ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/langevin/langevin.bib
(Generate patch)

Comparing trunk/langevin/langevin.bib (file contents):
Revision 3332 by xsun, Fri Jan 18 22:07:35 2008 UTC vs.
Revision 3333 by gezelter, Thu Jan 24 14:16:07 2008 UTC

# Line 2 | Line 2
2   %% http://bibdesk.sourceforge.net/
3  
4  
5 < %% Created for Dan Gezelter at 2008-01-11 16:20:18 -0500
5 > %% Created for Dan Gezelter at 2008-01-22 11:01:35 -0500
6  
7  
8   %% Saved with string encoding Western (ASCII)
9  
10 +
11 + @string{acp = {Adv. Chem. Phys.}}
12 +
13 + @string{ccp5 = {CCP5 Information Quarterly}}
14 +
15 + @string{cp = {Chem. Phys.}}
16 +
17 + @string{cpl = {Chem. Phys. Lett.}}
18 +
19 + @string{jacs = {J. Am. Chem. Soc.}}
20 +
21 + @string{jcc = {J. Comp. Chem.}}
22 +
23 + @string{jcop = {J. Comp. Phys.}}
24 +
25 + @string{jcp = {J. Chem. Phys.}}
26 +
27 + @string{jml = {J. Mol. Liq.}}
28 +
29 + @string{jpc = {J. Phys. Chem.}}
30 +
31 + @string{jpca = {J. Phys. Chem. A}}
32 +
33 + @string{jpcb = {J. Phys. Chem. B}}
34 +
35 + @string{mp = {Mol. Phys.}}
36 +
37 + @string{pams = {Proc. Am. Math Soc.}}
38 +
39 + @string{pccp = {Phys. Chem. Chem. Phys.}}
40 +
41 + @string{pnas = {Proc. Natl. Acad. Sci. USA}}
42 +
43 + @string{pr = {Phys. Rev.}}
44 +
45 + @string{pra = {Phys. Rev. A}}
46 +
47 + @string{prb = {Phys. Rev. B}}
48 +
49 + @string{pre = {Phys. Rev. E}}
50 +
51 + @string{prl = {Phys. Rev. Lett.}}
52 +
53 + @string{rmp = {Rev. Mod. Phys.}}
54 +
55 +
56 + @misc{Chun:2000fj,
57 +        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.},
58 +        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},
59 +        Date-Added = {2008-01-22 10:38:33 -0500},
60 +        Date-Modified = {2008-01-22 10:38:49 -0500},
61 +        Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
62 +        Note = {Journal of Computational Chemistry},
63 +        Pages = {159-184},
64 +        Timescited = {0},
65 +        Title = {MBO(N)D: A multibody method for long-time molecular dynamics simulations},
66 +        Volume = {21},
67 +        Year = {2000}}
68 +
69 + @article{Fogolari:1996lr,
70 +        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.},
71 +        Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.},
72 +        Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
73 +        Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
74 +        Da = {19960924},
75 +        Date-Added = {2008-01-22 10:19:04 -0500},
76 +        Date-Modified = {2008-01-22 10:19:09 -0500},
77 +        Dcom = {19960924},
78 +        Edat = {1996/03/01},
79 +        Issn = {0006-3495 (Print)},
80 +        Jid = {0370626},
81 +        Journal = {Biophys J},
82 +        Jt = {Biophysical journal},
83 +        Language = {eng},
84 +        Lr = {20071115},
85 +        Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; *Models, Molecular; Molecular Structure; Peptides/*chemistry; *Protein Conformation; Software; Thermodynamics},
86 +        Mhda = {1996/03/01 00:01},
87 +        Number = {3},
88 +        Own = {NLM},
89 +        Pages = {1183--1197},
90 +        Pl = {UNITED STATES},
91 +        Pmid = {8785277},
92 +        Pst = {ppublish},
93 +        Pt = {Journal Article},
94 +        Pubm = {Print},
95 +        Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)},
96 +        Sb = {IM},
97 +        So = {Biophys J. 1996 Mar;70(3):1183-97. },
98 +        Stat = {MEDLINE},
99 +        Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.},
100 +        Volume = {70},
101 +        Year = {1996}}
102 +
103 + @inbook{Ramachandran1996,
104 +        Address = {Providence, Rhode Island},
105 +        Author = {GOMATHI RAMACHANDRAN AND TAMAR SCHLICK},
106 +        Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
107 +        Date-Added = {2008-01-22 10:03:42 -0500},
108 +        Date-Modified = {2008-01-22 10:06:57 -0500},
109 +        Editor = {P. M. Pardalos and D. Shalloway and G. Xue},
110 +        Pages = {215-231},
111 +        Publisher = {American Mathematical Society},
112 +        Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
113 +        Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
114 +        Volume = {23},
115 +        Year = {1996}}
116 +
117 + @article{FIXMAN:1986lr,
118 +        Author = {FIXMAN, M},
119 +        Date-Added = {2008-01-22 09:59:29 -0500},
120 +        Date-Modified = {2008-01-22 09:59:35 -0500},
121 +        Journal = {Macromolecules},
122 +        Pages = {1204-1207},
123 +        Timescited = {0},
124 +        Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION},
125 +        Volume = {19},
126 +        Year = {1986}}
127 +
128 + @article{Berendsen87,
129 +        Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
130 +        Date-Added = {2008-01-22 09:53:15 -0500},
