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4  
5 < %% Created for Dan Gezelter at 2008-01-11 16:20:18 -0500
5 > %% Created for Xiuquan Sun at 2008-04-30 10:19:14 -0400
6  
7  
8   %% Saved with string encoding Western (ASCII)
9  
10  
11 + @string{acp = {Adv. Chem. Phys.}}
12  
13 + @string{bj = {Biophys. J.}}
14 +
15 + @string{ccp5 = {CCP5 Information Quarterly}}
16 +
17 + @string{cp = {Chem. Phys.}}
18 +
19 + @string{cpl = {Chem. Phys. Lett.}}
20 +
21 + @string{jacs = {J. Am. Chem. Soc.}}
22 +
23 + @string{jcc = {J. Comp. Chem.}}
24 +
25 + @string{jcop = {J. Comp. Phys.}}
26 +
27 + @string{jcp = {J. Chem. Phys.}}
28 +
29 + @string{jmb = {J. Mol. Bio.}}
30 +
31 + @string{jml = {J. Mol. Liq.}}
32 +
33 + @string{jpc = {J. Phys. Chem.}}
34 +
35 + @string{jpca = {J. Phys. Chem. A}}
36 +
37 + @string{jpcb = {J. Phys. Chem. B}}
38 +
39 + @string{mp = {Mol. Phys.}}
40 +
41 + @string{pams = {Proc. Am. Math Soc.}}
42 +
43 + @string{pccp = {Phys. Chem. Chem. Phys.}}
44 +
45 + @string{pnas = {Proc. Natl. Acad. Sci. USA}}
46 +
47 + @string{pr = {Phys. Rev.}}
48 +
49 + @string{pra = {Phys. Rev. A}}
50 +
51 + @string{prb = {Phys. Rev. B}}
52 +
53 + @string{pre = {Phys. Rev. E}}
54 +
55 + @string{prl = {Phys. Rev. Lett.}}
56 +
57 + @string{rmp = {Rev. Mod. Phys.}}
58 +
59 +
60 + @article{GarciadelaTorreJjp0647941,
61 +        Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain},
62 +        Author = {{Garc\'{i}a de la Torre}, Jose and del Rio Echenique, G. and Ortega, A.},
63 +        Date-Added = {2008-04-30 10:14:50 -0400},
64 +        Date-Modified = {2008-04-30 10:14:50 -0400},
65 +        Issn = {1520-6106},
66 +        Journal = jpcb,
67 +        Number = {5},
68 +        Pages = {955-961},
69 +        Title = {Improved Calculation of Rotational Diffusion and Intrinsic Viscosity of Bead Models for Macromolecules and Nanoparticles},
70 +        Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0647941},
71 +        Volume = {111},
72 +        Year = {2007}}
73 +
74 + @article{Garcia-de-la-Torre:2001wd,
75 +        Abstract = { The calculation of hydrodynamic and other solution properties of rigid macromolecules, using bead-shell model methodologies, requires the specification of the macromolecular shape in a format that can be interfaced with existing programs for hydrodynamic computations. Here, a procedure is presented for such a structural specification that is applicable to arbitrarily shaped particles. A computer program (), in which the user inserts the code needed to determine the structure, produces an structural file that is interpreted by another program () which is in charge of the computation of properties. As simple and yet illustrative examples we consider two cases: (1) dimeric structures composed of ellipsoidal subunits; and (2) toroidal structures, presenting simple equations that predict the properties of toroids with varying radial ratios.},
76 +        Author = {{Garc\'{i}a de la Torre}, Jose },
77 +        Date-Added = {2008-04-29 15:11:32 -0400},
78 +        Date-Modified = {2008-04-29 15:11:32 -0400},
79 +        Journal = {Biophysical Chemistry},
80 +        Keywords = {Rigid macromolecules; Hydrodynamic properties; Bead-shell model; Three-dimensional structure},
81 +        Number = {3},
82 +        Pages = {265--274},
83 +        Title = {Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape},
84 +        Ty = {JOUR},
85 +        Url = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953},
86 +        Volume = {94},
87 +        Year = {2001}}
88 +
89 + @article{Peters:1999uq,
90 +        Abstract = {The Fokker-Planck (FP) equation describing the dynamics of a single Brownian particle near a fixed external surface is derived using the multiple-time-scales perturbation method, previously used by Cukier and Deutch and Nienhuis in the absence of any external surfaces, and Piasecki ei LII. for two Brownian spheres in a hard fluid. The FP equation includes an explicit expression for the (time-independent) particle friction tensor in terms of the force autocorrelation Function and equilibrium average force on the particle by the surrounding fluid and in the presence of a fixed external surface. such as an adsorbate. The scaling and perturbation analysis given here also shows that the Force autocorrelation function must decay rapidly on the zeroth-order time scale tau(0), which physically requires N-Kn much less than 1, where N-Kn is the Knudsen number (ratio of the length scale for fluid intermolecular interactions to the Brownian particle length scale). This restricts the theory given here to liquid systems where N-Kn much less than 1. For a specified particle configuration with respect to the external surface, equilibrium canonical molecular dynamics (MD) calculations are conducted, as shown here, in order to obtain numerical values of the friction tensor from the force autocorrelation expression. Molecular dynamics computations of the friction tensor for a single spherical particle in the absence of a fixed external surface are shown to recover Stokes' law for various types of fluid molecule-particle interaction potentials. Analytical studies of the static force correlation function also demonstrate the remarkable principle of force-time parity whereby the particle friction coefficient is nearly independent of the fluid molecule-particle interaction potential. Molecular dynamics computations of the friction tensor for a single spherical particle near a fixed external spherical surface (adsorbate) demonstrate a breakdown in continuum hydrodynamic results at close particle surface separation distances on the order of several molecular diameters.},
