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Revision 3367 by gezelter, Thu Mar 13 22:16:01 2008 UTC vs.
Revision 3390 by xsun, Wed Apr 30 14:50:53 2008 UTC

# Line 2 | Line 2
2   %% http://bibdesk.sourceforge.net/
3  
4  
5 < %% Created for Dan Gezelter at 2008-03-13 17:04:26 -0400
5 > %% Created for Xiuquan Sun at 2008-04-30 10:19:14 -0400
6  
7  
8   %% Saved with string encoding Western (ASCII)
# Line 26 | Line 26
26  
27   @string{jcp = {J. Chem. Phys.}}
28  
29 – @string{jml = {J. Mol. Liq.}}
30 –
29   @string{jmb = {J. Mol. Bio.}}
30  
31 + @string{jml = {J. Mol. Liq.}}
32 +
33   @string{jpc = {J. Phys. Chem.}}
34  
35   @string{jpca = {J. Phys. Chem. A}}
# Line 57 | Line 57
57   @string{rmp = {Rev. Mod. Phys.}}
58  
59  
60 + @article{GarciadelaTorreJjp0647941,
61 +        Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain},
62 +        Author = {{Garc\'{i}a de la Torre}, Jose and del Rio Echenique, G. and Ortega, A.},
63 +        Date-Added = {2008-04-30 10:14:50 -0400},
64 +        Date-Modified = {2008-04-30 10:14:50 -0400},
65 +        Issn = {1520-6106},
66 +        Journal = jpcb,
67 +        Number = {5},
68 +        Pages = {955-961},
69 +        Title = {Improved Calculation of Rotational Diffusion and Intrinsic Viscosity of Bead Models for Macromolecules and Nanoparticles},
70 +        Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0647941},
71 +        Volume = {111},
72 +        Year = {2007}}
73 +
74 + @article{Garcia-de-la-Torre:2001wd,
75 +        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.},
76 +        Author = {{Garc\'{i}a de la Torre}, Jose },
77 +        Date-Added = {2008-04-29 15:11:32 -0400},
78 +        Date-Modified = {2008-04-29 15:11:32 -0400},
79 +        Journal = {Biophysical Chemistry},
80 +        Keywords = {Rigid macromolecules; Hydrodynamic properties; Bead-shell model; Three-dimensional structure},
81 +        Number = {3},
82 +        Pages = {265--274},
83 +        Title = {Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape},
84 +        Ty = {JOUR},
85 +        Url = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953},
86 +        Volume = {94},
87 +        Year = {2001}}
88 +
89   @article{Peters:1999uq,
90          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.},
91          Author = {Peters, MH},
# Line 97 | Line 126
126   @article{Nienhuis:1970lr,
127          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.},
128          Author = {Nienhuis, G. },
129 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413},
130          Date-Added = {2008-03-13 16:53:44 -0400},
131          Date-Modified = {2008-03-13 16:53:44 -0400},
132          Journal = {Physica},
# Line 106 | Line 136
136          Ty = {JOUR},
137          Url = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413},
138          Volume = {49},
139 <        Year = {1970},
110 <        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}}
139 >        Year = {1970}}
140  
141   @article{SunX._jp0762020,
142          Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556},
143          Author = {Sun, X. and Gezelter, J.D.},
144 +        Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020},
145          Date-Added = {2008-02-15 13:48:18 -0500},
146          Date-Modified = {2008-02-15 13:48:18 -0500},
147          Issn = {1520-6106},
# Line 121 | Line 151
151          Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes},
152          Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020},
153          Volume = {112},
154 <        Year = {2008},
125 <        Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}}
154 >        Year = {2008}}
155  
156   @book{Schlick2002,
157          Address = {Secaucus, NJ, USA},
# Line 139 | Line 168
168          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},
169          Date-Added = {2008-01-22 10:38:33 -0500},
170          Date-Modified = {2008-01-22 10:38:49 -0500},
142 –        Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
171          Journal = jcc,
172 +        Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