131 +        Date-Modified = {2008-01-22 09:53:15 -0500},
132 +        Journal = jpc,
133 +        Pages = {6269-6271},
134 +        Title = {The Missing Term in Effective Pair Potentials},
135 +        Volume = 91,
136 +        Year = 1987}
137 +
138 + @incollection{Berendsen81,
139 +        Address = {Dordrecht},
140 +        Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
141 +        Booktitle = {Intermolecular Forces},
142 +        Date-Added = {2008-01-22 09:52:49 -0500},
143 +        Date-Modified = {2008-01-22 09:52:49 -0500},
144 +        Editor = {B. Pullman},
145 +        Pages = {331-342},
146 +        Publisher = {Reidel},
147 +        Title = {Simple Point Charge Water},
148 +        Year = 1981}
149  
150 + @article{Stillinger74,
151 +        Author = {F.~H. Stillinger and A. Rahman},
152 +        Date-Added = {2008-01-22 09:51:43 -0500},
153 +        Date-Modified = {2008-01-22 09:51:43 -0500},
154 +        Journal = jcp,
155 +        Number = 4,
156 +        Pages = {1545-1557},
157 +        Title = {Improved simulation of liquid water by molecular dynamics},
158 +        Volume = 60,
159 +        Year = 1974}
160  
161   @article{Torre:1983lr,
162 <        Author = {de la Torre, Jose Garcia and Rodes, Vicente},
162 >        Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
163          Date-Added = {2008-01-11 16:16:43 -0500},
164          Date-Modified = {2008-01-11 16:16:43 -0500},
165          Journal = {The Journal of Chemical Physics},
# Line 24 | Line 173
173          Ty = {JOUR},
174          Url = {http://link.aip.org/link/?JCP/79/2454/1},
175          Volume = 79,
176 <        Year = 1983}
176 >        Year = 1983,
177 >        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}}
178  
179   @article{PhysRev.119.53,
180          Author = {Favro, L. Dale},
# Line 39 | Line 189
189          Publisher = {American Physical Society},
190          Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body},
191          Volume = 119,
192 <        Year = 1960}
192 >        Year = 1960,
193 >        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}}
194  
195   @article{hess:209,
196          Author = {Berk Hess},
# Line 54 | Line 205
205          Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
206          Url = {http://link.aip.org/link/?JCP/116/209/1},
207          Volume = 116,
208 <        Year = 2002}
208 >        Year = 2002,
209 >        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
210 >        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}}
211  
212   @article{Garcia-de-la-Torre:1997qy,
213          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.},
214          Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es},
215 <        Au = {Garcia de la Torre, J and Carrasco, B and Harding, SE},
216 <        Author = {Garcia de la Torre, J and Carrasco, B and Harding, S E},
215 >        Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE},
216 >        Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E},
217          Da = 19970709,
218          Date-Added = {2008-01-08 15:45:31 -0500},
219          Date-Modified = {2008-01-08 15:46:57 -0500},
# Line 122 | Line 275
275          Pages = {8062-8068},
276          Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
277          Volume = 119,
278 <        Year = 2003}
278 >        Year = 2003,
279 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}
280  
281   @article{Schmidt:2004fj,
282          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.},
# Line 134 | Line 288
288          Pages = {6767-6771},
289          Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
290          Volume = 108,
291 <        Year = 2004}
291 >        Year = 2004,
292 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}}
293  
294   @article{Klein01,
295          Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
# Line 428 | Line 583
583          Year = 2003}
584  
585   @article{Cascales98,
586 <        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
586 >        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and {Garc\'{i}a de la Torre}, Jose},
587          Date-Added = {2008-01-08 14:58:56 -0500},
588          Date-Modified = {2008-01-08 14:58:57 -0500},
589          Journal = {J. Phys. Chem. B},
# Line 617 | Line 772
772          Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}},
773          Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
774          Volume = 90,
775 <        Year = 2006}
775 >        Year = 2006,
776 >        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
777 >        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017}}
778  
779   @article{deJoannis06,
780          Author = {J. de~Joannis and F.~Y. Jiang and J.~T. Kindt},
# Line 773 | Line 930
930          Publisher = {American Physical Society},
