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Revision 3352 by gezelter, Fri Feb 29 22:02:46 2008 UTC vs.
Revision 3391 by gezelter, Wed Apr 30 16:16:25 2008 UTC

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2   %% http://bibdesk.sourceforge.net/
3  
4  
5 < %% Created for Dan Gezelter at 2008-02-15 13:48:27 -0500
5 > %% Created for Dan Gezelter at 2008-04-30 12:15:56 -0400
6  
7  
8   %% Saved with string encoding Western (ASCII)
# Line 10 | Line 10
10  
11   @string{acp = {Adv. Chem. Phys.}}
12  
13 + @string{bj = {Biophys. J.}}
14 +
15   @string{ccp5 = {CCP5 Information Quarterly}}
16  
17   @string{cp = {Chem. Phys.}}
# Line 24 | Line 26
26  
27   @string{jcp = {J. Chem. Phys.}}
28  
29 + @string{jmb = {J. Mol. Bio.}}
30 +
31   @string{jml = {J. Mol. Liq.}}
32  
33   @string{jpc = {J. Phys. Chem.}}
# Line 51 | Line 55
55   @string{prl = {Phys. Rev. Lett.}}
56  
57   @string{rmp = {Rev. Mod. Phys.}}
58 +
59 +
60 + @article{Jeffrey:2006dk,
61 +        Author = {Jeffrey,D. J. and Onishi,Y.},
62 +        Date-Added = {2008-04-30 12:15:31 -0400},
63 +        Date-Modified = {2008-04-30 12:15:31 -0400},
64 +        Journal = {Journal of Fluid Mechanics Digital Archive},
65 +        M3 = {10.1017/S0022112084000355},
66 +        Number = {-1},
67 +        Pages = {261--290},
68 +        Title = {Calculation of the resistance and mobility functions for two unequal rigid spheres in low-Reynolds-number flow},
69 +        Ty = {JOUR},
70 +        Volume = {139},
71 +        Year = {2006}}
72 +
73 + @article{Goldman:1966ph,
74 +        Abstract = { Bipolar coordinates are employed to determine the terminal settling motion of two, identical, homogeneous, unconstrained spheres in an unbounded fluid at small Reynolds numbers. Exact numerical values are obtained for the linear and angular velocities of the spheres as a function of their relative separation and of the orientation of their line-of-centers relative to the direction of gravity. Comparison with published experimental data indicates good agreement, especially when wall effects are taken into account.},
75 +        Author = {Goldman, A. J. and Cox, R. G. and Brenner, H.},
76 +        Date-Added = {2008-04-30 12:12:54 -0400},
77 +        Date-Modified = {2008-04-30 12:12:54 -0400},
78 +        Journal = {Chemical Engineering Science},
79 +        Number = {12},
80 +        Pages = {1151--1170},
81 +        Title = {The slow motion of two identical arbitrarily oriented spheres through a viscous fluid},
82 +        Ty = {JOUR},
83 +        Url = {http://www.sciencedirect.com/science/article/B6TFK-44360XJ-D0/1/c14cf5c48fab65f0aaa096e60d15fa87},
84 +        Volume = {21},
85 +        Year = {1966},
86 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-44360XJ-D0/1/c14cf5c48fab65f0aaa096e60d15fa87}}
87 +
88 + @article{Brenner:1972th,
89 +        Abstract = { A general theory is presented for determining the quasistatic Stokes resistance of a particle or an aggregate of particles of arbitrary shape which move with arbitrary translational and rotational velocities in an infinite viscous fluid subjected to a general linear shear flow in the absence of the particles. It is shown that the hydrodynamic resistance of the particles may be characterized by two intrinsic matrices-the grand resistance matrix and the shear resistance matrix, the elements of each matrix being dependent only upon the instantaneous geometrical configuration of the multiparticle system. Explicit expressions for these matrix elements are given for a single ellipsoidal particle and for two spheres. Analytical, closed-form expressions are given for the case where the spheres are widely spaced compared with their radii. When the separation between the spheres is arbitrary, the matrix elements are only determinate numerically for specified ratios of sphere radii and center-to-center separation distances. These numerical values are derived from available bipolar-coordinate system solutions for two spheres. Besides providing a compact and systematic representation of the intrinsic Stokes resistance of multiparticle systems subjected to shear, which does not depend upon the precise velocities of the particles or on the nature of the shear flow, it is demonstrated (by way of example) that the matrix representation permits an immediate determination of the translational and rotational velocities of the individual particles in a neutrally buoyant multiparticle system.},
90 +        Author = {Brenner, Howard and O'Neill, Michael E.},
91 +        Date-Added = {2008-04-30 12:12:49 -0400},
92 +        Date-Modified = {2008-04-30 12:12:49 -0400},
93 +        Journal = {Chemical Engineering Science},
94 +        Number = {7},
95 +        Pages = {1421--1439},
96 +        Title = {On the Stokes resistance of multiparticle systems in a linear shear field},
97 +        Ty = {JOUR},
98 +        Url = {http://www.sciencedirect.com/science/article/B6TFK-444GW12-16J/1/ba6bda9d1e50c88fea6cd92aac2f6bd7},
99 +        Volume = {27},
100 +        Year = {1972},
101 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-444GW12-16J/1/ba6bda9d1e50c88fea6cd92aac2f6bd7}}
102 +
103 + @article{GarciadelaTorreJjp0647941,
104 +        Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain},
105 +        Author = {{Garc\'{i}a de la Torre}, Jose and del Rio Echenique, G. and Ortega, A.},
106 +        Date-Added = {2008-04-30 10:14:50 -0400},
107 +        Date-Modified = {2008-04-30 10:14:50 -0400},
108 +        Issn = {1520-6106},
109 +        Journal = jpcb,
110 +        Number = {5},
111 +        Pages = {955-961},
112 +        Title = {Improved Calculation of Rotational Diffusion and Intrinsic Viscosity of Bead Models for Macromolecules and Nanoparticles},