173          Pages = {159--184},
174          Timescited = 0,
175          Title = {{MBO(N)D:} A multibody method for long-time molecular dynamics simulations},
# Line 183 | Line 212
212  
213   @inbook{Ramachandran1996,
214          Address = {Providence, Rhode Island},
215 <        author = {Gomathi Ramachandran and Tamar Schlick},
215 >        Author = {Gomathi Ramachandran and Tamar Schlick},
216          Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
217          Date-Added = {2008-01-22 10:03:42 -0500},
218          Date-Modified = {2008-01-22 10:06:57 -0500},
# Line 241 | Line 270
270  
271   @article{Torre:1983lr,
272          Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
273 +        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1},
274          Date-Added = {2008-01-11 16:16:43 -0500},
275          Date-Modified = {2008-01-11 16:16:43 -0500},
276          Journal = jcp,
# Line 254 | Line 284
284          Ty = {JOUR},
285          Url = {http://link.aip.org/link/?JCP/79/2454/1},
286          Volume = 79,
287 <        Year = 1983,
258 <        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}}
287 >        Year = 1983}
288  
289   @article{PhysRev.119.53,
290          Author = {Favro, L. Dale},
291 +        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53},
292          Date-Added = {2008-01-09 16:57:02 -0500},
293          Date-Modified = {2008-01-09 16:57:02 -0500},
294          Doi = {10.1103/PhysRev.119.53},
# Line 270 | Line 300
300          Publisher = {American Physical Society},
301          Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body},
302          Volume = 119,
303 <        Year = 1960,
274 <        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}}
303 >        Year = 1960}
304  
305   @article{hess:209,
306          Author = {Berk Hess},
307 +        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
308 +        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362},
309          Date-Added = {2008-01-08 16:41:06 -0500},
310          Date-Modified = {2008-01-08 16:41:06 -0500},
311          Doi = {10.1063/1.1421362},
# Line 286 | Line 317
317          Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
318          Url = {http://link.aip.org/link/?JCP/116/209/1},
319          Volume = 116,
320 <        Year = 2002,
290 <        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
291 <        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}}
320 >        Year = 2002}
321  
322   @article{Garcia-de-la-Torre:1997qy,
323          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.},
# Line 349 | Line 378
378   @article{Schmidt:2003kx,
379          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.},
380          Author = {Schmidt, JR and Skinner, JL},
381 +        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442},
382          Date-Added = {2008-01-08 15:12:53 -0500},
383          Date-Modified = {2008-01-08 15:13:21 -0500},
384          Doi = {DOI 10.1063/1.1610442},
# Line 356 | Line 386
386          Pages = {8062-8068},
387          Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
388          Volume = 119,
389 <        Year = 2003,
360 <        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}
389 >        Year = 2003}
390  
391   @article{Schmidt:2004fj,
392          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.},
393          Author = {Schmidt, JR and Skinner, JL},
394 +        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r},
395          Date-Added = {2008-01-08 15:12:53 -0500},
396          Date-Modified = {2008-01-08 15:13:20 -0500},
397          Doi = {DOI 10.1021/jp037185r},
# Line 369 | Line 399
399          Pages = {6767-6771},
400          Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
401          Volume = 108,
402 <        Year = 2004,
373 <        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}}
402 >        Year = 2004}
403  
404   @article{Klein01,
405          Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
# Line 843 | Line 872
872          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.
