,
->
+        Annote = {Nu461 Times Cited:40 Cited References Count:28},
->
+        Author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
->
+        Issn = {0006-3002},
->
+        Journal = {Biochimica Et Biophysica Acta},
->
+        Number = {2},
->
+        Pages = {388-398},
->
+        Title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - Evidence from Raman-Scattering},
->
+        Uri = {<Go to ISI>://A1982NU46100012},
->
+        Volume = {688},
->
+        Year = {1982}}
-<
+@BOOK{Leach2001,
-<
+  title = {Molecular Modeling: Principles and Applications},
-<
+  publisher = {Pearson Educated Limited},
-<
+  year = {2001},
-<
+  author = {A. Leach},
-<
+  address = {Harlow, England},
-<
+  edition = {2nd},
-<
+}
-<
-<
+@ARTICLE{Leimkuhler1999,
-<
+  author = {B. Leimkuhler},
-<
+  title = {Reversible adaptive regularization: perturbed Kepler motion and classical
-<
+    atomic trajectories},
-<
+  journal = {Philosophical Transactions of the Royal Society of London Series
-<
+    a-Mathematical Physical and Engineering Sciences},
-<
+  year = {1999},
-<
+  volume = {357},
-<
+  pages = {1101-1133},
-<
+  number = {1754},
-<
+  month = {Apr 15},
-<
+  abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
-<
+    regularization and modified Sundman transformations are applied
-<
+    to simulate general perturbed Kepler motion and to compute classical
-<
+    trajectories of atomic systems (e.g. Rydberg atoms). The new family
-<
+    of reversible adaptive regularization methods also conserves angular
-<
+    momentum and exhibits superior energy conservation and numerical
-<
+    stability in long-time integrations. The schemes are appropriate
-<
+    for scattering, for astronomical calculations of escape time and
-<
+    long-term stability, and for classical and semiclassical studies
-<
+    of atomic dynamics. The components of an algorithm for trajectory
-<
+    calculations are described. Numerical experiments illustrate the
-<
+    effectiveness of the reversible approach.},
-<
+  annote = {199EE Times Cited:11 Cited References Count:48},
-<
+  issn = {1364-503X},
-<
+  uri = {<Go to ISI>://000080466800007},
-<
+}
-<
-<
+@BOOK{Leimkuhler2004,
-<
+  title = {Simulating Hamiltonian Dynamics},
-<
+  publisher = {Cambridge University Press},
-<
+  year = {2004},
-<
+  author = {B. Leimkuhler and S. Reich},
-<
+  address = {Cambridge},
-<
+}
-<
-<
+@ARTICLE{Levelut1981,
-<
+  author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard
-<
+    and G. Sigaud},
-<
+  title = {Number of Sa Phases},
-<
+  journal = {Physical Review A},
-<
+  year = {1981},
-<
+  volume = {24},
-<
+  pages = {2180-2186},
-<
+  number = {4},
-<
+  annote = {Ml751 Times Cited:96 Cited References Count:16},
-<
+  issn = {1050-2947},
-<
+  uri = {<Go to ISI>://A1981ML75100057},
-<
+}
-<
-<
+@ARTICLE{Lieb1982,
-<
+  author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
-<
+  title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers -
-<
+    Evidence from Raman-Scattering},
-<
+  journal = {Biochimica Et Biophysica Acta},
-<
+  year = {1982},
-<
+  volume = {688},
-<
+  pages = {388-398},
-<
+  number = {2},
-<
+  annote = {Nu461 Times Cited:40 Cited References Count:28},
-<
+  issn = {0006-3002},
-<
+  uri = {<Go to ISI>://A1982NU46100012},
-<
+}
-<
-<
+@ARTICLE{Link1997,
-<
+  author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A.
-<
+    Clark and E. Korblova and D. M. Walba},
-<
+  title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic
-<
+    phase of achiral molecules},
-<
+  journal = {Science},
-<
+  year = {1997},
-<
+  volume = {278},
-<
+  pages = {1924-1927},
-<
+  number = {5345},
-<
+  month = {Dec 12},
-<
+  abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
->
+@article{Link1997,
->
+        Abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
+    cores was found to have fluid layers that exhibit two spontaneous
+    symmetry-breaking instabilities: polar molecular orientational ordering
+    about the layer normal and molecular tilt. These instabilities combine
+    from layer to layer, or antiferroelectric-chiral, which is of uniform
+    layer handedness. Both states exhibit an electric field-induced
+    transition from antiferroelectric to ferroelectric.},
-<
+  annote = {Yl002 Times Cited:407 Cited References Count:25},
-<
+  issn = {0036-8075},
-<
+  uri = {<Go to ISI>://A1997YL00200028},
-<
+}
->
+        Annote = {Yl002 Times Cited:407 Cited References Count:25},
->
+        Author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A. Clark and E. Korblova and D. M. Walba},
->
+        Issn = {0036-8075},
->
+        Journal = {Science},
->
+        Month = {Dec 12},
->
+        Number = {5345},
->
+        Pages = {1924-1927},
->
+        Title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic phase of achiral molecules},
->
+        Uri = {<Go to ISI>://A1997YL00200028},
->
+        Volume = {278},
->
+        Year = {1997}}
-<
+@ARTICLE{Liwo2005,
-<
+  author = {A. Liwo and M. Khalili and H. A. Scheraga},
-<
+  title = {Ab initio simulations of protein folding pathways by molecular dynamics
-<
+    with the united-residue (UNRES) model of polypeptide chains},
-<
+  journal = {Febs Journal},
-<
+  year = {2005},
-<
+  volume = {272},
-<
+  pages = {359-360},
-<
+  month = {Jul},
-<
+  annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
-<
+  issn = {1742-464X},
-<
+  uri = {<Go to ISI>://000234826102043},
-<
+}
->
+@article{Liwo2005,
->
+        Annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
->
+        Author = {A. Liwo and M. Khalili and H. A. Scheraga},
->
+        Issn = {1742-464X},
->
+        Journal = {Febs Journal},
->
+        Month = {Jul},
->
+        Pages = {359-360},
->
+        Title = {Ab initio simulations of protein folding pathways by molecular dynamics with the united-residue (UNRES) model of polypeptide chains},
->
+        Uri = {<Go to ISI>://000234826102043},
->
+        Volume = {272},
->
+        Year = {2005}}
-<
+@ARTICLE{Luty1994,
-<
+  author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
-<
+  title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods
-<
+    for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
-<
+  journal = {Molecular Simulation},
-<
+  year = {1994},
-<
+  volume = {14},
-<
+  pages = {11-20},
-<
+  number = {1},
-<
+  abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
->
+@article{Luty1994,
->
+        Abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
+    for calculating electrostatic interactions in periodic molecular
+    systems. A brief comparison of the theories shows that the methods
+    are very similar differing mainly in the technique which is used
+    utilizes the highly efficient numerical Fast Fourier Transform (FFT)
+    method it requires significantly less computational effort than
+    the Ewald method and scale's almost linearly with system size.},
-<
+  annote = {Qf464 Times Cited:50 Cited References Count:20},
-<
+  issn = {0892-7022},
-<
+  uri = {<Go to ISI>://A1994QF46400002},
-<
+}
->
+        Annote = {Qf464 Times Cited:50 Cited References Count:20},
->
+        Author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
->
+        Issn = {0892-7022},
->
+        Journal = {Molecular Simulation},
->
+        Number = {1},
->
+        Pages = {11-20},
->
+        Title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
->
+        Uri = {<Go to ISI>://A1994QF46400002},
->
+        Volume = {14},
->
+        Year = {1994}}
-<
+@BOOK{Marion1990,
-<
+  title = {Classical Dynamics of Particles and Systems},
-<
+  publisher = {Academic Press},
-<
+  year = {1990},
-<
+  author = {J.~B. Marion},
-<
+  address = {New York},
-<
+  edition = {2rd},
-<
+}
->
+@book{Marion1990,
->
+        Address = {New York},
->
+        Author = {J.~B. Marion},
->
+        Edition = {2rd},
->
+        Publisher = {Academic Press},
->
+        Title = {Classical Dynamics of Particles and Systems},
->
+        Year = {1990}}
-<
+@ARTICLE{Marrink1994,
-<
+  author = {S. J. Marrink and H. J. C. Berendsen},
-<
+  title = {Simulation of Water Transport through a Lipid-Membrane},
-<
+  journal = {Journal of Physical Chemistry},
-<
+  year = {1994},
-<
+  volume = {98},
-<
+  pages = {4155-4168},
-<
+  number = {15},
-<
+  month = {Apr 14},
-<
+  abstract = {To obtain insight in the process of water permeation through a lipid
->
+@article{Marrink1994,
->
+        Abstract = {To obtain insight in the process of water permeation through a lipid
+    membrane, we performed molecular dynamics simulations on a phospholipid
+    (DPPC)/water system with atomic detail. Since the actual process
+    of permeation is too slow to be studied directly, we deduced the
+    the inhomogeneity of the membrane into account, we define a new
+    ''four-region'' model which seems to be more realistic than the
+    ''two-phase'' solubility-diffusion model.},
-<
+  annote = {Ng219 Times Cited:187 Cited References Count:25},
-<
+  issn = {0022-3654},
-<
+  uri = {<Go to ISI>://A1994NG21900040},
-<
+}
->
+        Annote = {Ng219 Times Cited:187 Cited References Count:25},
->
+        Author = {S. J. Marrink and H. J. C. Berendsen},
->
+        Issn = {0022-3654},
->
+        Journal = {Journal of Physical Chemistry},
->
+        Month = {Apr 14},
->
+        Number = {15},
->
+        Pages = {4155-4168},
->
+        Title = {Simulation of Water Transport through a Lipid-Membrane},
->
+        Uri = {<Go to ISI>://A1994NG21900040},
->
+        Volume = {98},
->
+        Year = {1994}}
-<
+@ARTICLE{Marrink2004,
-<
+  author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
-<
+  title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
-<
+  journal = {J. Phys. Chem. B},
-<
+  year = {2004},
-<
+  volume = {108},
-<
+  pages = {750-760},
-<
+}
->
+@article{Marrink2004,
->
+        Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
->
+        Journal = {J. Phys. Chem. B},
->
+        Pages = {750-760},
->
+        Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
->
+        Volume = {108},
->
+        Year = {2004}}
-<
+@ARTICLE{Marsden1998,
-<
+  author = {J. E. Marsden and G. W. Patrick and S. Shkoller},
-<
+  title = {Multisymplectic geometry, variational integrators, and nonlinear
-<
+    PDEs},
-<
+  journal = {Communications in Mathematical Physics},
-<
+  year = {1998},
-<
+  volume = {199},
-<
+  pages = {351-395},
-<
+  number = {2},
-<
+  month = {Dec},
-<
+  abstract = {This paper presents a geometric-variational approach to continuous
->
+@article{Marsden1998,
->
+        Abstract = {This paper presents a geometric-variational approach to continuous
+    and discrete mechanics and field theories. Using multisymplectic
+    geometry, we show that the existence of the fundamental geometric
+    structures as well as their preservation along solutions can be
+    All of the aspects of our method are demonstrated with a nonlinear
+    sine-Gordon equation, including computational results and a comparison
+    with other discretization schemes.},
-<
+  annote = {154RH Times Cited:88 Cited References Count:36},
-<
+  issn = {0010-3616},
-<
+  uri = {<Go to ISI>://000077902200006},
-<
+}
->
+        Annote = {154RH Times Cited:88 Cited References Count:36},
->
+        Author = {J. E. Marsden and G. W. Patrick and S. Shkoller},
->
+        Issn = {0010-3616},
->
+        Journal = {Communications in Mathematical Physics},
->
+        Month = {Dec},
->
+        Number = {2},
->
+        Pages = {351-395},
->
+        Title = {Multisymplectic geometry, variational integrators, and nonlinear PDEs},
->
+        Uri = {<Go to ISI>://000077902200006},
->
+        Volume = {199},
->
+        Year = {1998}}
-<
+@ARTICLE{Matthey2004,
-<
+  author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and
-<
+    M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre},
-<
+  title = {ProtoMol, an object-oriented framework for prototyping novel algorithms
-<
+    for molecular dynamics},
-<
+  journal = {Acm Transactions on Mathematical Software},
-<
+  year = {2004},
-<
+  volume = {30},
-<
+  pages = {237-265},
-<
+  number = {3},
-<
+  month = {Sep},
-<
+  abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
->
+@article{Matthey2004,
->
+        Abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
+    of novel algorithms for molecular dynamics and related applications.