113 +        Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0647941},
114 +        Volume = {111},
115 +        Year = {2007},
116 +        Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0647941}}
117 +
118 + @article{Garcia-de-la-Torre:2001wd,
119 +        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.},
120 +        Author = {{Garc\'{i}a de la Torre}, Jose },
121 +        Date-Added = {2008-04-29 15:11:32 -0400},
122 +        Date-Modified = {2008-04-29 15:11:32 -0400},
123 +        Journal = {Biophysical Chemistry},
124 +        Keywords = {Rigid macromolecules; Hydrodynamic properties; Bead-shell model; Three-dimensional structure},
125 +        Number = {3},
126 +        Pages = {265--274},
127 +        Title = {Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape},
128 +        Ty = {JOUR},
129 +        Url = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953},
130 +        Volume = {94},
131 +        Year = {2001},
132 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953}}
133 +
134 + @article{Peters:1999uq,
135 +        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.},
136 +        Author = {Peters, MH},
137 +        Date-Added = {2008-03-13 16:54:59 -0400},
138 +        Date-Modified = {2008-03-13 16:56:54 -0400},
139 +        Journal = {Journal of Statistical Physics},
140 +        Keywords = {Brownian particle; Fokker Planck equation; adsorption; molecular friction; force autocorrelation function; molecular dynamics},
141 +        Pages = {557-586},
142 +        Timescited = {0},
143 +        Title = {Fokker-Planck equation, molecular friction, and molecular dynamics for Brownian particle transport near external solid surfaces},
144 +        Volume = {94},
145 +        Year = {1999}}
146  
147 + @article{Peters:1999qy,
148 +        Abstract = {The Fokker-Planck equation and molecular-based grand friction tensor are derived for the problem of rotational and translational motions of a structured Brownian particle, including the presence of a structured wall. Using the method of multiple time scales, it is shown that the time independent, grand friction tensor for the Brownian particle includes, in a general way, terms that account fur the fluid molecular mediated interactions with the wall. The resulting Fokker-Planck equation has important applications in processes involving site-specific adsorption of macromolecules, such as affinity chromotography, biological separations, and numerous cellular processes involving attachment of macromolecules. (C) 1999 American Institute of Physics. [S0021-9606(98)51748-5].},
149 +        Author = {Peters, MH},
150 +        Date-Added = {2008-03-13 16:54:59 -0400},
151 +        Date-Modified = {2008-03-13 16:56:44 -0400},
152 +        Journal = jcp,
153 +        Pages = {528-538},
154 +        Timescited = {0},
155 +        Title = {Fokker-Planck equation and the grand molecular friction tensor for coupled rotational and translational motions of structured Brownian particles near structured surfaces},
156 +        Volume = {110},
157 +        Year = {1999}}
158 +
159 + @article{Peters:2000fk,
160 +        Abstract = {Beginning with the molecular-based Fokker-Planck equation obtained previously [M. H. Peters, J. Chem. Phys. 110, 528 (1999); J. Stat. Phys. 94, 557 (1999)], the Smoluchowski diffusion equation is derived here to describe the spatial and orientational dynamics of molecularly structured macromolecules near molecularly structured surfaces. The formal scaling and perturbation methods employed allow the establishment of definite limits on the use of the Smoluchowski equation when surfaces are present. It is shown that the Smoluchowski equation reduces to that given previously [D. W. Condiff and J. S. Dahler, J. Chem. Phys. 44, 3988 (1966)] in the absence of external surfaces. A specific example application is given involving a spherical macromolecule with electrostatic charge segments near a planar surface with an arbitrary charge distribution. Finally, we show that the short-time solution to the Smoluchowski equation obtained here yields a Brownian dynamics method consistent with that given previously [E. Dickinson, S. A. Allison, and J. A. McCammon, J. Chem. Soc. Faraday Trans. 2 81, 591 (1985)] for orientable, interacting Brownian particles. This study has applications to problems involving site-specific adsorption of orientable, structured Brownian particles, such as association or adsorption of biological macromolecules to cellular surfaces and enzyme-substrate docking kinetics, to name a few. (C) 2000 American Institute of Physics. [S0021-9606(00)50112-3].},
161 +        Author = {Peters, MH},
162 +        Date-Added = {2008-03-13 16:54:59 -0400},
163 +        Date-Modified = {2008-03-13 16:56:20 -0400},
164 +        Journal = jcp,
165 +        Pages = {5488-5498},
166 +        Timescited = {0},
167 +        Title = {The Smoluchowski diffusion equation for structured macromolecules near structured surfaces},
168 +        Volume = {112},
169 +        Year = {2000}}
170 +
171 + @article{Nienhuis:1970lr,
172 +        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.},
173 +        Author = {Nienhuis, G. },
174 +        Date-Added = {2008-03-13 16:53:44 -0400},
175 +        Date-Modified = {2008-03-13 16:53:44 -0400},
176 +        Journal = {Physica},
177 +        Number = {1},
178 +        Pages = {26--48},
179 +        Title = {On the microscopic theory of Brownian motion with a rotational degree of freedom},
180 +        Ty = {JOUR},
181 +        Url = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413},
182 +        Volume = {49},
183 +        Year = {1970},
184 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}}
185  