931          Title = {Defects in flexible membranes with crystalline order},
932          Volume = 38,
933 <        Year = 1988}
933 >        Year = 1988,
934 >        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005}}
935  
936   @article{Monroe95,
937          Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
# Line 1095 | Line 1253
1253          Pages = {2496-2502},
1254          Title = {Electrostatics in periodic slab geometries. I},
1255          Volume = 117,
1256 <        Year = 2002}
1256 >        Year = 2002,
1257 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1258  
1259   @article{deJoannis02,
1260          Author = {J. {de Joannis} and A. Arnold and C. Holm},
# Line 1108 | Line 1267
1267          Pages = {2503-2512},
1268          Title = {Electrostatics in periodic slab geometries. II},
1269          Volume = 117,
1270 <        Year = 2002}
1270 >        Year = 2002,
1271 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1272  
1273   @article{Barenco95,
1274          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 1251 | Line 1411
1411          Pages = {62-67},
1412          Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
1413          Volume = 400,
1414 <        Year = 2004}
1414 >        Year = 2004,
1415 >        Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086}}
1416  
1417   @article{Chuang98,
1418          Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
# Line 1329 | Line 1490
1490          Ty = {JOUR},
1491          Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
1492          Volume = 88,
1493 <        Year = 2005}
1493 >        Year = 2005,
1494 >        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609}}
1495  
1496   @inbook{Blumen86,
1497          Address = {Amsterdam},
# Line 1607 | Line 1769
1769          Pages = {2213-2216},
1770          Title = {Model for Lamellar Phases of Interacting Lipid Membranes},
1771          Volume = 61,
1772 <        Year = 1988}
1772 >        Year = 1988,
1773 >        Bdsk-File-1 = {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}}
1774  
1775   @article{Daw89,
1776          Author = {Murray~S. Daw},
# Line 1721 | Line 1884
1884          Pages = {3668-3675},
1885          Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
1886          Volume = 104,
1887 <        Year = 2000}
1887 >        Year = 2000,
1888 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757}}
1889  
1890   @article{Venable00,
1891          Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
# Line 1862 | Line 2026
2026          Pages = {667-683},
2027          Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
2028          Volume = 15,
2029 <        Year = 1994}
2029 >        Year = 1994,
2030 >        Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150702}}
2031  
2032   @article{McKinnon92,
2033          Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
# Line 2589 | Line 2754
2754          Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}},
2755          Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2756          Volume = 88,
2757 <        Year = 2005}
2757 >        Year = 2005,
2758 >        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2759 >        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606}}
2760  
2761   @article{Lenz07,
2762          Author = {Olaf Lenz and Friederike Schmid},
# Line 3011 | Line 3178
3178          Publisher = {American Physical Society},
3179          Title = {Wrinkling transition in partially polymerized vesicles},
3180          Volume = 67,
3181 <        Year = 1991}
3181 >        Year = 1991,
3182 >        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923}}
3183  
3184   @article{Wendt78,
3185          Author = {H. Wendt and F.~F. Abraham},
# Line 3095 | Line 3263
3263          Ty = {JOUR},
3264          Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
3265          Volume = 24,
3266 <        Year = 1969}
3266 >        Year = 1969,
3267 >        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}}
3268  
3269   @article{Stimson:1926qy,
3270          Author = {Stimson, M and Jeffery, GB},
# Line 3136 | Line 3305
3305          Stat = {PubMed-not-MEDLINE},
3306          Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.},
3307          Volume = 124,
3308 <        Year = 2006}
3308 >        Year = 2006,
3309 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}}
3310  
3311   @article{sun:031602,
3312          Author = {Xiuquan Sun and J. Daniel Gezelter},
# Line 3153 | Line 3323
3323          Title = {Spontaneous corrugation of dipolar membranes},
3324          Url = {http://link.aps.org/abstract/PRE/v75/e031602},
3325          Volume = 75,
3326 <        Year = 2007}
3326 >        Year = 2007,
3327 >        Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602},
