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4
5	<	%% Created for Dan Gezelter at 2008-02-15 13:48:27 -0500
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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 53 \| 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},
92	+	Date-Added = {2008-03-13 16:54:59 -0400},
93	+	Date-Modified = {2008-03-13 16:56:54 -0400},
94	+	Journal = {Journal of Statistical Physics},
95	+	Keywords = {Brownian particle; Fokker Planck equation; adsorption; molecular friction; force autocorrelation function; molecular dynamics},
96	+	Pages = {557-586},
97	+	Timescited = {0},
98	+	Title = {Fokker-Planck equation, molecular friction, and molecular dynamics for Brownian particle transport near external solid surfaces},
99	+	Volume = {94},
100	+	Year = {1999}}
101	+
102	+	@article{Peters:1999qy,
103	+	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].},
104	+	Author = {Peters, MH},
105	+	Date-Added = {2008-03-13 16:54:59 -0400},
106	+	Date-Modified = {2008-03-13 16:56:44 -0400},
107	+	Journal = jcp,
108	+	Pages = {528-538},
109	+	Timescited = {0},
110	+	Title = {Fokker-Planck equation and the grand molecular friction tensor for coupled rotational and translational motions of structured Brownian particles near structured surfaces},
111	+	Volume = {110},
112	+	Year = {1999}}
113	+
114	+	@article{Peters:2000fk,
115	+	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].},
116	+	Author = {Peters, MH},
117	+	Date-Added = {2008-03-13 16:54:59 -0400},
118	+	Date-Modified = {2008-03-13 16:56:20 -0400},
119	+	Journal = jcp,
120	+	Pages = {5488-5498},
121	+	Timescited = {0},
122	+	Title = {The Smoluchowski diffusion equation for structured macromolecules near structured surfaces},
123	+	Volume = {112},
124	+	Year = {2000}}
125	+
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},
133	+	Number = {1},
134	+	Pages = {26--48},
135	+	Title = {On the microscopic theory of Brownian motion with a rotational degree of freedom},
136	+	Ty = {JOUR},
137	+	Url = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413},
138	+	Volume = {49},
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},
148	<	Journal = {Journal of Physical Chemistry B},
148	>	Journal = jpcb,
149		Number = {7},
150		Pages = {1968-1975},
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},
69	<	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 78 \| Line 163
163		Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
164		Year = {2002}}
165
166	<	@misc{Chun:2000fj,
166	>	@article{Chun:2000fj,
167		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.},
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},
171	+	Journal = jcc,
172		Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
173	<	Note = {Journal of Computational Chemistry},
174	<	Pages = {159-184},
175	<	Timescited = {0},
176	<	Title = {MBO(N)D: A multibody method for long-time molecular dynamics simulations},
177	<	Volume = {21},
92	<	Year = {2000}}
173	>	Pages = {159--184},
174	>	Timescited = 0,
175	>	Title = {{MBO(N)D:} A multibody method for long-time molecular dynamics simulations},
176	>	Volume = 21,
177	>	Year = 2000}
178
179		@article{Fogolari:1996lr,
180		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 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 140 \| Line 225
225		Year = {1996}}
226
227		@article{FIXMAN:1986lr,
228	<	Author = {FIXMAN, M},
228	>	Author = {Fixman, M},
229		Date-Added = {2008-01-22 09:59:29 -0500},
230		Date-Modified = {2008-01-22 09:59:35 -0500},
231		Journal = {Macromolecules},
#	Line 185 \| 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 = {The Journal of Chemical Physics},
276	>	Journal = jcp,
277		Journal1 = {The Journal of Chemical Physics},
278		Journal2 = {J. Chem. Phys.},
279		Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
#	Line 198 \| Line 284
284		Ty = {JOUR},
285		Url = {http://link.aip.org/link/?JCP/79/2454/1},
286		Volume = 79,
287	<	Year = 1983,
202	<	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 214 \| 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,
218	<	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},
312	<	Journal = {The Journal of Chemical Physics},
312	>	Journal = jcp,
313		Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
314		Number = 1,
315		Pages = {209-217},
#	Line 230 \| 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,
234	<	Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
235	<	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 273 \| Line 358
358		Author = {Ravichandran, S and Bagchi, B},
359		Date-Added = {2008-01-08 15:24:48 -0500},
360		Date-Modified = {2008-01-08 15:25:41 -0500},
361	<	Journal = {Journal of Chemical Physics},
361	>	Journal = jcp,
362		Pages = {7505-7511},
363		Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
364		Volume = 111,
#	Line 284 \| Line 369
369		Author = {TANG, SA and EVANS, GT},
370		Date-Added = {2008-01-08 15:23:42 -0500},
371		Date-Modified = {2008-01-08 15:24:09 -0500},
372	<	Journal = {Molecular Physics},
372	>	Journal = mp,
373		Pages = {1443-1457},
374		Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
375		Volume = 80,
#	Line 293 \| 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},
385	<	Journal = {Journal of Chemical Physics},
385	>	Journal = jcp,
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,
304	<	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},
398	<	Journal = {Journal of Physical Chemistry B},
398	>	Journal = jpcb,
399		Pages = {6767-6771},
400		Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
401		Volume = 108,
402	<	Year = 2004,
317	<	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 787 \| 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 797 \| 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,
801	<	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
802	<	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 944 \| 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 955 \| Line 1041
1041		Publisher = {American Physical Society},
1042		Title = {Defects in flexible membranes with crystalline order},
1043		Volume = 38,
1044	<	Year = 1988,
959	<	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 1137 \| Line 1222
1222		Author = {S.~J. Marrink and A.~E. Mark},
1223		Date-Added = {2008-01-08 14:58:56 -0500},
1224		Date-Modified = {2008-01-08 14:58:58 -0500},
1225	<	Journal = {Journal of Physical Chemistry B},
1225	>	Journal = jpcb,
1226		Pages = {6122-6127},
1227		Title = {Effect of undulations on surface tension in simulated bilayers},
1228		Volume = 105,
#	Line 1269 \| 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 1278 \| Line 1364
1364		Pages = {2496-2502},
1365		Title = {Electrostatics in periodic slab geometries. I},
1366		Volume = 117,
1367	<	Year = 2002,
1282	<	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 1292 \| Line 1378
1378		Pages = {2503-2512},
1379		Title = {Electrostatics in periodic slab geometries. II},
1380		Volume = 117,
1381	<	Year = 2002,
1296	<	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 1428 \| 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 1436 \| 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,
1440	<	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 1505 \| 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 = {Biophysical Journal},
1596	>	Journal = bj,
1597		Journal1 = {Biophys. J.},
1598		Number = 1,
1599		Pages = {609--622},
#	Line 1515 \| Line 1601
1601		Ty = {JOUR},
1602		Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
1603		Volume = 88,
1604	<	Year = 2005,
1519	<	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609}}
1604	>	Year = 2005}
1605
1606		@inbook{Blumen86,
1607		Address = {Amsterdam},
#	Line 1567 \| Line 1652
1652		Date-Added = {2008-01-08 14:58:56 -0500},
1653		Date-Modified = {2008-01-08 14:58:59 -0500},
1654		Eid = 157802,
1655	<	Journal = {Physical Review Letters},
1655	>	Journal = prl,
1656		Number = 15,
1657		Numpages = 4,
1658		Pages = 157802,
#	Line 1759 \| Line 1844
1844		Author = {E. Lindahl and O. Edholm},
1845		Date-Added = {2008-01-08 14:58:56 -0500},
1846		Date-Modified = {2008-01-08 14:58:59 -0500},
1847	<	Journal = {Biophysical Journal},
1847	>	Journal = bj,
1848		Month = {July},
1849		Pages = {426-433},
1850		Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
#	Line 1787 \| 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 1794 \| Line 1880
1880		Pages = {2213-2216},