186   @article{SunX._jp0762020,
187          Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556},
# Line 59 | Line 189
189          Date-Added = {2008-02-15 13:48:18 -0500},
190          Date-Modified = {2008-02-15 13:48:18 -0500},
191          Issn = {1520-6106},
192 <        Journal = {Journal of Physical Chemistry B},
192 >        Journal = jpcb,
193          Number = {7},
194          Pages = {1968-1975},
195          Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes},
# Line 78 | Line 208
208          Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
209          Year = {2002}}
210  
211 < @misc{Chun:2000fj,
211 > @article{Chun:2000fj,
212          Abstract = {A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5- to 30-fold over atomistic simulations have been realized in various applications of the method. (C) 2000 John Wiley \& Sons, Inc.},
213          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},
214          Date-Added = {2008-01-22 10:38:33 -0500},
215          Date-Modified = {2008-01-22 10:38:49 -0500},
216 +        Journal = jcc,
217          Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
218 <        Note = {Journal of Computational Chemistry},
219 <        Pages = {159-184},
220 <        Timescited = {0},
221 <        Title = {MBO(N)D: A multibody method for long-time molecular dynamics simulations},
222 <        Volume = {21},
92 <        Year = {2000}}
218 >        Pages = {159--184},
219 >        Timescited = 0,
220 >        Title = {{MBO(N)D:} A multibody method for long-time molecular dynamics simulations},
221 >        Volume = 21,
222 >        Year = 2000}
223  
224   @article{Fogolari:1996lr,
225          Abstract = {In an effort to reduce the number of degrees of freedom necessary to describe a polypeptide chain we analyze the statistical behavior of polypeptide chains when represented as C alpha chains, C alpha chains with C beta atoms attached, and C alpha chains with rotational ellipsoids as models of side chains. A statistical analysis on a restricted data set of 75 unrelated protein structures is performed. The comparison of the database distributions with those obtained by model calculation on very short polypeptide stretches allows the dissection of local versus nonlocal features of the distributions. The database distribution of the bend angles of polypeptide chains of pseudo bonded C alpha atoms spans a restricted range of values and shows a bimodal structure. On the other hand, the torsion angles of the C alpha chain may assume almost all possible values. The distribution is bimodal, but with a much broader probability distribution than for bend angles. The C alpha - C beta vectors may be taken as representative of the orientation of the lateral chain, as the direction of the bond is close to the direction of the vector joining C alpha to the ad hoc defined center of the "steric mass" of the side chain. Interestingly, both the bend angle defined by C alpha i-C alpha i+1-C beta i+1 and the torsional angle offset of the pseudo-dihedral C alpha i-C alpha i+1-C alpha i+2-C beta i+2 with respect to C alpha i-C alpha i+1-C alpha i+2-C alpha i+3 span a limited range of values. The latter results show that it is possible to give a more realistic representation of polypeptide chains without introducing additional degrees of freedom, i.e., by just adding to the C alpha chain a C beta with given side-chain properties. However, a more realistic description of side chains may be attained by modeling side chains as rotational ellipsoids that have roughly the same orientation and steric hindrance. To this end, we define the steric mass of an atom as proportional to its van der Waals volume and we calculate the side-chain inertia ellipsoid assuming that the steric mass of each atom is uniformly distributed within its van der Waals volume. Finally, we define the rotational ellipsoid representing the side chain as the uniform density ellipsoid possessing the same rotationally averaged inertia tensor of the side chain. The statistics of ellipsoid parameters support the possibility of representing a side chain via an ellipsoid, independently of the local conformation. To make this description useful for molecular modeling we describe ellipsoid-ellipsoid interactions via a Lennard-Jones potential that preserves the repulsive core of the interacting ellipsoids and takes into account their mutual orientation. Tests are performed for two different forms of the interaction potential on a set of high-resolution protein structures. Results are encouraging, in view of the drastic simplifications that were introduced.},
# Line 127 | Line 257
257  
258   @inbook{Ramachandran1996,
259          Address = {Providence, Rhode Island},
260 <        Author = {GOMATHI RAMACHANDRAN AND TAMAR SCHLICK},
260 >        Author = {Gomathi Ramachandran and Tamar Schlick},
261          Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
262          Date-Added = {2008-01-22 10:03:42 -0500},
263          Date-Modified = {2008-01-22 10:06:57 -0500},
# Line 140 | Line 270
270          Year = {1996}}
271  
272   @article{FIXMAN:1986lr,
273 <        Author = {FIXMAN, M},
273 >        Author = {Fixman, M},
274          Date-Added = {2008-01-22 09:59:29 -0500},
275          Date-Modified = {2008-01-22 09:59:35 -0500},
276          Journal = {Macromolecules},
# Line 187 | Line 317
317          Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
318          Date-Added = {2008-01-11 16:16:43 -0500},
319          Date-Modified = {2008-01-11 16:16:43 -0500},
320 <        Journal = {The Journal of Chemical Physics},
320 >        Journal = jcp,
321          Journal1 = {The Journal of Chemical Physics},
322          Journal2 = {J. Chem. Phys.},