3328 >        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}}
3329  
3330   @article{Ortega:2007lr,
3331          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.},
3332          Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.},
3333 <        Au = {Ortega, A and Garcia de la Torre, J},
3334 <        Author = {Ortega, A and Garcia de la Torre, J},
3333 >        Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3334 >        Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3335          Da = 20070813,
3336          Date-Added = {2008-01-08 14:38:03 -0500},
3337          Date-Modified = {2008-01-08 14:38:49 -0500},
# Line 3189 | Line 3361
3361          Stat = {MEDLINE},
3362          Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.},
3363          Volume = 8,
3364 <        Year = 2007}
3364 >        Year = 2007,
3365 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}}
3366  
3367   @article{Torre2003,
3368          Abstract = {While the prediction of hydrodynamic properties of rigid particles
# Line 3215 | Line 3388
3388      We provide an example of the application of this methodology to
3389      the dynamics of a semiflexible, wormlike DNA.},
3390          Annote = {724XK Times Cited:6 Cited References Count:64},
3391 <        Author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez},
3391 >        Author = {{Garc\'{i}a de la Torre}, Jose and H. E. Sanchez and A. Ortega and J. G. Hernandez and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez},
3392          Issn = {0175-7571},
3393          Journal = {European Biophysics Journal with Biophysics Letters},
3394          Month = {Aug},
# Line 3672 | Line 3845
3845          Year = 2002}
3846  
3847   @article{Bernal1980,
3848 <        Author = {J.M. Bernal and J. G. {de la Torre}},
3848 >        Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose},
3849          Journal = {Biopolymers},
3850          Pages = {751-766},
3851          Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape},
# Line 3813 | Line 3986
3986      them to some test cases, for which the properties are known a priori.
3987      We provide guidelines and computational tools for bead modeling.},
3988          Annote = {200TT Times Cited:46 Cited References Count:57},
3989 <        Author = {B. Carrasco and J. G. {de la Torre}},
3989 >        Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
3990          Issn = {0006-3495},
3991          Journal = {Biophysical Journal},
3992          Month = {Jun},
# Line 4234 | Line 4407
4407      its applicability. Examples include free diffusion, transport in
4408      an electric field, and diffusion in a restricting environment.},
4409          Annote = {633AD Times Cited:2 Cited References Count:43},
4410 <        Author = {M. X. Fernandes and J. G. {de la Torre}},
4410 >        Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4411          Issn = {0006-3495},
4412          Journal = {Biophysical Journal},
4413          Month = {Dec},
# Line 4659 | Line 4832
4832          Year = 2001}
4833  
4834   @article{Torre1977,
4835 <        Author = {Jose Garcia De La Torre, V.A. Bloomfield},
4835 >        Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield},
4836          Journal = {Biopolymers},
4837          Pages = {1747-1763},
4838          Title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
# Line 6434 | Line 6607
6607          Year = 1992}
6608  
6609   @article{HuseyinKaya07012005,
6610 <        Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun},
6438 <        title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}},
6439 <        journal = {Biophys. J.},
6440 <        volume = 89,
6441 <        number = 1,
6442 <        pages = {520-535},
6443 <        doi = {10.1529/biophysj.104.057471},
6444 <        year = 2005,
6445 <        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.
6610 >        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.
6611   },
6612 <       URL = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6613 <       eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf}
6614 < }
6612 >        Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun},
6613 >        Doi = {10.1529/biophysj.104.057471},
6614 >        Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf},
6615 >        Journal = {Biophys. J.},
6616 >        Number = 1,
6617 >        Pages = {520-535},
6618 >        Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}},
6619 >        Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6620 >        Volume = 89,
6621 >        Year = 2005,
6622 >        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6623 >        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}}

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines