--- trunk/langevin/langevin.bib 2008/03/13 22:16:01 3367 +++ trunk/langevin/langevin.bib 2008/04/30 14:50:53 3390 @@ -2,7 +2,7 @@ %% http://bibdesk.sourceforge.net/ -%% Created for Dan Gezelter at 2008-03-13 17:04:26 -0400 +%% Created for Xiuquan Sun at 2008-04-30 10:19:14 -0400 %% Saved with string encoding Western (ASCII) @@ -26,10 +26,10 @@ @string{jcp = {J. Chem. Phys.}} -@string{jml = {J. Mol. Liq.}} - @string{jmb = {J. Mol. Bio.}} +@string{jml = {J. Mol. Liq.}} + @string{jpc = {J. Phys. Chem.}} @string{jpca = {J. Phys. Chem. A}} @@ -57,6 +57,35 @@ @string{rmp = {Rev. Mod. Phys.}} +@article{GarciadelaTorreJjp0647941, + Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain}, + Author = {{Garc\'{i}a de la Torre}, Jose and del Rio Echenique, G. and Ortega, A.}, + Date-Added = {2008-04-30 10:14:50 -0400}, + Date-Modified = {2008-04-30 10:14:50 -0400}, + Issn = {1520-6106}, + Journal = jpcb, + Number = {5}, + Pages = {955-961}, + Title = {Improved Calculation of Rotational Diffusion and Intrinsic Viscosity of Bead Models for Macromolecules and Nanoparticles}, + Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0647941}, + Volume = {111}, + Year = {2007}} + +@article{Garcia-de-la-Torre:2001wd, + Abstract = { The calculation of hydrodynamic and other solution properties of rigid macromolecules, using bead-shell model methodologies, requires the specification of the macromolecular shape in a format that can be interfaced with existing programs for hydrodynamic computations. Here, a procedure is presented for such a structural specification that is applicable to arbitrarily shaped particles. A computer program (), in which the user inserts the code needed to determine the structure, produces an structural file that is interpreted by another program () which is in charge of the computation of properties. As simple and yet illustrative examples we consider two cases: (1) dimeric structures composed of ellipsoidal subunits; and (2) toroidal structures, presenting simple equations that predict the properties of toroids with varying radial ratios.}, + Author = {{Garc\'{i}a de la Torre}, Jose }, + Date-Added = {2008-04-29 15:11:32 -0400}, + Date-Modified = {2008-04-29 15:11:32 -0400}, + Journal = {Biophysical Chemistry}, + Keywords = {Rigid macromolecules; Hydrodynamic properties; Bead-shell model; Three-dimensional structure}, + Number = {3}, + Pages = {265--274}, + Title = {Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape}, + Ty = {JOUR}, + Url = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953}, + Volume = {94}, + Year = {2001}} + @article{Peters:1999uq, Abstract = {The Fokker-Planck (FP) equation describing the dynamics of a single Brownian particle near a fixed external surface is derived using the multiple-time-scales perturbation method, previously used by Cukier and Deutch and Nienhuis in the absence of any external surfaces, and Piasecki ei LII. for two Brownian spheres in a hard fluid. The FP equation includes an explicit expression for the (time-independent) particle friction tensor in terms of the force autocorrelation Function and equilibrium average force on the particle by the surrounding fluid and in the presence of a fixed external surface. such as an adsorbate. The scaling and perturbation analysis given here also shows that the Force autocorrelation function must decay rapidly on the zeroth-order time scale tau(0), which physically requires N-Kn much less than 1, where N-Kn is the Knudsen number (ratio of the length scale for fluid intermolecular interactions to the Brownian particle length scale). This restricts the theory given here to liquid systems where N-Kn much less than 1. For a specified particle configuration with respect to the external surface, equilibrium canonical molecular dynamics (MD) calculations are conducted, as shown here, in order to obtain numerical values of the friction tensor from the force autocorrelation expression. Molecular dynamics computations of the friction tensor for a single spherical particle in the absence of a fixed external surface are shown to recover Stokes' law for various types of fluid molecule-particle interaction potentials. Analytical studies of the static force correlation function also demonstrate the remarkable principle of force-time parity whereby the particle friction coefficient is nearly independent of the fluid molecule-particle interaction potential. Molecular dynamics computations of the friction tensor for a single spherical particle near a fixed external spherical surface (adsorbate) demonstrate a breakdown in continuum hydrodynamic results at close particle surface separation distances on the order of several molecular diameters.