323          Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
# Line 222 | Line 352
352          Date-Added = {2008-01-08 16:41:06 -0500},
353          Date-Modified = {2008-01-08 16:41:06 -0500},
354          Doi = {10.1063/1.1421362},
355 <        Journal = {The Journal of Chemical Physics},
355 >        Journal = jcp,
356          Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
357          Number = 1,
358          Pages = {209-217},
# Line 273 | Line 403
403          Author = {Ravichandran, S and Bagchi, B},
404          Date-Added = {2008-01-08 15:24:48 -0500},
405          Date-Modified = {2008-01-08 15:25:41 -0500},
406 <        Journal = {Journal of Chemical Physics},
406 >        Journal = jcp,
407          Pages = {7505-7511},
408          Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
409          Volume = 111,
# Line 284 | Line 414
414          Author = {TANG, SA and EVANS, GT},
415          Date-Added = {2008-01-08 15:23:42 -0500},
416          Date-Modified = {2008-01-08 15:24:09 -0500},
417 <        Journal = {Molecular Physics},
417 >        Journal = mp,
418          Pages = {1443-1457},
419          Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
420          Volume = 80,
# Line 296 | Line 426
426          Date-Added = {2008-01-08 15:12:53 -0500},
427          Date-Modified = {2008-01-08 15:13:21 -0500},
428          Doi = {DOI 10.1063/1.1610442},
429 <        Journal = {Journal of Chemical Physics},
429 >        Journal = jcp,
430          Pages = {8062-8068},
431          Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
432          Volume = 119,
# Line 309 | Line 439
439          Date-Added = {2008-01-08 15:12:53 -0500},
440          Date-Modified = {2008-01-08 15:13:20 -0500},
441          Doi = {DOI 10.1021/jp037185r},
442 <        Journal = {Journal of Physical Chemistry B},
442 >        Journal = jpcb,
443          Pages = {6767-6771},
444          Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
445          Volume = 108,
# Line 1137 | Line 1267
1267          Author = {S.~J. Marrink and A.~E. Mark},
1268          Date-Added = {2008-01-08 14:58:56 -0500},
1269          Date-Modified = {2008-01-08 14:58:58 -0500},
1270 <        Journal = {Journal of Physical Chemistry B},
1270 >        Journal = jpcb,
1271          Pages = {6122-6127},
1272          Title = {Effect of undulations on surface tension in simulated bilayers},
1273          Volume = 105,
# Line 1507 | Line 1637
1637          Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.},
1638          Date-Added = {2008-01-08 14:58:56 -0500},
1639          Date-Modified = {2008-01-08 14:58:59 -0500},
1640 <        Journal = {Biophysical Journal},
1640 >        Journal = bj,
1641          Journal1 = {Biophys. J.},
1642          Number = 1,
1643          Pages = {609--622},
# Line 1567 | Line 1697
1697          Date-Added = {2008-01-08 14:58:56 -0500},
1698          Date-Modified = {2008-01-08 14:58:59 -0500},
1699          Eid = 157802,
1700 <        Journal = {Physical Review Letters},
1700 >        Journal = prl,
1701          Number = 15,
1702          Numpages = 4,
1703          Pages = 157802,
# Line 1759 | Line 1889
1889          Author = {E. Lindahl and O. Edholm},
1890          Date-Added = {2008-01-08 14:58:56 -0500},
1891          Date-Modified = {2008-01-08 14:58:59 -0500},
1892 <        Journal = {Biophysical Journal},
1892 >        Journal = bj,
1893          Month = {July},
1894          Pages = {426-433},
1895          Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
# Line 1851 | Line 1981
1981          Author = {A.~M. Smondyrev and M.~L. Berkowitz},
1982          Date-Added = {2008-01-08 14:58:56 -0500},
1983          Date-Modified = {2008-01-08 14:59:00 -0500},
1984 <        Journal = {Biophysical Journal},
1984 >        Journal = bj,
1985          Pages = {2472-2478},
1986          Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1987          Volume = 76,
# Line 1861 | Line 1991
1991          Author = {S.~J. Marrink and D.~P. Teileman},
1992          Date-Added = {2008-01-08 14:58:56 -0500},
1993          Date-Modified = {2008-01-08 14:59:00 -0500},
1994 <        Journal = {Biophysical Journal},
1994 >        Journal = bj,
1995          Pages = {2386-2392},
1996          Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1997          Volume = 83,
# Line 1927 | Line 2057
2057          Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
2058          Date-Added = {2008-01-08 14:58:56 -0500},
2059          Date-Modified = {2008-01-08 14:59:00 -0500},
2060 <        Journal = {Biophysical Journal},
2060 >        Journal = bj,
2061          Pages = {3636-3645},
2062          Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
2063          Volume = 84,
# Line 1960 | Line 2090
2090          Author = {A.~K. Sum and J.~J. de~Pablo},
2091          Date-Added = {2008-01-08 14:58:56 -0500},
2092          Date-Modified = {2008-01-08 14:59:00 -0500},
2093 <        Journal = {Biophysical Journal},
2093 >        Journal = bj,
2094          Pages = {3636-3645},
2095          Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
2096          Volume = 85,
# Line 2149 | Line 2279
2279          Author = {J. Norberg and L. Nilsson},
2280          Date-Added = {2008-01-08 14:58:56 -0500},
2281          Date-Modified = {2008-01-08 14:59:00 -0500},
2282 <        Journal = {Biophysical Journal},
2282 >        Journal = bj,
2283          Pages = {1537-1553},
2284          Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
2285          Volume = 79,
# Line 2326 | Line 2456
2456          Volume = 51,
2457          Year = 1995}
2458  
2459 < @book{Cevc87,
2459 > @book{Cevc80,
2460          Address = {New York},