1881		Title = {Model for Lamellar Phases of Interacting Lipid Membranes},
1882		Volume = 61,
1883	<	Year = 1988,
1798	<	Bdsk-File-1 = {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}}
1883	>	Year = 1988}
1884
1885		@article{Daw89,
1886		Author = {Murray~S. Daw},
#	Line 1851 \| Line 1936
1936		Author = {A.~M. Smondyrev and M.~L. Berkowitz},
1937		Date-Added = {2008-01-08 14:58:56 -0500},
1938		Date-Modified = {2008-01-08 14:59:00 -0500},
1939	<	Journal = {Biophysical Journal},
1939	>	Journal = bj,
1940		Pages = {2472-2478},
1941		Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1942		Volume = 76,
#	Line 1861 \| Line 1946
1946		Author = {S.~J. Marrink and D.~P. Teileman},
1947		Date-Added = {2008-01-08 14:58:56 -0500},
1948		Date-Modified = {2008-01-08 14:59:00 -0500},
1949	<	Journal = {Biophysical Journal},
1949	>	Journal = bj,
1950		Pages = {2386-2392},
1951		Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1952		Volume = 83,
#	Line 1900 \| 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 1909 \| 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,
1913	<	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 1927 \| Line 2012
2012		Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
2013		Date-Added = {2008-01-08 14:58:56 -0500},
2014		Date-Modified = {2008-01-08 14:59:00 -0500},
2015	<	Journal = {Biophysical Journal},
2015	>	Journal = bj,
2016		Pages = {3636-3645},
2017		Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
2018		Volume = 84,
#	Line 1960 \| Line 2045
2045		Author = {A.~K. Sum and J.~J. de~Pablo},
2046		Date-Added = {2008-01-08 14:58:56 -0500},
2047		Date-Modified = {2008-01-08 14:59:00 -0500},
2048	<	Journal = {Biophysical Journal},
2048	>	Journal = bj,
2049		Pages = {3636-3645},
2050		Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
2051		Volume = 85,
#	Line 2043 \| 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 2051 \| 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,
2055	<	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 2149 \| Line 2234
2234		Author = {J. Norberg and L. Nilsson},
2235		Date-Added = {2008-01-08 14:58:56 -0500},
2236		Date-Modified = {2008-01-08 14:59:00 -0500},
2237	<	Journal = {Biophysical Journal},
2237	>	Journal = bj,
2238		Pages = {1537-1553},
2239		Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
2240		Volume = 79,
#	Line 2326 \| 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 2769 \| 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 2779 \| 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,
2783	<	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2784	<	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 3192 \| 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 3203 \| Line 3289
3289		Publisher = {American Physical Society},
3290		Title = {Wrinkling transition in partially polymerized vesicles},
3291		Volume = 67,
3292	<	Year = 1991,
3207	<	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 3279 \| 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 3288 \| Line 3374
3374		Ty = {JOUR},
3375		Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
3376		Volume = 24,
3377	<	Year = 1969,
3292	<	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 3306 \| 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 3330 \| 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,
3334	<	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 3348 \| 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,
3352	<	Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602},
3353	<	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 3386 \| 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,
3390	<	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
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3548		Author = {B. Alakent and M. C. Camurdan and P. Doruker},
3549		Issn = {0021-9606},
3550	<	Journal = {Journal of Chemical Physics},
3550	>	Journal = jcp,
3551		Month = {Oct 8},
3552		Number = 14,
3553		Pages = {-},
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3601		Annote = {Rq238 Times Cited:559 Cited References Count:14},
3602		Author = {H. C. Andersen},
3603		Issn = {0021-9991},