}, Author = {Peters, MH}, @@ -97,6 +126,7 @@ @article{Nienhuis:1970lr, Abstract = { A quantummechanical system consisting of N light bath particles and one heavy Brownian linear rotator is considered. By employing the multiple time scale technique and the Wigner representation of quantummechanics, a Fokker-Planck equation for the motion of the Brownian particle is derived. Some properties of this equation are briefly discussed.}, Author = {Nienhuis, G. }, + Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}, Date-Added = {2008-03-13 16:53:44 -0400}, Date-Modified = {2008-03-13 16:53:44 -0400}, Journal = {Physica}, @@ -106,12 +136,12 @@ Ty = {JOUR}, Url = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}, Volume = {49}, - Year = {1970}, - Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}} + Year = {1970}} @article{SunX._jp0762020, Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556}, Author = {Sun, X. and Gezelter, J.D.}, + Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}, Date-Added = {2008-02-15 13:48:18 -0500}, Date-Modified = {2008-02-15 13:48:18 -0500}, Issn = {1520-6106}, @@ -121,8 +151,7 @@ Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes}, Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}, Volume = {112}, - Year = {2008}, - Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}} + Year = {2008}} @book{Schlick2002, Address = {Secaucus, NJ, USA}, @@ -139,8 +168,8 @@ Author = {Chun, HM and Padilla, CE and Chin, DN and Watanabe, M and Karlov, VI and Alper, HE and Soosaar, K and Blair, KB and Becker, OM and Caves, LSD and Nagle, R and Haney, DN and Farmer, BL}, Date-Added = {2008-01-22 10:38:33 -0500}, Date-Modified = {2008-01-22 10:38:49 -0500}, - Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators}, Journal = jcc, + Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators}, Pages = {159--184}, Timescited = 0, Title = {{MBO(N)D:} A multibody method for long-time molecular dynamics simulations}, @@ -183,7 +212,7 @@ @inbook{Ramachandran1996, Address = {Providence, Rhode Island}, - author = {Gomathi Ramachandran and Tamar Schlick}, + Author = {Gomathi Ramachandran and Tamar Schlick}, Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model}, Date-Added = {2008-01-22 10:03:42 -0500}, Date-Modified = {2008-01-22 10:06:57 -0500}, @@ -241,6 +270,7 @@ @article{Torre:1983lr, Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente}, + Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}, Date-Added = {2008-01-11 16:16:43 -0500}, Date-Modified = {2008-01-11 16:16:43 -0500}, Journal = jcp, @@ -254,11 +284,11 @@ Ty = {JOUR}, Url = {http://link.aip.org/link/?JCP/79/2454/1}, Volume = 79, - Year = 1983, - Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}} + Year = 1983} @article{PhysRev.119.53, Author = {Favro, L. Dale}, + Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}, Date-Added = {2008-01-09 16:57:02 -0500}, Date-Modified = {2008-01-09 16:57:02 -0500}, Doi = {10.1103/PhysRev.119.53}, @@ -270,11 +300,12 @@ Publisher = {American Physical Society}, Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body}, Volume = 119, - Year = 1960, - Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}} + Year = 1960} @article{hess:209, Author = {Berk Hess}, + Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1}, + Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}, Date-Added = {2008-01-08 16:41:06 -0500}, Date-Modified = {2008-01-08 16:41:06 -0500}, Doi = {10.1063/1.1421362}, @@ -286,9 +317,7 @@ 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, - Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1}, - Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}} + 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.}, @@ -349,6 +378,7 @@ @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}, + Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}, Date-Added = {2008-01-08 15:12:53 -0500}, Date-Modified = {2008-01-08 15:13:21 -0500}, Doi = {DOI 10.1063/1.1610442}, @@ -356,12 +386,12 @@ Pages = {8062-8068}, Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit}, Volume = 119, - Year = 2003, - Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}} + 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}, + Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}, Date-Added = {2008-01-08 15:12:53 -0500}, Date-Modified = {2008-01-08 15:13:20 -0500}, Doi = {DOI 10.1021/jp037185r}, @@ -369,8 +399,7 @@ Pages = {6767-6771}, Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law}, Volume = 108, - Year = 2004, - Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}} + Year = 2004} @article{Klein01, Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein}, @@ -843,6 +872,8 @@ Abstract = {X-ray data are presented for the benchmark dipalmitoylphosphatidylcholine lipid bilayer in the most biologically relevant state in which the bilayers are fully hydrated and in the fluid (liquid-crystalline) phase. Form factors F(qz) are obtained from a combination of two sample preparations, oriented stacks of bilayers for qz extending to 0.85 A-1 and unilamellar vesicles for smaller qz. Modeling obtains the electron density profile and values for the area per molecule, for the locations of the component groups, and for the different types of thicknesses of the bilayer, such as the hydrocarbon thickness and the steric thickness. }, Author = {Kucerka, Norbert and Tristram-Nagle, Stephanie and Nagle, John F.}, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83}, + Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:57 -0500}, Doi = {10.1529/biophysj.106.086017}, @@ -853,9 +884,7 @@ Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}}, Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83}, Volume = 90, - Year = 2006, - Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83}, - Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017}} + Year = 2006} @article{deJoannis06, Author = {J. de~Joannis and F.~Y. Jiang and J.~T. Kindt}, @@ -1000,6 +1029,7 @@ @article{Seung1988, Author = {Seung, H. S. and Nelson, David R.}, + Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:58 -0500}, Doi = {10.1103/PhysRevA.38.1005}, @@ -1011,8 +1041,7 @@ Publisher = {American Physical Society}, Title = {Defects in flexible membranes with crystalline order}, Volume = 38, - Year = 1988, - Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005}} + Year = 1988} @article{Monroe95, Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland}, @@ -1325,6 +1354,7 @@ @article{Arnold02, Author = {A. Arnold and J. {de Joannis} and C. Holm}, + Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:58 -0500}, Doi = {10.1063/1.149195}, @@ -1334,11 +1364,11 @@ Pages = {2496-2502}, Title = {Electrostatics in periodic slab geometries. I}, Volume = 117, - Year = 2002, - Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}} + Year = 2002} @article{deJoannis02, Author = {J. {de Joannis} and A. Arnold and C. Holm}, + Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:58 -0500}, Doi = {10.1063/1.149195}, @@ -1348,8 +1378,7 @@ Pages = {2503-2512}, Title = {Electrostatics in periodic slab geometries. II}, Volume = 117, - Year = 2002, - Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}} + Year = 2002} @article{Barenco95, Author = {A. Barenco and C.~H. Bennett and R. Cleve and D.~P. DiVincenzo and N. Margolus and P. Shor and T. Sleator and J.~A. Smolin and H. Weinfurter}, @@ -1484,6 +1513,7 @@ @article{Brodka04, Author = {A. Br\'{o}dka}, + Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086}, 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}, @@ -1492,8 +1522,7 @@ Pages = {62-67}, Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry}, Volume = 400, - Year = 2004, - Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086}} + Year = 2004} @article{Chuang98, Author = {I. Chuang and N. Gershenfeld and M. Kubinec}, @@ -1561,6 +1590,7 @@ 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.}, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:59 -0500}, Journal = bj, @@ -1571,8 +1601,7 @@ Ty = {JOUR}, Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609}, Volume = 88, - Year = 2005, - Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609}} + Year = 2005} @inbook{Blumen86, Address = {Amsterdam}, @@ -1843,6 +1872,7 @@ @article{Goldstein88, Author = {Raymond E. Goldstein and Stanislas