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Revision 3302 by gezelter, Tue Jan 8 22:02:06 2008 UTC vs.
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3  
4  
5 < %% Created for Dan Gezelter at 2008-01-08 17:00:16 -0500
5 > %% Created for Xiuquan Sun at 2008-02-12 16:53:41 -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 + @book{Schlick2002,
57 +        Address = {Secaucus, NJ, USA},
58 +        Author = {Tamar Schlick},
59 +        Date-Added = {2008-02-12 16:52:19 -0500},
60 +        Date-Modified = {2008-02-12 16:53:15 -0500},
61 +        Isbn = {038795404X},
62 +        Publisher = {Springer-Verlag New York, Inc.},
63 +        Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
64 +        Year = {2002}}
65 +
66 + @misc{Chun:2000fj,
67 +        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.},
68 +        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},
69 +        Date-Added = {2008-01-22 10:38:33 -0500},
70 +        Date-Modified = {2008-01-22 10:38:49 -0500},
71 +        Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
72 +        Note = {Journal of Computational Chemistry},
73 +        Pages = {159-184},
74 +        Timescited = {0},
75 +        Title = {MBO(N)D: A multibody method for long-time molecular dynamics simulations},
76 +        Volume = {21},
77 +        Year = {2000}}
78 +
79 + @article{Fogolari:1996lr,
80 +        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.},
81 +        Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.},
82 +        Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
83 +        Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
84 +        Da = {19960924},
85 +        Date-Added = {2008-01-22 10:19:04 -0500},
86 +        Date-Modified = {2008-01-22 10:19:09 -0500},
87 +        Dcom = {19960924},
88 +        Edat = {1996/03/01},
89 +        Issn = {0006-3495 (Print)},
90 +        Jid = {0370626},
91 +        Journal = {Biophys J},
92 +        Jt = {Biophysical journal},
93 +        Language = {eng},
94 +        Lr = {20071115},
95 +        Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; *Models, Molecular; Molecular Structure; Peptides/*chemistry; *Protein Conformation; Software; Thermodynamics},
96 +        Mhda = {1996/03/01 00:01},
97 +        Number = {3},
98 +        Own = {NLM},
99 +        Pages = {1183--1197},
100 +        Pl = {UNITED STATES},
101 +        Pmid = {8785277},
102 +        Pst = {ppublish},
103 +        Pt = {Journal Article},
104 +        Pubm = {Print},
105 +        Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)},
106 +        Sb = {IM},
107 +        So = {Biophys J. 1996 Mar;70(3):1183-97. },
108 +        Stat = {MEDLINE},
109 +        Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.},
110 +        Volume = {70},
111 +        Year = {1996}}
112 +
113 + @inbook{Ramachandran1996,
114 +        Address = {Providence, Rhode Island},
115 +        Author = {GOMATHI RAMACHANDRAN AND TAMAR SCHLICK},
116 +        Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
117 +        Date-Added = {2008-01-22 10:03:42 -0500},
118 +        Date-Modified = {2008-01-22 10:06:57 -0500},
119 +        Editor = {P. M. Pardalos and D. Shalloway and G. Xue},
120 +        Pages = {215-231},
121 +        Publisher = {American Mathematical Society},
122 +        Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
123 +        Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
124 +        Volume = {23},
125 +        Year = {1996}}
126 +
127 + @article{FIXMAN:1986lr,
128 +        Author = {FIXMAN, M},
129 +        Date-Added = {2008-01-22 09:59:29 -0500},
130 +        Date-Modified = {2008-01-22 09:59:35 -0500},
131 +        Journal = {Macromolecules},
132 +        Pages = {1204-1207},
133 +        Timescited = {0},
134 +        Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION},
135 +        Volume = {19},
136 +        Year = {1986}}
137 +
138 + @article{Berendsen87,
139 +        Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
140 +        Date-Added = {2008-01-22 09:53:15 -0500},
141 +        Date-Modified = {2008-01-22 09:53:15 -0500},
142 +        Journal = jpc,
143 +        Pages = {6269-6271},
144 +        Title = {The Missing Term in Effective Pair Potentials},
145 +        Volume = 91,
146 +        Year = 1987}
147 +
148 + @incollection{Berendsen81,
149 +        Address = {Dordrecht},
150 +        Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
151 +        Booktitle = {Intermolecular Forces},
152 +        Date-Added = {2008-01-22 09:52:49 -0500},
153 +        Date-Modified = {2008-01-22 09:52:49 -0500},
154 +        Editor = {B. Pullman},
155 +        Pages = {331-342},
156 +        Publisher = {Reidel},
157 +        Title = {Simple Point Charge Water},
158 +        Year = 1981}
159 +
160 + @article{Stillinger74,
161 +        Author = {F.~H. Stillinger and A. Rahman},
162 +        Date-Added = {2008-01-22 09:51:43 -0500},
163 +        Date-Modified = {2008-01-22 09:51:43 -0500},
164 +        Journal = jcp,
165 +        Number = 4,
166 +        Pages = {1545-1557},
167 +        Title = {Improved simulation of liquid water by molecular dynamics},
168 +        Volume = 60,
169 +        Year = 1974}
170 +
171 + @article{Torre:1983lr,
172 +        Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
173 +        Date-Added = {2008-01-11 16:16:43 -0500},
174 +        Date-Modified = {2008-01-11 16:16:43 -0500},
175 +        Journal = {The Journal of Chemical Physics},
176 +        Journal1 = {The Journal of Chemical Physics},
177 +        Journal2 = {J. Chem. Phys.},
178 +        Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
179 +        Number = 5,
180 +        Pages = {2454--2460},
181 +        Publisher = {AIP},
182 +        Title = {Effects from bead size and hydrodynamic interactions on the translational and rotational coefficients of macromolecular bead models},
183 +        Ty = {JOUR},
184 +        Url = {http://link.aip.org/link/?JCP/79/2454/1},
185 +        Volume = 79,
186 +        Year = 1983,
187 +        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}}
188  
189 + @article{PhysRev.119.53,
190 +        Author = {Favro, L. Dale},
191 +        Date-Added = {2008-01-09 16:57:02 -0500},
192 +        Date-Modified = {2008-01-09 16:57:02 -0500},
193 +        Doi = {10.1103/PhysRev.119.53},
194 +        Journal = {Phys. Rev.},
195 +        Month = {Jul},
196 +        Number = 1,
197 +        Numpages = 9,
198 +        Pages = {53--62},
199 +        Publisher = {American Physical Society},
200 +        Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body},
201 +        Volume = 119,
202 +        Year = 1960,
203 +        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}}
204  
205   @article{hess:209,
206          Author = {Berk Hess},
# Line 16 | Line 209
209          Doi = {10.1063/1.1421362},
210          Journal = {The Journal of Chemical Physics},
211          Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
212 <        Number = {1},
212 >        Number = 1,
213          Pages = {209-217},
214          Publisher = {AIP},
215          Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
216          Url = {http://link.aip.org/link/?JCP/116/209/1},
217 <        Volume = {116},
218 <        Year = {2002}}
217 >        Volume = 116,
218 >        Year = 2002,
219 >        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
220 >        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}}
221  
222   @article{Garcia-de-la-Torre:1997qy,
223          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.},
224          Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es},
225 <        Au = {Garcia de la Torre, J and Carrasco, B and Harding, SE},
226 <        Author = {Garcia de la Torre, J and Carrasco, B and Harding, S E},
227 <        Da = {19970709},
225 >        Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE},
226 >        Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E},
227 >        Da = 19970709,
228          Date-Added = {2008-01-08 15:45:31 -0500},
229          Date-Modified = {2008-01-08 15:46:57 -0500},
230 <        Dcom = {19970709},
230 >        Dcom = 19970709,
231          Edat = {1997/01/01},
232          Issn = {0175-7571 (Print)},
233 <        Jid = {8409413},
233 >        Jid = 8409413,
234          Journal = {Eur Biophys J},
235          Jt = {European biophysics journal : EBJ},
236          Keywords = {Birefringence; Fluorescence Polarization; Humans; Immunoglobulin G/chemistry; Models, Structural; *Protein Conformation; Proteins/*chemistry; Scattering, Radiation; *Software; Ultracentrifugation/methods},
237          Language = {eng},
238 <        Lr = {20061115},
238 >        Lr = 20061115,
239          Mhda = {1997/01/01 00:01},
240          Number = {5-6},
241          Own = {NLM},
242          Pages = {361--372},
243          Pl = {GERMANY},
244 <        Pmid = {9213556},
244 >        Pmid = 9213556,
245          Pst = {ppublish},
246          Pt = {Journal Article; Research Support, Non-U.S. Gov't},
247          Pubm = {Print},
248          Rn = {0 (Immunoglobulin G); 0 (Proteins)},
249          Sb = {IM},
250 <        So = {Eur Biophys J. 1997;25(5-6):361-72. },
250 >        So = {Eur Biophys J. 1997;25(5-6):361-72.},
251          Stat = {MEDLINE},
252          Title = {SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.},
253 <        Volume = {25},
254 <        Year = {1997}}
253 >        Volume = 25,
254 >        Year = 1997}
255  
256   @article{Ravichandran:1999fk,
257          Abstract = {Detailed molecular dynamics simulations of the rotational and the translational motions of Gay-Berne ellipsoids in a sea of Lennard-Jones spheres have been carried out. It is found that while the translational motion of an ellipsoid is isotropic at low density, it becomes increasingly anisotropic with density until the ratio of the parallel to the perpendicular diffusion coefficients becomes nearly equal to the value of the aspect ratio at high density. The latter is in agreement with the prediction of Navier-Stokes hydrodynamics with slip boundary condition. The product of the translational diffusion coefficient and the rotational correlation time also attains a hydrodynamic-like density independent behavior only at high density. The reorientational correlation function becomes nonexponential at high density and low temperature where it also develops a slow decay. The perpendicular component of the velocity time correlation function exhibits a clear double minimum, only at high density, which becomes more pronounced as the aspect ratio is increased. (C) 1999 American Institute of Physics. [S0021-9606(99)51440-2].},
# Line 66 | Line 261
261          Journal = {Journal of Chemical Physics},
262          Pages = {7505-7511},
263          Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
264 <        Volume = {111},
265 <        Year = {1999}}
264 >        Volume = 111,
265 >        Year = 1999}
266  
267   @article{TANG:1993lr,
268          Abstract = {Translational friction coefficients of hard prolate ellipsoids (having aspect ratios of 1-10) have been calculated by solving the linearized Navier-Stokes equations of hydrodynamics, using the method of Faxen's theorem. When the stick boundary condition was used, the present results reproduce the famous work of Lamb. The new information derived from this study arises from the analysis of the friction under the influence of the slip hydrodynamic boundary condition. It was found that the slip friction perpendicular to the long axis of the prolate ellipsoid increases monotonically with aspect ratio, whereas the parallel component of the friction decreases monotonically to an apparent limiting value. The ratio f(perpendicular to)/f(parallel to) of friction coefficients perpendicular and parallel to the long axis of the particle, calculated using slip hydrodynamics, scales roughly as the aspect ratio of the ellipsoid, in accord with the findings from an Enskog (uncorrelated binary collision) kinetic theory of hard ellipsoids and from the estimate derived from molecular dynamics. In contrast, f(perpendicular to)/f(parallel to) derived by means of stick hydrodynamics shows a weak dependence on the aspect ratio and disagrees with kinetic theory and molecular dynamics findings.},
# Line 77 | Line 272
272          Journal = {Molecular Physics},
273          Pages = {1443-1457},
274          Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
275 <        Volume = {80},
276 <        Year = {1993}}
275 >        Volume = 80,
276 >        Year = 1993}
277  
278   @article{Schmidt:2003kx,
279          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.},
# Line 89 | Line 284
284          Journal = {Journal of Chemical Physics},
285          Pages = {8062-8068},
286          Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
287 <        Volume = {119},
288 <        Year = {2003}}
287 >        Volume = 119,
288 >        Year = 2003,
289 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}
290  
291   @article{Schmidt:2004fj,
292          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 101 | Line 297
297          Journal = {Journal of Physical Chemistry B},
298          Pages = {6767-6771},
299          Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
300 <        Volume = {108},
301 <        Year = {2004}}
300 >        Volume = 108,
301 >        Year = 2004,
302 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}}
303  
304   @article{Klein01,
305          Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
# Line 242 | Line 439
439          Date-Modified = {2008-01-08 14:58:56 -0500},
440          Journal = {J. Chem. Phys.},
441          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf},
442 <        Number = {19},
442 >        Number = 19,
443          Pages = {8577-8593},
444          Title = {A smooth particle mesh Ewald method},
445 <        Volume = {103},
446 <        Year = {1995}}
445 >        Volume = 103,
446 >        Year = 1995}
447  
448   @article{Ricci94,
449          Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
