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Revision 3317 by xsun, Fri Jan 18 22:07:35 2008 UTC vs.
Revision 3352 by gezelter, Fri Feb 29 22:02:46 2008 UTC

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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 2008-02-15 13:48:27 -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 + @article{SunX._jp0762020,
57 +        Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556},
58 +        Author = {Sun, X. and Gezelter, J.D.},
59 +        Date-Added = {2008-02-15 13:48:18 -0500},
60 +        Date-Modified = {2008-02-15 13:48:18 -0500},
61 +        Issn = {1520-6106},
62 +        Journal = {Journal of Physical Chemistry B},
63 +        Number = {7},
64 +        Pages = {1968-1975},
65 +        Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes},
66 +        Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020},
67 +        Volume = {112},
68 +        Year = {2008},
69 +        Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}}
70 +
71 + @book{Schlick2002,
72 +        Address = {Secaucus, NJ, USA},
73 +        Author = {Tamar Schlick},
74 +        Date-Added = {2008-02-12 16:52:19 -0500},
75 +        Date-Modified = {2008-02-12 16:53:15 -0500},
76 +        Isbn = {038795404X},
77 +        Publisher = {Springer-Verlag New York, Inc.},
78 +        Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
79 +        Year = {2002}}
80 +
81 + @misc{Chun:2000fj,
82 +        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.},
83 +        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},
84 +        Date-Added = {2008-01-22 10:38:33 -0500},
85 +        Date-Modified = {2008-01-22 10:38:49 -0500},
86 +        Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
87 +        Note = {Journal of Computational Chemistry},
88 +        Pages = {159-184},
89 +        Timescited = {0},
90 +        Title = {MBO(N)D: A multibody method for long-time molecular dynamics simulations},
91 +        Volume = {21},
92 +        Year = {2000}}
93 +
94 + @article{Fogolari:1996lr,
95 +        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.},
96 +        Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.},
97 +        Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
98 +        Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
99 +        Da = {19960924},
100 +        Date-Added = {2008-01-22 10:19:04 -0500},
101 +        Date-Modified = {2008-01-22 10:19:09 -0500},
102 +        Dcom = {19960924},
103 +        Edat = {1996/03/01},
104 +        Issn = {0006-3495 (Print)},
105 +        Jid = {0370626},
106 +        Journal = {Biophys J},
107 +        Jt = {Biophysical journal},
108 +        Language = {eng},
109 +        Lr = {20071115},
110 +        Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; *Models, Molecular; Molecular Structure; Peptides/*chemistry; *Protein Conformation; Software; Thermodynamics},
111 +        Mhda = {1996/03/01 00:01},
112 +        Number = {3},
113 +        Own = {NLM},
114 +        Pages = {1183--1197},
115 +        Pl = {UNITED STATES},
116 +        Pmid = {8785277},
117 +        Pst = {ppublish},
118 +        Pt = {Journal Article},
119 +        Pubm = {Print},
120 +        Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)},
121 +        Sb = {IM},
122 +        So = {Biophys J. 1996 Mar;70(3):1183-97. },
123 +        Stat = {MEDLINE},
124 +        Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.},
125 +        Volume = {70},
126 +        Year = {1996}}
127 +
128 + @inbook{Ramachandran1996,
129 +        Address = {Providence, Rhode Island},
130 +        Author = {GOMATHI RAMACHANDRAN AND TAMAR SCHLICK},
131 +        Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
132 +        Date-Added = {2008-01-22 10:03:42 -0500},
133 +        Date-Modified = {2008-01-22 10:06:57 -0500},
134 +        Editor = {P. M. Pardalos and D. Shalloway and G. Xue},
135 +        Pages = {215-231},
136 +        Publisher = {American Mathematical Society},
137 +        Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
138 +        Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
139 +        Volume = {23},
140 +        Year = {1996}}
141 +
142 + @article{FIXMAN:1986lr,
143 +        Author = {FIXMAN, M},
144 +        Date-Added = {2008-01-22 09:59:29 -0500},
145 +        Date-Modified = {2008-01-22 09:59:35 -0500},
146 +        Journal = {Macromolecules},
147 +        Pages = {1204-1207},
148 +        Timescited = {0},
149 +        Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION},
150 +        Volume = {19},
151 +        Year = {1986}}
152 +
153 + @article{Berendsen87,
154 +        Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
155 +        Date-Added = {2008-01-22 09:53:15 -0500},
156 +        Date-Modified = {2008-01-22 09:53:15 -0500},
157 +        Journal = jpc,
158 +        Pages = {6269-6271},