2461          Author = {Gregor Cevc and Derek Marsh},
2462          Date-Added = {2008-01-08 14:58:56 -0500},
2463 <        Date-Modified = {2008-01-08 14:59:01 -0500},
2463 >        Date-Modified = {2008-03-20 12:27:15 -0400},
2464          Publisher = {Wiley-Interscience},
2465          Title = {Phospholipid Bilayers},
2466          Year = 1980}
# Line 3462 | Line 3592
3592          Annote = {973OH Times Cited:1 Cited References Count:33},
3593          Author = {B. Alakent and M. C. Camurdan and P. Doruker},
3594          Issn = {0021-9606},
3595 <        Journal = {Journal of Chemical Physics},
3595 >        Journal = jcp,
3596          Month = {Oct 8},
3597          Number = 14,
3598          Pages = {-},
# Line 3516 | Line 3646
3646          Annote = {Rq238 Times Cited:559 Cited References Count:14},
3647          Author = {H. C. Andersen},
3648          Issn = {0021-9991},
3649 <        Journal = {Journal of Computational Physics},
3649 >        Journal = jcop,
3650          Number = 1,
3651          Pages = {24-34},
3652          Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
# Line 3547 | Line 3677
3677          Annote = {895QF Times Cited:9 Cited References Count:33},
3678          Author = {A. Auerbach},
3679          Issn = {0027-8424},
3680 <        Journal = {Proceedings of the National Academy of Sciences of the United States of America},
3680 >        Journal = pnas,
3681          Month = {Feb 1},
3682          Number = 5,
3683          Pages = {1408-1412},
# Line 3608 | Line 3738
3738          Annote = {816YY Times Cited:8 Cited References Count:35},
3739          Author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
3740          Issn = {0021-9606},
3741 <        Journal = {Journal of Chemical Physics},
3741 >        Journal = jcp,
3742          Month = {May 15},
3743          Number = 19,
3744          Pages = {8960-8972},
# Line 3655 | Line 3785
3785          Annote = {105HH Times Cited:29 Cited References Count:49},
3786          Author = {E. Barth and T. Schlick},
3787          Issn = {0021-9606},
3788 <        Journal = {Journal of Chemical Physics},
3788 >        Journal = jcp,
3789          Month = {Aug 1},
3790          Number = 5,
3791          Pages = {1617-1632},
# Line 3679 | Line 3809
3809          Annote = {469KV Times Cited:6 Cited References Count:30},
3810          Author = {P. F. Batcho and T. Schlick},
3811          Issn = {0021-9606},
3812 <        Journal = {Journal of Chemical Physics},
3812 >        Journal = jcp,
3813          Month = {Sep 1},
3814          Number = 9,
3815          Pages = {4019-4029},
# Line 3732 | Line 3862
3862          Annote = {736UA Times Cited:0 Cited References Count:11},
3863          Author = {D. A. Beard and T. Schlick},
3864          Issn = {0006-3495},
3865 <        Journal = {Biophysical Journal},
3865 >        Journal = bj,
3866          Month = {Nov 1},
3867          Number = 5,
3868          Pages = {2973-2976},
# Line 3889 | Line 4019
4019          Annote = {Qp423 Times Cited:6414 Cited References Count:96},
4020          Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus},
4021          Issn = {0192-8651},
4022 <        Journal = {Journal of Computational Chemistry},
4022 >        Journal = jcc,
4023          Number = 2,
4024          Pages = {187-217},
4025          Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
# Line 3962 | Line 4092
4092          Annote = {255TC Times Cited:24 Cited References Count:38},
4093          Author = {P. J. Camp and M. P. Allen and A. J. Masters},
4094          Issn = {0021-9606},
4095 <        Journal = {Journal of Chemical Physics},
4095 >        Journal = jcp,
4096          Month = {Dec 1},
4097          Number = 21,
4098          Pages = {9871-9881},
# Line 4013 | Line 4143
4143          Annote = {200TT Times Cited:46 Cited References Count:57},
4144          Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
4145          Issn = {0006-3495},
4146 <        Journal = {Biophysical Journal},
4146 >        Journal = bj,
4147          Month = {Jun},
4148          Number = 6,
4149          Pages = {3044-3057},
# Line 4044 | Line 4174
4174          Annote = {221EN Times Cited:14 Cited References Count:66},
4175          Author = {A. Chandra and T. Ichiye},
4176          Issn = {0021-9606},
4177 <        Journal = {Journal of Chemical Physics},
4177 >        Journal = jcp,
4178          Month = {Aug 8},
4179          Number = 6,
4180          Pages = {2701-2709},
# Line 4104 | Line 4234
4234          Annote = {866UM Times Cited:4 Cited References Count:61},
4235          Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
4236          Issn = {0021-9606},
4237 <        Journal = {Journal of Chemical Physics},
4237 >        Journal = jcp,
4238          Month = {Nov 8},
4239          Number = 18,
4240          Pages = {9131-9139},
# Line 4155 | Line 4285
4285          Annote = {757TK Times Cited:1 Cited References Count:22},
4286          Author = {S. A. Chin},
4287          Issn = {0021-9606},
4288 <        Journal = {Journal of Chemical Physics},
4288 >        Journal = jcp,
4289          Month = {Jan 1},
4290          Number = 1,
4291          Pages = {8-13},
# Line 4214 | Line 4344
4344          Annote = {689LC Times Cited:3 Cited References Count:48},
4345          Author = {B. X. Cui and M. Y. Shen and K. F. Freed},
4346          Issn = {0027-8424},
4347 <        Journal = {Proceedings of the National Academy of Sciences of the United States of America},
4347 >        Journal = pnas,
4348          Month = {Jun 10},
4349          Number = 12,
4350          Pages = {7087-7092},
# Line 4274 | Line 4404
4404          Annote = {Zl046 Times Cited:30 Cited References Count:29},
4405          Author = {P. Derreumaux and T. Schlick},