# Line 296 | Line 493
493          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf},
494          Pages = {7320-7327},
495          Title = {Acceleration of Convergence for Lattice Sums},
496 <        Volume = {93},
497 <        Year = {1989}}
496 >        Volume = 93,
497 >        Year = 1989}
498  
499   @article{Petersen95,
500          Author = {H.~G. Petersen},
# Line 306 | Line 503
503          Journal = {J. Chem. Phys.},
504          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
505          Month = {September},
506 <        Number = {9},
506 >        Number = 9,
507          Pages = {3668-3679},
508          Title = {Accuracy and efficiency of the particle mesh Ewald method},
509 <        Volume = {103},
510 <        Year = {1995}}
509 >        Volume = 103,
510 >        Year = 1995}
511  
512   @article{Duncan06,
513          Author = {Peter D. Duncan and Philip J. Camp},
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593          Year = 2003}
594  
595   @article{Cascales98,
596 <        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
596 >        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and {Garc\'{i}a de la Torre}, Jose},
597          Date-Added = {2008-01-08 14:58:56 -0500},
598          Date-Modified = {2008-01-08 14:58:57 -0500},
599          Journal = {J. Phys. Chem. B},
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641          Pages = {1057-1066},
642          Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
643 <        Volume = {75},
644 <        Year = {1997}}
643 >        Volume = 75,
644 >        Year = 1997}
645  
646   @inproceedings{Gotze89,
647          Address = {Amsterdam},
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694          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
695          Pages = {1322-1331},
696          Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
697 <        Volume = {99},
698 <        Year = {1995}}
697 >        Volume = 99,
698 >        Year = 1995}
699  
700   @article{Ayton02,
701          Author = {G. Ayton and G.~A. Voth},
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777          Doi = {10.1529/biophysj.106.086017},
778          Eprint = {http://www.biophysj.org/cgi/reprint/90/11/L83.pdf},
779          Journal = {Biophys. J.},
780 <        Number = {11},
780 >        Number = 11,
781          Pages = {L83-85},
782          Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}},
783          Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
784 <        Volume = {90},
785 <        Year = {2006}}
784 >        Volume = 90,
785 >        Year = 2006,
786 >        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
787 >        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017}}
788  
789   @article{deJoannis06,
790          Author = {J. de~Joannis and F.~Y. Jiang and J.~T. Kindt},
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915          Pages = {351-368},
916          Title = {Cutoff Errors in the Ewald. Summation Formulae for Point Charge Systems},
917 <        Volume = {9},
918 <        Year = {1992}}
917 >        Volume = 9,
918 >        Year = 1992}
919  
920   @article{Tlusty00,
921          Author = {T. Tlusty and S.~A. Safran},
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935          Journal = {Phys. Rev. A},
936          Month = {Jul},
937 <        Number = {2},
938 <        Numpages = {13},
937 >        Number = 2,
938 >        Numpages = 13,
939          Pages = {1005--1018},
940          Publisher = {American Physical Society},
941          Title = {Defects in flexible membranes with crystalline order},
942 <        Volume = {38},
943 <        Year = {1988}}
942 >        Volume = 38,
943 >        Year = 1988,
944 >        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005}}
945  
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947          Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
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1051          Date-Modified = {2008-01-08 14:58:58 -0500},
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1056 >        Year = 1999}
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1104          Pages = {69-88},
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1106 <        Volume = {78},
1107 <        Year = {1999}}
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1112          Date-Modified = {2008-01-08 14:58:58 -0500},
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1114          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
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1228 >        Number = 3,
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1253 <        Year = {2001}}
1252 >        Volume = 11,
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1256          Author = {A. Arnold and J. {de Joannis} and C. Holm},
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1260          Journal = {J. Chem. Phys.},
1261          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Arnold_SlabElectrostatics_02.pdf},
1262 <        Number = {6},
1262 >        Number = 6,
1263          Pages = {2496-2502},
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1267 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1268  
1269   @article{deJoannis02,
1270          Author = {J. {de Joannis} and A. Arnold and C. Holm},
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1274          Journal = {J. Chem. Phys.},
1275          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf},
1276 <        Number = {6},
1276 >        Number = 6,
1277          Pages = {2503-2512},
1278          Title = {Electrostatics in periodic slab geometries. II},
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1280 <        Year = {2002}}
1279 >        Volume = 117,
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1281 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
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1709          Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
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1779          Pages = {2213-2216},
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1781          Volume = 61,
1782 <        Year = 1988}
1782 >        Year = 1988,
1783 >        Bdsk-File-1 = {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}}
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1797          Date-Added = {2008-01-08 14:58:56 -0500},
1798          Date-Modified = {2008-01-08 14:58:59 -0500},
1799          Journal = {J. Chem. Soc., Faraday Trans. II},
1800 <        Number = {7},
1800 >        Number = 7,
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1891          Journal = {J. Phys. Chem. B},
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1893 <        Number = {15},
1893 >        Number = 15,
1894          Pages = {3668-3675},
1895          Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
1896 <        Volume = {104},
1897 <        Year = {2000}}
1896 >        Volume = 104,
1897 >        Year = 2000,
1898 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757}}
1899  
1900   @article{Venable00,
1901          Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
# Line 1729 | Line 1935
1935          Journal = {J. Chem. Phys.},
1936          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
1937          Month = {October},
1938 <        Number = {7},
1938 >        Number = 7,
1939          Pages = {3336-3359},
1940          Title = {Molecular Dynamics Study of Liquid Water},
1941 <        Volume = {55},
1942 <        Year = {1971}}
1941 >        Volume = 55,
1942 >        Year = 1971}
1943  
1944   @article{Sum03,
1945          Author = {A.~K. Sum and J.~J. de~Pablo},
# Line 1794 | Line 2000
2000          Journal = {Mol. Phys.},
2001          Pages = {789-792},
2002          Title = {Monte Carlo studies of the dielectric properties of water-like models},
2003 <        Volume = {26},
2004 <        Year = {1973}}
2003 >        Volume = 26,
2004 >        Year = 1973}
2005  
2006   @article{Brush66,
2007          Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
# Line 1804 | Line 2010
2010          Journal = {J. Chem. Phys.},
2011          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
2012          Month = {September},
2013 <        Number = {6},
2013 >        Number = 6,
2014          Pages = {2102-2118},
2015          Title = {Monte Carlo Study of a One-Component Plasma. I},
2016 <        Volume = {45},
2017 <        Year = {1966}}
2016 >        Volume = 45,
2017 >        Year = 1966}
2018  
2019   @article{Tenchov2001,
2020          Author = {Boris Tenchov and Rumiana Koynova and Gert Rapp},
# Line 1826 | Line 2032
2032          Date-Modified = {2008-01-08 14:59:00 -0500},
2033          Doi = {10.1002/jcc.540150702},
2034          Journal = {J. Comput. Chem.},
2035 <        Number = {7},
2035 >        Number = 7,
2036          Pages = {667-683},
2037          Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
2038 <        Volume = {15},
2039 <        Year = {1994}}
2038 >        Volume = 15,
2039 >        Year = 1994,
2040 >        Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150702}}
2041  
2042   @article{McKinnon92,
2043          Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
# Line 1962 | Line 2169
2169          Date-Modified = {2008-01-08 14:59:00 -0500},
2170          Journal = {J. Chem. Phys.},
2171          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
2172 <        Number = {5},
2172 >        Number = 5,
2173          Pages = {1062-1063},
2174          Title = {Optimum Atomic Shape for Bertaut Series},
2175 <        Volume = {25},
2176 <        Year = {1956}}
2175 >        Volume = 25,
2176 >        Year = 1956}
2177  
2178   @article{Renard1966,
2179          Author = {R\'emi Renard and Carl W. Garland},
# Line 2231 | Line 2438
2438          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Kawata_Rapid2DEwald_01.pdf},
2439          Pages = {157-164},
2440          Title = {Rapid calculation of two-dimensional Ewald summation},
2441 <        Volume = {340},
2442 <        Year = {2001}}
2441 >        Volume = 340,
2442 >        Year = 2001}
2443  
2444   @inproceedings{Barker80,
2445          Author = {J.~A. Barker},
# Line 2435 | Line 2642
2642          Date-Modified = {2008-01-08 14:59:01 -0500},
2643          Journal = {Proc. R. Soc. London Ser. A},
2644          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
2645 <        Number = {1752},
2645 >        Number = 1752,
2646          Pages = {27-56},
2647          Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
2648 <        Volume = {373},
2649 <        Year = {1980}}
2648 >        Volume = 373,
2649 >        Year = 1980}
2650  
2651   @article{Ercolessi88,
2652          Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
# Line 2552 | Line 2759
2759          Doi = {10.1529/biophysj.104.056606},
2760          Eprint = {http://www.biophysj.org/cgi/reprint/88/4/2626.pdf},
2761          Journal = {Biophys. J.},
2762 <        Number = {4},
2762 >        Number = 4,
2763          Pages = {2626-2637},
2764          Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}},
2765          Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2766 <        Volume = {88},
2767 <        Year = {2005}}
2766 >        Volume = 88,
2767 >        Year = 2005,
2768 >        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2769 >        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606}}
2770  
2771   @article{Lenz07,
2772          Author = {Olaf Lenz and Friederike Schmid},
# Line 2667 | Line 2876
2876          Date-Added = {2008-01-08 14:58:56 -0500},
2877          Date-Modified = {2008-01-08 14:59:02 -0500},
2878          Journal = {Mol. Phys.},
2879 <        Number = {2},
2879 >        Number = 2,
2880          Pages = {387-400},
2881          Title = {The computer simulation of polar liquids},
2882 <        Volume = {38},
2883 <        Year = {1979}}
2882 >        Volume = 38,
2883 >        Year = 1979}
2884  
2885   @article{Pense92,
2886          Author = {A. W. Pense},
# Line 2711 | Line 2920
2920          Journal = {Surf. Sci.},
2921          Pages = {433-440},
2922          Title = {The electrostatic potential in the surface region of an ionic crystal},
2923 <        Volume = {49},
2924 <        Year = {1975}}
2923 >        Volume = 49,
2924 >        Year = 1975}
2925  
2926   @article{Daw93,
2927          Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes},
# Line 2760 | Line 2969
2969          Date-Modified = {2008-01-08 14:59:02 -0500},
2970          Journal = {J. Chem. Phys.},
2971          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
2972 <        Number = {9},
2972 >        Number = 9,
2973          Pages = {4576-4584},
2974          Title = {The role of long ranged forces in determining the structure and properties of liquid water},
2975 <        Volume = {79},
2976 <        Year = {1983}}
2975 >        Volume = 79,
2976 >        Year = 1983}
2977  
2978   @article{Brannigan04b,
2979          Author = {G. Brannigan and A.~C. Tamboli and F.~L.~H. Brown},
# Line 2973 | Line 3182
3182          Doi = {10.1103/PhysRevLett.67.923},
3183          Journal = {Phys. Rev. Lett.},
3184          Month = {Aug},
3185 <        Number = {7},
3186 <        Numpages = {3},
3185 >        Number = 7,
3186 >        Numpages = 3,
3187          Pages = {923--926},
3188          Publisher = {American Physical Society},
3189          Title = {Wrinkling transition in partially polymerized vesicles},
3190 <        Volume = {67},
3191 <        Year = {1991}}
3190 >        Volume = 67,
3191 >        Year = 1991,
3192 >        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923}}
3193  
3194   @article{Wendt78,
3195          Author = {H. Wendt and F.~F. Abraham},
# Line 2995 | Line 3205
3205          Date-Added = {2008-01-08 14:58:56 -0500},
3206          Date-Modified = {2008-01-08 14:59:03 -0500},
3207          Note = {private correspondence},
3208 <        Year = {2000}}
3208 >        Year = 2000}
3209  
3210   @article{Dwyer1977,