+    Its flexibility is achieved primarily through the use of inheritance
+    and design patterns (object-oriented programming): Performance is
+    of processors. Binaries and source codes for Windows, Linux, Solaris,
+    IRIX, HP-UX, and AIX platforms are available under open source license
+    at http://protomol.sourceforge.net.},
-<
+  annote = {860EP Times Cited:2 Cited References Count:52},
-<
+  issn = {0098-3500},
-<
+  uri = {<Go to ISI>://000224325600001},
-<
+}
->
+        Annote = {860EP Times Cited:2 Cited References Count:52},
->
+        Author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre},
->
+        Issn = {0098-3500},
->
+        Journal = {Acm Transactions on Mathematical Software},
->
+        Month = {Sep},
->
+        Number = {3},
->
+        Pages = {237-265},
->
+        Title = {ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics},
->
+        Uri = {<Go to ISI>://000224325600001},
->
+        Volume = {30},
->
+        Year = {2004}}
-<
+@ARTICLE{McLachlan1993,
-<
+  author = {R.~I McLachlan},
-<
+  title = {Explicit Lie-Poisson integration and the Euler equations},
-<
+  journal = {prl},
-<
+  year = {1993},
-<
+  volume = {71},
-<
+  pages = {3043-3046},
-<
+}
->
+@article{McLachlan1993,
->
+        Author = {R.~I McLachlan},
->
+        Journal = {prl},
->
+        Pages = {3043-3046},
->
+        Title = {Explicit Lie-Poisson integration and the Euler equations},
->
+        Volume = {71},
->
+        Year = {1993}}
-<
+@ARTICLE{McLachlan1998,
-<
+  author = {R. I. McLachlan and G. R. W. Quispel},
-<
+  title = {Generating functions for dynamical systems with symmetries, integrals,
-<
+    and differential invariants},
-<
+  journal = {Physica D},
-<
+  year = {1998},
-<
+  volume = {112},
-<
+  pages = {298-309},
-<
+  number = {1-2},
-<
+  month = {Jan 15},
-<
+  abstract = {We give a survey and some new examples of generating functions for
->
+@article{McLachlan1998,
->
+        Abstract = {We give a survey and some new examples of generating functions for
+    systems with symplectic structure, systems with a first integral,
+    systems that preserve volume, and systems with symmetries and/or
+    time-reversing symmetries. Both ODEs and maps are treated, and we
+    discuss how generating functions may be used in the structure-preserving
+    numerical integration of ODEs with the above properties.},
-<
+  annote = {Yt049 Times Cited:7 Cited References Count:26},
-<
+  issn = {0167-2789},
-<
+  uri = {<Go to ISI>://000071558900021},
-<
+}
->
+        Annote = {Yt049 Times Cited:7 Cited References Count:26},
->
+        Author = {R. I. McLachlan and G. R. W. Quispel},
->
+        Issn = {0167-2789},
->
+        Journal = {Physica D},
->
+        Month = {Jan 15},
->
+        Number = {1-2},
->
+        Pages = {298-309},
->
+        Title = {Generating functions for dynamical systems with symmetries, integrals, and differential invariants},
->
+        Uri = {<Go to ISI>://000071558900021},
->
+        Volume = {112},
->
+        Year = {1998}}
-<
+@ARTICLE{McLachlan1998a,
-<
+  author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner},
-<
+  title = {Numerical integrators that preserve symmetries and reversing symmetries},
-<
+  journal = {Siam Journal on Numerical Analysis},
-<
+  year = {1998},
-<
+  volume = {35},
-<
+  pages = {586-599},
-<
+  number = {2},
-<
+  month = {Apr},
-<
+  abstract = {We consider properties of flows, the relationships between them, and
->
+@article{McLachlan1998a,
->
+        Abstract = {We consider properties of flows, the relationships between them, and
+    whether numerical integrators can be made to preserve these properties.
+    This is done in the context of automorphisms and antiautomorphisms
+    of a certain group generated by maps associated to vector fields.
+    to a group of coordinate transformations. The main application is
+    to explore the relationship between spatial symmetries, reversing
+    symmetries, and time symmetry of flows and numerical integrators.},
-<
+  annote = {Zc449 Times Cited:14 Cited References Count:33},
-<
+  issn = {0036-1429},
-<
+  uri = {<Go to ISI>://000072580500010},
-<
+}
->
+        Annote = {Zc449 Times Cited:14 Cited References Count:33},
->
+        Author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner},
->
+        Issn = {0036-1429},
->
+        Journal = {Siam Journal on Numerical Analysis},
->
+        Month = {Apr},
->
+        Number = {2},
->
+        Pages = {586-599},
->
+        Title = {Numerical integrators that preserve symmetries and reversing symmetries},
->
+        Uri = {<Go to ISI>://000072580500010},
->
+        Volume = {35},
->
+        Year = {1998}}
-<
+@ARTICLE{McLachlan2005,
-<
+  author = {R. I. McLachlan and A. Zanna},
-<
+  title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
-<
+  journal = {Foundations of Computational Mathematics},
-<
+  year = {2005},
-<
+  volume = {5},
-<
+  pages = {87-123},
-<
+  number = {1},
-<
+  month = {Feb},
-<
+  abstract = {In this paper we revisit the Moser-Veselov description of the free
->
+@article{McLachlan2005,
->
+        Abstract = {In this paper we revisit the Moser-Veselov description of the free
+    rigid body in body coordinates, which, in the 3 x 3 case, can be
+    implemented as an explicit, second-order, integrable approximation
+    of the continuous solution. By backward error analysis, we study
+    algorithm. Numerical integration with these preprocessed initial
+    data is several orders of magnitude more accurate than the original
+    DMV and RATTLE approach.},
-<
+  annote = {911NS Times Cited:0 Cited References Count:14},
-<
+  issn = {1615-3375},
-<
+  uri = {<Go to ISI>://000228011900003},
-<
+}
->
+        Annote = {911NS Times Cited:0 Cited References Count:14},
->
+        Author = {R. I. McLachlan and A. Zanna},
->
+        Issn = {1615-3375},
->
+        Journal = {Foundations of Computational Mathematics},
->
+        Month = {Feb},
->
+        Number = {1},
->
+        Pages = {87-123},
->
+        Title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
->
+        Uri = {<Go to ISI>://000228011900003},
->
+        Volume = {5},
->
+        Year = {2005}}
-<
+@ARTICLE{Meineke2005,
-<
+  author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and
-<
+    J. D. Gezelter},
-<
+  title = {OOPSE: An object-oriented parallel simulation engine for molecular
-<
+    dynamics},
-<
+  journal = {Journal of Computational Chemistry},
-<
+  year = {2005},
-<
+  volume = {26},
-<
+  pages = {252-271},
-<
+  number = {3},
-<
+  month = {Feb},
-<
+  abstract = {OOPSE is a new molecular dynamics simulation program that is capable
->
+@article{Meineke2005,
->
+        Abstract = {OOPSE is a new molecular dynamics simulation program that is capable
+    of efficiently integrating equations of motion for atom types with
+    orientational degrees of freedom (e.g. #sticky# atoms and point
+    dipoles). Transition metals can also be simulated using the embedded
+    number of advanced integrators are included, and the basic integrator
+    for orientational dynamics provides substantial improvements over
+    older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.},
-<
+  annote = {891CF Times Cited:1 Cited References Count:56},
-<
+  issn = {0192-8651},
-<
+  uri = {<Go to ISI>://000226558200006},
-<
+}
->
+        Annote = {891CF Times Cited:1 Cited References Count:56},
->
+        Author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and J. D. Gezelter},
->
+        Issn = {0192-8651},
->
+        Journal = {Journal of Computational Chemistry},
->
+        Month = {Feb},
->
+        Number = {3},
->
+        Pages = {252-271},
->
+        Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
->
+        Uri = {<Go to ISI>://000226558200006},
->
+        Volume = {26},
->
+        Year = {2005}}
-<
+@ARTICLE{Melchionna1993,
-<
+  author = {S. Melchionna and G. Ciccotti and B. L. Holian},
-<
+  title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
-<
+  journal = {Molecular Physics},
-<
+  year = {1993},
-<
+  volume = {78},
-<
+  pages = {533-544},
-<
+  number = {3},
-<
+  month = {Feb 20},
-<
+  abstract = {In this paper we write down equations of motion (following the approach
->
+@article{Melchionna1993,
->
+        Abstract = {In this paper we write down equations of motion (following the approach
+    pioneered by Hoover) for an exact isothermal-isobaric molecular
+    dynamics simulation, and we extend them to multiple thermostating
+    rates, to a shape-varying cell and to molecular systems, coherently
+    with the previous 'extended system method'. An integration scheme
+    is proposed together with a numerical illustration of the method.},
-<
+  annote = {Kq355 Times Cited:172 Cited References Count:17},
-<
+  issn = {0026-8976},
-<
+  uri = {<Go to ISI>://A1993KQ35500002},
-<
+}
->
+        Annote = {Kq355 Times Cited:172 Cited References Count:17},
->
+        Author = {S. Melchionna and G. Ciccotti and B. L. Holian},
->
+        Issn = {0026-8976},
->
+        Journal = {Molecular Physics},
->
+        Month = {Feb 20},
->
+        Number = {3},
->
+        Pages = {533-544},
->
+        Title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
->
+        Uri = {<Go to ISI>://A1993KQ35500002},
->
+        Volume = {78},
->
+        Year = {1993}}
-<
+@ARTICLE{Memmer2002,
-<
+  author = {R. Memmer},
-<
+  title = {Liquid crystal phases of achiral banana-shaped molecules: a computer
-<
+    simulation study},
-<
+  journal = {Liquid Crystals},
-<
+  year = {2002},
-<
+  volume = {29},
-<
+  pages = {483-496},
-<
+  number = {4},
-<
+  month = {Apr},
-<
+  abstract = {The phase behaviour of achiral banana-shaped molecules was studied
->
+@article{Memmer2002,
->
+        Abstract = {The phase behaviour of achiral banana-shaped molecules was studied
+    by computer simulation. The banana-shaped molecules were described
+    by model intermolecular interactions based on the Gay-Berne potential.