3604	<	Journal = {Journal of Computational Physics},
3604	>	Journal = jcop,
3605		Number = 1,
3606		Pages = {24-34},
3607		Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
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3632		Annote = {895QF Times Cited:9 Cited References Count:33},
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3634		Issn = {0027-8424},
3635	<	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
3635	>	Journal = pnas,
3636		Month = {Feb 1},
3637		Number = 5,
3638		Pages = {1408-1412},
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3693		Annote = {816YY Times Cited:8 Cited References Count:35},
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3695		Issn = {0021-9606},
3696	<	Journal = {Journal of Chemical Physics},
3696	>	Journal = jcp,
3697		Month = {May 15},
3698		Number = 19,
3699		Pages = {8960-8972},
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3740		Annote = {105HH Times Cited:29 Cited References Count:49},
3741		Author = {E. Barth and T. Schlick},
3742		Issn = {0021-9606},
3743	<	Journal = {Journal of Chemical Physics},
3743	>	Journal = jcp,
3744		Month = {Aug 1},
3745		Number = 5,
3746		Pages = {1617-1632},
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3764		Annote = {469KV Times Cited:6 Cited References Count:30},
3765		Author = {P. F. Batcho and T. Schlick},
3766		Issn = {0021-9606},
3767	<	Journal = {Journal of Chemical Physics},
3767	>	Journal = jcp,
3768		Month = {Sep 1},
3769		Number = 9,
3770		Pages = {4019-4029},
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3817		Annote = {736UA Times Cited:0 Cited References Count:11},
3818		Author = {D. A. Beard and T. Schlick},
3819		Issn = {0006-3495},
3820	<	Journal = {Biophysical Journal},
3820	>	Journal = bj,
3821		Month = {Nov 1},
3822		Number = 5,
3823		Pages = {2973-2976},
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3976		Issn = {0192-8651},
3977	<	Journal = {Journal of Computational Chemistry},
3977	>	Journal = jcc,
3978		Number = 2,
3979		Pages = {187-217},
3980		Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
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4049		Issn = {0021-9606},
4050	<	Journal = {Journal of Chemical Physics},
4050	>	Journal = jcp,
4051		Month = {Dec 1},
4052		Number = 21,
4053		Pages = {9871-9881},
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4098		Annote = {200TT Times Cited:46 Cited References Count:57},
4099		Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
4100		Issn = {0006-3495},
4101	<	Journal = {Biophysical Journal},
4101	>	Journal = bj,
4102		Month = {Jun},
4103		Number = 6,
4104		Pages = {3044-3057},
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4131		Issn = {0021-9606},
4132	<	Journal = {Journal of Chemical Physics},
4132	>	Journal = jcp,
4133		Month = {Aug 8},
4134		Number = 6,
4135		Pages = {2701-2709},
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4191		Issn = {0021-9606},
4192	<	Journal = {Journal of Chemical Physics},
4192	>	Journal = jcp,
4193		Month = {Nov 8},
4194		Number = 18,
4195		Pages = {9131-9139},
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4242		Issn = {0021-9606},
4243	<	Journal = {Journal of Chemical Physics},
4243	>	Journal = jcp,
4244		Month = {Jan 1},
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4246		Pages = {8-13},
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4301		Issn = {0027-8424},
4302	<	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
4302	>	Journal = pnas,
4303		Month = {Jun 10},
4304		Number = 12,
4305		Pages = {7087-7092},
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4359		Annote = {Zl046 Times Cited:30 Cited References Count:29},
4360		Author = {P. Derreumaux and T. Schlick},
4361		Issn = {0006-3495},
4362	<	Journal = {Biophysical Journal},
4362	>	Journal = bj,
4363		Month = {Jan},
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4393		Issn = {0021-9606},
4394	<	Journal = {Journal of Chemical Physics},
4394	>	Journal = jcp,
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4396		Number = 15,
4397		Pages = {5840-5851},
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4437		Issn = {0021-9606},
4438	<	Journal = {Journal of Chemical Physics},