3211          Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
# Line 3057 | Line 3267
3267          Date-Added = {2008-01-08 14:57:14 -0500},
3268          Date-Modified = {2008-01-08 14:57:14 -0500},
3269          Journal = {Chemical Engineering Science},
3270 <        Number = {12},
3270 >        Number = 12,
3271          Pages = {1769--1776},
3272          Title = {The slow translation and rotation of two unequal spheres in a viscous fluid},
3273          Ty = {JOUR},
3274          Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
3275 <        Volume = {24},
3276 <        Year = {1969}}
3275 >        Volume = 24,
3276 >        Year = 1969,
3277 >        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}}
3278  
3279   @article{Stimson:1926qy,
3280          Author = {Stimson, M and Jeffery, GB},
# Line 3072 | Line 3283
3283          Journal = {Proceedings of the Royal Society of London Series A-Containing Papers of a Mathematical and Physical Character},
3284          Pages = {110-116},
3285          Title = {The motion of two spheres in a viscous fluid},
3286 <        Volume = {111},
3287 <        Year = {1926}}
3286 >        Volume = 111,
3287 >        Year = 1926}
3288  
3289   @article{Orlandi:2006fk,
3290          Abstract = {Liquid crystal phases formed by bent-shaped (or {\tt{}"{}}banana{\tt{}"{}}) molecules are currently of great interest. Here we investigate by Monte Carlo computer simulations the phases formed by rigid banana molecules modeled combining three Gay-Berne sites and containing either one central or two lateral and transversal dipoles. We show that changing the dipole position and orientation has a profound effect on the mesophase stability and molecular organization. In particular, we find a uniaxial nematic phase only for off-center dipolar models and tilted phases only for the one with terminal dipoles.},
3291          Address = {Dipartimento di Chimica Fisica e Inorganica, and INSTM, Universita di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.},
3292          Au = {Orlandi, S and Berardi, R and Steltzer, J and Zannoni, C},
3293          Author = {Orlandi, Silvia and Berardi, Roberto and Steltzer, Joachim and Zannoni, Claudio},
3294 <        Da = {20060407},
3294 >        Da = 20060407,
3295          Date-Added = {2008-01-08 14:47:56 -0500},
3296          Date-Modified = {2008-01-08 14:48:06 -0500},
3297 <        Dcom = {20070727},
3297 >        Dcom = 20070727,
3298          Doi = {10.1063/1.2176622},
3299          Edat = {2006/04/08 09:00},
3300          Issn = {0021-9606 (Print)},
3301 <        Jid = {0375360},
3301 >        Jid = 0375360,
3302          Journal = {J Chem Phys},
3303          Jt = {The Journal of chemical physics},
3304          Language = {eng},
3305          Mhda = {2006/04/08 09:01},
3306 <        Number = {12},
3306 >        Number = 12,
3307          Own = {NLM},
3308 <        Pages = {124907},
3308 >        Pages = 124907,
3309          Pl = {United States},
3310 <        Pmid = {16599725},
3310 >        Pmid = 16599725,
3311          Pst = {ppublish},
3312          Pt = {Journal Article},
3313          Pubm = {Print},
3314          So = {J Chem Phys. 2006 Mar 28;124(12):124907.},
3315          Stat = {PubMed-not-MEDLINE},
3316          Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.},
3317 <        Volume = {124},
3318 <        Year = {2006}}
3317 >        Volume = 124,
3318 >        Year = 2006,
3319 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}}
3320  
3321   @article{sun:031602,
3322          Author = {Xiuquan Sun and J. Daniel Gezelter},
3323          Date-Added = {2008-01-08 14:42:33 -0500},
3324          Date-Modified = {2008-01-08 14:42:33 -0500},
3325          Doi = {10.1103/PhysRevE.75.031602},
3326 <        Eid = {031602},
3326 >        Eid = 031602,
3327          Journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)},
3328          Keywords = {lattice theory; membranes},
3329 <        Number = {3},
3330 <        Numpages = {7},
3331 <        Pages = {031602},
3329 >        Number = 3,
3330 >        Numpages = 7,
3331 >        Pages = 031602,
3332          Publisher = {APS},
3333          Title = {Spontaneous corrugation of dipolar membranes},
3334          Url = {http://link.aps.org/abstract/PRE/v75/e031602},
3335 <        Volume = {75},
3336 <        Year = {2007}}
3335 >        Volume = 75,
3336 >        Year = 2007,
3337 >        Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602},
3338 >        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}}
3339  
3340   @article{Ortega:2007lr,
3341          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.},
3342          Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.},
3343 <        Au = {Ortega, A and Garcia de la Torre, J},
3344 <        Author = {Ortega, A and Garcia de la Torre, J},
3345 <        Da = {20070813},
3343 >        Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3344 >        Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3345 >        Da = 20070813,
3346          Date-Added = {2008-01-08 14:38:03 -0500},
3347          Date-Modified = {2008-01-08 14:38:49 -0500},
3348 <        Dcom = {20071017},
3349 <        Dep = {20070724},
3348 >        Dcom = 20071017,
3349 >        Dep = 20070724,
3350          Doi = {10.1021/bm700473f},
3351          Edat = {2007/07/25 09:00},
3352          Issn = {1525-7797 (Print)},
3353 <        Jid = {100892849},
3353 >        Jid = 100892849,
3354          Journal = {Biomacromolecules},
3355          Jt = {Biomacromolecules},
3356          Keywords = {Computer Simulation; Heparin/chemistry; Macromolecular Substances/*chemistry; *Models, Chemical; *Models, Molecular; Molecular Conformation; Particle Size; Protein Conformation; Proteins/chemistry; Software; Solutions},
3357          Language = {eng},
3358          Mhda = {2007/10/18 09:00},
3359 <        Number = {8},
3359 >        Number = 8,
3360          Own = {NLM},
3361          Pages = {2464--2475},
3362          Phst = {2007/07/24 {$[$}aheadofprint{$]$}},
3363          Pl = {United States},
3364 <        Pmid = {17645309},
3364 >        Pmid = 17645309,
3365          Pst = {ppublish},
3366          Pt = {Journal Article; Research Support, Non-U.S. Gov't},
3367          Pubm = {Print-Electronic},
# Line 3156 | Line 3370
3370          So = {Biomacromolecules. 2007 Aug;8(8):2464-75. Epub 2007 Jul 24.},
3371          Stat = {MEDLINE},
3372          Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.},
3373 <        Volume = {8},
3374 <        Year = {2007}}
3373 >        Volume = 8,
3374 >        Year = 2007,
3375 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}}
3376  
3377   @article{Torre2003,
3378          Abstract = {While the prediction of hydrodynamic properties of rigid particles
# Line 3183 | Line 3398
3398      We provide an example of the application of this methodology to
3399      the dynamics of a semiflexible, wormlike DNA.},
3400          Annote = {724XK Times Cited:6 Cited References Count:64},
3401 <        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},
3401 >        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},
3402          Issn = {0175-7571},
3403          Journal = {European Biophysics Journal with Biophysics Letters},
3404          Month = {Aug},
3405 <        Number = {5},
3405 >        Number = 5,
3406          Pages = {477-486},
3407          Title = {Calculation of the solution properties of flexible macromolecules: methods and applications},
3408          Uri = {<Go to ISI>://000185513400011},
3409 <        Volume = {32},
3410 <        Year = {2003}}
3409 >        Volume = 32,
3410 >        Year = 2003}
3411  
3412   @article{Alakent2005,
3413          Abstract = {Time series analysis tools are employed on the principal modes obtained
# Line 3234 | Line 3449
3449          Issn = {0021-9606},
3450          Journal = {Journal of Chemical Physics},
3451          Month = {Oct 8},
3452 <        Number = {14},
3452 >        Number = 14,
3453          Pages = {-},
3454          Title = {Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects},
3455          Uri = {<Go to ISI>://000232532000064},
3456 <        Volume = {123},
3457 <        Year = {2005}}
3456 >        Volume = 123,
3457 >        Year = 2005}
3458  
3459   @book{Alexander1987,
3460          Address = {New York},
3461          Author = {C. Alexander},
3462          Publisher = {Oxford University Press},
3463          Title = {A Pattern Language: Towns, Buildings, Construction},
3464 <        Year = {1987}}
3464 >        Year = 1987}
3465  
3466   @book{Allen1987,
3467          Address = {New York},
3468          Author = {M.~P. Allen and D.~J. Tildesley},
3469          Publisher = {Oxford University Press},
3470          Title = {Computer Simulations of Liquids},
3471 <        Year = {1987}}
3471 >        Year = 1987}
3472  
3473   @article{Allison1991,
3474          Abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
# Line 3275 | Line 3490
3490          Issn = {0024-9297},
3491          Journal = {Macromolecules},
3492          Month = {Jan 21},
3493 <        Number = {2},
3493 >        Number = 2,
3494          Pages = {530-536},
3495          Title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application to Polarized Dynamic Light-Scattering},
3496          Uri = {<Go to ISI>://A1991EU81400029},
3497 <        Volume = {24},
3498 <        Year = {1991}}
3497 >        Volume = 24,
3498 >        Year = 1991}
3499  
3500   @article{Andersen1983,
3501          Annote = {Rq238 Times Cited:559 Cited References Count:14},
3502          Author = {H. C. Andersen},
3503          Issn = {0021-9991},
3504          Journal = {Journal of Computational Physics},
3505 <        Number = {1},
3505 >        Number = 1,
3506          Pages = {24-34},
3507          Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
3508          Uri = {<Go to ISI>://A1983RQ23800002},
3509 <        Volume = {52},
3510 <        Year = {1983}}
3509 >        Volume = 52,
3510 >        Year = 1983}
3511  
3512   @article{Auerbach2005,
3513          Abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
# Line 3319 | Line 3534
3534          Issn = {0027-8424},
3535          Journal = {Proceedings of the National Academy of Sciences of the United States of America},
3536          Month = {Feb 1},
3537 <        Number = {5},
3537 >        Number = 5,
3538          Pages = {1408-1412},
3539          Title = {Gating of acetylcholine receptor channels: Brownian motion across a broad transition state},
3540          Uri = {<Go to ISI>://000226877300030},
3541 <        Volume = {102},
3542 <        Year = {2005}}
3541 >        Volume = 102,
3542 >        Year = 2005}
3543  
3544   @article{Baber1995,
3545          Abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
# Line 3353 | Line 3568
3568          Issn = {0006-2960},
3569          Journal = {Biochemistry},
3570          Month = {May 16},
3571 <        Number = {19},
3571 >        Number = 19,
3572          Pages = {6533-6539},
3573          Title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
3574          Uri = {<Go to ISI>://A1995QZ71600035},
3575 <        Volume = {34},
3576 <        Year = {1995}}
3575 >        Volume = 34,
3576 >        Year = 1995}
3577  
3578   @article{Banerjee2004,
3579          Abstract = {Based on a coherent state representation of noise operator and an
# Line 3380 | Line 3595
3595          Issn = {0021-9606},
3596          Journal = {Journal of Chemical Physics},
3597          Month = {May 15},
3598 <        Number = {19},
3598 >        Number = 19,
3599          Pages = {8960-8972},
3600          Title = {Solution of quantum Langevin equation: Approximations, theoretical and numerical aspects},
3601          Uri = {<Go to ISI>://000221146400009},
3602 <        Volume = {120},
3603 <        Year = {2004}}
3602 >        Volume = 120,
3603 >        Year = 2004}
3604  
3605   @article{Barojas1973,
3606          Author = {J. Barojas and D. Levesque},
3607          Journal = {Phys. Rev. A},
3608          Pages = {1092-1105},
3609          Title = {Simulation of Diatomic Homonuclear Liquids},
3610 <        Volume = {7},
3611 <        Year = {1973}}
3610 >        Volume = 7,
3611 >        Year = 1973}
3612  
3613   @article{Barth1998,
3614          Abstract = {We present an efficient new method termed LN for propagating biomolecular
# Line 3427 | Line 3642
3642          Issn = {0021-9606},
3643          Journal = {Journal of Chemical Physics},
3644          Month = {Aug 1},
3645 <        Number = {5},
3645 >        Number = 5,
3646          Pages = {1617-1632},
3647          Title = {Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN},
3648          Uri = {<Go to ISI>://000075066300006},
3649 <        Volume = {109},
3650 <        Year = {1998}}
3649 >        Volume = 109,
3650 >        Year = 1998}
3651  
3652   @article{Batcho2001,
3653          Abstract = {We present an analysis for a simple two-component harmonic oscillator
# Line 3451 | Line 3666
3666          Issn = {0021-9606},
3667          Journal = {Journal of Chemical Physics},
3668          Month = {Sep 1},
3669 <        Number = {9},
3669 >        Number = 9,
3670          Pages = {4019-4029},
3671          Title = {Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration},
3672          Uri = {<Go to ISI>://000170813800005},
3673 <        Volume = {115},
3674 <        Year = {2001}}
3673 >        Volume = 115,
3674 >        Year = 2001}
3675  
3676   @article{Bates2005,
3677          Abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
# Line 3482 | Line 3697
3697          Issn = {1539-3755},
3698          Journal = {Physical Review E},
3699          Month = {Nov},
3700 <        Number = {5},
3700 >        Number = 5,
3701          Pages = {-},
3702          Title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation study},
3703          Uri = {<Go to ISI>://000233603100030},
3704 <        Volume = {72},
3705 <        Year = {2005}}
3704 >        Volume = 72,
3705 >        Year = 2005}
3706  
3707   @article{Beard2003,
3708          Abstract = {We introduce an unbiased protocol for performing rotational moves
# Line 3504 | Line 3719
3719          Issn = {0006-3495},
3720          Journal = {Biophysical Journal},
3721          Month = {Nov 1},
3722 <        Number = {5},
3722 >        Number = 5,
3723          Pages = {2973-2976},
3724          Title = {Unbiased rotational moves for rigid-body dynamics},
3725          Uri = {<Go to ISI>://000186190500018},
3726 <        Volume = {85},
3727 <        Year = {2003}}
3726 >        Volume = 85,
3727 >        Year = 2003}
3728  
3729   @article{Beloborodov1998,
3730          Abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
# Line 3526 | Line 3741
3741          Issn = {1090-7807},
3742          Journal = {Journal of Magnetic Resonance},
3743          Month = {Jun},
3744 <        Number = {2},
3744 >        Number = 2,
3745          Pages = {328-329},
3746          Title = {Effect of coupling between rotational and translational Brownian motions on NMR spin relaxation: Consideration using green function of rigid body diffusion},
3747          Uri = {<Go to ISI>://000074214800017},
3748 <        Volume = {132},
3749 <        Year = {1998}}
3748 >        Volume = 132,
3749 >        Year = 1998}
3750  
3751   @article{Berardi1996,
3752          Abstract = {We demonstrate that the overall molecular dipole organization in a
# Line 3548 | Line 3763
3763          Issn = {0009-2614},
3764          Journal = {Chemical Physics Letters},
3765          Month = {Oct 18},
3766 <        Number = {3},
3766 >        Number = 3,
3767          Pages = {357-362},
3768          Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
3769          Uri = {<Go to ISI>://A1996VN63700023},
3770 <        Volume = {261},
3771 <        Year = {1996}}
3770 >        Volume = 261,
3771 >        Year = 1996}
3772  
3773   @article{Berkov2005,
3774          Abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
# Line 3578 | Line 3793
3793          Issn = {1098-0121},
3794          Journal = {Physical Review B},
3795          Month = {Sep},
3796 <        Number = {9},
3796 >        Number = 9,
3797          Pages = {-},
3798          Title = {Magnetization precession due to a spin-polarized current in a thin nanoelement: Numerical simulation study},
3799          Uri = {<Go to ISI>://000232228500058},
3800 <        Volume = {72},
3801 <        Year = {2005}}
3800 >        Volume = 72,
3801 >        Year = 2005}
3802  
3803   @article{Berkov2005a,
3804          Abstract = {Numerical simulations of fast remagnetization processes using stochastic
# Line 3609 | Line 3824
3824          Pages = {442-448},
3825          Title = {Stochastic dynamic simulations of fast remagnetization processes: recent advances and applications},
3826          Uri = {<Go to ISI>://000228837600109},
3827 <        Volume = {290},
3828 <        Year = {2005}}
3827 >        Volume = 290,
3828 >        Year = 2005}
3829  
3830   @article{Berkov2002,
3831          Abstract = {We report on recent progress achieved by the development of numerical
# Line 3632 | Line 3847
3847          Issn = {0031-8965},
3848          Journal = {Physica Status Solidi a-Applied Research},
3849          Month = {Feb 16},
3850 <        Number = {2},
3850 >        Number = 2,
3851          Pages = {409-421},
3852          Title = {Magnetization dynamics in nanoparticle systems: Numerical simulation using Langevin dynamics},
3853          Uri = {<Go to ISI>://000174145200026},
3854 <        Volume = {189},
3855 <        Year = {2002}}
3854 >        Volume = 189,
3855 >        Year = 2002}
3856  
3857   @article{Bernal1980,
3858 <        Author = {J.M. Bernal and J. G. {de la Torre}},
3858 >        Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose},
3859          Journal = {Biopolymers},
3860          Pages = {751-766},
3861          Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape},
3862 <        Volume = {19},
3863 <        Year = {1980}}
3862 >        Volume = 19,
3863 >        Year = 1980}
3864  
3865   @article{Brenner1967,
3866          Author = {H. Brenner},
3867          Journal = {J. Collid. Int. Sci.},
3868          Pages = {407-436},
3869          Title = {Coupling between the Translational and Rotational Brownian Motions of Rigid Particles of Arbitrary shape},
3870 <        Volume = {23},
3871 <        Year = {1967}}
3870 >        Volume = 23,
3871 >        Year = 1967}
3872  
3873   @article{Brooks1983,
3874          Annote = {Qp423 Times Cited:6414 Cited References Count:96},
3875          Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus},
3876          Issn = {0192-8651},
3877          Journal = {Journal of Computational Chemistry},
3878 <        Number = {2},
3878 >        Number = 2,
3879          Pages = {187-217},
3880          Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
3881          Uri = {<Go to ISI>://A1983QP42300010},
3882 <        Volume = {4},
3883 <        Year = {1983}}
3882 >        Volume = 4,
3883 >        Year = 1983}
3884  
3885   @article{Brunger1984,
3886          Annote = {Sm173 Times Cited:143 Cited References Count:22},
3887          Author = {A. Brunger and C. L. Brooks and M. Karplus},
3888          Issn = {0009-2614},
3889          Journal = {Chemical Physics Letters},
3890 <        Number = {5},
3890 >        Number = 5,
3891          Pages = {495-500},
3892          Title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations of St2 Water},
3893          Uri = {<Go to ISI>://A1984SM17300007},
3894 <        Volume = {105},
3895 <        Year = {1984}}
3894 >        Volume = 105,
3895 >        Year = 1984}
3896  
3897   @article{Budd1999,
3898          Abstract = {This paper examines a synthesis of adaptive mesh methods with the
# Line 3691 | Line 3906
3906          Issn = {1364-503X},
3907          Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
3908          Month = {Apr 15},
3909 <        Number = {1754},
3909 >        Number = 1754,
3910          Pages = {1047-1077},
3911          Title = {Self-similar numerical solutions of the porous-medium equation using moving mesh methods},
3912          Uri = {<Go to ISI>://000080466800005},
3913 <        Volume = {357},
3914 <        Year = {1999}}
3913 >        Volume = 357,
3914 >        Year = 1999}
3915  
3916   @article{Camp1999,
3917          Abstract = {Fluids of hard bent-core molecules have been studied using theory
# Line 3734 | Line 3949
3949          Issn = {0021-9606},
3950          Journal = {Journal of Chemical Physics},
3951          Month = {Dec 1},
3952 <        Number = {21},
3952 >        Number = 21,
3953          Pages = {9871-9881},
3954          Title = {Theory and computer simulation of bent-core molecules},
3955          Uri = {<Go to ISI>://000083685400056},
3956 <        Volume = {111},
3957 <        Year = {1999}}
3956 >        Volume = 111,
3957 >        Year = 1999}
3958  
3959   @article{Care2005,
3960          Abstract = {A review is presented of molecular and mesoscopic computer simulations
# Line 3754 | Line 3969
3969          Issn = {0034-4885},
3970          Journal = {Reports on Progress in Physics},
3971          Month = {Nov},
3972 <        Number = {11},
3972 >        Number = 11,
3973          Pages = {2665-2700},
3974          Title = {Computer simulation of liquid crystals},
3975          Uri = {<Go to ISI>://000233697600004},
3976 <        Volume = {68},
3977 <        Year = {2005}}
3976 >        Volume = 68,
3977 >        Year = 2005}
3978  
3979   @article{Carrasco1999,
3980          Abstract = {The hydrodynamic properties of rigid particles are calculated from
# Line 3781 | Line 3996
3996      them to some test cases, for which the properties are known a priori.
3997      We provide guidelines and computational tools for bead modeling.},
3998          Annote = {200TT Times Cited:46 Cited References Count:57},
3999 <        Author = {B. Carrasco and J. G. {de la Torre}},
3999 >        Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
4000          Issn = {0006-3495},
4001          Journal = {Biophysical Journal},
4002          Month = {Jun},
4003 <        Number = {6},
4003 >        Number = 6,
4004          Pages = {3044-3057},
4005          Title = {Hydrodynamic properties of rigid particles: Comparison of different modeling and computational procedures},
4006          Uri = {<Go to ISI>://000080556700016},
4007 <        Volume = {76},
4008 <        Year = {1999}}
4007 >        Volume = 76,
4008 >        Year = 1999}
4009  
4010   @article{Chandra1999,
4011          Abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
# Line 3816 | Line 4031
4031          Issn = {0021-9606},
4032          Journal = {Journal of Chemical Physics},
4033          Month = {Aug 8},
4034 <        Number = {6},
4034 >        Number = 6,
4035          Pages = {2701-2709},
4036          Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations},
4037          Uri = {<Go to ISI>://000081711200038},
4038 <        Volume = {111},
4039 <        Year = {1999}}
4038 >        Volume = 111,
4039 >        Year = 1999}
4040  
4041   @article{Channell1990,
4042          Annote = {Dk631 Times Cited:152 Cited References Count:34},
# Line 3829 | Line 4044
4044          Issn = {0951-7715},
4045          Journal = {Nonlinearity},
4046          Month = {may},
4047 <        Number = {2},
4047 >        Number = 2,
4048          Pages = {231-259},
4049          Title = {Symplectic Integration of Hamiltonian-Systems},
4050          Uri = {<Go to ISI>://A1990DK63100001},
4051 <        Volume = {3},
4052 <        Year = {1990}}
4051 >        Volume = 3,
4052 >        Year = 1990}
4053  
4054   @article{Chen2003,
4055          Abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
# Line 3855 | Line 4070
4070          Pages = {21-30},
4071          Title = {Explicit mixed finite order Runge-Kutta methods},
4072          Uri = {<Go to ISI>://000180314200002},
4073 <        Volume = {44},
4074 <        Year = {2003}}
4073 >        Volume = 44,
4074 >        Year = 2003}
4075  
4076   @article{Cheung2004,
4077          Abstract = {Equilibrium molecular dynamics calculations have been performed for
# Line 3876 | Line 4091
4091          Issn = {0021-9606},
4092          Journal = {Journal of Chemical Physics},
4093          Month = {Nov 8},
4094 <        Number = {18},
4094 >        Number = 18,
4095          Pages = {9131-9139},
4096          Title = {Calculation of flexoelectric coefficients for a nematic liquid crystal by atomistic simulation},
4097          Uri = {<Go to ISI>://000224798900053},
4098 <        Volume = {121},
4099 <        Year = {2004}}
4098 >        Volume = 121,
4099 >        Year = 2004}
4100  
4101   @article{Cheung2002,
4102          Abstract = {Equilibrium molecular dynamics calculations have been performed for
# Line 3903 | Line 4118
4118          Pages = {140-146},
4119          Title = {Calculation of the rotational viscosity of a nematic liquid crystal},
4120          Uri = {<Go to ISI>://000175331000020},
4121 <        Volume = {356},
4122 <        Year = {2002}}
4121 >        Volume = 356,
4122 >        Year = 2002}
4123  
4124   @article{Chin2004,
4125          Abstract = {Current molecular dynamics simulations of biomolecules using multiple
# Line 3927 | Line 4142
4142          Issn = {0021-9606},
4143          Journal = {Journal of Chemical Physics},
4144          Month = {Jan 1},
4145 <        Number = {1},
4145 >        Number = 1,
4146          Pages = {8-13},
4147          Title = {Dynamical multiple-time stepping methods for overcoming resonance instabilities},
4148          Uri = {<Go to ISI>://000187577400003},
4149 <        Volume = {120},
4150 <        Year = {2004}}
4149 >        Volume = 120,
4150 >        Year = 2004}
4151  
4152   @article{Cook2000,
4153          Abstract = {The Kirkwood correlation factor g(1) determines the preference for
# Line 3956 | Line 4171
4171          Issn = {0267-8292},
4172          Journal = {Liquid Crystals},
4173          Month = {Dec},
4174 <        Number = {12},
4174 >        Number = 12,
4175          Pages = {1573-1583},
4176          Title = {Simulation studies of dipole correlation in the isotropic liquid phase},
4177          Uri = {<Go to ISI>://000165437800002},
4178 <        Volume = {27},
4179 <        Year = {2000}}
4178 >        Volume = 27,
4179 >        Year = 2000}
4180  
4181   @article{Cui2003,
4182          Abstract = {All-atom Langevin dynamics simulations have been performed to study
# Line 3986 | Line 4201
4201          Issn = {0027-8424},
4202          Journal = {Proceedings of the National Academy of Sciences of the United States of America},
4203          Month = {Jun 10},
4204 <        Number = {12},
4204 >        Number = 12,
4205          Pages = {7087-7092},
4206          Title = {Folding and misfolding of the papillomavirus E6 interacting peptide E6ap},
4207          Uri = {<Go to ISI>://000183493500037},
4208 <        Volume = {100},
4209 <        Year = {2003}}
4208 >        Volume = 100,
4209 >        Year = 2003}
4210  
4211   @article{Denisov2003,
4212          Abstract = {We study the slow phase of thermally activated magnetic relaxation
# Line 4009 | Line 4224
4224          Issn = {1098-0121},
4225          Journal = {Physical Review B},
4226          Month = {Jan 1},
4227 <        Number = {1},
4227 >        Number = 1,
4228          Pages = {-},
4229          Title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
4230          Uri = {<Go to ISI>://000180830400056},
4231 <        Volume = {67},
4232 <        Year = {2003}}
4231 >        Volume = 67,
4232 >        Year = 2003}
4233  
4234   @article{Derreumaux1998,
4235          Abstract = {To explore the origin of the large-scale motion of triosephosphate
# Line 4046 | Line 4261
4261          Issn = {0006-3495},
4262          Journal = {Biophysical Journal},
4263          Month = {Jan},
4264 <        Number = {1},
4264 >        Number = 1,
4265          Pages = {72-81},
4266          Title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
4267          Uri = {<Go to ISI>://000073393400009},
4268 <        Volume = {74},
4269 <        Year = {1998}}
4268 >        Volume = 74,
4269 >        Year = 1998}
4270  
4271   @article{Dullweber1997,
4272          Abstract = {Rigid body molecular models possess symplectic structure and time-reversal
# Line 4078 | Line 4293
4293          Issn = {0021-9606},
4294          Journal = {Journal of Chemical Physics},
4295          Month = {Oct 15},
4296 <        Number = {15},
4296 >        Number = 15,
4297          Pages = {5840-5851},
4298          Title = {Symplectic splitting methods for rigid body molecular dynamics},
4299          Uri = {<Go to ISI>://A1997YA58700024},
4300 <        Volume = {107},
4301 <        Year = {1997}}
4300 >        Volume = 107,
4301 >        Year = 1997}
4302  
4303   @book{Gamma1994,
4304          Address = {London},
4305          Author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
4306 <        Chapter = {7},
4306 >        Chapter = 7,
4307          Publisher = {Perason Education},
4308          Title = {Design Patterns: Elements of Reusable Object-Oriented Software},
4309 <        Year = {1994}}
4309 >        Year = 1994}
4310  
4311   @article{Edwards2005,
4312          Abstract = {Using the Langevin dynamics technique, we have carried out simulations
# Line 4109 | Line 4324
4324          Issn = {0024-9297},
4325          Journal = {Macromolecules},
4326          Month = {Dec 13},
4327 <        Number = {25},
4327 >        Number = 25,
4328          Pages = {10590-10595},
4329          Title = {Stretching a single diblock copolymer in a selective solvent: Langevin dynamics simulations},
4330          Uri = {<Go to ISI>://000233866200035},
4331 <        Volume = {38},
4332 <        Year = {2005}}
4331 >        Volume = 38,
4332 >        Year = 2005}
4333  
4334   @article{Egberts1988,
4335          Annote = {Q0188 Times Cited:219 Cited References Count:43},
# Line 4122 | Line 4337
4337          Issn = {0021-9606},
4338          Journal = {Journal of Chemical Physics},
4339          Month = {Sep 15},
4340 <        Number = {6},
4340 >        Number = 6,
4341          Pages = {3718-3732},
4342          Title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic Detail},
4343          Uri = {<Go to ISI>://A1988Q018800036},
4344 <        Volume = {89},
4345 <        Year = {1988}}
4344 >        Volume = 89,
4345 >        Year = 1988}
4346  
4347   @article{Ermak1978,
4348          Annote = {Fp216 Times Cited:785 Cited References Count:42},
4349          Author = {D. L. Ermak and J. A. Mccammon},
4350          Issn = {0021-9606},
4351          Journal = {Journal of Chemical Physics},
4352 <        Number = {4},
4352 >        Number = 4,
4353          Pages = {1352-1360},
4354          Title = {Brownian Dynamics with Hydrodynamic Interactions},
4355          Uri = {<Go to ISI>://A1978FP21600004},
4356 <        Volume = {69},
4357 <        Year = {1978}}
4356 >        Volume = 69,
4357 >        Year = 1978}
4358  
4359   @article{Evans1977,
4360          Annote = {Ds757 Times Cited:271 Cited References Count:18},
4361          Author = {D. J. Evans},
4362          Issn = {0026-8976},
4363          Journal = {Molecular Physics},
4364 <        Number = {2},
4364 >        Number = 2,
4365          Pages = {317-325},
4366          Title = {Representation of Orientation Space},
4367          Uri = {<Go to ISI>://A1977DS75700002},
4368 <        Volume = {34},
4369 <        Year = {1977}}
4368 >        Volume = 34,
4369 >        Year = 1977}
4370  
4371   @article{Fennell2004,
4372          Abstract = {The density maximum and temperature dependence of the self-diffusion
# Line 4182 | Line 4397
4397          Issn = {0021-9606},
4398          Journal = {Journal of Chemical Physics},
4399          Month = {May 15},
4400 <        Number = {19},
4400 >        Number = 19,
4401          Pages = {9175-9184},
4402          Title = {On the structural and transport properties of the soft sticky dipole and related single-point water models},
4403          Uri = {<Go to ISI>://000221146400032},
4404 <        Volume = {120},
4405 <        Year = {2004}}
4404 >        Volume = 120,
4405 >        Year = 2004}
4406  
4407   @article{Fernandes2002,
4408          Abstract = {We have developed a Brownian dynamics simulation algorithm to generate
# Line 4202 | Line 4417
4417      its applicability. Examples include free diffusion, transport in
4418      an electric field, and diffusion in a restricting environment.},
4419          Annote = {633AD Times Cited:2 Cited References Count:43},
4420 <        Author = {M. X. Fernandes and J. G. {de la Torre}},
4420 >        Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4421          Issn = {0006-3495},
4422          Journal = {Biophysical Journal},
4423          Month = {Dec},
4424 <        Number = {6},
4424 >        Number = 6,
4425          Pages = {3039-3048},
4426          Title = {Brownian dynamics simulation of rigid particles of arbitrary shape in external fields},
4427          Uri = {<Go to ISI>://000180256300012},
4428 <        Volume = {83},
4429 <        Year = {2002}}
4428 >        Volume = 83,
4429 >        Year = 2002}
4430  
4431   @book{Frenkel1996,
4432          Address = {New York},
4433          Author = {D. Frenkel and B. Smit},
4434          Publisher = {Academic Press},
4435          Title = {Understanding Molecular Simulation : From Algorithms to Applications},
4436 <        Year = {1996}}
4436 >        Year = 1996}
4437  
4438   @article{Gay1981,
4439          Annote = {Lj347 Times Cited:482 Cited References Count:13},
4440          Author = {J. G. Gay and B. J. Berne},
4441          Issn = {0021-9606},
4442          Journal = {Journal of Chemical Physics},
4443 <        Number = {6},
4443 >        Number = 6,
4444          Pages = {3316-3319},
4445          Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
4446          Uri = {<Go to ISI>://A1981LJ34700029},
4447 <        Volume = {74},
4448 <        Year = {1981}}
4447 >        Volume = 74,
4448 >        Year = 1981}
4449  
4450   @article{Gelin1999,
4451          Abstract = {To investigate the influence of inertial effects on the dynamics of
# Line 4256 | Line 4471
4471          Issn = {1022-1344},
4472          Journal = {Macromolecular Theory and Simulations},
4473          Month = {Nov},
4474 <        Number = {6},
4474 >        Number = 6,
4475          Pages = {529-543},
4476          Title = {Inertial effects in the Brownian dynamics with rigid constraints},
4477          Uri = {<Go to ISI>://000083785700002},
4478 <        Volume = {8},
4479 <        Year = {1999}}
4478 >        Volume = 8,
4479 >        Year = 1999}
4480  
4481   @article{Goetz1998,
4482          Author = {R. Goetz and R. Lipowsky},
4483          Journal = {Journal of Chemical Physics},
4484 <        Number = {17},
4485 <        Pages = {7397},
4484 >        Number = 17,
4485 >        Pages = 7397,
4486          Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
4487 <        Volume = {108},
4488 <        Year = {1998}}
4487 >        Volume = 108,
4488 >        Year = 1998}
4489  
4490   @book{Goldstein2001,
4491          Address = {San Francisco},
# Line 4278 | Line 4493
4493          Edition = {3rd},
4494          Publisher = {Addison Wesley},
4495          Title = {Classical Mechanics},
4496 <        Year = {2001}}
4496 >        Year = 2001}
4497  
4498   @article{Gray2003,
4499          Abstract = {Protein-protein docking algorithms provide a means to elucidate structural
# Line 4310 | Line 4525
4525          Issn = {0022-2836},
4526          Journal = {Journal of Molecular Biology},
4527          Month = {Aug 1},
4528 <        Number = {1},
4528 >        Number = 1,
4529          Pages = {281-299},
4530          Title = {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations},
4531          Uri = {<Go to ISI>://000184351300022},
4532 <        Volume = {331},
4533 <        Year = {2003}}
4532 >        Volume = 331,
4533 >        Year = 2003}
4534  
4535   @article{Greengard1994,
4536          Abstract = {Some of the recently developed fast summation methods that have arisen
# Line 4332 | Line 4547
4547          Issn = {0036-8075},
4548          Journal = {Science},
4549          Month = {Aug 12},
4550 <        Number = {5174},
4550 >        Number = 5174,
4551          Pages = {909-914},
4552          Title = {Fast Algorithms for Classical Physics},
4553          Uri = {<Go to ISI>://A1994PB49900031},
4554 <        Volume = {265},
4555 <        Year = {1994}}
4554 >        Volume = 265,
4555 >        Year = 1994}
4556  
4557   @article{Greengard1987,
4558          Annote = {L0498 Times Cited:899 Cited References Count:7},
# Line 4345 | Line 4560
4560          Issn = {0021-9991},
4561          Journal = {Journal of Computational Physics},
4562          Month = {Dec},
4563 <        Number = {2},
4563 >        Number = 2,
4564          Pages = {325-348},
4565          Title = {A Fast Algorithm for Particle Simulations},
4566          Uri = {<Go to ISI>://A1987L049800006},
4567 <        Volume = {73},
4568 <        Year = {1987}}
4567 >        Volume = 73,
4568 >        Year = 1987}
4569  
4570   @article{Hairer1997,
4571          Abstract = {Backward error analysis is a useful tool for the study of numerical
# Line 4371 | Line 4586
4586          Issn = {0029-599X},
4587          Journal = {Numerische Mathematik},
4588          Month = {Jun},
4589 <        Number = {4},
4589 >        Number = 4,
4590          Pages = {441-462},
4591          Title = {The life-span of backward error analysis for numerical integrators},
4592          Uri = {<Go to ISI>://A1997XJ48800002},
4593 <        Volume = {76},
4594 <        Year = {1997}}
4593 >        Volume = 76,
4594 >        Year = 1997}
4595  
4596   @article{Hao1993,
4597          Abstract = {A new procedure for studying the folding and unfolding of proteins,
# Line 4418 | Line 4633
4633          Issn = {0006-2960},
4634          Journal = {Biochemistry},
4635          Month = {Sep 21},
4636 <        Number = {37},
4636 >        Number = 37,
4637          Pages = {9614-9631},
4638          Title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic Trypsin-Inhibitor Studied by Computer-Simulations},
4639          Uri = {<Go to ISI>://A1993LY29400014},
4640 <        Volume = {32},
4641 <        Year = {1993}}
4640 >        Volume = 32,
4641 >        Year = 1993}
4642  
4643   @article{Hinsen2000,
4644          Abstract = {The slow dynamics of proteins around its native folded state is usually
# Line 4462 | Line 4677
4677          Pages = {25-37},
4678          Title = {Harmonicity in slow protein dynamics},
4679          Uri = {<Go to ISI>://000090121700003},
4680 <        Volume = {261},
4681 <        Year = {2000}}
4680 >        Volume = 261,
4681 >        Year = 2000}
4682  
4683   @article{Ho1992,
4684          Abstract = {Evidence has been found for the existence water at the protein-lipid
# Line 4498 | Line 4713
4713          Issn = {0006-3495},
4714          Journal = {Biophysical Journal},
4715          Month = {Oct},
4716 <        Number = {4},
4716 >        Number = 4,
4717          Pages = {897-902},
4718          Title = {Hydration at the Membrane Protein-Lipid Interface},
4719          Uri = {<Go to ISI>://A1992JU25100002},
4720 <        Volume = {63},
4721 <        Year = {1992}}
4720 >        Volume = 63,
4721 >        Year = 1992}
4722  
4723   @book{Hockney1981,
4724          Address = {New York},
4725          Author = {R.W. Hockney and J.W. Eastwood},
4726          Publisher = {McGraw-Hill},
4727          Title = {Computer Simulation Using Particles},
4728 <        Year = {1981}}
4728 >        Year = 1981}
4729  
4730   @article{Hoover1985,
4731          Annote = {Acr30 Times Cited:1809 Cited References Count:11},
4732          Author = {W. G. Hoover},
4733          Issn = {1050-2947},
4734          Journal = {Physical Review A},
4735 <        Number = {3},
4735 >        Number = 3,
4736          Pages = {1695-1697},
4737          Title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
4738          Uri = {<Go to ISI>://A1985ACR3000056},
4739 <        Volume = {31},
4740 <        Year = {1985}}
4739 >        Volume = 31,
4740 >        Year = 1985}
4741  
4742   @article{Huh2004,
4743          Abstract = {Racemic fluids of chiral calamitic molecules are investigated with
# Line 4540 | Line 4755
4755          Issn = {0021-9606},
4756          Journal = {Journal of Chemical Physics},
4757          Month = {Nov 22},
4758 <        Number = {20},
4758 >        Number = 20,
4759          Pages = {10299-10308},
4760          Title = {Discrimination in isotropic, nematic, and smectic phases of chiral calamitic molecules: A computer simulation study},
4761          Uri = {<Go to ISI>://000225042700059},
4762 <        Volume = {121},
4763 <        Year = {2004}}
4762 >        Volume = 121,
4763 >        Year = 2004}
4764  
4765   @article{Humphrey1996,
4766          Abstract = {VMD is a molecular graphics program designed for the display and analysis
# Line 4579 | Line 4794
4794          Issn = {0263-7855},
4795          Journal = {Journal of Molecular Graphics},
4796          Month = {Feb},
4797 <        Number = {1},
4797 >        Number = 1,
4798          Pages = {33-\&},
4799          Title = {VMD: Visual molecular dynamics},
4800          Uri = {<Go to ISI>://A1996UH51500005},
4801 <        Volume = {14},
4802 <        Year = {1996}}
4801 >        Volume = 14,
4802 >        Year = 1996}
4803  
4804   @article{Izaguirre2001,
4805          Abstract = {In this paper we show the possibility of using very mild stochastic
# Line 4619 | Line 4834
4834          Issn = {0021-9606},
4835          Journal = {Journal of Chemical Physics},
4836          Month = {Feb 1},
4837 <        Number = {5},
4837 >        Number = 5,
4838          Pages = {2090-2098},
4839          Title = {Langevin stabilization of molecular dynamics},
4840          Uri = {<Go to ISI>://000166676100020},
4841 <        Volume = {114},
4842 <        Year = {2001}}
4841 >        Volume = 114,
4842 >        Year = 2001}
4843  
4844   @article{Torre1977,
4845 <        Author = {Jose Garcia De La Torre, V.A. Bloomfield},
4845 >        Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield},
4846          Journal = {Biopolymers},
4847          Pages = {1747-1763},