+    The characteristic molecular structure was considered by joining
+    phases have been characterized by visual representations of selected
+    configurations, scalar and pseudoscalar correlation functions, and
+    order parameters.},
-<
+  annote = {531HT Times Cited:12 Cited References Count:37},
-<
+  issn = {0267-8292},
-<
+  uri = {<Go to ISI>://000174410500001},
-<
+}
->
+        Annote = {531HT Times Cited:12 Cited References Count:37},
->
+        Author = {R. Memmer},
->
+        Issn = {0267-8292},
->
+        Journal = {Liquid Crystals},
->
+        Month = {Apr},
->
+        Number = {4},
->
+        Pages = {483-496},
->
+        Title = {Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study},
->
+        Uri = {<Go to ISI>://000174410500001},
->
+        Volume = {29},
->
+        Year = {2002}}
-<
+@ARTICLE{Metropolis1949,
-<
+  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{Metropolis1949,
->
+        Author = {N. Metropolis and S. Ulam},
->
+        Journal = {J. Am. Stat. Ass.},
->
+        Pages = {335-341},
->
+        Title = {The $\mbox{Monte Carlo}$ Method},
->
+        Volume = {44},
->
+        Year = {1949}}
-<
+@ARTICLE{Mielke2004,
-<
+  author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen
-<
+    and C. J. Benham},
-<
+  title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian
-<
+    dynamics study},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2004},
-<
+  volume = {121},
-<
+  pages = {8104-8112},
-<
+  number = {16},
-<
+  month = {Oct 22},
-<
+  abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
->
+@article{Mielke2004,
->
+        Abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
+    DNA can potentially induce long-range structural deformations integral
+    to mechanisms of biological significance in both prokaryotes and
+    eukaryotes. In this paper, we introduce a dynamic computer model
+    agree well with predictions from theory, and the generated stress
+    is ample for driving secondary structural transitions in physiological
+    DNA. (C) 2004 American Institute of Physics.},
-<
+  annote = {861ZF Times Cited:3 Cited References Count:34},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000224456500064},
-<
+}
->
+        Annote = {861ZF Times Cited:3 Cited References Count:34},
->
+        Author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen and C. J. Benham},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Oct 22},
->
+        Number = {16},
->
+        Pages = {8104-8112},
->
+        Title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study},
->
+        Uri = {<Go to ISI>://000224456500064},
->
+        Volume = {121},
->
+        Year = {2004}}
-<
+@ARTICLE{Naess2001,
-<
+  author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter},
-<
+  title = {Brownian dynamics simulation of rigid bodies and segmented polymer
-<
+    chains. Use of Cartesian rotation vectors as the generalized coordinates
-<
+    describing angular orientations},
-<
+  journal = {Physica A},
-<
+  year = {2001},
-<
+  volume = {294},
-<
+  pages = {323-339},
-<
+  number = {3-4},
-<
+  month = {May 15},
-<
+  abstract = {The three Eulerian angles constitute the classical choice of generalized
->
+@article{Naess2001,
->
+        Abstract = {The three Eulerian angles constitute the classical choice of generalized
+    coordinates used to describe the three degrees of rotational freedom
+    of a rigid body, but it has long been known that this choice yields
+    singular equations of motion. The latter is also true when Eulerian
+    The suitability of Cartesian rotation vectors in Brownian dynamics
+    simulations of segmented polymer chains with spring-like or ball-socket
+    joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.},
-<
+  annote = {433TA Times Cited:7 Cited References Count:19},
-<
+  issn = {0378-4371},
-<
+  uri = {<Go to ISI>://000168774800005},
-<
+}
->
+        Annote = {433TA Times Cited:7 Cited References Count:19},
->
+        Author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter},
->
+        Issn = {0378-4371},
->
+        Journal = {Physica A},
->
+        Month = {May 15},
->
+        Number = {3-4},
->
+        Pages = {323-339},
->
+        Title = {Brownian dynamics simulation of rigid bodies and segmented polymer chains. Use of Cartesian rotation vectors as the generalized coordinates describing angular orientations},
->
+        Uri = {<Go to ISI>://000168774800005},
->
+        Volume = {294},
->
+        Year = {2001}}
-<
+@ARTICLE{Niori1996,
-<
+  author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe},
-<
+  title = {Distinct ferroelectric smectic liquid crystals consisting of banana
-<
+    shaped achiral molecules},
-<
+  journal = {Journal of Materials Chemistry},
-<
+  year = {1996},
-<
+  volume = {6},
-<
+  pages = {1231-1233},
-<
+  number = {7},
-<
+  month = {Jul},
-<
+  abstract = {The synthesis of a banana-shaped molecule is reported and it is found
->
+@article{Niori1996,
->
+        Abstract = {The synthesis of a banana-shaped molecule is reported and it is found
+    that the smectic phase which it forms is biaxial with the molecules
+    packed in the best,direction into a layer. Because of this characteristic
+    packing, spontaneous polarization appears parallel to the layer
+    and switches on reversal of an applied electric field. This is the
+    first obvious example of ferroelectricity in an achiral smectic
+    phase and is ascribed to the C-2v symmetry of the molecular packing.},
-<
+  annote = {Ux855 Times Cited:447 Cited References Count:18},
-<
+  issn = {0959-9428},
-<
+  uri = {<Go to ISI>://A1996UX85500025},
-<
+}
->
+        Annote = {Ux855 Times Cited:447 Cited References Count:18},
->
+        Author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe},
->
+        Issn = {0959-9428},
->
+        Journal = {Journal of Materials Chemistry},
->
+        Month = {Jul},
->
+        Number = {7},
->
+        Pages = {1231-1233},
->
+        Title = {Distinct ferroelectric smectic liquid crystals consisting of banana shaped achiral molecules},
->
+        Uri = {<Go to ISI>://A1996UX85500025},
->
+        Volume = {6},
->
+        Year = {1996}}
-<
+@ARTICLE{Noguchi2002,
-<
+  author = {H. Noguchi and M. Takasu},
-<
+  title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
-<
+  journal = {Physical Review E},
-<
+  year = {2002},
-<
+  volume = {65},
-<
+  pages = {-},
-<
+  number = {5},
-<
+  month = {may},
-<
+  abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
->
+@article{Noguchi2002,
->
+        Abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
+    forces using a Brownian dynamics simulation. Two nanoparticles,
+    which interact repulsively with amphiphilic molecules, are put inside
+    a vesicle. The position of one nanoparticle is fixed, and the other
+    after this the cylindrical region shrinks. The trapping force similar
+    to 100 pN is needed to induce the formation of the cylindrical structure
+    and fission.},
-<
+  annote = {Part 1 568PX Times Cited:5 Cited References Count:39},
-<
+  issn = {1063-651X},
-<
+  uri = {<Go to ISI>://000176552300084},
-<
+}
->
+        Annote = {Part 1 568PX Times Cited:5 Cited References Count:39},
->
+        Author = {H. Noguchi and M. Takasu},
->
+        Issn = {1063-651X},
->
+        Journal = {Physical Review E},
->
+        Month = {may},
->
+        Number = {5},
->
+        Pages = {-},
->
+        Title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
->
+        Uri = {<Go to ISI>://000176552300084},
->
+        Volume = {65},
->
+        Year = {2002}}
-<
+@ARTICLE{Noguchi2001,
-<
+  author = {H. Noguchi and M. Takasu},
-<
+  title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2001},
-<
+  volume = {115},
-<
+  pages = {9547-9551},
-<
+  number = {20},
-<
+  month = {Nov 22},
-<
+  abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
->
+@article{Noguchi2001,
->
+        Abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
+    simulation. Amphiphilic molecules spontaneously form vesicles with
+    a bilayer structure. Two vesicles come into contact and form a stalk
+    intermediate, in which a necklike structure only connects the outer
+    that the pore-opening process at low temperature agrees with the
+    modified stalk model: a pore is induced by contact between the inner
+    monolayers inside the stalk. (C) 2001 American Institute of Physics.},
-<
+  annote = {491UW Times Cited:48 Cited References Count:25},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000172129300049},
-<
+}
->
+        Annote = {491UW Times Cited:48 Cited References Count:25},
->
+        Author = {H. Noguchi and M. Takasu},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Nov 22},
->
+        Number = {20},
->
+        Pages = {9547-9551},
->
+        Title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
->
+        Uri = {<Go to ISI>://000172129300049},
->
+        Volume = {115},
->
+        Year = {2001}}
-<
+@BOOK{Olver1986,
-<
+  title = {Applications of Lie groups to differential equatitons},
-<
+  publisher = {Springer},
-<
+  year = {1986},
-<
+  author = {P.J. Olver},
-<
+  address = {New York},
-<
+}
->
+@book{Olver1986,
->
+        Address = {New York},
->
+        Author = {P.J. Olver},
->
+        Publisher = {Springer},
->
+        Title = {Applications of Lie groups to differential equatitons},
->
+        Year = {1986}}
-<
+@ARTICLE{Omelyan1998,
-<
+  author = {I. P. Omelyan},
-<
+  title = {On the numerical integration of motion for rigid polyatomics: The
-<
+    modified quaternion approach},
-<
+  journal = {Computers in Physics},
-<
+  year = {1998},
-<
+  volume = {12},
-<
+  pages = {97-103},
-<
+  number = {1},
-<
+  month = {Jan-Feb},
-<
+  abstract = {A revised version of the quaternion approach for numerical integration
->
+@article{Omelyan1998,
->
+        Abstract = {A revised version of the quaternion approach for numerical integration
+    of the equations of motion for rigid polyatomic molecules is proposed.
+    The modified approach is based on a formulation of the quaternion
+    dynamics with constraints. This allows one to resolve the rigidity
+    stability with respect to the usual quaternion rescaling scheme
+    and it is roughly as good as the cumbersome atomic-constraint technique.
+    (C) 1998 American Institute of Physics.},
-<
+  annote = {Yx279 Times Cited:12 Cited References Count:28},
-<
+  issn = {0894-1866},
-<
+  uri = {<Go to ISI>://000072024300025},
-<
+}
->
+        Annote = {Yx279 Times Cited:12 Cited References Count:28},
->
+        Author = {I. P. Omelyan},
->
+        Issn = {0894-1866},
->
+        Journal = {Computers in Physics},
->
+        Month = {Jan-Feb},
->
+        Number = {1},
->
+        Pages = {97-103},
->
+        Title = {On the numerical integration of motion for rigid polyatomics: The modified quaternion approach},
->
+        Uri = {<Go to ISI>://000072024300025},
->
+        Volume = {12},
->
+        Year = {1998}}
-<
+@ARTICLE{Omelyan1998a,
-<
+  author = {I. P. Omelyan},
-<
+  title = {Algorithm for numerical integration of the rigid-body equations of
-<
+    motion},
-<
+  journal = {Physical Review E},
-<
+  year = {1998},
-<
+  volume = {58},
-<
+  pages = {1169-1172},
-<
+  number = {1},
-<
+  month = {Jul},
-<
+  abstract = {An algorithm for numerical integration of the rigid-body equations
->
+@article{Omelyan1998a,
->
+        Abstract = {An algorithm for numerical integration of the rigid-body equations
+    of motion is proposed. The algorithm uses the leapfrog scheme and
+    the quantities involved are angular velocities and orientational
+    variables that can be expressed in terms of either principal axes
+    despite an approximate character of the produced trajectories. It
+    is shown that the method presented appears to be the most efficient
+    among all such algorithms known.},
-<
+  annote = {101XL Times Cited:8 Cited References Count:22},
-<
+  issn = {1063-651X},
-<
+  uri = {<Go to ISI>://000074893400151},
-<
+}
->
+        Annote = {101XL Times Cited:8 Cited References Count:22},
->
+        Author = {I. P. Omelyan},
->
+        Issn = {1063-651X},
->
+        Journal = {Physical Review E},
->
+        Month = {Jul},
->
+        Number = {1},
->
+        Pages = {1169-1172},
->
+        Title = {Algorithm for numerical integration of the rigid-body equations of motion},
->
+        Uri = {<Go to ISI>://000074893400151},
->
+        Volume = {58},
->
+        Year = {1998}}
-<
+@ARTICLE{Orlandi2006,
-<
+  author = {S. Orlandi and R. Berardi and J. Steltzer and C. Zannoni},
-<
+  title = {A Monte Carlo study of the mesophases formed by polar bent-shaped
-<
+    molecules},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2006},
-<
+  volume = {124},
-<
+  pages = {-},
-<
+  number = {12},
-<
+  month = {Mar 28},
-<
+  abstract = {Liquid crystal phases formed by bent-shaped (or #banana#) molecules
-<
+    are currently of great interest. Here we investigate by Monte Carlo
-<
+    computer simulations the phases formed by rigid banana molecules
-<
+    modeled combining three Gay-Berne sites and containing either one
-<
+    central or two lateral and transversal dipoles. We show that changing
-<
+    the dipole position and orientation has a profound effect on the
-<
+    mesophase stability and molecular organization. In particular, we
-<
+    find a uniaxial nematic phase only for off-center dipolar models
-<
+    and tilted phases only for the one with terminal dipoles. (c) 2006
-<
+    American Institute of Physics.},
-<
+  annote = {028CP Times Cited:0 Cited References Count:42},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000236464000072},
-<
+}
-<
-<
+@ARTICLE{Owren1992,
-<
+  author = {B. Owren and M. Zennaro},
-<
+  title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
-<
+  journal = {Siam Journal on Scientific and Statistical Computing},
-<
+  year = {1992},
-<
+  volume = {13},
-<
+  pages = {1488-1501},
-<
+  number = {6},
-<
+  month = {Nov},
-<
+  abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
->
+@article{Owren1992,
->
+        Abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
+    stages are considered. These methods are continuously differentiable
+    if and only if one of the stages is the FSAL evaluation. A characterization
+    of a subclass of these methods is developed for orders 3, 4, and
+    implementation of the Dormand-Prince 5(4) pair with interpolant,
+    showing a significant advantage in the new method for the chosen
+    problems.},
-<
+  annote = {Ju936 Times Cited:25 Cited References Count:20},
-<
+  issn = {0196-5204},
-<
+  uri = {<Go to ISI>://A1992JU93600013},
-<
+}
->
+        Annote = {Ju936 Times Cited:25 Cited References Count:20},
->
+        Author = {B. Owren and M. Zennaro},
->
+        Issn = {0196-5204},
->
+        Journal = {Siam Journal on Scientific and Statistical Computing},
->
+        Month = {Nov},
->
+        Number = {6},
->
+        Pages = {1488-1501},
->
+        Title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
->
+        Uri = {<Go to ISI>://A1992JU93600013},
->
+        Volume = {13},
->
+        Year = {1992}}
-<
+@ARTICLE{Palacios1998,
-<
+  author = {J. L. Garcia-Palacios and F. J. Lazaro},
-<
+  title = {Langevin-dynamics study of the dynamical properties of small magnetic
-<
+    particles},
-<
+  journal = {Physical Review B},
-<
+  year = {1998},
-<
+  volume = {58},
-<
+  pages = {14937-14958},
-<
+  number = {22},
-<
+  month = {Dec 1},
-<
+  abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
->
+@article{Palacios1998,
->
+        Abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
+    magnetic moment is numerically solved (properly observing the customary
+    interpretation of it as a Stratonovich stochastic differential equation),
+    in order to study the dynamics of magnetic nanoparticles. The corresponding
+    frequencies of the magnetic moment in the anisotropy field to the
+    dynamic response at intermediate-to-high temperatures. [S0163-1829
+    (98)00446-9].},
-<
+  annote = {146XW Times Cited:66 Cited References Count:45},
-<
+  issn = {0163-1829},
-<
+  uri = {<Go to ISI>://000077460000052},
-<
+}
->
+        Annote = {146XW Times Cited:66 Cited References Count:45},
->
+        Author = {J. L. Garcia-Palacios and F. J. Lazaro},
->
+        Issn = {0163-1829},
->
+        Journal = {Physical Review B},
->
+        Month = {Dec 1},
->
+        Number = {22},
->
+        Pages = {14937-14958},
->
+        Title = {Langevin-dynamics study of the dynamical properties of small magnetic particles},
->
+        Uri = {<Go to ISI>://000077460000052},
->
+        Volume = {58},
->
+        Year = {1998}}
-<
+@ARTICLE{Parr1995,
-<
+  author = {T. J. Parr and R. W. Quong},
-<
+  title = {Antlr - a Predicated-Ll(K) Parser Generator},
-<
+  journal = {Software-Practice \& Experience},
-<
+  year = {1995},
-<
+  volume = {25},
-<
+  pages = {789-810},
-<
+  number = {7},
-<
+  month = {Jul},
-<
+  abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
->
+@article{Parr1995,
->
+        Abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
+    often choose to write recursive-descent parsers by hand to obtain
+    increased flexibility, better error handling, and ease of debugging.
+    We introduce ANTLR, a public-domain parser generator that combines
+    the PC, Macintosh, and a variety of UNIX platforms; a commercial
+    C++ front-end has been developed as a result of one of our industrial
+    collaborations.},
-<
+  annote = {Rk104 Times Cited:19 Cited References Count:10},
-<
+  issn = {0038-0644},
-<
+  uri = {<Go to ISI>://A1995RK10400004},
-<
+}
->
+        Annote = {Rk104 Times Cited:19 Cited References Count:10},
->
+        Author = {T. J. Parr and R. W. Quong},
->
+        Issn = {0038-0644},
->
+        Journal = {Software-Practice \& Experience},
->
+        Month = {Jul},
->
+        Number = {7},
->
+        Pages = {789-810},
->
+        Title = {Antlr - a Predicated-Ll(K) Parser Generator},
->
+        Uri = {<Go to ISI>://A1995RK10400004},
->
+        Volume = {25},
->
+        Year = {1995}}
-<
+@ARTICLE{Pastor1988,
-<
+  author = {R. W. Pastor and B. R. Brooks and A. Szabo},
-<
+  title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
-<
+  journal = {Molecular Physics},
-<
+  year = {1988},
-<
+  volume = {65},
-<
+  pages = {1409-1419},
-<
+  number = {6},
-<
+  month = {Dec 20},
-<
+  annote = {T1302 Times Cited:61 Cited References Count:26},
-<
+  issn = {0026-8976},
-<
+  uri = {<Go to ISI>://A1988T130200011},
-<
+}
->
+@article{Pastor1988,
->
+        Annote = {T1302 Times Cited:61 Cited References Count:26},
->
+        Author = {R. W. Pastor and B. R. Brooks and A. Szabo},
->
+        Issn = {0026-8976},
->
+        Journal = {Molecular Physics},
->
+        Month = {Dec 20},
->
+        Number = {6},
->
+        Pages = {1409-1419},
->
+        Title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
->
+        Uri = {<Go to ISI>://A1988T130200011},
->
+        Volume = {65},
->
+        Year = {1988}}
-<
+@ARTICLE{Pelzl1999,
-<
+  author = {G. Pelzl and S. Diele and W. Weissflog},
-<
+  title = {Banana-shaped compounds - A new field of liquid crystals},
-<
+  journal = {Advanced Materials},
-<
+  year = {1999},
-<
+  volume = {11},
-<
+  pages = {707-724},
-<
+  number = {9},
-<
+  month = {Jul 5},
-<
+  annote = {220RC Times Cited:313 Cited References Count:49},
-<
+  issn = {0935-9648},
-<
+  uri = {<Go to ISI>://000081680400007},
-<
+}
->
+@article{Pelzl1999,
->
+        Annote = {220RC Times Cited:313 Cited References Count:49},
->
+        Author = {G. Pelzl and S. Diele and W. Weissflog},
->
+        Issn = {0935-9648},
->
+        Journal = {Advanced Materials},
->
+        Month = {Jul 5},
->
+        Number = {9},
->
+        Pages = {707-724},
->
+        Title = {Banana-shaped compounds - A new field of liquid crystals},
->
+        Uri = {<Go to ISI>://000081680400007},
->
+        Volume = {11},
->
+        Year = {1999}}
-<
+@ARTICLE{Perram1985,
-<
+  author = {J. W. Perram and M. S. Wertheim},
-<
+  title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and
-<
+    the Contact Function},
-<
+  journal = {Journal of Computational Physics},
-<
+  year = {1985},
-<
+  volume = {58},
-<
+  pages = {409-416},
-<
+  number = {3},
-<
+  annote = {Akb93 Times Cited:71 Cited References Count:12},
-<
+  issn = {0021-9991},
-<
+  uri = {<Go to ISI>://A1985AKB9300008},
-<
+}
->
+@article{Perram1985,
->
+        Annote = {Akb93 Times Cited:71 Cited References Count:12},
->
+        Author = {J. W. Perram and M. S. Wertheim},
->
+        Issn = {0021-9991},
->
+        Journal = {Journal of Computational Physics},
->
+        Number = {3},
->
+        Pages = {409-416},
->
+        Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function},
->
+        Uri = {<Go to ISI>://A1985AKB9300008},
->
+        Volume = {58},
->
+        Year = {1985}}
-<
+@ARTICLE{Rotne1969,
-<
+  author = {F. Perrin},
-<
+  title = {Variational treatment of hydrodynamic interaction in polymers},
-<
+  journal = {J. Chem. Phys.},
-<
+  year = {1969},
-<
+  volume = {50},
-<
+  pages = {4831�C4837},
-<
+}
->
+@article{Rotne1969,
->
+        Author = {F. Perrin},
->
+        Journal = {J. Chem. Phys.},
->
+        Pages = {4831-4837},
->
+        Title = {Variational treatment of hydrodynamic interaction in polymers},
->
+        Volume = {50},
->
+        Year = {1969}}
-<
+@ARTICLE{Perrin1936,
-<
+  author = {F. Perrin},
-<
+  title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation
-<
+    des fluorescences. Translation et diffusion de moleculese ellipsoidales},
-<
+  journal = {J. Phys. Radium},
-<
+  year = {1936},
-<
+  volume = {7},
-<
+  pages = {1-11},
-<
+}
->
+@article{Perrin1936,
->
+        Author = {F. Perrin},
->
+        Journal = {J. Phys. Radium},
->
+        Pages = {1-11},
->
+        Title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation des fluorescences. Translation et diffusion de moleculese ellipsoidales},
->
+        Volume = {7},
->
+        Year = {1936}}
-<
+@ARTICLE{Perrin1934,
-<
+  author = {F. Perrin},
-<
+  title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour
-<
+    des molecules ellipsoidales},
-<
+  journal = {J. Phys. Radium},
-<
+  year = {1934},
-<
+  volume = {5},
-<
+  pages = {497-511},
-<
+}
->
+@article{Perrin1934,
->
+        Author = {F. Perrin},
->
+        Journal = {J. Phys. Radium},
->
+        Pages = {497-511},
->
+        Title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour des molecules ellipsoidales},
->
+        Volume = {5},
->
+        Year = {1934}}
-<
+@ARTICLE{Petrache2000,
-<
+  author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
-<
+  title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines
-<
+    Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
-<
+  journal = {Biophysical Journal},
-<
+  year = {2000},
-<
+  volume = {79},
-<
+  pages = {3172-3192},
-<
+}
->
+@article{Petrache2000,
->
+        Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
->
+        Journal = {Biophysical Journal},
->
+        Pages = {3172-3192},
->
+        Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
->
+        Volume = {79},
->
+        Year = {2000}}
-<
+@ARTICLE{Petrache1998,
-<
+  author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle},
-<
+  title = {Fluid phase structure of EPC and DMPC bilayers},
-<
+  journal = {Chemistry and Physics of Lipids},
-<
+  year = {1998},
-<
+  volume = {95},
-<
+  pages = {83-94},
-<
+  number = {1},
-<
+  month = {Sep},
-<
+  abstract = {X-ray diffraction data taken at high instrumental resolution were
->
+@article{Petrache1998,
->
+        Abstract = {X-ray diffraction data taken at high instrumental resolution were
+    obtained for EPC and DMPC under various osmotic pressures, primarily
+    at T = 30 degrees C. The headgroup thickness D-HH was obtained from
+    relative electron density profiles. By using volumetric results
+    increased water spacing reported by Simon et al. (1995) Biophys.