159 +        Title = {The Missing Term in Effective Pair Potentials},
160 +        Volume = 91,
161 +        Year = 1987}
162 +
163 + @incollection{Berendsen81,
164 +        Address = {Dordrecht},
165 +        Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
166 +        Booktitle = {Intermolecular Forces},
167 +        Date-Added = {2008-01-22 09:52:49 -0500},
168 +        Date-Modified = {2008-01-22 09:52:49 -0500},
169 +        Editor = {B. Pullman},
170 +        Pages = {331-342},
171 +        Publisher = {Reidel},
172 +        Title = {Simple Point Charge Water},
173 +        Year = 1981}
174 +
175 + @article{Stillinger74,
176 +        Author = {F.~H. Stillinger and A. Rahman},
177 +        Date-Added = {2008-01-22 09:51:43 -0500},
178 +        Date-Modified = {2008-01-22 09:51:43 -0500},
179 +        Journal = jcp,
180 +        Number = 4,
181 +        Pages = {1545-1557},
182 +        Title = {Improved simulation of liquid water by molecular dynamics},
183 +        Volume = 60,
184 +        Year = 1974}
185 +
186   @article{Torre:1983lr,
187 <        Author = {de la Torre, Jose Garcia and Rodes, Vicente},
187 >        Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
188          Date-Added = {2008-01-11 16:16:43 -0500},
189          Date-Modified = {2008-01-11 16:16:43 -0500},
190          Journal = {The Journal of Chemical Physics},
# Line 24 | Line 198
198          Ty = {JOUR},
199          Url = {http://link.aip.org/link/?JCP/79/2454/1},
200          Volume = 79,
201 <        Year = 1983}
201 >        Year = 1983,
202 >        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}}
203  
204   @article{PhysRev.119.53,
205          Author = {Favro, L. Dale},
# Line 39 | Line 214
214          Publisher = {American Physical Society},
215          Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body},
216          Volume = 119,
217 <        Year = 1960}
217 >        Year = 1960,
218 >        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}}
219  
220   @article{hess:209,
221          Author = {Berk Hess},
# Line 54 | Line 230
230          Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
231          Url = {http://link.aip.org/link/?JCP/116/209/1},
232          Volume = 116,
233 <        Year = 2002}
233 >        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}}
236  
237   @article{Garcia-de-la-Torre:1997qy,
238          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.},
239          Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es},
240 <        Au = {Garcia de la Torre, J and Carrasco, B and Harding, SE},
241 <        Author = {Garcia de la Torre, J and Carrasco, B and Harding, S E},
240 >        Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE},
241 >        Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E},
242          Da = 19970709,
243          Date-Added = {2008-01-08 15:45:31 -0500},
244          Date-Modified = {2008-01-08 15:46:57 -0500},
# Line 122 | Line 300
300          Pages = {8062-8068},
301          Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
302          Volume = 119,
303 <        Year = 2003}
303 >        Year = 2003,
304 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}
305  
306   @article{Schmidt:2004fj,
307          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 313
313          Pages = {6767-6771},
314          Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
315          Volume = 108,
316 <        Year = 2004}
316 >        Year = 2004,
317 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}}
318  
319   @article{Klein01,
320          Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
# Line 428 | Line 608
608          Year = 2003}
609  
610   @article{Cascales98,
611 <        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
611 >        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and {Garc\'{i}a de la Torre}, Jose},
612          Date-Added = {2008-01-08 14:58:56 -0500},
613          Date-Modified = {2008-01-08 14:58:57 -0500},
614          Journal = {J. Phys. Chem. B},
# Line 617 | Line 797
797          Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}},
798          Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
799          Volume = 90,
800 <        Year = 2006}
800 >        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}}
803  
804   @article{deJoannis06,
805          Author = {J. de~Joannis and F.~Y. Jiang and J.~T. Kindt},
# Line 773 | Line 955
955          Publisher = {American Physical Society},
956          Title = {Defects in flexible membranes with crystalline order},
957          Volume = 38,
958 <        Year = 1988}
958 >        Year = 1988,
959 >        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005}}
960  
961   @article{Monroe95,
962          Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
# Line 1095 | Line 1278
1278          Pages = {2496-2502},