91 +        Author = {Peters, MH},
92 +        Date-Added = {2008-03-13 16:54:59 -0400},
93 +        Date-Modified = {2008-03-13 16:56:54 -0400},
94 +        Journal = {Journal of Statistical Physics},
95 +        Keywords = {Brownian particle; Fokker Planck equation; adsorption; molecular friction; force autocorrelation function; molecular dynamics},
96 +        Pages = {557-586},
97 +        Timescited = {0},
98 +        Title = {Fokker-Planck equation, molecular friction, and molecular dynamics for Brownian particle transport near external solid surfaces},
99 +        Volume = {94},
100 +        Year = {1999}}
101 +
102 + @article{Peters:1999qy,
103 +        Abstract = {The Fokker-Planck equation and molecular-based grand friction tensor are derived for the problem of rotational and translational motions of a structured Brownian particle, including the presence of a structured wall. Using the method of multiple time scales, it is shown that the time independent, grand friction tensor for the Brownian particle includes, in a general way, terms that account fur the fluid molecular mediated interactions with the wall. The resulting Fokker-Planck equation has important applications in processes involving site-specific adsorption of macromolecules, such as affinity chromotography, biological separations, and numerous cellular processes involving attachment of macromolecules. (C) 1999 American Institute of Physics. [S0021-9606(98)51748-5].},
104 +        Author = {Peters, MH},
105 +        Date-Added = {2008-03-13 16:54:59 -0400},
106 +        Date-Modified = {2008-03-13 16:56:44 -0400},
107 +        Journal = jcp,
108 +        Pages = {528-538},
109 +        Timescited = {0},
110 +        Title = {Fokker-Planck equation and the grand molecular friction tensor for coupled rotational and translational motions of structured Brownian particles near structured surfaces},
111 +        Volume = {110},
112 +        Year = {1999}}
113 +
114 + @article{Peters:2000fk,
115 +        Abstract = {Beginning with the molecular-based Fokker-Planck equation obtained previously [M. H. Peters, J. Chem. Phys. 110, 528 (1999); J. Stat. Phys. 94, 557 (1999)], the Smoluchowski diffusion equation is derived here to describe the spatial and orientational dynamics of molecularly structured macromolecules near molecularly structured surfaces. The formal scaling and perturbation methods employed allow the establishment of definite limits on the use of the Smoluchowski equation when surfaces are present. It is shown that the Smoluchowski equation reduces to that given previously [D. W. Condiff and J. S. Dahler, J. Chem. Phys. 44, 3988 (1966)] in the absence of external surfaces. A specific example application is given involving a spherical macromolecule with electrostatic charge segments near a planar surface with an arbitrary charge distribution. Finally, we show that the short-time solution to the Smoluchowski equation obtained here yields a Brownian dynamics method consistent with that given previously [E. Dickinson, S. A. Allison, and J. A. McCammon, J. Chem. Soc. Faraday Trans. 2 81, 591 (1985)] for orientable, interacting Brownian particles. This study has applications to problems involving site-specific adsorption of orientable, structured Brownian particles, such as association or adsorption of biological macromolecules to cellular surfaces and enzyme-substrate docking kinetics, to name a few. (C) 2000 American Institute of Physics. [S0021-9606(00)50112-3].},
116 +        Author = {Peters, MH},
117 +        Date-Added = {2008-03-13 16:54:59 -0400},
118 +        Date-Modified = {2008-03-13 16:56:20 -0400},
119 +        Journal = jcp,
120 +        Pages = {5488-5498},
121 +        Timescited = {0},
122 +        Title = {The Smoluchowski diffusion equation for structured macromolecules near structured surfaces},
123 +        Volume = {112},
124 +        Year = {2000}}
125 +
126 + @article{Nienhuis:1970lr,
127 +        Abstract = { A quantummechanical system consisting of N light bath particles and one heavy Brownian linear rotator is considered. By employing the multiple time scale technique and the Wigner representation of quantummechanics, a Fokker-Planck equation for the motion of the Brownian particle is derived. Some properties of this equation are briefly discussed.},
128 +        Author = {Nienhuis, G. },
129 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413},
130 +        Date-Added = {2008-03-13 16:53:44 -0400},
131 +        Date-Modified = {2008-03-13 16:53:44 -0400},
132 +        Journal = {Physica},
133 +        Number = {1},
134 +        Pages = {26--48},
135 +        Title = {On the microscopic theory of Brownian motion with a rotational degree of freedom},
136 +        Ty = {JOUR},
137 +        Url = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413},
138 +        Volume = {49},
139 +        Year = {1970}}
140 +
141 + @article{SunX._jp0762020,
142 +        Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556},
143 +        Author = {Sun, X. and Gezelter, J.D.},
144 +        Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020},
145 +        Date-Added = {2008-02-15 13:48:18 -0500},
146 +        Date-Modified = {2008-02-15 13:48:18 -0500},
147 +        Issn = {1520-6106},
148 +        Journal = jpcb,
149 +        Number = {7},
150 +        Pages = {1968-1975},
151 +        Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes},
152 +        Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020},
153 +        Volume = {112},
154 +        Year = {2008}}
155 +
156 + @book{Schlick2002,
157 +        Address = {Secaucus, NJ, USA},
158 +        Author = {Tamar Schlick},
159 +        Date-Added = {2008-02-12 16:52:19 -0500},
160 +        Date-Modified = {2008-02-12 16:53:15 -0500},
161 +        Isbn = {038795404X},
162 +        Publisher = {Springer-Verlag New York, Inc.},
163 +        Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
164 +        Year = {2002}}
165 +
166 + @article{Chun:2000fj,
167 +        Abstract = {A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5- to 30-fold over atomistic simulations have been realized in various applications of the method. (C) 2000 John Wiley \& Sons, Inc.},
168 +        Author = {Chun, HM and Padilla, CE and Chin, DN and Watanabe, M and Karlov, VI and Alper, HE and Soosaar, K and Blair, KB and Becker, OM and Caves, LSD and Nagle, R and Haney, DN and Farmer, BL},
169 +        Date-Added = {2008-01-22 10:38:33 -0500},
170 +        Date-Modified = {2008-01-22 10:38:49 -0500},
171 +        Journal = jcc,
172 +        Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
173 +        Pages = {159--184},
174 +        Timescited = 0,
175 +        Title = {{MBO(N)D:} A multibody method for long-time molecular dynamics simulations},
176 +        Volume = 21,
177 +        Year = 2000}
178 +
179 + @article{Fogolari:1996lr,
180 +        Abstract = {In an effort to reduce the number of degrees of freedom necessary to describe a polypeptide chain we analyze the statistical behavior of polypeptide chains when represented as C alpha chains, C alpha chains with C beta atoms attached, and C alpha chains with rotational ellipsoids as models of side chains. A statistical analysis on a restricted data set of 75 unrelated protein structures is performed. The comparison of the database distributions with those obtained by model calculation on very short polypeptide stretches allows the dissection of local versus nonlocal features of the distributions. The database distribution of the bend angles of polypeptide chains of pseudo bonded C alpha atoms spans a restricted range of values and shows a bimodal structure. On the other hand, the torsion angles of the C alpha chain may assume almost all possible values. The distribution is bimodal, but with a much broader probability distribution than for bend angles. The C alpha - C beta vectors may be taken as representative of the orientation of the lateral chain, as the direction of the bond is close to the direction of the vector joining C alpha to the ad hoc defined center of the "steric mass" of the side chain. Interestingly, both the bend angle defined by C alpha i-C alpha i+1-C beta i+1 and the torsional angle offset of the pseudo-dihedral C alpha i-C alpha i+1-C alpha i+2-C beta i+2 with respect to C alpha i-C alpha i+1-C alpha i+2-C alpha i+3 span a limited range of values. The latter results show that it is possible to give a more realistic representation of polypeptide chains without introducing additional degrees of freedom, i.e., by just adding to the C alpha chain a C beta with given side-chain properties. However, a more realistic description of side chains may be attained by modeling side chains as rotational ellipsoids that have roughly the same orientation and steric hindrance. To this end, we define the steric mass of an atom as proportional to its van der Waals volume and we calculate the side-chain inertia ellipsoid assuming that the steric mass of each atom is uniformly distributed within its van der Waals volume. Finally, we define the rotational ellipsoid representing the side chain as the uniform density ellipsoid possessing the same rotationally averaged inertia tensor of the side chain. The statistics of ellipsoid parameters support the possibility of representing a side chain via an ellipsoid, independently of the local conformation. To make this description useful for molecular modeling we describe ellipsoid-ellipsoid interactions via a Lennard-Jones potential that preserves the repulsive core of the interacting ellipsoids and takes into account their mutual orientation. Tests are performed for two different forms of the interaction potential on a set of high-resolution protein structures. Results are encouraging, in view of the drastic simplifications that were introduced.},
181 +        Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.},
182 +        Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
183 +        Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
184 +        Da = {19960924},
185 +        Date-Added = {2008-01-22 10:19:04 -0500},
186 +        Date-Modified = {2008-01-22 10:19:09 -0500},
187 +        Dcom = {19960924},
188 +        Edat = {1996/03/01},
189 +        Issn = {0006-3495 (Print)},
190 +        Jid = {0370626},
191 +        Journal = {Biophys J},
192 +        Jt = {Biophysical journal},
193 +        Language = {eng},
194 +        Lr = {20071115},
195 +        Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; *Models, Molecular; Molecular Structure; Peptides/*chemistry; *Protein Conformation; Software; Thermodynamics},
196 +        Mhda = {1996/03/01 00:01},
197 +        Number = {3},
198 +        Own = {NLM},
199 +        Pages = {1183--1197},
200 +        Pl = {UNITED STATES},
201 +        Pmid = {8785277},
202 +        Pst = {ppublish},
203 +        Pt = {Journal Article},
204 +        Pubm = {Print},
205 +        Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)},
206 +        Sb = {IM},
207 +        So = {Biophys J. 1996 Mar;70(3):1183-97. },
208 +        Stat = {MEDLINE},
209 +        Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.},
210 +        Volume = {70},
211 +        Year = {1996}}
212 +
213 + @inbook{Ramachandran1996,
214 +        Address = {Providence, Rhode Island},
215 +        Author = {Gomathi Ramachandran and Tamar Schlick},
216 +        Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
217 +        Date-Added = {2008-01-22 10:03:42 -0500},
218 +        Date-Modified = {2008-01-22 10:06:57 -0500},
219 +        Editor = {P. M. Pardalos and D. Shalloway and G. Xue},
220 +        Pages = {215-231},
221 +        Publisher = {American Mathematical Society},
222 +        Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
223 +        Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
224 +        Volume = {23},
225 +        Year = {1996}}
226 +
227 + @article{FIXMAN:1986lr,
228 +        Author = {Fixman, M},
229 +        Date-Added = {2008-01-22 09:59:29 -0500},
230 +        Date-Modified = {2008-01-22 09:59:35 -0500},
231 +        Journal = {Macromolecules},
232 +        Pages = {1204-1207},
233 +        Timescited = {0},
234 +        Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION},
235 +        Volume = {19},
236 +        Year = {1986}}
237 +
238 + @article{Berendsen87,
239 +        Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
240 +        Date-Added = {2008-01-22 09:53:15 -0500},
241 +        Date-Modified = {2008-01-22 09:53:15 -0500},
242 +        Journal = jpc,
243 +        Pages = {6269-6271},
244 +        Title = {The Missing Term in Effective Pair Potentials},
245 +        Volume = 91,
246 +        Year = 1987}
247 +
248 + @incollection{Berendsen81,
249 +        Address = {Dordrecht},
250 +        Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
251 +        Booktitle = {Intermolecular Forces},
252 +        Date-Added = {2008-01-22 09:52:49 -0500},
253 +        Date-Modified = {2008-01-22 09:52:49 -0500},
254 +        Editor = {B. Pullman},
255 +        Pages = {331-342},
256 +        Publisher = {Reidel},
257 +        Title = {Simple Point Charge Water},
258 +        Year = 1981}
259 +
260 + @article{Stillinger74,
261 +        Author = {F.~H. Stillinger and A. Rahman},
262 +        Date-Added = {2008-01-22 09:51:43 -0500},
263 +        Date-Modified = {2008-01-22 09:51:43 -0500},
264 +        Journal = jcp,
265 +        Number = 4,
266 +        Pages = {1545-1557},
267 +        Title = {Improved simulation of liquid water by molecular dynamics},
268 +        Volume = 60,
269 +        Year = 1974}
270 +
271   @article{Torre:1983lr,
272 <        Author = {de la Torre, Jose Garcia and Rodes, Vicente},
272 >        Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
273 >        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1},
274          Date-Added = {2008-01-11 16:16:43 -0500},
275          Date-Modified = {2008-01-11 16:16:43 -0500},
276 <        Journal = {The Journal of Chemical Physics},
276 >        Journal = jcp,
277          Journal1 = {The Journal of Chemical Physics},
278          Journal2 = {J. Chem. Phys.},
279          Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
280 <        Number = {5},
280 >        Number = 5,
281          Pages = {2454--2460},
282          Publisher = {AIP},
283          Title = {Effects from bead size and hydrodynamic interactions on the translational and rotational coefficients of macromolecular bead models},
284          Ty = {JOUR},
285          Url = {http://link.aip.org/link/?JCP/79/2454/1},
286 <        Volume = {79},
287 <        Year = {1983}}
286 >        Volume = 79,
287 >        Year = 1983}
288  
289   @article{PhysRev.119.53,
290          Author = {Favro, L. Dale},
291 +        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53},
292          Date-Added = {2008-01-09 16:57:02 -0500},
293          Date-Modified = {2008-01-09 16:57:02 -0500},
294          Doi = {10.1103/PhysRev.119.53},
295          Journal = {Phys. Rev.},
296          Month = {Jul},
297 <        Number = {1},
298 <        Numpages = {9},
297 >        Number = 1,
298 >        Numpages = 9,
299          Pages = {53--62},
300          Publisher = {American Physical Society},
301          Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body},
302 <        Volume = {119},
303 <        Year = {1960}}
302 >        Volume = 119,
303 >        Year = 1960}
304  
305   @article{hess:209,
306          Author = {Berk Hess},
307 +        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
308 +        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362},
309          Date-Added = {2008-01-08 16:41:06 -0500},
310          Date-Modified = {2008-01-08 16:41:06 -0500},
311          Doi = {10.1063/1.1421362},
312 <        Journal = {The Journal of Chemical Physics},
312 >        Journal = jcp,
313          Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
314 <        Number = {1},
314 >        Number = 1,
315          Pages = {209-217},
316          Publisher = {AIP},
317          Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
318          Url = {http://link.aip.org/link/?JCP/116/209/1},
319 <        Volume = {116},
320 <        Year = {2002}}
319 >        Volume = 116,
320 >        Year = 2002}
321  
322   @article{Garcia-de-la-Torre:1997qy,
323          Abstract = {Single-valued hydrodynamic coefficients of a rigid particle can be calculated from existing theories and computer programs for either bead models or ellipsoids. Starting from these coefficients, we review the procedures for the calculation of complex solution properties depending on rotational diffusion, such as the decays of electric birefringence and fluorescence anisotropy. We also describe the calculation of the scattering from factor of bead models. The hydrodynamic coefficients and solution properties can be combined to give universal, shape-dependent functions, which were initially intended for ellipsoidal particles, and are extended here for the most general case. We have implemented all three developments in a new computer program. SOLPRO, for calculation of SOLution PROperties, which can be linked to existing software for bead models or ellipsoids.},
324          Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es},
325 <        Au = {Garcia de la Torre, J and Carrasco, B and Harding, SE},
326 <        Author = {Garcia de la Torre, J and Carrasco, B and Harding, S E},
327 <        Da = {19970709},
325 >        Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE},
326 >        Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E},
327 >        Da = 19970709,
328          Date-Added = {2008-01-08 15:45:31 -0500},
329          Date-Modified = {2008-01-08 15:46:57 -0500},
330 <        Dcom = {19970709},
330 >        Dcom = 19970709,
331          Edat = {1997/01/01},
332          Issn = {0175-7571 (Print)},
333 <        Jid = {8409413},
333 >        Jid = 8409413,
334          Journal = {Eur Biophys J},
335          Jt = {European biophysics journal : EBJ},
336          Keywords = {Birefringence; Fluorescence Polarization; Humans; Immunoglobulin G/chemistry; Models, Structural; *Protein Conformation; Proteins/*chemistry; Scattering, Radiation; *Software; Ultracentrifugation/methods},
337          Language = {eng},
338 <        Lr = {20061115},
338 >        Lr = 20061115,
339          Mhda = {1997/01/01 00:01},
340          Number = {5-6},
341          Own = {NLM},
342          Pages = {361--372},
343          Pl = {GERMANY},
344 <        Pmid = {9213556},
344 >        Pmid = 9213556,
345          Pst = {ppublish},
346          Pt = {Journal Article; Research Support, Non-U.S. Gov't},
347          Pubm = {Print},
# Line 87 | Line 350
350          So = {Eur Biophys J. 1997;25(5-6):361-72.},
351          Stat = {MEDLINE},
352          Title = {SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.},
353 <        Volume = {25},
354 <        Year = {1997}}
353 >        Volume = 25,
354 >        Year = 1997}
355  
356   @article{Ravichandran:1999fk,
357          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].},
358          Author = {Ravichandran, S and Bagchi, B},
359          Date-Added = {2008-01-08 15:24:48 -0500},
360          Date-Modified = {2008-01-08 15:25:41 -0500},
361 <        Journal = {Journal of Chemical Physics},
361 >        Journal = jcp,
362          Pages = {7505-7511},
363          Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
364 <        Volume = {111},
365 <        Year = {1999}}
364 >        Volume = 111,
365 >        Year = 1999}
366  
367   @article{TANG:1993lr,
368          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.},
369          Author = {TANG, SA and EVANS, GT},
370          Date-Added = {2008-01-08 15:23:42 -0500},
371          Date-Modified = {2008-01-08 15:24:09 -0500},
372 <        Journal = {Molecular Physics},
372 >        Journal = mp,
373          Pages = {1443-1457},
374          Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
375 <        Volume = {80},
376 <        Year = {1993}}
375 >        Volume = 80,
376 >        Year = 1993}
377  
378   @article{Schmidt:2003kx,
379          Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a spherical solute in a dense fluid of spherical solvent particles. The size and mass of the solute particle are related in such a way that we can naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that as long as the solute radius is interpreted as an effective hydrodynamic radius, the Stokes-Einstein law with slip boundary conditions is satisfied as the Brownian limit is approached (specifically, when the solute is roughly 100 times more massive than the solvent particles). In contrast, the Stokes-Einstein law is not satisfied for a tagged particle of the neat solvent. We also find that in the Brownian limit the amplitude of the long-time tail of the solute's velocity autocorrelation function is in good agreement with theoretical hydrodynamic predictions. When the solvent density is substantially lower than the triple density, the Stokes-Einstein law is no longer satisfied, and the amplitude of the long-time tail is not in good agreement with theoretical predictions, signaling the breakdown of hydrodynamics. (C) 2003 American Institute of Physics.},
380          Author = {Schmidt, JR and Skinner, JL},
381 +        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442},
382          Date-Added = {2008-01-08 15:12:53 -0500},
383          Date-Modified = {2008-01-08 15:13:21 -0500},
384          Doi = {DOI 10.1063/1.1610442},
385 <        Journal = {Journal of Chemical Physics},
385 >        Journal = jcp,
386          Pages = {8062-8068},
387          Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
388 <        Volume = {119},
389 <        Year = {2003}}
388 >        Volume = 119,
389 >        Year = 2003}
390  
391   @article{Schmidt:2004fj,
392          Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a variety of solutes in a dense fluid of spherical solvent particles. We explore the effects of surface roughness of the solute on the resulting hydrodynamic boundary condition as we naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that when the solute and solvent interact through a purely repulsive isotropic potential, in the Brownian limit the Stokes-Einstein law is satisfied with slip boundary conditions. However, when surface roughness is introduced through an anisotropic solute-solvent interaction potential, we find that the Stokes-Einstein law is satisfied with stick boundary conditions. In addition, when the attractive strength of a short-range isotropic solute-solvent potential is increased, the solute becomes dressed with solvent particles, making it effectively rough, and so stick boundary conditions are again recovered.},
393          Author = {Schmidt, JR and Skinner, JL},
394 +        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r},
395          Date-Added = {2008-01-08 15:12:53 -0500},
396          Date-Modified = {2008-01-08 15:13:20 -0500},
397          Doi = {DOI 10.1021/jp037185r},
398 <        Journal = {Journal of Physical Chemistry B},
398 >        Journal = jpcb,
399          Pages = {6767-6771},
400          Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
401 <        Volume = {108},
402 <        Year = {2004}}
401 >        Volume = 108,
402 >        Year = 2004}
403  
404   @article{Klein01,
405          Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
# Line 274 | Line 539
539          Date-Modified = {2008-01-08 14:58:56 -0500},
540          Journal = {J. Chem. Phys.},
541          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf},
542 <        Number = {19},
542 >        Number = 19,
543          Pages = {8577-8593},
544          Title = {A smooth particle mesh Ewald method},
545 <        Volume = {103},
546 <        Year = {1995}}
545 >        Volume = 103,
546 >        Year = 1995}
547  
548   @article{Ricci94,
549          Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
# Line 328 | Line 593
593          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf},
594          Pages = {7320-7327},
595          Title = {Acceleration of Convergence for Lattice Sums},
596 <        Volume = {93},
597 <        Year = {1989}}
596 >        Volume = 93,
597 >        Year = 1989}
598  
599   @article{Petersen95,
600          Author = {H.~G. Petersen},
# Line 338 | Line 603
603          Journal = {J. Chem. Phys.},
604          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
605          Month = {September},
606 <        Number = {9},
606 >        Number = 9,
607          Pages = {3668-3679},
608          Title = {Accuracy and efficiency of the particle mesh Ewald method},
609 <        Volume = {103},
610 <        Year = {1995}}
609 >        Volume = 103,
610 >        Year = 1995}
611  
612   @article{Duncan06,
613          Author = {Peter D. Duncan and Philip J. Camp},
# Line 428 | Line 693
693          Year = 2003}
694  
695   @article{Cascales98,
696 <        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
696 >        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and {Garc\'{i}a de la Torre}, Jose},
697          Date-Added = {2008-01-08 14:58:56 -0500},
698          Date-Modified = {2008-01-08 14:58:57 -0500},
699          Journal = {J. Phys. Chem. B},
# Line 475 | Line 740
740          Journal = {Phil. Mag. A},
741          Pages = {1057-1066},
742          Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
743 <        Volume = {75},
744 <        Year = {1997}}
743 >        Volume = 75,
744 >        Year = 1997}
745  
746   @inproceedings{Gotze89,
747          Address = {Amsterdam},
# Line 529 | Line 794
794          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
795          Pages = {1322-1331},
796          Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
797 <        Volume = {99},
798 <        Year = {1995}}
797 >        Volume = 99,
798 >        Year = 1995}
799  
800   @article{Ayton02,
801          Author = {G. Ayton and G.~A. Voth},
# Line 607 | Line 872
872          Abstract = {X-ray data are presented for the benchmark dipalmitoylphosphatidylcholine lipid bilayer in the most biologically relevant state in which the bilayers are fully hydrated and in the fluid (liquid-crystalline) phase. Form factors F(qz) are obtained from a combination of two sample preparations, oriented stacks of bilayers for qz extending to 0.85 A-1 and unilamellar vesicles for smaller qz. Modeling obtains the electron density profile and values for the area per molecule, for the locations of the component groups, and for the different types of thicknesses of the bilayer, such as the hydrocarbon thickness and the steric thickness.