873   },
874          Author = {Kucerka, Norbert and Tristram-Nagle, Stephanie and Nagle, John F.},
875 +        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
876 +        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017},
877          Date-Added = {2008-01-08 14:58:56 -0500},
878          Date-Modified = {2008-01-08 14:58:57 -0500},
879          Doi = {10.1529/biophysj.106.086017},
# Line 853 | Line 884
884          Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}},
885          Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
886          Volume = 90,
887 <        Year = 2006,
857 <        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
858 <        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017}}
887 >        Year = 2006}
888  
889   @article{deJoannis06,
890          Author = {J. de~Joannis and F.~Y. Jiang and J.~T. Kindt},
# Line 1000 | Line 1029
1029  
1030   @article{Seung1988,
1031          Author = {Seung, H. S. and Nelson, David R.},
1032 +        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005},
1033          Date-Added = {2008-01-08 14:58:56 -0500},
1034          Date-Modified = {2008-01-08 14:58:58 -0500},
1035          Doi = {10.1103/PhysRevA.38.1005},
# Line 1011 | Line 1041
1041          Publisher = {American Physical Society},
1042          Title = {Defects in flexible membranes with crystalline order},
1043          Volume = 38,
1044 <        Year = 1988,
1015 <        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005}}
1044 >        Year = 1988}
1045  
1046   @article{Monroe95,
1047          Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
# Line 1325 | Line 1354
1354  
1355   @article{Arnold02,
1356          Author = {A. Arnold and J. {de Joannis} and C. Holm},
1357 +        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195},
1358          Date-Added = {2008-01-08 14:58:56 -0500},
1359          Date-Modified = {2008-01-08 14:58:58 -0500},
1360          Doi = {10.1063/1.149195},
# Line 1334 | Line 1364
1364          Pages = {2496-2502},
1365          Title = {Electrostatics in periodic slab geometries. I},
1366          Volume = 117,
1367 <        Year = 2002,
1338 <        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1367 >        Year = 2002}
1368  
1369   @article{deJoannis02,
1370          Author = {J. {de Joannis} and A. Arnold and C. Holm},
1371 +        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195},
1372          Date-Added = {2008-01-08 14:58:56 -0500},
1373          Date-Modified = {2008-01-08 14:58:58 -0500},
1374          Doi = {10.1063/1.149195},
# Line 1348 | Line 1378
1378          Pages = {2503-2512},
1379          Title = {Electrostatics in periodic slab geometries. II},
1380          Volume = 117,
1381 <        Year = 2002,
1352 <        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1381 >        Year = 2002}
1382  
1383   @article{Barenco95,
1384          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},
# Line 1484 | Line 1513
1513  
1514   @article{Brodka04,
1515          Author = {A. Br\'{o}dka},
1516 +        Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086},
1517          Date-Added = {2008-01-08 14:58:56 -0500},
1518          Date-Modified = {2008-01-08 14:58:59 -0500},
1519          Doi = {10.1016/j.cplett.2004.10.086},
# Line 1492 | Line 1522
1522          Pages = {62-67},
1523          Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
1524          Volume = 400,
1525 <        Year = 2004,
1496 <        Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086}}
1525 >        Year = 2004}
1526  
1527   @article{Chuang98,
1528          Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
# Line 1561 | Line 1590
1590          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. },
1591          Annote = {10.1529/biophysj.104.050096},
1592          Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.},
1593 +        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
1594          Date-Added = {2008-01-08 14:58:56 -0500},
1595          Date-Modified = {2008-01-08 14:58:59 -0500},
1596          Journal = bj,
# Line 1571 | Line 1601
1601          Ty = {JOUR},
1602          Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
1603          Volume = 88,
1604 <        Year = 2005,
1575 <        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609}}
1604 >        Year = 2005}
1605  
1606   @inbook{Blumen86,
1607          Address = {Amsterdam},
# Line 1843 | Line 1872
1872  
1873   @article{Goldstein88,
1874          Author = {Raymond E. Goldstein and Stanislas Leibler},
1875 +        Bdsk-File-1 = {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},
1876          Date-Added = {2008-01-08 14:58:56 -0500},