Leibler}, + Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUGCQpYJHZlcnNpb25UJHRvcFkkYXJjaGl2ZXJYJG9iamVjdHMSAAGGoNEHCFRyb290gAFfEA9OU0tleWVkQXJjaGl2ZXKoCwwXGBkdJCVVJG51bGzTDQ4PEBEUViRjbGFzc1dOUy5rZXlzWk5TLm9iamVjdHOAB6ISE4ACgAOiFRaABIAGWWFsaWFzRGF0YVxyZWxhdGl2ZVBhdGjSDRobHFdOUy5kYXRhgAVPEQHUAAAAAAHUAAIAAAhnZXplbHRlcgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATkoAAf////8fY2l0LWFicy1lbmRub3RlLTI0I0ZGRkZGRkZGLnJpcwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA/////wAAAAAAAAAAAAAAAAADAAIAABKBY3UAAAAAAAAAAAAAAAAACURvd25sb2FkcwAAAgBILzpob21lOm1hdWw6Z2V6ZWx0ZXI6Z2V6ZWx0ZXI6RG93bmxvYWRzOmNpdC1hYnMtZW5kbm90ZS0yNDIzODAwOC5lbncucmlzAA4AQgAgAGMAaQB0AC0AYQBiAHMALQBlAG4AZABuAG8AdABlAC0AMgA0ADIAMwA4ADAAMAA4AC4AZQBuAHcALgByAGkAcwAPABIACABnAGUAegBlAGwAdABlAHIAEgArL0Rvd25sb2Fkcy9jaXQtYWJzLWVuZG5vdGUtMjQyMzgwMDguZW53LnJpcwAAEwAcL2hvbWUvbWF1bC9nZXplbHRlci9nZXplbHRlcgAJACkAKWNyYm0AAHBvc3gvaG9tZS9tYXVsL2dlemVsdGVyL2dlemVsdGVyAAAAFQACABz//wAA0h4fICFYJGNsYXNzZXNaJGNsYXNzbmFtZaMhIiNdTlNNdXRhYmxlRGF0YVZOU0RhdGFYTlNPYmplY3RfEDMuLi8uLi8uLi9Eb3dubG9hZHMvY2l0LWFicy1lbmRub3RlLTI0MjM4MDA4LmVudy5yaXPSHh8mJ6InI1xOU0RpY3Rpb25hcnkACAARABoAHwApADIANwA6AD8AQQBTAFwAYgBpAHAAeACDAIUAiACKAIwAjwCRAJMAnQCqAK8AtwC5ApEClgKfAqoCrgK8AsMCzAMCAwcDCgAAAAAAAAIBAAAAAAAAACgAAAAAAAAAAAAAAAAAAAMX}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:59 -0500}, Journal = prl, @@ -1850,8 +1880,7 @@ Pages = {2213-2216}, Title = {Model for Lamellar Phases of Interacting Lipid Membranes}, Volume = 61, - Year = 1988, - Bdsk-File-1 = {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}} + Year = 1988} @article{Daw89, Author = {Murray~S. Daw}, @@ -1956,6 +1985,7 @@ @article{Weber00, Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon}, + Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:00 -0500}, Doi = {10.1021/jp9937757}, @@ -1965,8 +1995,7 @@ Pages = {3668-3675}, Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation}, Volume = 104, - Year = 2000, - Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757}} + Year = 2000} @article{Venable00, Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor}, @@ -2099,6 +2128,7 @@ @article{Steinbach94, Author = {P.~J. Steinbach and B.~R. Brooks}, + Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150702}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:00 -0500}, Doi = {10.1002/jcc.540150702}, @@ -2107,8 +2137,7 @@ Pages = {667-683}, Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation}, Volume = 15, - Year = 1994, - Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150702}} + Year = 1994} @article{McKinnon92, Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks}, @@ -2382,11 +2411,11 @@ Volume = 51, Year = 1995} -@book{Cevc87, +@book{Cevc80, Address = {New York}, Author = {Gregor Cevc and Derek Marsh}, Date-Added = {2008-01-08 14:58:56 -0500}, - Date-Modified = {2008-01-08 14:59:01 -0500}, + Date-Modified = {2008-03-20 12:27:15 -0400}, Publisher = {Wiley-Interscience}, Title = {Phospholipid Bilayers}, Year = 1980} @@ -2825,6 +2854,8 @@ 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.}, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626}, + Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:02 -0500}, Doi = {10.1529/biophysj.104.056606}, @@ -2835,9 +2866,7 @@ 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, - Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626}, - Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606}} + Year = 2005} @article{Lenz07, Author = {Olaf Lenz and Friederike Schmid}, @@ -3248,6 +3277,7 @@ @article{Mutz1991, Author = {Mutz, M. and Bensimon, D. and Brienne, M. J.}, + Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:03 -0500}, Doi = {10.1103/PhysRevLett.67.923}, @@ -3259,8 +3289,7 @@ Publisher = {American Physical Society}, Title = {Wrinkling transition in partially polymerized vesicles}, Volume = 67, - Year = 1991, - Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923}} + Year = 1991} @article{Wendt78, Author = {H. Wendt and F.~F. Abraham}, @@ -3335,6 +3364,7 @@ @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.}, + Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}, Date-Added = {2008-01-08 14:57:14 -0500}, Date-Modified = {2008-01-08 14:57:14 -0500}, Journal = {Chemical Engineering Science}, @@ -3344,8 +3374,7 @@ Ty = {JOUR}, Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}, Volume = 24, - Year = 1969, - Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}} + Year = 1969} @article{Stimson:1926qy, Author = {Stimson, M and Jeffery, GB}, @@ -3362,6 +3391,7 @@ 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}, + Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}, Da = 20060407, Date-Added = {2008-01-08 14:47:56 -0500}, Date-Modified = {2008-01-08 14:48:06 -0500}, @@ -3386,11 +3416,12 @@ Stat = {PubMed-not-MEDLINE}, Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.