873   },
874          Author = {Kucerka, Norbert and Tristram-Nagle, Stephanie and Nagle, John F.},
875 +        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
876 +        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017},
877          Date-Added = {2008-01-08 14:58:56 -0500},
878          Date-Modified = {2008-01-08 14:58:57 -0500},
879          Doi = {10.1529/biophysj.106.086017},
880          Eprint = {http://www.biophysj.org/cgi/reprint/90/11/L83.pdf},
881          Journal = {Biophys. J.},
882 <        Number = {11},
882 >        Number = 11,
883          Pages = {L83-85},
884          Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}},
885          Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
886 <        Volume = {90},
887 <        Year = {2006}}
886 >        Volume = 90,
887 >        Year = 2006}
888  
889   @article{deJoannis06,
890          Author = {J. de~Joannis and F.~Y. Jiang and J.~T. Kindt},
# Line 747 | Line 1014
1014          Journal = {Mol. Simul.},
1015          Pages = {351-368},
1016          Title = {Cutoff Errors in the Ewald. Summation Formulae for Point Charge Systems},
1017 <        Volume = {9},
1018 <        Year = {1992}}
1017 >        Volume = 9,
1018 >        Year = 1992}
1019  
1020   @article{Tlusty00,
1021          Author = {T. Tlusty and S.~A. Safran},
# Line 762 | Line 1029
1029  
1030   @article{Seung1988,
1031          Author = {Seung, H. S. and Nelson, David R.},
1032 +        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005},
1033          Date-Added = {2008-01-08 14:58:56 -0500},
1034          Date-Modified = {2008-01-08 14:58:58 -0500},
1035          Doi = {10.1103/PhysRevA.38.1005},
1036          Journal = {Phys. Rev. A},
1037          Month = {Jul},
1038 <        Number = {2},
1039 <        Numpages = {13},
1038 >        Number = 2,
1039 >        Numpages = 13,
1040          Pages = {1005--1018},
1041          Publisher = {American Physical Society},
1042          Title = {Defects in flexible membranes with crystalline order},
1043 <        Volume = {38},
1044 <        Year = {1988}}
1043 >        Volume = 38,
1044 >        Year = 1988}
1045  
1046   @article{Monroe95,
1047          Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
# Line 834 | Line 1102
1102          Journal = {Ann. Physik},
1103          Pages = {253-287},
1104          Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
1105 <        Volume = {64},
1106 <        Year = {1921}}
1105 >        Volume = 64,
1106 >        Year = 1921}
1107  
1108   @article{Zwanzig88,
1109          Author = {R. Zwanzig},
# Line 882 | Line 1150
1150          Date-Added = {2008-01-08 14:58:56 -0500},
1151          Date-Modified = {2008-01-08 14:58:58 -0500},
1152          Journal = prl,
1153 <        Pages = {3649},
1153 >        Pages = 3649,
1154          Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
1155          Volume = 82,
1156 <        Year = {1999}}
1156 >        Year = 1999}
1157  
1158   @article{Ngai81,
1159          Author = {K.~L. Ngai and F.-S. Liu},
# Line 935 | Line 1203
1203          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
1204          Pages = {69-88},
1205          Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
1206 <        Volume = {78},
1207 <        Year = {1999}}
1206 >        Volume = 78,
1207 >        Year = 1999}
1208  
1209   @article{Spohr97,
1210          Author = {E. Spohr},
# Line 944 | Line 1212
1212          Date-Modified = {2008-01-08 14:58:58 -0500},
1213          Journal = {J. Chem. Phys.},
1214          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
1215 <        Number = {16},
1215 >        Number = 16,
1216          Pages = {6342-6348},
1217          Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
1218 <        Volume = {107},
1219 <        Year = {1997}}
1218 >        Volume = 107,
1219 >        Year = 1997}
1220  
1221   @article{Marrink01b,
1222          Author = {S.~J. Marrink and A.~E. Mark},
1223          Date-Added = {2008-01-08 14:58:56 -0500},
1224          Date-Modified = {2008-01-08 14:58:58 -0500},
1225 <        Journal = {Journal of Physical Chemistry B},
1225 >        Journal = jpcb,
1226          Pages = {6122-6127},
1227          Title = {Effect of undulations on surface tension in simulated bilayers},
1228          Volume = 105,
# Line 1047 | Line 1315
1315          Journal = {Mol. Phys.},