1877          Date-Modified = {2008-01-08 14:58:59 -0500},
1878          Journal = prl,
# Line 1850 | Line 1880
1880          Pages = {2213-2216},
1881          Title = {Model for Lamellar Phases of Interacting Lipid Membranes},
1882          Volume = 61,
1883 <        Year = 1988,
1854 <        Bdsk-File-1 = {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}}
1883 >        Year = 1988}
1884  
1885   @article{Daw89,
1886          Author = {Murray~S. Daw},
# Line 1956 | Line 1985
1985  
1986   @article{Weber00,
1987          Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
1988 +        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757},
1989          Date-Added = {2008-01-08 14:58:56 -0500},
1990          Date-Modified = {2008-01-08 14:59:00 -0500},
1991          Doi = {10.1021/jp9937757},
# Line 1965 | Line 1995
1995          Pages = {3668-3675},
1996          Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
1997          Volume = 104,
1998 <        Year = 2000,
1969 <        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757}}
1998 >        Year = 2000}
1999  
2000   @article{Venable00,
2001          Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
# Line 2099 | Line 2128
2128  
2129   @article{Steinbach94,
2130          Author = {P.~J. Steinbach and B.~R. Brooks},
2131 +        Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150702},
2132          Date-Added = {2008-01-08 14:58:56 -0500},
2133          Date-Modified = {2008-01-08 14:59:00 -0500},
2134          Doi = {10.1002/jcc.540150702},
# Line 2107 | Line 2137
2137          Pages = {667-683},
2138          Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
2139          Volume = 15,
2140 <        Year = 1994,
2111 <        Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150702}}
2140 >        Year = 1994}
2141  
2142   @article{McKinnon92,
2143          Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
# Line 2382 | Line 2411
2411          Volume = 51,
2412          Year = 1995}
2413  
2414 < @book{Cevc87,
2414 > @book{Cevc80,
2415          Address = {New York},
2416          Author = {Gregor Cevc and Derek Marsh},
2417          Date-Added = {2008-01-08 14:58:56 -0500},
2418 <        Date-Modified = {2008-01-08 14:59:01 -0500},
2418 >        Date-Modified = {2008-03-20 12:27:15 -0400},
2419          Publisher = {Wiley-Interscience},
2420          Title = {Phospholipid Bilayers},
2421          Year = 1980}
# Line 2825 | Line 2854
2854          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.
2855   },
2856          Author = {Kucerka, Norbert and Liu, Yufeng and Chu, Nanjun and Petrache, Horia I. and Tristram-Nagle, Stephanie and Nagle, John F.},
2857 +        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2858 +        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606},
2859          Date-Added = {2008-01-08 14:58:56 -0500},
2860          Date-Modified = {2008-01-08 14:59:02 -0500},
2861          Doi = {10.1529/biophysj.104.056606},
# Line 2835 | Line 2866
2866          Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}},
2867          Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2868          Volume = 88,
2869 <        Year = 2005,
2839 <        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2840 <        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606}}
2869 >        Year = 2005}
2870  
2871   @article{Lenz07,
2872          Author = {Olaf Lenz and Friederike Schmid},
# Line 3248 | Line 3277
3277  
3278   @article{Mutz1991,
3279          Author = {Mutz, M. and Bensimon, D. and Brienne, M. J.},
3280 +        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923},
3281          Date-Added = {2008-01-08 14:58:56 -0500},
3282          Date-Modified = {2008-01-08 14:59:03 -0500},
3283          Doi = {10.1103/PhysRevLett.67.923},
# Line 3259 | Line 3289
3289          Publisher = {American Physical Society},
3290          Title = {Wrinkling transition in partially polymerized vesicles},
3291          Volume = 67,
3292 <        Year = 1991,
3263 <        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923}}
3292 >        Year = 1991}
3293  
3294   @article{Wendt78,
3295          Author = {H. Wendt and F.~F. Abraham},
# Line 3335 | Line 3364
3364   @article{Davis:1969uq,
3365          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.},
3366          Author = {Davis, M. H.},
3367 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
3368          Date-Added = {2008-01-08 14:57:14 -0500},
3369          Date-Modified = {2008-01-08 14:57:14 -0500},
3370          Journal = {Chemical Engineering Science},
# Line 3344 | Line 3374
3374          Ty = {JOUR},
3375          Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
3376          Volume = 24,
3377 <        Year = 1969,