1279          Title = {Electrostatics in periodic slab geometries. I},
1280          Volume = 117,
1281 <        Year = 2002}
1281 >        Year = 2002,
1282 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1283  
1284   @article{deJoannis02,
1285          Author = {J. {de Joannis} and A. Arnold and C. Holm},
# Line 1108 | Line 1292
1292          Pages = {2503-2512},
1293          Title = {Electrostatics in periodic slab geometries. II},
1294          Volume = 117,
1295 <        Year = 2002}
1295 >        Year = 2002,
1296 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1297  
1298   @article{Barenco95,
1299          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 1436
1436          Pages = {62-67},
1437          Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
1438          Volume = 400,
1439 <        Year = 2004}
1439 >        Year = 2004,
1440 >        Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086}}
1441  
1442   @article{Chuang98,
1443          Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
# Line 1329 | Line 1515
1515          Ty = {JOUR},
1516          Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
1517          Volume = 88,
1518 <        Year = 2005}
1518 >        Year = 2005,
1519 >        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609}}
1520  
1521   @inbook{Blumen86,
1522          Address = {Amsterdam},
# Line 1607 | Line 1794
1794          Pages = {2213-2216},
1795          Title = {Model for Lamellar Phases of Interacting Lipid Membranes},
1796          Volume = 61,
1797 <        Year = 1988}
1797 >        Year = 1988,
1798 >        Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUGCQpYJHZlcnNpb25UJHRvcFkkYXJjaGl2ZXJYJG9iamVjdHMSAAGGoNEHCFRyb290gAFfEA9OU0tleWVkQXJjaGl2ZXKoCwwXGBkdJCVVJG51bGzTDQ4PEBEUViRjbGFzc1dOUy5rZXlzWk5TLm9iamVjdHOAB6ISE4ACgAOiFRaABIAGWWFsaWFzRGF0YVxyZWxhdGl2ZVBhdGjSDRobHFdOUy5kYXRhgAVPEQHUAAAAAAHUAAIAAAhnZXplbHRlcgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATkoAAf////8fY2l0LWFicy1lbmRub3RlLTI0I0ZGRkZGRkZGLnJpcwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA/////wAAAAAAAAAAAAAAAAADAAIAABKBY3UAAAAAAAAAAAAAAAAACURvd25sb2FkcwAAAgBILzpob21lOm1hdWw6Z2V6ZWx0ZXI6Z2V6ZWx0ZXI6RG93bmxvYWRzOmNpdC1hYnMtZW5kbm90ZS0yNDIzODAwOC5lbncucmlzAA4AQgAgAGMAaQB0AC0AYQBiAHMALQBlAG4AZABuAG8AdABlAC0AMgA0ADIAMwA4ADAAMAA4AC4AZQBuAHcALgByAGkAcwAPABIACABnAGUAegBlAGwAdABlAHIAEgArL0Rvd25sb2Fkcy9jaXQtYWJzLWVuZG5vdGUtMjQyMzgwMDguZW53LnJpcwAAEwAcL2hvbWUvbWF1bC9nZXplbHRlci9nZXplbHRlcgAJACkAKWNyYm0AAHBvc3gvaG9tZS9tYXVsL2dlemVsdGVyL2dlemVsdGVyAAAAFQACABz//wAA0h4fICFYJGNsYXNzZXNaJGNsYXNzbmFtZaMhIiNdTlNNdXRhYmxlRGF0YVZOU0RhdGFYTlNPYmplY3RfEDMuLi8uLi8uLi9Eb3dubG9hZHMvY2l0LWFicy1lbmRub3RlLTI0MjM4MDA4LmVudy5yaXPSHh8mJ6InI1xOU0RpY3Rpb25hcnkACAARABoAHwApADIANwA6AD8AQQBTAFwAYgBpAHAAeACDAIUAiACKAIwAjwCRAJMAnQCqAK8AtwC5ApEClgKfAqoCrgK8AsMCzAMCAwcDCgAAAAAAAAIBAAAAAAAAACgAAAAAAAAAAAAAAAAAAAMX}}
1799  
1800   @article{Daw89,
1801          Author = {Murray~S. Daw},
# Line 1721 | Line 1909
1909          Pages = {3668-3675},
1910          Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
1911          Volume = 104,
1912 <        Year = 2000}
1912 >        Year = 2000,
1913 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757}}
1914  
1915   @article{Venable00,
1916          Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
# Line 1862 | Line 2051
2051          Pages = {667-683},
2052          Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
2053          Volume = 15,
2054 <        Year = 1994}
2054 >        Year = 1994,
2055 >        Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150702}}
2056  
2057   @article{McKinnon92,
2058          Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
# Line 2589 | Line 2779
2779          Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}},
2780          Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2781          Volume = 88,
2782 <        Year = 2005}
2782 >        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}}
2785  
2786   @article{Lenz07,
2787          Author = {Olaf Lenz and Friederike Schmid},
# Line 3011 | Line 3203
3203          Publisher = {American Physical Society},
3204          Title = {Wrinkling transition in partially polymerized vesicles},
3205          Volume = 67,
3206 <        Year = 1991}
3206 >        Year = 1991,
3207 >        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923}}
3208  
3209   @article{Wendt78,
3210          Author = {H. Wendt and F.~F. Abraham},
# Line 3095 | Line 3288
3288          Ty = {JOUR},
3289          Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
3290          Volume = 24,
3291 <        Year = 1969}
3291 >        Year = 1969,
3292 >        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}}
3293  
3294   @article{Stimson:1926qy,
3295          Author = {Stimson, M and Jeffery, GB},
# Line 3136 | Line 3330
3330          Stat = {PubMed-not-MEDLINE},
3331          Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.},
3332          Volume = 124,
3333 <        Year = 2006}
3333 >        Year = 2006,
3334 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}}
3335  
3336   @article{sun:031602,
3337          Author = {Xiuquan Sun and J. Daniel Gezelter},
# Line 3153 | Line 3348
3348          Title = {Spontaneous corrugation of dipolar membranes},
3349          Url = {http://link.aps.org/abstract/PRE/v75/e031602},
3350          Volume = 75,
3351 <        Year = 2007}
3351 >        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}}
3354  
3355   @article{Ortega:2007lr,
3356          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.},
3357          Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.},
3358 <        Au = {Ortega, A and Garcia de la Torre, J},
3359 <        Author = {Ortega, A and Garcia de la Torre, J},
3358 >        Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3359 >        Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3360          Da = 20070813,
3361          Date-Added = {2008-01-08 14:38:03 -0500},
3362          Date-Modified = {2008-01-08 14:38:49 -0500},
# Line 3189 | Line 3386
3386          Stat = {MEDLINE},
3387          Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.},
3388          Volume = 8,
3389 <        Year = 2007}
3389 >        Year = 2007,
3390 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}}
3391  
3392   @article{Torre2003,
3393          Abstract = {While the prediction of hydrodynamic properties of rigid particles
# Line 3215 | Line 3413
3413      We provide an example of the application of this methodology to
3414      the dynamics of a semiflexible, wormlike DNA.},
3415          Annote = {724XK Times Cited:6 Cited References Count:64},
3416 <        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},
3416 >        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},
3417          Issn = {0175-7571},
3418          Journal = {European Biophysics Journal with Biophysics Letters},
3419          Month = {Aug},
# Line 3672 | Line 3870
3870          Year = 2002}
3871  
3872   @article{Bernal1980,
3873 <        Author = {J.M. Bernal and J. G. {de la Torre}},
3873 >        Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose},
3874          Journal = {Biopolymers},
3875          Pages = {751-766},
3876          Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape},
# Line 3813 | Line 4011
4011      them to some test cases, for which the properties are known a priori.
4012      We provide guidelines and computational tools for bead modeling.},
4013          Annote = {200TT Times Cited:46 Cited References Count:57},
4014 <        Author = {B. Carrasco and J. G. {de la Torre}},
4014 >        Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
4015          Issn = {0006-3495},
4016          Journal = {Biophysical Journal},
4017          Month = {Jun},
# Line 4234 | Line 4432
4432      its applicability. Examples include free diffusion, transport in
4433      an electric field, and diffusion in a restricting environment.},
4434          Annote = {633AD Times Cited:2 Cited References Count:43},
4435 <        Author = {M. X. Fernandes and J. G. {de la Torre}},
4435 >        Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4436          Issn = {0006-3495},
4437          Journal = {Biophysical Journal},
4438          Month = {Dec},
# Line 4659 | Line 4857
4857          Year = 2001}
4858  
4859   @article{Torre1977,
4860 <        Author = {Jose Garcia De La Torre, V.A. Bloomfield},
4860 >        Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield},
4861          Journal = {Biopolymers},
4862          Pages = {1747-1763},
4863          Title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
# Line 6434 | Line 6632
6632          Year = 1992}
6633  
6634   @article{HuseyinKaya07012005,
6635 <        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.
6635 >        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.
6636   },
6637 <       URL = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6638 <       eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf}
6639 < }
6637 >        Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun},
6638 >        Doi = {10.1529/biophysj.104.057471},
6639 >        Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf},
6640 >        Journal = {Biophys. J.},
6641 >        Number = 1,
6642 >        Pages = {520-535},
6643 >        Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}},
6644 >        Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6645 >        Volume = 89,
6646 >        Year = 2005,
6647 >        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6648 >        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}}

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