+    J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights
+    reserved.},
-<
+  annote = {130AT Times Cited:98 Cited References Count:39},
-<
+  issn = {0009-3084},
-<
+  uri = {<Go to ISI>://000076497600007},
-<
+}
->
+        Annote = {130AT Times Cited:98 Cited References Count:39},
->
+        Author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle},
->
+        Issn = {0009-3084},
->
+        Journal = {Chemistry and Physics of Lipids},
->
+        Month = {Sep},
->
+        Number = {1},
->
+        Pages = {83-94},
->
+        Title = {Fluid phase structure of EPC and DMPC bilayers},
->
+        Uri = {<Go to ISI>://000076497600007},
->
+        Volume = {95},
->
+        Year = {1998}}
->
->
+@article{Powles1973,
->
+        Author = {J.~G. Powles},
->
+        Journal = {Advan. Phys.},
->
+        Pages = {1-56},
->
+        Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
->
+        Volume = {22},
->
+        Year = {1973}}
-<
+@ARTICLE{Powles1973,
-<
+  author = {J.~G. Powles},
-<
+  title = {A general ellipsoid can not always serve as a modle for the rotational
-<
+    diffusion properties of arbitrary shaped rigid molecules},
-<
+  journal = {Advan. Phys.},
-<
+  year = {1973},
-<
+  volume = {22},
-<
+  pages = {1-56},
-<
+}
-<
-<
+@ARTICLE{Recio2004,
-<
+  author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
-<
+  title = {Identification of protein-protein interaction sites from docking
-<
+    energy landscapes},
-<
+  journal = {Journal of Molecular Biology},
-<
+  year = {2004},
-<
+  volume = {335},
-<
+  pages = {843-865},
-<
+  number = {3},
-<
+  month = {Jan 16},
-<
+  abstract = {Protein recognition is one of the most challenging and intriguing
->
+@article{Recio2004,
->
+        Abstract = {Protein recognition is one of the most challenging and intriguing
+    problems in structural biology. Despite all the available structural,
+    sequence and biophysical information about protein-protein complexes,
+    the physico-chemical patterns, if any, that make a protein surface
+    of proteins, provide geometrical details of a possible interaction,
+    and help to annotate protein surfaces in structural proteomics.
+    (C) 2003 Elsevier Ltd. All rights reserved.},
-<
+  annote = {763GQ Times Cited:21 Cited References Count:59},
-<
+  issn = {0022-2836},
-<
+  uri = {<Go to ISI>://000188066900016},
-<
+}
->
+        Annote = {763GQ Times Cited:21 Cited References Count:59},
->
+        Author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
->
+        Issn = {0022-2836},
->
+        Journal = {Journal of Molecular Biology},
->
+        Month = {Jan 16},
->
+        Number = {3},
->
+        Pages = {843-865},
->
+        Title = {Identification of protein-protein interaction sites from docking energy landscapes},
->
+        Uri = {<Go to ISI>://000188066900016},
->
+        Volume = {335},
->
+        Year = {2004}}
-<
+@ARTICLE{Reddy2006,
-<
+  author = {R. A. Reddy and C. Tschierske},
-<
+  title = {Bent-core liquid crystals: polar order, superstructural chirality
-<
+    and spontaneous desymmetrisation in soft matter systems},
-<
+  journal = {Journal of Materials Chemistry},
-<
+  year = {2006},
-<
+  volume = {16},
-<
+  pages = {907-961},
-<
+  number = {10},
-<
+  abstract = {An overview on the recent developments in the field of liquid crystalline
->
+@article{Reddy2006,
->
+        Abstract = {An overview on the recent developments in the field of liquid crystalline
+    bent-core molecules (so-called banana liquid crystals) is given.
+    After some basic issues, dealing with general aspects of the systematisation
+    of the mesophases, development of polar order and chirality in this
+    polar order in smectic and columnar phases, amplification and switching
+    of chirality and the spontaneous formation of superstructural and
+    supramolecular chirality.},
-<
+  annote = {021NS Times Cited:2 Cited References Count:316},
-<
+  issn = {0959-9428},
-<
+  uri = {<Go to ISI>://000235990500001},
-<
+}
->
+        Annote = {021NS Times Cited:2 Cited References Count:316},
->
+        Author = {R. A. Reddy and C. Tschierske},
->
+        Issn = {0959-9428},
->
+        Journal = {Journal of Materials Chemistry},
->
+        Number = {10},
->
+        Pages = {907-961},
->
+        Title = {Bent-core liquid crystals: polar order, superstructural chirality and spontaneous desymmetrisation in soft matter systems},
->
+        Uri = {<Go to ISI>://000235990500001},
->
+        Volume = {16},
->
+        Year = {2006}}
-<
+@ARTICLE{Reich1999,
-<
+  author = {S. Reich},
-<
+  title = {Backward error analysis for numerical integrators},
-<
+  journal = {Siam Journal on Numerical Analysis},
-<
+  year = {1999},
-<
+  volume = {36},
-<
+  pages = {1549-1570},
-<
+  number = {5},
-<
+  month = {Sep 8},
-<
+  abstract = {Backward error analysis has become an important tool for understanding
->
+@article{Reich1999,
->
+        Abstract = {Backward error analysis has become an important tool for understanding
+    the long time behavior of numerical integration methods. This is
+    true in particular for the integration of Hamiltonian systems where
+    backward error analysis can be used to show that a symplectic method
+    an application we discuss the long time integration of chaotic Hamiltonian
+    systems and the approximation of time averages along numerically
+    computed trajectories.},
-<
+  annote = {237HV Times Cited:43 Cited References Count:41},
-<
+  issn = {0036-1429},
-<
+  uri = {<Go to ISI>://000082650600010},
-<
+}
->
+        Annote = {237HV Times Cited:43 Cited References Count:41},
->
+        Author = {S. Reich},
->
+        Issn = {0036-1429},
->
+        Journal = {Siam Journal on Numerical Analysis},
->
+        Month = {Sep 8},
->
+        Number = {5},
->
+        Pages = {1549-1570},
->
+        Title = {Backward error analysis for numerical integrators},
->
+        Uri = {<Go to ISI>://000082650600010},
->
+        Volume = {36},
->
+        Year = {1999}}
-<
+@ARTICLE{Ros2005,
-<
+  author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
-<
+  title = {Banana-shaped liquid crystals: a new field to explore},
-<
+  journal = {Journal of Materials Chemistry},
-<
+  year = {2005},
-<
+  volume = {15},
-<
+  pages = {5093-5098},
-<
+  number = {48},
-<
+  abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
->
+@article{Ros2005,
->
+        Abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
+    mesogenic materials represent a bewitching and stimulating field
+    of research that is interesting both academically and in terms of
+    applications. Numerous topics are open to investigation in this
+    these materials offer. The principal concepts in this area are reviewed
+    along with recent results. In addition, new directions to stimulate
+    further research activities are highlighted.},
-<
+  annote = {990XA Times Cited:3 Cited References Count:72},
-<
+  issn = {0959-9428},
-<
+  uri = {<Go to ISI>://000233775500001},
-<
+}
->
+        Annote = {990XA Times Cited:3 Cited References Count:72},
->
+        Author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
->
+        Issn = {0959-9428},
->
+        Journal = {Journal of Materials Chemistry},
->
+        Number = {48},
->
+        Pages = {5093-5098},
->
+        Title = {Banana-shaped liquid crystals: a new field to explore},
->
+        Uri = {<Go to ISI>://000233775500001},
->
+        Volume = {15},
->
+        Year = {2005}}
-<
+@ARTICLE{Roux1991,
-<
+  author = {B. Roux and M. Karplus},
-<
+  title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
-<
+  journal = {Journal of Physical Chemistry},
-<
+  year = {1991},
-<
+  volume = {95},
-<
+  pages = {4856-4868},
-<
+  number = {12},
-<
+  month = {Jun 13},
-<
+  abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
->
+@article{Roux1991,
->
+        Abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
+    poly-(L,D)-alanine beta-helix, a model for the interior of the gramicidin
+    channel. Because of the different dynamical regimes for the three
+    species (high barrier for Na+, low barrier for K+, almost free diffusion
+    and their dynamics is overdamped and noninertial. Thus, the selectivity
+    sequence of ions in the beta-helix is not influenced strongly by
+    their masses.},
-<
+  annote = {Fr756 Times Cited:97 Cited References Count:65},
-<
+  issn = {0022-3654},
-<
+  uri = {<Go to ISI>://A1991FR75600049},
-<
+}
->
+        Annote = {Fr756 Times Cited:97 Cited References Count:65},
->
+        Author = {B. Roux and M. Karplus},
->
+        Issn = {0022-3654},
->
+        Journal = {Journal of Physical Chemistry},
->
+        Month = {Jun 13},
->
+        Number = {12},
->
+        Pages = {4856-4868},
->
+        Title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
->
+        Uri = {<Go to ISI>://A1991FR75600049},
->
+        Volume = {95},
->
+        Year = {1991}}
-<
+@ARTICLE{Roy2005,
-<
+  author = {A. Roy and N. V. Madhusudana},
-<
+  title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases
-<
+    in banana shaped molecules},
-<
+  journal = {European Physical Journal E},
-<
+  year = {2005},
-<
+  volume = {18},
-<
+  pages = {253-258},
-<
+  number = {3},
-<
+  month = {Nov},
-<
+  abstract = {A vast majority of compounds with bent core or banana shaped molecules
->
+@article{Roy2005,
->
+        Abstract = {A vast majority of compounds with bent core or banana shaped molecules
+    exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased
+    in a homologous series. The B-6 phase has an intercalated fluid
+    lamellar structure with a layer spacing of half the molecular length.