4406          Issn = {0006-3495},
4407 <        Journal = {Biophysical Journal},
4407 >        Journal = bj,
4408          Month = {Jan},
4409          Number = 1,
4410          Pages = {72-81},
# Line 4306 | Line 4436
4436          Annote = {Ya587 Times Cited:35 Cited References Count:32},
4437          Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
4438          Issn = {0021-9606},
4439 <        Journal = {Journal of Chemical Physics},
4439 >        Journal = jcp,
4440          Month = {Oct 15},
4441          Number = 15,
4442          Pages = {5840-5851},
# Line 4350 | Line 4480
4480          Annote = {Q0188 Times Cited:219 Cited References Count:43},
4481          Author = {E. Egberts and H. J. C. Berendsen},
4482          Issn = {0021-9606},
4483 <        Journal = {Journal of Chemical Physics},
4483 >        Journal = jcp,
4484          Month = {Sep 15},
4485          Number = 6,
4486          Pages = {3718-3732},
# Line 4363 | Line 4493
4493          Annote = {Fp216 Times Cited:785 Cited References Count:42},
4494          Author = {D. L. Ermak and J. A. Mccammon},
4495          Issn = {0021-9606},
4496 <        Journal = {Journal of Chemical Physics},
4496 >        Journal = jcp,
4497          Number = 4,
4498          Pages = {1352-1360},
4499          Title = {Brownian Dynamics with Hydrodynamic Interactions},
# Line 4375 | Line 4505
4505          Annote = {Ds757 Times Cited:271 Cited References Count:18},
4506          Author = {D. J. Evans},
4507          Issn = {0026-8976},
4508 <        Journal = {Molecular Physics},
4508 >        Journal = mp,
4509          Number = 2,
4510          Pages = {317-325},
4511          Title = {Representation of Orientation Space},
# Line 4410 | Line 4540
4540          Annote = {816YY Times Cited:5 Cited References Count:39},
4541          Author = {C. J. Fennell and J. D. Gezelter},
4542          Issn = {0021-9606},
4543 <        Journal = {Journal of Chemical Physics},
4543 >        Journal = jcp,
4544          Month = {May 15},
4545          Number = 19,
4546          Pages = {9175-9184},
# Line 4434 | Line 4564
4564          Annote = {633AD Times Cited:2 Cited References Count:43},
4565          Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4566          Issn = {0006-3495},
4567 <        Journal = {Biophysical Journal},
4567 >        Journal = bj,
4568          Month = {Dec},
4569          Number = 6,
4570          Pages = {3039-3048},
# Line 4454 | Line 4584
4584          Annote = {Lj347 Times Cited:482 Cited References Count:13},
4585          Author = {J. G. Gay and B. J. Berne},
4586          Issn = {0021-9606},
4587 <        Journal = {Journal of Chemical Physics},
4587 >        Journal = jcp,
4588          Number = 6,
4589          Pages = {3316-3319},
4590          Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
# Line 4495 | Line 4625
4625  
4626   @article{Goetz1998,
4627          Author = {R. Goetz and R. Lipowsky},
4628 <        Journal = {Journal of Chemical Physics},
4628 >        Journal = jcp,
4629          Number = 17,
4630          Pages = 7397,
4631          Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
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4668          Annote = {704QL Times Cited:48 Cited References Count:60},
4669          Author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and B. Kuhlman and C. A. Rohl and D. Baker},
4670          Issn = {0022-2836},
4671 <        Journal = {Journal of Molecular Biology},
4671 >        Journal = jmb,
4672          Month = {Aug 1},
4673          Number = 1,
4674          Pages = {281-299},
# Line 4573 | Line 4703
4703          Annote = {L0498 Times Cited:899 Cited References Count:7},
4704          Author = {L. Greengard and V. Rokhlin},
4705          Issn = {0021-9991},
4706 <        Journal = {Journal of Computational Physics},
4706 >        Journal = jcop,
4707          Month = {Dec},
4708          Number = 2,
4709          Pages = {325-348},
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4856          Annote = {Ju251 Times Cited:55 Cited References Count:44},
4857          Author = {C. Ho and C. D. Stubbs},
4858          Issn = {0006-3495},
4859 <        Journal = {Biophysical Journal},
4859 >        Journal = bj,
4860          Month = {Oct},
4861          Number = 4,
4862          Pages = {897-902},
# Line 4768 | Line 4898
4898          Annote = {870FJ Times Cited:0 Cited References Count:63},
4899          Author = {Y. Huh and N. M. Cann},
4900          Issn = {0021-9606},
4901 <        Journal = {Journal of Chemical Physics},
4901 >        Journal = jcp,
4902          Month = {Nov 22},
4903          Number = 20,
4904          Pages = {10299-10308},
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4977          Annote = {397CQ Times Cited:14 Cited References Count:36},
4978          Author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
4979          Issn = {0021-9606},
4980 <        Journal = {Journal of Chemical Physics},
4980 >        Journal = jcp,
4981          Month = {Feb 1},
4982          Number = 5,
4983          Pages = {2090-2098},
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5020          Annote = {194FM Times Cited:373 Cited References Count:51},
5021          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},
5022          Issn = {0021-9991},
5023 <        Journal = {Journal of Computational Physics},
5023 >        Journal = jcop,
5024          Month = {May 1},
5025          Number = 1,
5026          Pages = {283-312},
# Line 4943 | Line 5073
5073          Annote = {Xk293 Times Cited:77 Cited References Count:17},
5074          Author = {D. K. Klimov and D. Thirumalai},
5075          Issn = {0031-9007},
5076 <        Journal = {Physical Review Letters},