4848          Title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
4849 <        Volume = {16},
4850 <        Year = {1977}}
4849 >        Volume = 16,
4850 >        Year = 1977}
4851  
4852   @article{Kale1999,
4853          Abstract = {Molecular dynamics programs simulate the behavior of biomolecular
# Line 4662 | Line 4877
4877          Issn = {0021-9991},
4878          Journal = {Journal of Computational Physics},
4879          Month = {May 1},
4880 <        Number = {1},
4880 >        Number = 1,
4881          Pages = {283-312},
4882          Title = {NAMD2: Greater scalability for parallel molecular dynamics},
4883          Uri = {<Go to ISI>://000080181500013},
4884 <        Volume = {151},
4885 <        Year = {1999}}
4884 >        Volume = 151,
4885 >        Year = 1999}
4886  
4887   @article{Kane2000,
4888          Abstract = {The purpose of this work is twofold. First, we demonstrate analytically
# Line 4691 | Line 4906
4906          Issn = {0029-5981},
4907          Journal = {International Journal for Numerical Methods in Engineering},
4908          Month = {Dec 10},
4909 <        Number = {10},
4909 >        Number = 10,
4910          Pages = {1295-1325},
4911          Title = {Variational integrators and the Newmark algorithm for conservative and dissipative mechanical systems},
4912          Uri = {<Go to ISI>://000165270600004},
4913 <        Volume = {49},
4914 <        Year = {2000}}
4913 >        Volume = 49,
4914 >        Year = 2000}
4915  
4916   @article{Klimov1997,
4917          Abstract = {The viscosity (eta) dependence of the folding rates for four sequences
# Line 4715 | Line 4930
4930          Issn = {0031-9007},
4931          Journal = {Physical Review Letters},
4932          Month = {Jul 14},
4933 <        Number = {2},
4933 >        Number = 2,
4934          Pages = {317-320},
4935          Title = {Viscosity dependence of the folding rates of proteins},
4936          Uri = {<Go to ISI>://A1997XK29300035},
4937 <        Volume = {79},
4938 <        Year = {1997}}
4937 >        Volume = 79,
4938 >        Year = 1997}
4939  
4940   @article{Kol1997,
4941          Abstract = {Rigid-body molecular dynamics simulations typically are performed
# Line 4748 | Line 4963
4963          Issn = {0021-9606},
4964          Journal = {Journal of Chemical Physics},
4965          Month = {Aug 15},
4966 <        Number = {7},
4966 >        Number = 7,
4967          Pages = {2580-2588},
4968          Title = {A symplectic method for rigid-body molecular simulation},
4969          Uri = {<Go to ISI>://A1997XQ33200046},
4970 <        Volume = {107},
4971 <        Year = {1997}}
4970 >        Volume = 107,
4971 >        Year = 1997}
4972  
4973   @article{Lansac2001,
4974          Abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
# Line 4782 | Line 4997
4997          Issn = {1063-651X},
4998          Journal = {Physical Review E},
4999          Month = {Nov},
5000 <        Number = {5},
5000 >        Number = 5,
5001          Pages = {-},
5002          Title = {Microscopic structure and dynamics of a partial bilayer smectic liquid crystal},
5003          Uri = {<Go to ISI>://000172406900063},
5004 <        Volume = {6405},
5005 <        Year = {2001}}
5004 >        Volume = 6405,
5005 >        Year = 2001}
5006  
5007   @article{Lansac2003,
5008          Abstract = {Recently, a new class of smectic liquid crystal phases characterized
# Line 4810 | Line 5025
5025          Issn = {1063-651X},
5026          Journal = {Physical Review E},
5027          Month = {Jan},
5028 <        Number = {1},
5028 >        Number = 1,
5029          Pages = {-},
5030          Title = {Phase behavior of bent-core molecules},
5031          Uri = {<Go to ISI>://000181017300042},
5032 <        Volume = {67},
5033 <        Year = {2003}}
5032 >        Volume = 67,
5033 >        Year = 2003}
5034  
5035   @book{Leach2001,
5036          Address = {Harlow, England},
# Line 4823 | Line 5038
5038          Edition = {2nd},
5039          Publisher = {Pearson Educated Limited},
5040          Title = {Molecular Modeling: Principles and Applications},
5041 <        Year = {2001}}
5041 >        Year = 2001}
5042  
5043   @article{Leimkuhler1999,
5044          Abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
# Line 4843 | Line 5058
5058          Issn = {1364-503X},
5059          Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
5060          Month = {Apr 15},
5061 <        Number = {1754},
5061 >        Number = 1754,
5062          Pages = {1101-1133},
5063          Title = {Reversible adaptive regularization: perturbed Kepler motion and classical atomic trajectories},
5064          Uri = {<Go to ISI>://000080466800007},
5065 <        Volume = {357},
5066 <        Year = {1999}}
5065 >        Volume = 357,
5066 >        Year = 1999}
5067  
5068   @book{Leimkuhler2004,
5069          Address = {Cambridge},
5070          Author = {B. Leimkuhler and S. Reich},
5071          Publisher = {Cambridge University Press},
5072          Title = {Simulating Hamiltonian Dynamics},
5073 <        Year = {2004}}
5073 >        Year = 2004}
5074  
5075   @article{Levelut1981,
5076          Annote = {Ml751 Times Cited:96 Cited References Count:16},
5077          Author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard and G. Sigaud},
5078          Issn = {1050-2947},
5079          Journal = {Physical Review A},
5080 <        Number = {4},
5080 >        Number = 4,
5081          Pages = {2180-2186},
5082          Title = {Number of Sa Phases},
5083          Uri = {<Go to ISI>://A1981ML75100057},
5084 <        Volume = {24},
5085 <        Year = {1981}}
5084 >        Volume = 24,
5085 >        Year = 1981}
5086  
5087   @article{Lieb1982,
5088          Annote = {Nu461 Times Cited:40 Cited References Count:28},
5089          Author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
5090          Issn = {0006-3002},
5091          Journal = {Biochimica Et Biophysica Acta},
5092 <        Number = {2},
5092 >        Number = 2,
5093          Pages = {388-398},
5094          Title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - Evidence from Raman-Scattering},
5095          Uri = {<Go to ISI>://A1982NU46100012},
5096 <        Volume = {688},
5097 <        Year = {1982}}
5096 >        Volume = 688,
5097 >        Year = 1982}
5098  
5099   @article{Link1997,
5100          Abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
# Line 4897 | Line 5112
5112          Issn = {0036-8075},
5113          Journal = {Science},
5114          Month = {Dec 12},
5115 <        Number = {5345},
5115 >        Number = 5345,
5116          Pages = {1924-1927},
5117          Title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic phase of achiral molecules},
5118          Uri = {<Go to ISI>://A1997YL00200028},
5119 <        Volume = {278},
5120 <        Year = {1997}}
5119 >        Volume = 278,
5120 >        Year = 1997}
5121  
5122   @article{Liwo2005,
5123          Annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
# Line 4913 | Line 5128
5128          Pages = {359-360},
5129          Title = {Ab initio simulations of protein folding pathways by molecular dynamics with the united-residue (UNRES) model of polypeptide chains},
5130          Uri = {<Go to ISI>://000234826102043},
5131 <        Volume = {272},
5132 <        Year = {2005}}
5131 >        Volume = 272,
5132 >        Year = 2005}
5133  
5134   @article{Luty1994,
5135          Abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
# Line 4929 | Line 5144
5144          Author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
5145          Issn = {0892-7022},
5146          Journal = {Molecular Simulation},
5147 <        Number = {1},
5147 >        Number = 1,
5148          Pages = {11-20},
5149          Title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
5150          Uri = {<Go to ISI>://A1994QF46400002},
5151 <        Volume = {14},
5152 <        Year = {1994}}
5151 >        Volume = 14,
5152 >        Year = 1994}
5153  
5154   @book{Marion1990,
5155          Address = {New York},
# Line 4942 | Line 5157
5157          Edition = {2rd},
5158          Publisher = {Academic Press},
5159          Title = {Classical Dynamics of Particles and Systems},
5160 <        Year = {1990}}
5160 >        Year = 1990}
5161  
5162   @article{Marrink1994,
5163          Abstract = {To obtain insight in the process of water permeation through a lipid
# Line 4974 | Line 5189
5189          Issn = {0022-3654},
5190          Journal = {Journal of Physical Chemistry},
5191          Month = {Apr 14},
5192 <        Number = {15},
5192 >        Number = 15,
5193          Pages = {4155-4168},
5194          Title = {Simulation of Water Transport through a Lipid-Membrane},
5195          Uri = {<Go to ISI>://A1994NG21900040},
5196 <        Volume = {98},
5197 <        Year = {1994}}
5196 >        Volume = 98,
5197 >        Year = 1994}
5198  
5199   @article{Marrink2004,
5200          Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
5201          Journal = {J. Phys. Chem. B},
5202          Pages = {750-760},
5203          Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
5204 <        Volume = {108},
5205 <        Year = {2004}}
5204 >        Volume = 108,
5205 >        Year = 2004}
5206  
5207   @article{Marsden1998,
5208          Abstract = {This paper presents a geometric-variational approach to continuous
# Line 5015 | Line 5230
5230          Issn = {0010-3616},
5231          Journal = {Communications in Mathematical Physics},
5232          Month = {Dec},
5233 <        Number = {2},
5233 >        Number = 2,
5234          Pages = {351-395},
5235          Title = {Multisymplectic geometry, variational integrators, and nonlinear PDEs},
5236          Uri = {<Go to ISI>://000077902200006},
5237 <        Volume = {199},
5238 <        Year = {1998}}
5237 >        Volume = 199,
5238 >        Year = 1998}
5239  
5240   @article{Matthey2004,
5241          Abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
# Line 5045 | Line 5260
5260          Issn = {0098-3500},
5261          Journal = {Acm Transactions on Mathematical Software},
5262          Month = {Sep},
5263 <        Number = {3},
5263 >        Number = 3,
5264          Pages = {237-265},
5265          Title = {ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics},
5266          Uri = {<Go to ISI>://000224325600001},
5267 <        Volume = {30},
5268 <        Year = {2004}}
5267 >        Volume = 30,
5268 >        Year = 2004}
5269  
5270   @article{McLachlan1993,
5271          Author = {R.~I McLachlan},
5272          Journal = {prl},
5273          Pages = {3043-3046},
5274          Title = {Explicit Lie-Poisson integration and the Euler equations},
5275 <        Volume = {71},
5276 <        Year = {1993}}
5275 >        Volume = 71,
5276 >        Year = 1993}
5277  
5278   @article{McLachlan1998,
5279          Abstract = {We give a survey and some new examples of generating functions for
# Line 5076 | Line 5291
5291          Pages = {298-309},
5292          Title = {Generating functions for dynamical systems with symmetries, integrals, and differential invariants},
5293          Uri = {<Go to ISI>://000071558900021},
5294 <        Volume = {112},
5295 <        Year = {1998}}
5294 >        Volume = 112,
5295 >        Year = 1998}
5296  
5297   @article{McLachlan1998a,
5298          Abstract = {We consider properties of flows, the relationships between them, and
# Line 5094 | Line 5309
5309          Issn = {0036-1429},
5310          Journal = {Siam Journal on Numerical Analysis},
5311          Month = {Apr},
5312 <        Number = {2},
5312 >        Number = 2,
5313          Pages = {586-599},
5314          Title = {Numerical integrators that preserve symmetries and reversing symmetries},
5315          Uri = {<Go to ISI>://000072580500010},
5316 <        Volume = {35},
5317 <        Year = {1998}}
5316 >        Volume = 35,
5317 >        Year = 1998}
5318  
5319   @article{McLachlan2005,
5320          Abstract = {In this paper we revisit the Moser-Veselov description of the free
# Line 5120 | Line 5335
5335          Issn = {1615-3375},
5336          Journal = {Foundations of Computational Mathematics},
5337          Month = {Feb},
5338 <        Number = {1},
5338 >        Number = 1,
5339          Pages = {87-123},
5340          Title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
5341          Uri = {<Go to ISI>://000228011900003},
5342 <        Volume = {5},
5343 <        Year = {2005}}
5342 >        Volume = 5,
5343 >        Year = 2005}
5344  
5345   @article{Meineke2005,
5346          Abstract = {OOPSE is a new molecular dynamics simulation program that is capable
# Line 5143 | Line 5358
5358          Issn = {0192-8651},
5359          Journal = {Journal of Computational Chemistry},
5360          Month = {Feb},
5361 <        Number = {3},
5361 >        Number = 3,
5362          Pages = {252-271},
5363          Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
5364          Uri = {<Go to ISI>://000226558200006},
5365 <        Volume = {26},
5366 <        Year = {2005}}
5365 >        Volume = 26,
5366 >        Year = 2005}
5367  
5368   @article{Melchionna1993,
5369          Abstract = {In this paper we write down equations of motion (following the approach
# Line 5162 | Line 5377
5377          Issn = {0026-8976},
5378          Journal = {Molecular Physics},
5379          Month = {Feb 20},
5380 <        Number = {3},
5380 >        Number = 3,
5381          Pages = {533-544},
5382          Title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
5383          Uri = {<Go to ISI>://A1993KQ35500002},
5384 <        Volume = {78},
5385 <        Year = {1993}}
5384 >        Volume = 78,
5385 >        Year = 1993}
5386  
5387   @article{Memmer2002,
5388          Abstract = {The phase behaviour of achiral banana-shaped molecules was studied
# Line 5200 | Line 5415
5415          Issn = {0267-8292},
5416          Journal = {Liquid Crystals},
5417          Month = {Apr},
5418 <        Number = {4},
5418 >        Number = 4,
5419          Pages = {483-496},
5420          Title = {Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study},