+    a frustrated packing model to describe this phase sequence qualitatively.
+    The model has some analogy with that of the frustrated smectics
+    exhibited by highly polar rod like molecules.},
-<
+  annote = {985FW Times Cited:0 Cited References Count:30},
-<
+  issn = {1292-8941},
-<
+  uri = {<Go to ISI>://000233363300002},
-<
+}
->
+        Annote = {985FW Times Cited:0 Cited References Count:30},
->
+        Author = {A. Roy and N. V. Madhusudana},
->
+        Issn = {1292-8941},
->
+        Journal = {European Physical Journal E},
->
+        Month = {Nov},
->
+        Number = {3},
->
+        Pages = {253-258},
->
+        Title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases in banana shaped molecules},
->
+        Uri = {<Go to ISI>://000233363300002},
->
+        Volume = {18},
->
+        Year = {2005}}
-<
+@ARTICLE{Ryckaert1977,
-<
+  author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
-<
+  title = {Numerical-Integration of Cartesian Equations of Motion of a System
-<
+    with Constraints - Molecular-Dynamics of N-Alkanes},
-<
+  journal = {Journal of Computational Physics},
-<
+  year = {1977},
-<
+  volume = {23},
-<
+  pages = {327-341},
-<
+  number = {3},
-<
+  annote = {Cz253 Times Cited:3680 Cited References Count:7},
-<
+  issn = {0021-9991},
-<
+  uri = {<Go to ISI>://A1977CZ25300007},
-<
+}
->
+@article{Ryckaert1977,
->
+        Annote = {Cz253 Times Cited:3680 Cited References Count:7},
->
+        Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
->
+        Issn = {0021-9991},
->
+        Journal = {Journal of Computational Physics},
->
+        Number = {3},
->
+        Pages = {327-341},
->
+        Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes},
->
+        Uri = {<Go to ISI>://A1977CZ25300007},
->
+        Volume = {23},
->
+        Year = {1977}}
-<
+@ARTICLE{Sagui1999,
-<
+  author = {C. Sagui and T. A. Darden},
-<
+  title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic
-<
+    effects},
-<
+  journal = {Annual Review of Biophysics and Biomolecular Structure},
-<
+  year = {1999},
-<
+  volume = {28},
-<
+  pages = {155-179},
-<
+  abstract = {Current computer simulations of biomolecules typically make use of
->
+@article{Sagui1999,
->
+        Abstract = {Current computer simulations of biomolecules typically make use of
+    classical molecular dynamics methods, as a very large number (tens
+    to hundreds of thousands) of atoms are involved over timescales
+    of many nanoseconds. The methodology for treating short-range bonded
+    methods. We also review recent efforts to understand the role of
+    boundary conditions in systems with long-range interactions, and
+    conclude with a short perspective on future trends.},
-<
+  annote = {213KJ Times Cited:126 Cited References Count:73},
-<
+  issn = {1056-8700},
-<
+  uri = {<Go to ISI>://000081271400008},
-<
+}
->
+        Annote = {213KJ Times Cited:126 Cited References Count:73},
->
+        Author = {C. Sagui and T. A. Darden},
->
+        Issn = {1056-8700},
->
+        Journal = {Annual Review of Biophysics and Biomolecular Structure},
->
+        Pages = {155-179},
->
+        Title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic effects},
->
+        Uri = {<Go to ISI>://000081271400008},
->
+        Volume = {28},
->
+        Year = {1999}}
-<
+@ARTICLE{Sandu1999,
-<
+  author = {A. Sandu and T. Schlick},
-<
+  title = {Masking resonance artifacts in force-splitting methods for biomolecular
-<
+    simulations by extrapolative Langevin dynamics},
-<
+  journal = {Journal of Computational Physics},
-<
+  year = {1999},
-<
+  volume = {151},
-<
+  pages = {74-113},
-<
+  number = {1},
-<
+  month = {May 1},
-<
+  abstract = {Numerical resonance artifacts have become recognized recently as a
->
+@article{Sandu1999,
->
+        Abstract = {Numerical resonance artifacts have become recognized recently as a
+    limiting factor to increasing the timestep in multiple-timestep
+    (MTS) biomolecular dynamics simulations. At certain timesteps correlated
+    to internal motions (e.g., 5 fs, around half the period of the fastest
+    spectral density functions also show how the Newtonian modes can
+    be approximated by using a small gamma in the range Of 5-20 ps(-1).
+    (C) 1999 Academic Press.},
-<
+  annote = {194FM Times Cited:14 Cited References Count:32},
-<
+  issn = {0021-9991},
-<
+  uri = {<Go to ISI>://000080181500004},
-<
+}
->
+        Annote = {194FM Times Cited:14 Cited References Count:32},
->
+        Author = {A. Sandu and T. Schlick},
->
+        Issn = {0021-9991},
->
+        Journal = {Journal of Computational Physics},
->
+        Month = {May 1},
->
+        Number = {1},
->
+        Pages = {74-113},
->
+        Title = {Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics},
->
+        Uri = {<Go to ISI>://000080181500004},
->
+        Volume = {151},
->
+        Year = {1999}}
-<
+@ARTICLE{Sasaki2004,
-<
+  author = {Y. Sasaki and R. Shukla and B. D. Smith},
-<
+  title = {Facilitated phosphatidylserine flip-flop across vesicle and cell
-<
+    membranes using urea-derived synthetic translocases},
-<
+  journal = {Organic \& Biomolecular Chemistry},
-<
+  year = {2004},
-<
+  volume = {2},
-<
+  pages = {214-219},
-<
+  number = {2},
-<
+  abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
->
+@article{Sasaki2004,
->
+        Abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
+    groups are shown to facilitate the translocation of fluorescent
+    phospholipid probes and endogenous phosphatidylserine across vesicle
+    and erythrocyte cell membranes. The synthetic translocases appear
+    to operate by binding to the phospholipid head groups and forming
+    lipophilic supramolecular complexes which diffuse through the non-polar
+    interior of the bilayer membrane.},
-<
+  annote = {760PX Times Cited:8 Cited References Count:25},
-<
+  issn = {1477-0520},
-<
+  uri = {<Go to ISI>://000187843800012},
-<
+}
->
+        Annote = {760PX Times Cited:8 Cited References Count:25},
->
+        Author = {Y. Sasaki and R. Shukla and B. D. Smith},
->
+        Issn = {1477-0520},
->
+        Journal = {Organic \& Biomolecular Chemistry},
->
+        Number = {2},
->
+        Pages = {214-219},
->
+        Title = {Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases},
->
+        Uri = {<Go to ISI>://000187843800012},
->
+        Volume = {2},
->
+        Year = {2004}}
-<
+@ARTICLE{Satoh1996,
-<
+  author = {K. Satoh and S. Mita and S. Kondo},
-<
+  title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect
-<
+    of terminal dipole moment on mesophase formation},
-<
+  journal = {Chemical Physics Letters},
-<
+  year = {1996},
-<
+  volume = {255},
-<
+  pages = {99-104},
-<
+  number = {1-3},
-<
+  month = {Jun 7},
-<
+  abstract = {The effects of dipole-dipole interaction on mesophase formation are
->
+@article{Satoh1996,
->
+        Abstract = {The effects of dipole-dipole interaction on mesophase formation are
+    investigated with a Monte Carlo simulation using the dipolar Gay-Berne
+    potential. It is shown that the dipole moment at the end of a molecule
+    causes a shift in the nematic-isotropic transition toward higher
+    temperature and a spread of the temperature range of the nematic
+    phase and that layer structures with various interdigitations are
+    formed in the smectic phase.},
-<
+  annote = {Uq975 Times Cited:32 Cited References Count:33},
-<
+  issn = {0009-2614},
-<
+  uri = {<Go to ISI>://A1996UQ97500017},
-<
+}
->
+        Annote = {Uq975 Times Cited:32 Cited References Count:33},
->
+        Author = {K. Satoh and S. Mita and S. Kondo},
->
+        Issn = {0009-2614},
->
+        Journal = {Chemical Physics Letters},
->
+        Month = {Jun 7},
->
+        Number = {1-3},
->
+        Pages = {99-104},
->
+        Title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect of terminal dipole moment on mesophase formation},
->
+        Uri = {<Go to ISI>://A1996UQ97500017},
->
+        Volume = {255},
->
+        Year = {1996}}
-<
+@ARTICLE{Schaps1999,
-<
+  author = {G. L. Schaps},
-<
+  title = {Compiler construction with ANTLR and Java - Tools for building tools},
-<
+  journal = {Dr Dobbs Journal},
-<
+  year = {1999},
-<
+  volume = {24},
-<
+  pages = {84-+},
-<
+  number = {3},
-<
+  month = {Mar},
-<
+  annote = {163EC Times Cited:0 Cited References Count:0},
-<
+  issn = {1044-789X},
-<
+  uri = {<Go to ISI>://000078389200023},
-<
+}
->
+@article{Schaps1999,
->
+        Annote = {163EC Times Cited:0 Cited References Count:0},
->
+        Author = {G. L. Schaps},
->
+        Issn = {1044-789X},
->
+        Journal = {Dr Dobbs Journal},
->
+        Month = {Mar},
->
+        Number = {3},
->
+        Pages = {84-+},
->
+        Title = {Compiler construction with ANTLR and Java - Tools for building tools},
->
+        Uri = {<Go to ISI>://000078389200023},
->
+        Volume = {24},
->
+        Year = {1999}}
-<
+@ARTICLE{Shen2002,
-<
+  author = {M. Y. Shen and K. F. Freed},
-<
+  title = {Long time dynamics of met-enkephalin: Comparison of explicit and
-<
+    implicit solvent models},
-<
+  journal = {Biophysical Journal},
-<
+  year = {2002},
-<
+  volume = {82},
-<
+  pages = {1791-1808},
-<
+  number = {4},
-<
+  month = {Apr},
-<
+  abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
->
+@article{Shen2002,
->
+        Abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
+    structure and receptor docking mechanism are still not well understood.