5076 >        Journal = prl,
5077          Month = {Jul 14},
5078          Number = 2,
5079          Pages = {317-320},
# Line 4976 | Line 5106
5106          Annote = {Xq332 Times Cited:11 Cited References Count:18},
5107          Author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
5108          Issn = {0021-9606},
5109 <        Journal = {Journal of Chemical Physics},
5109 >        Journal = jcp,
5110          Month = {Aug 15},
5111          Number = 7,
5112          Pages = {2580-2588},
# Line 5371 | Line 5501
5501          Annote = {891CF Times Cited:1 Cited References Count:56},
5502          Author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and J. D. Gezelter},
5503          Issn = {0192-8651},
5504 <        Journal = {Journal of Computational Chemistry},
5504 >        Journal = jcc,
5505          Month = {Feb},
5506          Number = 3,
5507          Pages = {252-271},
# Line 5390 | Line 5520
5520          Annote = {Kq355 Times Cited:172 Cited References Count:17},
5521          Author = {S. Melchionna and G. Ciccotti and B. L. Holian},
5522          Issn = {0026-8976},
5523 <        Journal = {Molecular Physics},
5523 >        Journal = mp,
5524          Month = {Feb 20},
5525          Number = 3,
5526          Pages = {533-544},
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5604          Annote = {861ZF Times Cited:3 Cited References Count:34},
5605          Author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen and C. J. Benham},
5606          Issn = {0021-9606},
5607 <        Journal = {Journal of Chemical Physics},
5607 >        Journal = jcp,
5608          Month = {Oct 22},
5609          Number = 16,
5610          Pages = {8104-8112},
# Line 5569 | Line 5699
5699          Annote = {491UW Times Cited:48 Cited References Count:25},
5700          Author = {H. Noguchi and M. Takasu},
5701          Issn = {0021-9606},
5702 <        Journal = {Journal of Chemical Physics},
5702 >        Journal = jcp,
5703          Month = {Nov 22},
5704          Number = 20,
5705          Pages = {9547-9551},
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5866          Annote = {T1302 Times Cited:61 Cited References Count:26},
5867          Author = {R. W. Pastor and B. R. Brooks and A. Szabo},
5868          Issn = {0026-8976},
5869 <        Journal = {Molecular Physics},
5869 >        Journal = mp,
5870          Month = {Dec 20},
5871          Number = 6,
5872          Pages = {1409-1419},
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5892          Annote = {Akb93 Times Cited:71 Cited References Count:12},
5893          Author = {J. W. Perram and M. S. Wertheim},
5894          Issn = {0021-9991},
5895 <        Journal = {Journal of Computational Physics},
5895 >        Journal = jcop,
5896          Number = 3,
5897          Pages = {409-416},
5898          Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function},
# Line 5796 | Line 5926
5926  
5927   @article{Petrache2000,
5928          Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
5929 <        Journal = {Biophysical Journal},
5929 >        Journal = bj,
5930          Pages = {3172-3192},
5931          Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
5932          Volume = 79,
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5997          Annote = {763GQ Times Cited:21 Cited References Count:59},
5998          Author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
5999          Issn = {0022-2836},
6000 <        Journal = {Journal of Molecular Biology},
6000 >        Journal = jmb,
6001          Month = {Jan 16},
6002          Number = 3,
6003          Pages = {843-865},
# Line 6015 | Line 6145
6145          Annote = {Cz253 Times Cited:3680 Cited References Count:7},
6146          Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
6147          Issn = {0021-9991},
6148 <        Journal = {Journal of Computational Physics},
6148 >        Journal = jcop,
6149          Number = 3,
6150          Pages = {327-341},
6151          Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes},
# Line 6090 | Line 6220
6220          Annote = {194FM Times Cited:14 Cited References Count:32},
6221          Author = {A. Sandu and T. Schlick},
6222          Issn = {0021-9991},
6223 <        Journal = {Journal of Computational Physics},
6223 >        Journal = jcop,
6224          Month = {May 1},
6225          Number = 1,
6226          Pages = {74-113},
# Line 6174 | Line 6304
6304          Annote = {540MH Times Cited:36 Cited References Count:45},
6305          Author = {M. Y. Shen and K. F. Freed},
6306          Issn = {0006-3495},
6307 <        Journal = {Biophysical Journal},
6307 >        Journal = bj,
6308          Month = {Apr},
6309          Number = 4,
6310          Pages = {1791-1808},
# Line 6217 | Line 6347
6347          Annote = {Lh164 Times Cited:27 Cited References Count:47},
6348          Author = {J. Shimada and H. Kaneko and T. Takada},
6349          Issn = {0192-8651},
6350 <        Journal = {Journal of Computational Chemistry},
6350 >        Journal = jcc,
6351          Month = {Jul},
6352          Number = 7,
6353          Pages = {867-878},
# Line 6240 | Line 6370
6370          Annote = {633RX Times Cited:8 Cited References Count:22},
6371          Author = {R. D. Skeel and J. A. Izaguirre},
6372          Issn = {0026-8976},
6373 <        Journal = {Molecular Physics},
6373 >        Journal = mp,
6374          Month = {Dec 20},
6375          Number = 24,
6376          Pages = {3885-3891},
# Line 6299 | Line 6429
6429          Annote = {943DN Times Cited:3 Cited References Count:26},
6430          Author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont and W. J. Briels},
6431          Issn = {0021-9606},