5421          Uri = {<Go to ISI>://000174410500001},
5422 <        Volume = {29},
5423 <        Year = {2002}}
5422 >        Volume = 29,
5423 >        Year = 2002}
5424  
5425   @article{Metropolis1949,
5426          Author = {N. Metropolis and S. Ulam},
5427          Journal = {J. Am. Stat. Ass.},
5428          Pages = {335-341},
5429          Title = {The $\mbox{Monte Carlo}$ Method},
5430 <        Volume = {44},
5431 <        Year = {1949}}
5430 >        Volume = 44,
5431 >        Year = 1949}
5432  
5433   @article{Mielke2004,
5434          Abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
# Line 5246 | Line 5461
5461          Issn = {0021-9606},
5462          Journal = {Journal of Chemical Physics},
5463          Month = {Oct 22},
5464 <        Number = {16},
5464 >        Number = 16,
5465          Pages = {8104-8112},
5466          Title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study},
5467          Uri = {<Go to ISI>://000224456500064},
5468 <        Volume = {121},
5469 <        Year = {2004}}
5468 >        Volume = 121,
5469 >        Year = 2004}
5470  
5471   @article{Naess2001,
5472          Abstract = {The three Eulerian angles constitute the classical choice of generalized
# Line 5276 | Line 5491
5491          Pages = {323-339},
5492          Title = {Brownian dynamics simulation of rigid bodies and segmented polymer chains. Use of Cartesian rotation vectors as the generalized coordinates describing angular orientations},
5493          Uri = {<Go to ISI>://000168774800005},
5494 <        Volume = {294},
5495 <        Year = {2001}}
5494 >        Volume = 294,
5495 >        Year = 2001}
5496  
5497   @article{Niori1996,
5498          Abstract = {The synthesis of a banana-shaped molecule is reported and it is found
# Line 5292 | Line 5507
5507          Issn = {0959-9428},
5508          Journal = {Journal of Materials Chemistry},
5509          Month = {Jul},
5510 <        Number = {7},
5510 >        Number = 7,
5511          Pages = {1231-1233},
5512          Title = {Distinct ferroelectric smectic liquid crystals consisting of banana shaped achiral molecules},
5513          Uri = {<Go to ISI>://A1996UX85500025},
5514 <        Volume = {6},
5515 <        Year = {1996}}
5514 >        Volume = 6,
5515 >        Year = 1996}
5516  
5517   @article{Noguchi2002,
5518          Abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
# Line 5317 | Line 5532
5532          Issn = {1063-651X},
5533          Journal = {Physical Review E},
5534          Month = {may},
5535 <        Number = {5},
5535 >        Number = 5,
5536          Pages = {-},
5537          Title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
5538          Uri = {<Go to ISI>://000176552300084},
5539 <        Volume = {65},
5540 <        Year = {2002}}
5539 >        Volume = 65,
5540 >        Year = 2002}
5541  
5542   @article{Noguchi2001,
5543          Abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
# Line 5341 | Line 5556
5556          Issn = {0021-9606},
5557          Journal = {Journal of Chemical Physics},
5558          Month = {Nov 22},
5559 <        Number = {20},
5559 >        Number = 20,
5560          Pages = {9547-9551},
5561          Title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
5562          Uri = {<Go to ISI>://000172129300049},
5563 <        Volume = {115},
5564 <        Year = {2001}}
5563 >        Volume = 115,
5564 >        Year = 2001}
5565  
5566   @book{Olver1986,
5567          Address = {New York},
5568          Author = {P.J. Olver},
5569          Publisher = {Springer},
5570          Title = {Applications of Lie groups to differential equatitons},
5571 <        Year = {1986}}
5571 >        Year = 1986}
5572  
5573   @article{Omelyan1998,
5574          Abstract = {A revised version of the quaternion approach for numerical integration
# Line 5372 | Line 5587
5587          Issn = {0894-1866},
5588          Journal = {Computers in Physics},
5589          Month = {Jan-Feb},
5590 <        Number = {1},
5590 >        Number = 1,
5591          Pages = {97-103},
5592          Title = {On the numerical integration of motion for rigid polyatomics: The modified quaternion approach},
5593          Uri = {<Go to ISI>://000072024300025},
5594 <        Volume = {12},
5595 <        Year = {1998}}
5594 >        Volume = 12,
5595 >        Year = 1998}
5596  
5597   @article{Omelyan1998a,
5598          Abstract = {An algorithm for numerical integration of the rigid-body equations
# Line 5394 | Line 5609
5609          Issn = {1063-651X},
5610          Journal = {Physical Review E},
5611          Month = {Jul},
5612 <        Number = {1},
5612 >        Number = 1,
5613          Pages = {1169-1172},
5614          Title = {Algorithm for numerical integration of the rigid-body equations of motion},
5615          Uri = {<Go to ISI>://000074893400151},
5616 <        Volume = {58},
5617 <        Year = {1998}}
5616 >        Volume = 58,
5617 >        Year = 1998}
5618  
5619   @article{Owren1992,
5620          Abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
# Line 5420 | Line 5635
5635          Issn = {0196-5204},
5636          Journal = {Siam Journal on Scientific and Statistical Computing},
5637          Month = {Nov},
5638 <        Number = {6},
5638 >        Number = 6,
5639          Pages = {1488-1501},
5640          Title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
5641          Uri = {<Go to ISI>://A1992JU93600013},
5642 <        Volume = {13},
5643 <        Year = {1992}}
5642 >        Volume = 13,
5643 >        Year = 1992}
5644  
5645   @article{Palacios1998,
5646          Abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
# Line 5463 | Line 5678
5678          Issn = {0163-1829},
5679          Journal = {Physical Review B},
5680          Month = {Dec 1},
5681 <        Number = {22},
5681 >        Number = 22,
5682          Pages = {14937-14958},
5683          Title = {Langevin-dynamics study of the dynamical properties of small magnetic particles},
5684          Uri = {<Go to ISI>://000077460000052},
5685 <        Volume = {58},
5686 <        Year = {1998}}
5685 >        Volume = 58,
5686 >        Year = 1998}
5687  
5688   @article{Parr1995,
5689          Abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
# Line 5495 | Line 5710
5710          Issn = {0038-0644},
5711          Journal = {Software-Practice \& Experience},
5712          Month = {Jul},
5713 <        Number = {7},
5713 >        Number = 7,
5714          Pages = {789-810},
5715          Title = {Antlr - a Predicated-Ll(K) Parser Generator},
5716          Uri = {<Go to ISI>://A1995RK10400004},
5717 <        Volume = {25},
5718 <        Year = {1995}}
5717 >        Volume = 25,
5718 >        Year = 1995}
5719  
5720   @article{Pastor1988,
5721          Annote = {T1302 Times Cited:61 Cited References Count:26},
# Line 5508 | Line 5723
5723          Issn = {0026-8976},
5724          Journal = {Molecular Physics},
5725          Month = {Dec 20},
5726 <        Number = {6},
5726 >        Number = 6,
5727          Pages = {1409-1419},
5728          Title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
5729          Uri = {<Go to ISI>://A1988T130200011},
5730 <        Volume = {65},
5731 <        Year = {1988}}
5730 >        Volume = 65,
5731 >        Year = 1988}
5732  
5733   @article{Pelzl1999,
5734          Annote = {220RC Times Cited:313 Cited References Count:49},
# Line 5521 | Line 5736
5736          Issn = {0935-9648},
5737          Journal = {Advanced Materials},
5738          Month = {Jul 5},
5739 <        Number = {9},
5739 >        Number = 9,
5740          Pages = {707-724},
5741          Title = {Banana-shaped compounds - A new field of liquid crystals},
5742          Uri = {<Go to ISI>://000081680400007},
5743 <        Volume = {11},
5744 <        Year = {1999}}
5743 >        Volume = 11,
5744 >        Year = 1999}
5745  
5746   @article{Perram1985,
5747          Annote = {Akb93 Times Cited:71 Cited References Count:12},
5748          Author = {J. W. Perram and M. S. Wertheim},
5749          Issn = {0021-9991},
5750          Journal = {Journal of Computational Physics},
5751 <        Number = {3},
5751 >        Number = 3,
5752          Pages = {409-416},
5753          Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function},
5754          Uri = {<Go to ISI>://A1985AKB9300008},
5755 <        Volume = {58},
5756 <        Year = {1985}}
5755 >        Volume = 58,
5756 >        Year = 1985}
5757  
5758   @article{Rotne1969,
5759          Author = {F. Perrin},
5760          Journal = {J. Chem. Phys.},
5761          Pages = {4831-4837},
5762          Title = {Variational treatment of hydrodynamic interaction in polymers},
5763 <        Volume = {50},
5764 <        Year = {1969}}
5763 >        Volume = 50,
5764 >        Year = 1969}
5765  
5766   @article{Perrin1936,
5767          Author = {F. Perrin},
5768          Journal = {J. Phys. Radium},
5769          Pages = {1-11},
5770          Title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation des fluorescences. Translation et diffusion de moleculese ellipsoidales},
5771 <        Volume = {7},
5772 <        Year = {1936}}
5771 >        Volume = 7,
5772 >        Year = 1936}
5773  
5774   @article{Perrin1934,
5775          Author = {F. Perrin},
5776          Journal = {J. Phys. Radium},
5777          Pages = {497-511},
5778          Title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour des molecules ellipsoidales},
5779 <        Volume = {5},
5780 <        Year = {1934}}
5779 >        Volume = 5,
5780 >        Year = 1934}
5781  
5782   @article{Petrache2000,
5783          Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
5784          Journal = {Biophysical Journal},
5785          Pages = {3172-3192},
5786          Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
5787 <        Volume = {79},
5788 <        Year = {2000}}
5787 >        Volume = 79,
5788 >        Year = 2000}
5789  
5790   @article{Petrache1998,
5791          Abstract = {X-ray diffraction data taken at high instrumental resolution were
# Line 5595 | Line 5810
5810          Issn = {0009-3084},
5811          Journal = {Chemistry and Physics of Lipids},
5812          Month = {Sep},
5813 <        Number = {1},
5813 >        Number = 1,
5814          Pages = {83-94},
5815          Title = {Fluid phase structure of EPC and DMPC bilayers},
5816          Uri = {<Go to ISI>://000076497600007},
5817 <        Volume = {95},
5818 <        Year = {1998}}
5817 >        Volume = 95,
5818 >        Year = 1998}
5819  
5820   @article{Powles1973,
5821          Author = {J.~G. Powles},
5822          Journal = {Advan. Phys.},
5823          Pages = {1-56},
5824          Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
5825 <        Volume = {22},
5826 <        Year = {1973}}
5825 >        Volume = 22,
5826 >        Year = 1973}
5827  
5828   @article{Recio2004,
5829          Abstract = {Protein recognition is one of the most challenging and intriguing
# Line 5639 | Line 5854
5854          Issn = {0022-2836},
5855          Journal = {Journal of Molecular Biology},
5856          Month = {Jan 16},
5857 <        Number = {3},
5857 >        Number = 3,
5858          Pages = {843-865},
5859          Title = {Identification of protein-protein interaction sites from docking energy landscapes},
5860          Uri = {<Go to ISI>://000188066900016},
5861 <        Volume = {335},
5862 <        Year = {2004}}
5861 >        Volume = 335,
5862 >        Year = 2004}
5863  
5864   @article{Reddy2006,
5865          Abstract = {An overview on the recent developments in the field of liquid crystalline
# Line 5662 | Line 5877
5877          Author = {R. A. Reddy and C. Tschierske},
5878          Issn = {0959-9428},
5879          Journal = {Journal of Materials Chemistry},
5880 <        Number = {10},
5880 >        Number = 10,
5881          Pages = {907-961},
5882          Title = {Bent-core liquid crystals: polar order, superstructural chirality and spontaneous desymmetrisation in soft matter systems},
5883          Uri = {<Go to ISI>://000235990500001},
5884 <        Volume = {16},
5885 <        Year = {2006}}
5884 >        Volume = 16,
5885 >        Year = 2006}
5886  
5887   @article{Reich1999,
5888          Abstract = {Backward error analysis has become an important tool for understanding
# Line 5697 | Line 5912
5912          Issn = {0036-1429},
5913          Journal = {Siam Journal on Numerical Analysis},
5914          Month = {Sep 8},
5915 <        Number = {5},
5915 >        Number = 5,
5916          Pages = {1549-1570},
5917          Title = {Backward error analysis for numerical integrators},
5918          Uri = {<Go to ISI>://000082650600010},
5919 <        Volume = {36},
5920 <        Year = {1999}}
5919 >        Volume = 36,
5920 >        Year = 1999}
5921  
5922   @article{Ros2005,
5923          Abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
# Line 5717 | Line 5932
5932          Author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
5933          Issn = {0959-9428},
5934          Journal = {Journal of Materials Chemistry},
5935 <        Number = {48},
5935 >        Number = 48,
5936          Pages = {5093-5098},
5937          Title = {Banana-shaped liquid crystals: a new field to explore},
5938          Uri = {<Go to ISI>://000233775500001},
5939 <        Volume = {15},
5940 <        Year = {2005}}
5939 >        Volume = 15,
5940 >        Year = 2005}
5941  
5942   @article{Roux1991,
5943          Abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
# Line 5750 | Line 5965
5965          Issn = {0022-3654},
5966          Journal = {Journal of Physical Chemistry},
5967          Month = {Jun 13},
5968 <        Number = {12},
5968 >        Number = 12,
5969          Pages = {4856-4868},
5970          Title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
5971          Uri = {<Go to ISI>://A1991FR75600049},
5972 <        Volume = {95},
5973 <        Year = {1991}}
5972 >        Volume = 95,
5973 >        Year = 1991}
5974  
5975   @article{Roy2005,
5976          Abstract = {A vast majority of compounds with bent core or banana shaped molecules