+    The conformational dynamics of this neuron peptide in liquid water
+    are studied here by using all-atom molecular dynamics (MID) and
+    The simulations provide insights into the conformational restrictions
+    that are associated with the bioactivity of the opiate peptide dermorphin
+    for the delta-receptor.},
-<
+  annote = {540MH Times Cited:36 Cited References Count:45},
-<
+  issn = {0006-3495},
-<
+  uri = {<Go to ISI>://000174932400010},
-<
+}
->
+        Annote = {540MH Times Cited:36 Cited References Count:45},
->
+        Author = {M. Y. Shen and K. F. Freed},
->
+        Issn = {0006-3495},
->
+        Journal = {Biophysical Journal},
->
+        Month = {Apr},
->
+        Number = {4},
->
+        Pages = {1791-1808},
->
+        Title = {Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models},
->
+        Uri = {<Go to ISI>://000174932400010},
->
+        Volume = {82},
->
+        Year = {2002}}
-<
+@ARTICLE{Shillcock2005,
-<
+  author = {J. C. Shillcock and R. Lipowsky},
-<
+  title = {Tension-induced fusion of bilayer membranes and vesicles},
-<
+  journal = {Nature Materials},
-<
+  year = {2005},
-<
+  volume = {4},
-<
+  pages = {225-228},
-<
+  number = {3},
-<
+  month = {Mar},
-<
+  annote = {901QJ Times Cited:9 Cited References Count:23},
-<
+  issn = {1476-1122},
-<
+  uri = {<Go to ISI>://000227296700019},
-<
+}
->
+@article{Shillcock2005,
->
+        Annote = {901QJ Times Cited:9 Cited References Count:23},
->
+        Author = {J. C. Shillcock and R. Lipowsky},
->
+        Issn = {1476-1122},
->
+        Journal = {Nature Materials},
->
+        Month = {Mar},
->
+        Number = {3},
->
+        Pages = {225-228},
->
+        Title = {Tension-induced fusion of bilayer membranes and vesicles},
->
+        Uri = {<Go to ISI>://000227296700019},
->
+        Volume = {4},
->
+        Year = {2005}}
-<
+@ARTICLE{Shimada1993,
-<
+  author = {J. Shimada and H. Kaneko and T. Takada},
-<
+  title = {Efficient Calculations of Coulombic Interactions in Biomolecular
-<
+    Simulations with Periodic Boundary-Conditions},
-<
+  journal = {Journal of Computational Chemistry},
-<
+  year = {1993},
-<
+  volume = {14},
-<
+  pages = {867-878},
-<
+  number = {7},
-<
+  month = {Jul},
-<
+  abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
->
+@article{Shimada1993,
->
+        Abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
+    simulations, two possibilities are considered. The first is the
+    famous particle-particle and particle-mesh (PPPM) method developed
+    by Hockney and Eastwood, and the second is a new one developed here
+    first method has the drawback that the accuracy in the total electrostatic
+    energy is not high for configurations of charged particles randomly
+    generated.},
-<
+  annote = {Lh164 Times Cited:27 Cited References Count:47},
-<
+  issn = {0192-8651},
-<
+  uri = {<Go to ISI>://A1993LH16400011},
-<
+}
->
+        Annote = {Lh164 Times Cited:27 Cited References Count:47},
->
+        Author = {J. Shimada and H. Kaneko and T. Takada},
->
+        Issn = {0192-8651},
->
+        Journal = {Journal of Computational Chemistry},
->
+        Month = {Jul},
->
+        Number = {7},
->
+        Pages = {867-878},
->
+        Title = {Efficient Calculations of Coulombic Interactions in Biomolecular Simulations with Periodic Boundary-Conditions},
->
+        Uri = {<Go to ISI>://A1993LH16400011},
->
+        Volume = {14},
->
+        Year = {1993}}
-<
+@ARTICLE{Skeel2002,
-<
+  author = {R. D. Skeel and J. A. Izaguirre},
-<
+  title = {An impulse integrator for Langevin dynamics},
-<
+  journal = {Molecular Physics},
-<
+  year = {2002},
-<
+  volume = {100},
-<
+  pages = {3885-3891},
-<
+  number = {24},
-<
+  month = {Dec 20},
-<
+  abstract = {The best simple method for Newtonian molecular dynamics is indisputably
->
+@article{Skeel2002,
->
+        Abstract = {The best simple method for Newtonian molecular dynamics is indisputably
+    the leapfrog Stormer-Verlet method. The appropriate generalization
+    to simple Langevin dynamics is unclear. An analysis is presented
+    comparing an 'impulse method' (kick; fluctuate; kick), the 1982
+    considerations suggest that the impulse method is the best basic
+    method for simple Langevin dynamics, with the van Gunsteren-Berendsen
+    method a close contender.},
-<
+  annote = {633RX Times Cited:8 Cited References Count:22},
-<
+  issn = {0026-8976},
-<
+  uri = {<Go to ISI>://000180297200014},
-<
+}
->
+        Annote = {633RX Times Cited:8 Cited References Count:22},
->
+        Author = {R. D. Skeel and J. A. Izaguirre},
->
+        Issn = {0026-8976},
->
+        Journal = {Molecular Physics},
->
+        Month = {Dec 20},
->
+        Number = {24},
->
+        Pages = {3885-3891},
->
+        Title = {An impulse integrator for Langevin dynamics},
->
+        Uri = {<Go to ISI>://000180297200014},
->
+        Volume = {100},
->
+        Year = {2002}}
-<
+@ARTICLE{Skeel1997,
-<
+  author = {R. D. Skeel and G. H. Zhang and T. Schlick},
-<
+  title = {A family of symplectic integrators: Stability, accuracy, and molecular
-<
+    dynamics applications},
-<
+  journal = {Siam Journal on Scientific Computing},
-<
+  year = {1997},
-<
+  volume = {18},
-<
+  pages = {203-222},
-<
+  number = {1},
-<
+  month = {Jan},
-<
+  abstract = {The following integration methods for special second-order ordinary
->
+@article{Skeel1997,
->
+        Abstract = {The following integration methods for special second-order ordinary
+    differential equations are studied: leapfrog, implicit midpoint,
+    trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all
+    are members, or equivalent to members, of a one-parameter family
+    leads to higher accuracy and better energy conservation. Hence,
+    we suggest that the straightforward analysis of energy conservation
+    is misleading.},
-<
+  annote = {We981 Times Cited:30 Cited References Count:35},
-<
+  issn = {1064-8275},
-<
+  uri = {<Go to ISI>://A1997WE98100012},
-<
+}
->
+        Annote = {We981 Times Cited:30 Cited References Count:35},
->
+        Author = {R. D. Skeel and G. H. Zhang and T. Schlick},
->
+        Issn = {1064-8275},
->
+        Journal = {Siam Journal on Scientific Computing},
->
+        Month = {Jan},
->
+        Number = {1},
->
+        Pages = {203-222},
->
+        Title = {A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications},
->
+        Uri = {<Go to ISI>://A1997WE98100012},
->
+        Volume = {18},
->
+        Year = {1997}}
-<
+@ARTICLE{Tao2005,
-<
+  author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont
-<
+    and W. J. Briels},
-<
+  title = {Brownian dynamics simulations of the self- and collective rotational
-<
+    diffusion coefficients of rigid long thin rods},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2005},
-<
+  volume = {122},
-<
+  pages = {-},
-<
+  number = {24},
-<
+  month = {Jun 22},
-<
+  abstract = {Recently a microscopic theory for the dynamics of suspensions of long
->
+@article{Tao2005,
->
+        Abstract = {Recently a microscopic theory for the dynamics of suspensions of long
+    thin rigid rods was presented, confirming and expanding the well-known
+    theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon,
+    Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here
+    predicted by the theory, which is attributed to an oversimplification
+    of dynamic correlations in the theory. (c) 2005 American Institute
+    of Physics.},
-<
+  annote = {943DN Times Cited:3 Cited References Count:26},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000230332400077},
-<
+}
-<
-<
+@BOOK{Tolman1979,
-<
+  title = {The Principles of Statistical Mechanics},
-<
+  publisher = {Dover Publications, Inc.},
-<
+  year = {1979},
-<
+  author = {R.~C. Tolman},
-<
+  address = {New York},
-<
+  chapter = {2},
-<
+  pages = {19-22},
-<
+}
->
+        Annote = {943DN Times Cited:3 Cited References Count:26},
->
+        Author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont and W. J. Briels},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Jun 22},
->
+        Number = {24},
->
+        Pages = {-},
->
+        Title = {Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods},
->
+        Uri = {<Go to ISI>://000230332400077},
->
+        Volume = {122},
->
+        Year = {2005}}
-<
+@ARTICLE{Tu1995,
-<
+  author = {K. Tu and D. J. Tobias and M. L. Klein},
-<
+  title = {Constant pressure and temperature molecular dynamics simulation of
-<
+    a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine
-<
+    bilayer},
-<
+  journal = {Biophysical Journal},
-<
+  year = {1995},
-<
+  volume = {69},
-<
+  pages = {2558-2562},
-<
+  number = {6},
-<
+  month = {Dec},
-<
+  abstract = {We report a constant pressure and temperature molecular dynamics simulation
->
+@book{Tolman1979,
->
+        Address = {New York},
->
+        Author = {R.~C. Tolman},
->
+        Chapter = {2},
->
+        Pages = {19-22},
->
+        Publisher = {Dover Publications, Inc.},
->
+        Title = {The Principles of Statistical Mechanics},
->
+        Year = {1979}}
->
->
+@article{Tu1995,
->
+        Abstract = {We report a constant pressure and temperature molecular dynamics simulation
+    of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine
+    at 50 degrees C and 28 water molecules/lipid. We have shown that
+    the bilayer is stable throughout the 1550-ps simulation and have
+    order parameters for the glycerol and choline groups, as well as
+    the phosphorus chemical shift anisotropy, are in qualitative agreement
+    with those extracted from NMR measurements.},
-<
+  annote = {Tv018 Times Cited:108 Cited References Count:34},
-<
+  issn = {0006-3495},
-<
+  uri = {<Go to ISI>://A1995TV01800037},
-<
+}
->
+        Annote = {Tv018 Times Cited:108 Cited References Count:34},
->
+        Author = {K. Tu and D. J. Tobias and M. L. Klein},
->
+        Issn = {0006-3495},
->
+        Journal = {Biophysical Journal},
->
+        Month = {Dec},
->
+        Number = {6},
->
+        Pages = {2558-2562},
->
+        Title = {Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer},
->
+        Uri = {<Go to ISI>://A1995TV01800037},
->
+        Volume = {69},
->
+        Year = {1995}}
-<
+@ARTICLE{Tuckerman1992,
-<
+  author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
-<
+  title = {Reversible Multiple Time Scale Molecular-Dynamics},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {1992},
-<
+  volume = {97},
-<
+  pages = {1990-2001},
-<
+  number = {3},
-<
+  month = {Aug 1},
-<
+  abstract = {The Trotter factorization of the Liouville propagator is used to generate
->
+@article{Tuckerman1992,
->
+        Abstract = {The Trotter factorization of the Liouville propagator is used to generate
+    new reversible molecular dynamics integrators. This strategy is
+    applied to derive reversible reference system propagator algorithms
+    (RESPA) that greatly accelerate simulations of systems with a separation
+    integrators. Finally, we show how these methods can be used to accelerate
+    the integration of the equations of motion of systems with Nose
+    thermostats.},
-<
+  annote = {Je891 Times Cited:680 Cited References Count:19},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://A1992JE89100044},
-<
+}
->
+        Annote = {Je891 Times Cited:680 Cited References Count:19},
->
+        Author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Aug 1},
->
+        Number = {3},
->
+        Pages = {1990-2001},
->
+        Title = {Reversible Multiple Time Scale Molecular-Dynamics},
->
+        Uri = {<Go to ISI>://A1992JE89100044},
->
+        Volume = {97},
->
+        Year = {1992}}
-<
+@BOOK{Varadarajan1974,
-<
+  title = {Lie groups, Lie algebras, and their representations},
-<
+  publisher = {Prentice-Hall},
-<
+  year = {1974},
-<
+  author = {V.S. Varadarajan},
-<
+  address = {New York},
-<
+}
->
+@book{Varadarajan1974,
->
+        Address = {New York},
->
+        Author = {V.S. Varadarajan},
->
+        Publisher = {Prentice-Hall},
->
+        Title = {Lie groups, Lie algebras, and their representations},
->
+        Year = {1974}}
-<
+@ARTICLE{Vincent1995,
-<
+  author = {J. J. Vincent and K. M. Merz},
-<
+  title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing
-<
+    Interface Standard},
-<
+  journal = {Journal of Computational Chemistry},
-<
+  year = {1995},
-<
+  volume = {16},
-<
+  pages = {1420-1427},
-<
+  number = {11},
-<
+  month = {Nov},
-<
+  abstract = {We have implemented a portable parallel version of the macromolecular
->
+@article{Vincent1995,
->
+        Abstract = {We have implemented a portable parallel version of the macromolecular
+    modeling package AMBER4. The message passing paradigm was used.