6432 <        Journal = {Journal of Chemical Physics},
6432 >        Journal = jcp,
6433          Month = {Jun 22},
6434          Number = 24,
6435          Pages = {-},
# Line 6340 | Line 6470
6470          Annote = {Tv018 Times Cited:108 Cited References Count:34},
6471          Author = {K. Tu and D. J. Tobias and M. L. Klein},
6472          Issn = {0006-3495},
6473 <        Journal = {Biophysical Journal},
6473 >        Journal = bj,
6474          Month = {Dec},
6475          Number = 6,
6476          Pages = {2558-2562},
# Line 6365 | Line 6495
6495          Annote = {Je891 Times Cited:680 Cited References Count:19},
6496          Author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
6497          Issn = {0021-9606},
6498 <        Journal = {Journal of Chemical Physics},
6498 >        Journal = jcp,
6499          Month = {Aug 1},
6500          Number = 3,
6501          Pages = {1990-2001},
# Line 6399 | Line 6529
6529          Annote = {Ta403 Times Cited:16 Cited References Count:23},
6530          Author = {J. J. Vincent and K. M. Merz},
6531          Issn = {0192-8651},
6532 <        Journal = {Journal of Computational Chemistry},
6532 >        Journal = jcc,
6533          Month = {Nov},
6534          Number = 11,
6535          Pages = {1420-1427},
# Line 6455 | Line 6585
6585          Annote = {738EF Times Cited:3 Cited References Count:43},
6586          Author = {I. M. Withers},
6587          Issn = {0021-9606},
6588 <        Journal = {Journal of Chemical Physics},
6588 >        Journal = jcp,
6589          Month = {Nov 15},
6590          Number = 19,
6591          Pages = {10209-10223},
# Line 6489 | Line 6619
6619          Annote = {189PD Times Cited:70 Cited References Count:34},
6620          Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
6621          Issn = {0021-9606},
6622 <        Journal = {Journal of Chemical Physics},
6622 >        Journal = jcp,
6623          Month = {May 1},
6624          Number = 17,
6625          Pages = {8254-8282},
# Line 6513 | Line 6643
6643  
6644   @article{Blum1972,
6645          Author = {L. Blum and A.~J. Torruella},
6646 <        Journal = {Journal of Chemical Physics},
6646 >        Journal = jcp,
6647          Number = 1,
6648          Pages = {303-309},
6649          Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
# Line 6522 | Line 6652
6652  
6653   @article{Stone1978,
6654          Author = {A.~J. Stone},
6655 <        Journal = {Molecular Physics},
6655 >        Journal = mp,
6656          Number = 1,
6657          Pages = {241-256},
6658          Title = {The description of bimolecular potentials, forces and torques: the S and V function expansions},
# Line 6531 | Line 6661
6661  
6662   @article{Berardi2003,
6663          Author = {R. Berardi, M. Cecchini and C. Zannoni},
6664 <        Journal = {Journal of Chemical Physics},
6664 >        Journal = jcp,
6665          Number = 18,
6666          Pages = {9933-9946},
6667          Title = {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
# Line 6540 | Line 6670
6670  
6671   @article{Beard2000,
6672          Author = {D. A. Beard and T. Schlick},
6673 <        Journal = {Journal of Chemical Physics},
6673 >        Journal = jcp,
6674          Number = 17,
6675          Pages = {7313-7322},
6676          Title = {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
# Line 6570 | Line 6700
6700  
6701   @article{Matubayasi1999,
6702          Author = {N. Matubayasi and M. Nakahara},
6703 <        Journal = {Journal of Chemical Physics},
6703 >        Journal = jcp,
6704          Number = 7,
6705          Pages = {3291-3301},
6706          Title = {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
# Line 6579 | Line 6709
6709  
6710   @article{Miller2002,
6711          Author = {T.F. Miller III, M. Eleftheriou},
6712 <        Journal = {Journal of Chemical Physics},
6712 >        Journal = jcp,
6713          Number = 20,
6714          Pages = {8649-8659},
6715          Title = {Symplectic quaternion scheme for biophysical molecular dynamics},
# Line 6588 | Line 6718
6718  
6719   @article{McMillan1971,
6720          Author = {W.L. McMillan},
6721 <        Journal = {Journal of Chemical Physics},
6721 >        Journal = jcp,
6722          Number = 3,
6723          Pages = {1238-1246},
6724          Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},
# Line 6646 | Line 6776
6776          Year = 2005,
6777          Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6778          Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}}
6779 +
6780 + @article{JoseGarciadelaTorre02012000,
6781 +        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.
6782 + },
6783 +        Author = {{Garc\'{i}a de la Torre}, Jose and Huertas, Maria L. and Carrasco, Beatriz},
6784 +        Eprint = {http://www.biophysj.org/cgi/reprint/78/2/719.pdf},
6785 +        Journal = bj,
6786 +        Number = {2},
6787 +        Pages = {719-730},
6788 +        Title = {{Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure}},
6789 +        Url = {http://www.biophysj.org/cgi/content/abstract/78/2/719},
6790 +        Volume = {78},
6791 +        Year = {2000},
6792 +        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/78/2/719}}
6793 +
6794 + @article{GarciadelaTorreJ2002,
6795 +        Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain},
6796 +        Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B.},
6797 +        Journal = {Biopolymers},
6798 +        Number = {3},
6799 +        Pages = {163-167},
6800 +        Title = {Hydrodynamic Properties of Rigid Macromolecules Composed of Ellipsoidal and Cylindrical Subunits},
6801 +        Volume = {63},
6802 +        Year = {2002}}

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