3348 <        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}}
3377 >        Year = 1969}
3378  
3379   @article{Stimson:1926qy,
3380          Author = {Stimson, M and Jeffery, GB},
# Line 3362 | Line 3391
3391          Address = {Dipartimento di Chimica Fisica e Inorganica, and INSTM, Universita di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.},
3392          Au = {Orlandi, S and Berardi, R and Steltzer, J and Zannoni, C},
3393          Author = {Orlandi, Silvia and Berardi, Roberto and Steltzer, Joachim and Zannoni, Claudio},
3394 +        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622},
3395          Da = 20060407,
3396          Date-Added = {2008-01-08 14:47:56 -0500},
3397          Date-Modified = {2008-01-08 14:48:06 -0500},
# Line 3386 | Line 3416
3416          Stat = {PubMed-not-MEDLINE},
3417          Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.},
3418          Volume = 124,
3419 <        Year = 2006,
3390 <        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}}
3419 >        Year = 2006}
3420  
3421   @article{sun:031602,
3422          Author = {Xiuquan Sun and J. Daniel Gezelter},
3423 +        Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602},
3424 +        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602},
3425          Date-Added = {2008-01-08 14:42:33 -0500},
3426          Date-Modified = {2008-01-08 14:42:33 -0500},
3427          Doi = {10.1103/PhysRevE.75.031602},
# Line 3404 | Line 3435
3435          Title = {Spontaneous corrugation of dipolar membranes},
3436          Url = {http://link.aps.org/abstract/PRE/v75/e031602},
3437          Volume = 75,
3438 <        Year = 2007,
3408 <        Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602},
3409 <        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}}
3438 >        Year = 2007}
3439  
3440   @article{Ortega:2007lr,
3441          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.},
3442          Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.},
3443          Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3444          Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3445 +        Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f},
3446          Da = 20070813,
3447          Date-Added = {2008-01-08 14:38:03 -0500},
3448          Date-Modified = {2008-01-08 14:38:49 -0500},
# Line 3442 | Line 3472
3472          Stat = {MEDLINE},
3473          Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.},
3474          Volume = 8,
3475 <        Year = 2007,
3446 <        Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}}
3475 >        Year = 2007}
3476  
3477   @article{Torre2003,
3478          Abstract = {While the prediction of hydrodynamic properties of rigid particles
# Line 6691 | Line 6720
6720          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.
6721   },
6722          Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun},
6723 +        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6724 +        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471},
6725          Doi = {10.1529/biophysj.104.057471},
6726          Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf},
6727          Journal = {Biophys. J.},
# Line 6699 | Line 6730
6730          Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}},
6731          Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6732          Volume = 89,
6733 <        Year = 2005,
6734 <        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6735 <        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}}
6733 >        Year = 2005}
6734 >
6735 > @article{JoseGarciadelaTorre02012000,
6736 >        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.
6737 > },
6738 >        Author = {{Garc\'{i}a de la Torre}, Jose and Huertas, Maria L. and Carrasco, Beatriz},
6739 >        Eprint = {http://www.biophysj.org/cgi/reprint/78/2/719.pdf},
6740 >        Journal = bj,
6741 >        Number = {2},
6742 >        Pages = {719-730},
6743 >        Title = {{Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure}},
6744 >        Url = {http://www.biophysj.org/cgi/content/abstract/78/2/719},
6745 >        Volume = {78},
6746 >        Year = {2000}}
6747 >
6748 > @article{GarciadelaTorreJ2002,
6749 >        Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain},
6750 >        Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B.},
6751 >        Journal = {Biopolymers},
6752 >        Number = {3},
6753 >        Pages = {163-167},
6754 >        Title = {Hydrodynamic Properties of Rigid Macromolecules Composed of Ellipsoidal and Cylindrical Subunits},
6755 >        Volume = {63},
6756 >        Year = {2002}}

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