+    All message passing constructs are compliant with the Message Passing
+    Interface (MPI) standard. The molecular dynamics/minimization module
+    Performance results for a Lipid bilayer molecular dynamics simulation
+    on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995
+    by John Wiley & Sons, Inc.},
-<
+  annote = {Ta403 Times Cited:16 Cited References Count:23},
-<
+  issn = {0192-8651},
-<
+  uri = {<Go to ISI>://A1995TA40300009},
-<
+}
->
+        Annote = {Ta403 Times Cited:16 Cited References Count:23},
->
+        Author = {J. J. Vincent and K. M. Merz},
->
+        Issn = {0192-8651},
->
+        Journal = {Journal of Computational Chemistry},
->
+        Month = {Nov},
->
+        Number = {11},
->
+        Pages = {1420-1427},
->
+        Title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing Interface Standard},
->
+        Uri = {<Go to ISI>://A1995TA40300009},
->
+        Volume = {16},
->
+        Year = {1995}}
-<
+@ARTICLE{Wegener1979,
-<
+  author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
-<
+  title = {A general ellipsoid can not always serve as a modle for the rotational
-<
+    diffusion properties of arbitrary shaped rigid molecules},
-<
+  journal = {Proc. Natl. Acad. Sci.},
-<
+  year = {1979},
-<
+  volume = {76},
-<
+  pages = {6356-6360},
-<
+  number = {12},
-<
+}
->
+@article{Wegener1979,
->
+        Author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
->
+        Journal = {Proc. Natl. Acad. Sci.},
->
+        Number = {12},
->
+        Pages = {6356-6360},
->
+        Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
->
+        Volume = {76},
->
+        Year = {1979}}
-<
+@ARTICLE{Wilson2006,
-<
+  author = {G.~V. Wilson },
-<
+  title = {Where's the Real Bottleneck in Scientific Computing?},
-<
+  journal = {American Scientist},
-<
+  year = {2006},
-<
+  volume = {94},
-<
+}
->
+@article{Wilson2006,
->
+        Author = {G.~V. Wilson},
->
+        Journal = {American Scientist},
->
+        Title = {Where's the Real Bottleneck in Scientific Computing?},
->
+        Volume = {94},
->
+        Year = {2006}}
-<
+@ARTICLE{Withers2003,
-<
+  author = {I. M. Withers},
-<
+  title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne
-<
+    fluid},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {2003},
-<
+  volume = {119},
-<
+  pages = {10209-10223},
-<
+  number = {19},
-<
+  month = {Nov 15},
-<
+  abstract = {The effects of longitudinal quadrupole moments on the formation of
->
+@article{Withers2003,
->
+        Abstract = {The effects of longitudinal quadrupole moments on the formation of
+    liquid crystalline phases are studied by means of constant NPT Monte
+    Carlo simulation methods. The popular Gay-Berne model mesogen is
+    used as the reference fluid, which displays the phase sequences
+    This behavior is in much closer agreement with experimental findings
+    than has been observed previously for nonpolar Gay-Berne and hard
+    spherocylinder models. (C) 2003 American Institute of Physics.},
-<
+  annote = {738EF Times Cited:3 Cited References Count:43},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000186273200027},
-<
+}
->
+        Annote = {738EF Times Cited:3 Cited References Count:43},
->
+        Author = {I. M. Withers},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
->
+        Month = {Nov 15},
->
+        Number = {19},
->
+        Pages = {10209-10223},
->
+        Title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne fluid},
->
+        Uri = {<Go to ISI>://000186273200027},
->
+        Volume = {119},
->
+        Year = {2003}}
-<
+@ARTICLE{Wolf1999,
-<
+  author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
-<
+  title = {Exact method for the simulation of Coulombic systems by spherically
-<
+    truncated, pairwise r(-1) summation},
-<
+  journal = {Journal of Chemical Physics},
-<
+  year = {1999},
-<
+  volume = {110},
-<
+  pages = {8254-8282},
-<
+  number = {17},
-<
+  month = {May 1},
-<
+  abstract = {Based on a recent result showing that the net Coulomb potential in
->
+@article{Wolf1999,
->
+        Abstract = {Based on a recent result showing that the net Coulomb potential in
+    condensed ionic systems is rather short ranged, an exact and physically
+    transparent method permitting the evaluation of the Coulomb potential
+    by direct summation over the r(-1) Coulomb pair potential is presented.
+    simulations of crystals, liquids, and interfacial systems, such
+    as free surfaces and grain boundaries. (C) 1999 American Institute
+    of Physics. [S0021-9606(99)51517-1].},
-<
+  annote = {189PD Times Cited:70 Cited References Count:34},
-<
+  issn = {0021-9606},
-<
+  uri = {<Go to ISI>://000079913000008},
-<
+}
->
+        Annote = {189PD Times Cited:70 Cited References Count:34},
->
+        Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
->
+        Issn = {0021-9606},
->
+        Journal = {Journal of Chemical Physics},
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+        Uri = {<Go to ISI>://000079913000008},
->
+        Volume = {110},
->
+        Year = {1999}}
-<
+@ARTICLE{Yoshida1990,
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+  author = {H. Yoshida},
-<
+  title = {Construction of Higher-Order Symplectic Integrators},
-<
+  journal = {Physics Letters A},
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+  year = {1990},
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+  volume = {150},
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+  pages = {262-268},
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+  number = {5-7},
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+  month = {Nov 12},
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+  annote = {Ej798 Times Cited:492 Cited References Count:9},
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+  issn = {0375-9601},
-<
+  uri = {<Go to ISI>://A1990EJ79800009},
-<
+}
->
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+        Annote = {Ej798 Times Cited:492 Cited References Count:9},
->
+        Author = {H. Yoshida},
->
+        Issn = {0375-9601},
->
+        Journal = {Physics Letters A},
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->
+        Pages = {262-268},
->
+        Title = {Construction of Higher-Order Symplectic Integrators},
->
+        Uri = {<Go to ISI>://A1990EJ79800009},
->
+        Volume = {150},
->
+        Year = {1990}}
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+  author =   {L. Blum and A.~J. Torruella},
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+}
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->
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+        Pages = {303-309},
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+        Year = 1972}
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+  author =   {A.~J. Stone},
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+}
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->
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->
+        Journal = {Molecular Physics},
->
+        Number = 1,
->
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->
+        Title = {The description of bimolecular potentials, forces and torques: the S and V function expansions},
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+@Article{Berardi2003,
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+  author =   {R. Berardi, M. Cecchini and C. Zannoni},
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+        Author = {R. Berardi, M. Cecchini and C. Zannoni},
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+        Title = {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
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+        Year = 2003}
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+}
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+        Year = 1999}
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+}
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+        Pages = {1238-1246},
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+        Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},
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+        Year = 1971}
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+  author =   {R. Gilmore},
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+}
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+        Author = {R. Gilmore},
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+        Title = {Baker-Campbell-Hausdorff Formulas},
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+        Volume = 15,
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+        Year = 1974}
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+  author =   {G. Strang},
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+        Author = {G. Strang},
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+        Journal = {SIAM Journal on Numerical Analysis},
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+        Title = {On the construction and comparision of difference schemes},
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+        Volume = 5,
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+        Year = 1968}
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+        Journal = {SIAM Journal on Numerical Analysis},
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+        Number = 14,
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+        Pages = {545-551},
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+        Title = {On the product of semi-groups of operators},
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+        Volume = 10,
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+        Year = 1959}
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+}
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+@article{Cartwright1992,
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+        Author = {J.H.E. Cartwright and O. Piro},
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+        Journal = {International Journal of Bifurcation and Chaos},
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+        Title = {The Dynamics of Runge-Kutta Methods},
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+        Volume = 2,
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+        Year = 1992}

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Comparing trunk/langevin/langevin.bib (file contents): Revision 2999 by tim, Mon Sep 4 15:05:46 2006 UTC vs. Revision 3302 by gezelter, Tue Jan 8 22:02:06 2008 UTC

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Comparing trunk/langevin/langevin.bib (file contents):
Revision 2999 by tim, Mon Sep 4 15:05:46 2006 UTC vs.
Revision 3302 by gezelter, Tue Jan 8 22:02:06 2008 UTC