}, Volume = 124, - Year = 2006, - Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}} + Year = 2006} @article{sun:031602, Author = {Xiuquan Sun and J. Daniel Gezelter}, + Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602}, + Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}, Date-Added = {2008-01-08 14:42:33 -0500}, Date-Modified = {2008-01-08 14:42:33 -0500}, Doi = {10.1103/PhysRevE.75.031602}, @@ -3404,15 +3435,14 @@ Title = {Spontaneous corrugation of dipolar membranes}, Url = {http://link.aps.org/abstract/PRE/v75/e031602}, Volume = 75, - Year = 2007, - Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602}, - Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}} + 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 {Garc\'{i}a de la Torre}, Jose}, Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose}, + Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}, Da = 20070813, Date-Added = {2008-01-08 14:38:03 -0500}, Date-Modified = {2008-01-08 14:38:49 -0500}, @@ -3442,8 +3472,7 @@ Stat = {MEDLINE}, Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.}, Volume = 8, - Year = 2007, - Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}} + Year = 2007} @article{Torre2003, Abstract = {While the prediction of hydrodynamic properties of rigid particles @@ -6691,6 +6720,8 @@ Abstract = {It has been demonstrated that a "near-Levinthal" cooperative mechanism, whereby the common G[o] interaction scheme is augmented by an extra favorability for the native state as a whole, can lead to apparent two-state folding/unfolding kinetics over a broad range of native stabilities in lattice models of proteins. Here such a mechanism is shown to be generalizable to a simplified continuum (off-lattice) Langevin dynamics model with a C{alpha} protein chain representation, with the resulting chevron plots exhibiting an extended quasilinear regime reminiscent of that of apparent two-state real proteins. Similarly high degrees of cooperativity are possible in G[o]-like continuum models with rudimentary pairwise desolvation barriers as well. In these models, cooperativity increases with increasing desolvation barrier height, suggesting strongly that two-state-like folding/unfolding kinetics would be achievable when the pairwise desolvation barrier becomes sufficiently high. Besides cooperativity, another generic folding property of interest that has emerged from published experiments on several apparent two-state proteins is that their folding relaxation under constant native stability (isostability) conditions is essentially Arrhenius, entailing high intrinsic enthalpic folding barriers of [~]17-30 kcal/mol. Based on a new analysis of published data on barnase, here we propose that a similar property should also apply to a certain class of non-two-state proteins that fold with chevron rollovers. However, several continuum G[o]-like constructs considered here fail to predict any significant intrinsic enthalpic folding barrier under isostability conditions; thus the physical origin of such barriers in real proteins remains to be elucidated. }, Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun}, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520}, + Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}, Doi = {10.1529/biophysj.104.057471}, Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf}, Journal = {Biophys. J.}, @@ -6699,6 +6730,27 @@ Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}}, Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520}, Volume = 89, - Year = 2005, - Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520}, - Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}} + Year = 2005} + +@article{JoseGarciadelaTorre02012000, + Abstract = {The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (Carrasco and Garcia de la Torre, 1999, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overlapping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 proteins. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 A, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A computational shortcut makes the procedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer program. +}, + Author = {{Garc\'{i}a de la Torre}, Jose and Huertas, Maria L. and Carrasco, Beatriz}, + Eprint = {http://www.biophysj.org/cgi/reprint/78/2/719.pdf}, + Journal = bj, + Number = {2}, + Pages = {719-730}, + Title = {{Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure}}, + Url = {http://www.biophysj.org/cgi/content/abstract/78/2/719}, + Volume = {78}, + Year = {2000}} + +@article{GarciadelaTorreJ2002, + Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain}, + Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B.}, + Journal = {Biopolymers}, + Number = {3}, + Pages = {163-167}, + Title = {Hydrodynamic Properties of Rigid Macromolecules Composed of Ellipsoidal and Cylindrical Subunits}, + Volume = {63}, + Year = {2002}}