# Line 5774 | Line 5989
5989          Issn = {1292-8941},
5990          Journal = {European Physical Journal E},
5991          Month = {Nov},
5992 <        Number = {3},
5992 >        Number = 3,
5993          Pages = {253-258},
5994          Title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases in banana shaped molecules},
5995          Uri = {<Go to ISI>://000233363300002},
5996 <        Volume = {18},
5997 <        Year = {2005}}
5996 >        Volume = 18,
5997 >        Year = 2005}
5998  
5999   @article{Ryckaert1977,
6000          Annote = {Cz253 Times Cited:3680 Cited References Count:7},
6001          Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
6002          Issn = {0021-9991},
6003          Journal = {Journal of Computational Physics},
6004 <        Number = {3},
6004 >        Number = 3,
6005          Pages = {327-341},
6006          Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes},
6007          Uri = {<Go to ISI>://A1977CZ25300007},
6008 <        Volume = {23},
6009 <        Year = {1977}}
6008 >        Volume = 23,
6009 >        Year = 1977}
6010  
6011   @article{Sagui1999,
6012          Abstract = {Current computer simulations of biomolecules typically make use of
# Line 5816 | Line 6031
6031          Pages = {155-179},
6032          Title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic effects},
6033          Uri = {<Go to ISI>://000081271400008},
6034 <        Volume = {28},
6035 <        Year = {1999}}
6034 >        Volume = 28,
6035 >        Year = 1999}
6036  
6037   @article{Sandu1999,
6038          Abstract = {Numerical resonance artifacts have become recognized recently as a
# Line 5862 | Line 6077
6077          Issn = {0021-9991},
6078          Journal = {Journal of Computational Physics},
6079          Month = {May 1},
6080 <        Number = {1},
6080 >        Number = 1,
6081          Pages = {74-113},
6082          Title = {Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics},
6083          Uri = {<Go to ISI>://000080181500004},
6084 <        Volume = {151},
6085 <        Year = {1999}}
6084 >        Volume = 151,
6085 >        Year = 1999}
6086  
6087   @article{Sasaki2004,
6088          Abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
# Line 5881 | Line 6096
6096          Author = {Y. Sasaki and R. Shukla and B. D. Smith},
6097          Issn = {1477-0520},
6098          Journal = {Organic \& Biomolecular Chemistry},
6099 <        Number = {2},
6099 >        Number = 2,
6100          Pages = {214-219},
6101          Title = {Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases},
6102          Uri = {<Go to ISI>://000187843800012},
6103 <        Volume = {2},
6104 <        Year = {2004}}
6103 >        Volume = 2,
6104 >        Year = 2004}
6105  
6106   @article{Satoh1996,
6107          Abstract = {The effects of dipole-dipole interaction on mesophase formation are
# Line 5905 | Line 6120
6120          Pages = {99-104},
6121          Title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect of terminal dipole moment on mesophase formation},
6122          Uri = {<Go to ISI>://A1996UQ97500017},
6123 <        Volume = {255},
6124 <        Year = {1996}}
6123 >        Volume = 255,
6124 >        Year = 1996}
6125  
6126   @article{Schaps1999,
6127          Annote = {163EC Times Cited:0 Cited References Count:0},
# Line 5914 | Line 6129
6129          Issn = {1044-789X},
6130          Journal = {Dr Dobbs Journal},
6131          Month = {Mar},
6132 <        Number = {3},
6132 >        Number = 3,
6133          Pages = {84-+},
6134          Title = {Compiler construction with ANTLR and Java - Tools for building tools},
6135          Uri = {<Go to ISI>://000078389200023},
6136 <        Volume = {24},
6137 <        Year = {1999}}
6136 >        Volume = 24,
6137 >        Year = 1999}
6138  
6139   @article{Shen2002,
6140          Abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
# Line 5946 | Line 6161
6161          Issn = {0006-3495},
6162          Journal = {Biophysical Journal},
6163          Month = {Apr},
6164 <        Number = {4},
6164 >        Number = 4,
6165          Pages = {1791-1808},
6166          Title = {Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models},
6167          Uri = {<Go to ISI>://000174932400010},
6168 <        Volume = {82},
6169 <        Year = {2002}}
6168 >        Volume = 82,
6169 >        Year = 2002}
6170  
6171   @article{Shillcock2005,
6172          Annote = {901QJ Times Cited:9 Cited References Count:23},
# Line 5959 | Line 6174
6174          Issn = {1476-1122},
6175          Journal = {Nature Materials},
6176          Month = {Mar},
6177 <        Number = {3},
6177 >        Number = 3,
6178          Pages = {225-228},
6179          Title = {Tension-induced fusion of bilayer membranes and vesicles},
6180          Uri = {<Go to ISI>://000227296700019},
6181 <        Volume = {4},
6182 <        Year = {2005}}
6181 >        Volume = 4,
6182 >        Year = 2005}
6183  
6184   @article{Shimada1993,
6185          Abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
# Line 5989 | Line 6204
6204          Issn = {0192-8651},
6205          Journal = {Journal of Computational Chemistry},
6206          Month = {Jul},
6207 <        Number = {7},
6207 >        Number = 7,
6208          Pages = {867-878},
6209          Title = {Efficient Calculations of Coulombic Interactions in Biomolecular Simulations with Periodic Boundary-Conditions},
6210          Uri = {<Go to ISI>://A1993LH16400011},
6211 <        Volume = {14},
6212 <        Year = {1993}}
6211 >        Volume = 14,
6212 >        Year = 1993}
6213  
6214   @article{Skeel2002,
6215          Abstract = {The best simple method for Newtonian molecular dynamics is indisputably
# Line 6012 | Line 6227
6227          Issn = {0026-8976},
6228          Journal = {Molecular Physics},
6229          Month = {Dec 20},
6230 <        Number = {24},
6230 >        Number = 24,
6231          Pages = {3885-3891},
6232          Title = {An impulse integrator for Langevin dynamics},
6233          Uri = {<Go to ISI>://000180297200014},
6234 <        Volume = {100},
6235 <        Year = {2002}}
6234 >        Volume = 100,
6235 >        Year = 2002}
6236  
6237   @article{Skeel1997,
6238          Abstract = {The following integration methods for special second-order ordinary
# Line 6038 | Line 6253
6253          Issn = {1064-8275},
6254          Journal = {Siam Journal on Scientific Computing},
6255          Month = {Jan},
6256 <        Number = {1},
6256 >        Number = 1,
6257          Pages = {203-222},
6258          Title = {A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications},
6259          Uri = {<Go to ISI>://A1997WE98100012},
6260 <        Volume = {18},
6261 <        Year = {1997}}
6260 >        Volume = 18,
6261 >        Year = 1997}
6262  
6263   @article{Tao2005,
6264          Abstract = {Recently a microscopic theory for the dynamics of suspensions of long
# Line 6071 | Line 6286
6286          Issn = {0021-9606},
6287          Journal = {Journal of Chemical Physics},
6288          Month = {Jun 22},
6289 <        Number = {24},
6289 >        Number = 24,
6290          Pages = {-},
6291          Title = {Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods},
6292          Uri = {<Go to ISI>://000230332400077},
6293 <        Volume = {122},
6294 <        Year = {2005}}
6293 >        Volume = 122,
6294 >        Year = 2005}
6295  
6296   @book{Tolman1979,
6297          Address = {New York},
6298          Author = {R.~C. Tolman},
6299 <        Chapter = {2},
6299 >        Chapter = 2,
6300          Pages = {19-22},
6301          Publisher = {Dover Publications, Inc.},
6302          Title = {The Principles of Statistical Mechanics},
6303 <        Year = {1979}}
6303 >        Year = 1979}
6304  
6305   @article{Tu1995,
6306          Abstract = {We report a constant pressure and temperature molecular dynamics simulation
# Line 6112 | Line 6327
6327          Issn = {0006-3495},
6328          Journal = {Biophysical Journal},
6329          Month = {Dec},
6330 <        Number = {6},
6330 >        Number = 6,
6331          Pages = {2558-2562},
6332          Title = {Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer},
6333          Uri = {<Go to ISI>://A1995TV01800037},
6334 <        Volume = {69},
6335 <        Year = {1995}}
6334 >        Volume = 69,
6335 >        Year = 1995}
6336  
6337   @article{Tuckerman1992,
6338          Abstract = {The Trotter factorization of the Liouville propagator is used to generate
# Line 6137 | Line 6352
6352          Issn = {0021-9606},
6353          Journal = {Journal of Chemical Physics},
6354          Month = {Aug 1},
6355 <        Number = {3},
6355 >        Number = 3,
6356          Pages = {1990-2001},
6357          Title = {Reversible Multiple Time Scale Molecular-Dynamics},
6358          Uri = {<Go to ISI>://A1992JE89100044},
6359 <        Volume = {97},
6360 <        Year = {1992}}
6359 >        Volume = 97,
6360 >        Year = 1992}
6361  
6362   @book{Varadarajan1974,
6363          Address = {New York},
6364          Author = {V.S. Varadarajan},
6365          Publisher = {Prentice-Hall},
6366          Title = {Lie groups, Lie algebras, and their representations},
6367 <        Year = {1974}}
6367 >        Year = 1974}
6368  
6369   @article{Vincent1995,
6370          Abstract = {We have implemented a portable parallel version of the macromolecular
# Line 6171 | Line 6386
6386          Issn = {0192-8651},
6387          Journal = {Journal of Computational Chemistry},
6388          Month = {Nov},
6389 <        Number = {11},
6389 >        Number = 11,
6390          Pages = {1420-1427},
6391          Title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing Interface Standard},
6392          Uri = {<Go to ISI>://A1995TA40300009},
6393 <        Volume = {16},
6394 <        Year = {1995}}
6393 >        Volume = 16,
6394 >        Year = 1995}
6395  
6396   @article{Wegener1979,
6397          Author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
6398          Journal = {Proc. Natl. Acad. Sci.},
6399 <        Number = {12},
6399 >        Number = 12,
6400          Pages = {6356-6360},
6401          Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
6402 <        Volume = {76},
6403 <        Year = {1979}}
6402 >        Volume = 76,
6403 >        Year = 1979}
6404  
6405   @article{Wilson2006,
6406          Author = {G.~V. Wilson},
6407          Journal = {American Scientist},
6408          Title = {Where's the Real Bottleneck in Scientific Computing?},
6409 <        Volume = {94},
6410 <        Year = {2006}}
6409 >        Volume = 94,
6410 >        Year = 2006}
6411  
6412   @article{Withers2003,
6413          Abstract = {The effects of longitudinal quadrupole moments on the formation of
# Line 6227 | Line 6442
6442          Issn = {0021-9606},
6443          Journal = {Journal of Chemical Physics},
6444          Month = {Nov 15},
6445 <        Number = {19},
6445 >        Number = 19,
6446          Pages = {10209-10223},
6447          Title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne fluid},
6448          Uri = {<Go to ISI>://000186273200027},
6449 <        Volume = {119},
6450 <        Year = {2003}}
6449 >        Volume = 119,
6450 >        Year = 2003}
6451  
6452   @article{Wolf1999,
6453          Abstract = {Based on a recent result showing that the net Coulomb potential in
# Line 6261 | Line 6476
6476          Issn = {0021-9606},
6477          Journal = {Journal of Chemical Physics},
6478          Month = {May 1},
6479 <        Number = {17},
6479 >        Number = 17,
6480          Pages = {8254-8282},
6481          Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r(-1) summation},
6482          Uri = {<Go to ISI>://000079913000008},
6483 <        Volume = {110},
6484 <        Year = {1999}}
6483 >        Volume = 110,
6484 >        Year = 1999}
6485  
6486   @article{Yoshida1990,
6487          Annote = {Ej798 Times Cited:492 Cited References Count:9},
# Line 6278 | Line 6493
6493          Pages = {262-268},
6494          Title = {Construction of Higher-Order Symplectic Integrators},
6495          Uri = {<Go to ISI>://A1990EJ79800009},
6496 <        Volume = {150},
6497 <        Year = {1990}}
6496 >        Volume = 150,
6497 >        Year = 1990}
6498  
6499   @article{Blum1972,
6500          Author = {L. Blum and A.~J. Torruella},
# Line 6322 | Line 6537
6537          Author = {M.W. Hirsch},
6538          Publisher = {Springer},
6539          Title = {Differential Topology},
6540 <        Year = {1997}}
6540 >        Year = 1997}
6541  
6542   @book{Jost2002,
6543          Address = {Berlin},
6544          Author = {J. Jost},
6545          Publisher = {Springer-Verlag},
6546          Title = {Riemannian Geometry and Geometric Analysis},
6547 <        Year = {2002}}
6547 >        Year = 2002}
6548  
6549   @book{McDuff1998,
6550          Address = {Oxford},
6551          Author = {D. McDuff and D. Salamon},
6552          Publisher = {Oxford Mathematical Monographs},
6553          Title = {Introduction to Symplectic Topology},
6554 <        Year = {1998}}
6554 >        Year = 1998}
6555  
6556   @article{Matubayasi1999,
6557          Author = {N. Matubayasi and M. Nakahara},
# Line 6400 | Line 6615
6615          Title = {The Dynamics of Runge-Kutta Methods},
6616          Volume = 2,
6617          Year = 1992}
6618 +
6619 + @article{HuseyinKaya07012005,
6620 +        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.
6621 + },
6622 +        Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun},
6623 +        Doi = {10.1529/biophysj.104.057471},
6624 +        Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf},
6625 +        Journal = {Biophys. J.},
6626 +        Number = 1,
6627 +        Pages = {520-535},
6628 +        Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}},
6629 +        Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6630 +        Volume = 89,
6631 +        Year = 2005,
6632 +        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6633 +        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}}

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