4438	>	Journal = jcp,
4439		Month = {Sep 15},
4440		Number = 6,
4441		Pages = {3718-3732},
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4450		Issn = {0021-9606},
4451	<	Journal = {Journal of Chemical Physics},
4451	>	Journal = jcp,
4452		Number = 4,
4453		Pages = {1352-1360},
4454		Title = {Brownian Dynamics with Hydrodynamic Interactions},
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4461		Author = {D. J. Evans},
4462		Issn = {0026-8976},
4463	<	Journal = {Molecular Physics},
4463	>	Journal = mp,
4464		Number = 2,
4465		Pages = {317-325},
4466		Title = {Representation of Orientation Space},
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4497		Issn = {0021-9606},
4498	<	Journal = {Journal of Chemical Physics},
4498	>	Journal = jcp,
4499		Month = {May 15},
4500		Number = 19,
4501		Pages = {9175-9184},
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4519		Annote = {633AD Times Cited:2 Cited References Count:43},
4520		Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4521		Issn = {0006-3495},
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4522	>	Journal = bj,
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4541		Issn = {0021-9606},
4542	<	Journal = {Journal of Chemical Physics},
4542	>	Journal = jcp,
4543		Number = 6,
4544		Pages = {3316-3319},
4545		Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
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4581		@article{Goetz1998,
4582		Author = {R. Goetz and R. Lipowsky},
4583	<	Journal = {Journal of Chemical Physics},
4583	>	Journal = jcp,
4584		Number = 17,
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4625		Issn = {0022-2836},
4626	<	Journal = {Journal of Molecular Biology},
4626	>	Journal = jmb,
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5478	<	Journal = {Molecular Physics},
5478	>	Journal = mp,
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5480		Number = 3,
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5563		Month = {Oct 22},
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5565		Pages = {8104-8112},
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5823		Issn = {0026-8976},
5824	<	Journal = {Molecular Physics},
5824	>	Journal = mp,
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5826		Number = 6,
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5852		Pages = {409-416},
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5881
5882		@article{Petrache2000,
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6626		@article{Beard2000,
6627		Author = {D. A. Beard and T. Schlick},
6628	<	Journal = {Journal of Chemical Physics},
6628	>	Journal = jcp,
6629		Number = 17,
6630		Pages = {7313-7322},
6631		Title = {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
#	Line 6570 \| Line 6655
6655
6656		@article{Matubayasi1999,
6657		Author = {N. Matubayasi and M. Nakahara},
6658	<	Journal = {Journal of Chemical Physics},
6658	>	Journal = jcp,
6659		Number = 7,
6660		Pages = {3291-3301},
6661		Title = {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
#	Line 6579 \| Line 6664
6664
6665		@article{Miller2002,
6666		Author = {T.F. Miller III, M. Eleftheriou},
6667	<	Journal = {Journal of Chemical Physics},
6667	>	Journal = jcp,
6668		Number = 20,
6669		Pages = {8649-8659},
6670		Title = {Symplectic quaternion scheme for biophysical molecular dynamics},
#	Line 6588 \| Line 6673
6673
6674		@article{McMillan1971,
6675		Author = {W.L. McMillan},
6676	<	Journal = {Journal of Chemical Physics},
6676	>	Journal = jcp,
6677		Number = 3,
6678		Pages = {1238-1246},
6679		Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},
#	Line 6635 \| 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 6643 \| 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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Comparing trunk/langevin/langevin.bib (file contents): Revision 3352 by gezelter, Fri Feb 29 22:02:46 2008 UTC vs. Revision 3390 by xsun, Wed Apr 30 14:50:53 2008 UTC

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Comparing trunk/langevin/langevin.bib (file contents):
Revision 3352 by gezelter, Fri Feb 29 22:02:46 2008 UTC vs.
Revision 3390 by xsun, Wed Apr 30 14:50:53 2008 UTC