1316          Pages = {1313-1327},
1317          Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices},
1318 <        Volume = {37},
1319 <        Year = {1979}}
1318 >        Volume = 37,
1319 >        Year = 1979}
1320  
1321   @article{Heyes81,
1322          Author = {D.~M. Heyes},
# Line 1057 | Line 1325
1325          Journal = {J. Chem. Phys.},
1326          Keywords = {Empty Keywords},
1327          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
1328 <        Number = {3},
1328 >        Number = 3,
1329          Pages = {1924-1929},
1330          Title = {Electrostatic potentials and fields in infinite point charge lattices},
1331 <        Volume = {74},
1332 <        Year = {1981}}
1331 >        Volume = 74,
1332 >        Year = 1981}
1333  
1334   @article{Tsonchev04,
1335          Author = {Stefan Tsonchev and George C. Schatz and Mark A. Ratner},
# Line 1081 | Line 1349
1349          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
1350          Pages = {253-261},
1351          Title = {Electrostatics calculations: recent methodological advances and applications to membranes},
1352 <        Volume = {11},
1353 <        Year = {2001}}
1352 >        Volume = 11,
1353 >        Year = 2001}
1354  
1355   @article{Arnold02,
1356          Author = {A. Arnold and J. {de Joannis} and C. Holm},
1357 +        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195},
1358          Date-Added = {2008-01-08 14:58:56 -0500},
1359          Date-Modified = {2008-01-08 14:58:58 -0500},
1360          Doi = {10.1063/1.149195},
1361          Journal = {J. Chem. Phys.},
1362          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Arnold_SlabElectrostatics_02.pdf},
1363 <        Number = {6},
1363 >        Number = 6,
1364          Pages = {2496-2502},
1365          Title = {Electrostatics in periodic slab geometries. I},
1366 <        Volume = {117},
1367 <        Year = {2002}}
1366 >        Volume = 117,
1367 >        Year = 2002}
1368  
1369   @article{deJoannis02,
1370          Author = {J. {de Joannis} and A. Arnold and C. Holm},
1371 +        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195},
1372          Date-Added = {2008-01-08 14:58:56 -0500},
1373          Date-Modified = {2008-01-08 14:58:58 -0500},
1374          Doi = {10.1063/1.149195},
1375          Journal = {J. Chem. Phys.},
1376          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf},
1377 <        Number = {6},
1377 >        Number = 6,
1378          Pages = {2503-2512},
1379          Title = {Electrostatics in periodic slab geometries. II},
1380 <        Volume = {117},
1381 <        Year = {2002}}
1380 >        Volume = 117,
1381 >        Year = 2002}
1382  
1383   @article{Barenco95,
1384          Author = {A. Barenco and C.~H. Bennett and R. Cleve and D.~P. DiVincenzo and N. Margolus and P. Shor and T. Sleator and J.~A. Smolin and H. Weinfurter},
# Line 1158 | Line 1428
1428          Date-Modified = {2008-01-08 14:58:58 -0500},
1429          Journal = {J. Phys. Chem. B},
1430          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
1431 <        Number = {41},
1431 >        Number = 41,
1432          Pages = {10725-10732},
1433          Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
1434 <        Volume = {106},
1435 <        Year = {2002}}
1434 >        Volume = 106,
1435 >        Year = 2002}
1436  
1437   @article{Metropolis53,
1438          Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
# Line 1180 | Line 1450
1450          Date-Added = {2008-01-08 14:58:56 -0500},
1451          Date-Modified = {2008-01-08 14:58:58 -0500},
1452          Journal = {Surf. Sci.},
1453 <        Pages = {195},
1453 >        Pages = 195,
1454          Title = {Errata: The electrostatic potential in the surface region of an ionic crystal},
1455 <        Volume = {54},
1456 <        Year = {1976}}
1455 >        Volume = 54,
1456 >        Year = 1976}
1457  
1458   @article{Steane96,
1459          Author = {A.~M. Steane},
# Line 1211 | Line 1481
1481          Date-Modified = {2008-01-08 14:58:59 -0500},
1482          Journal = {J. Chem. Phys.},
1483          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
1484 <        Number = {4},
1484 >        Number = 4,
1485          Pages = {1856-1872},
1486          Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study},
1487 <        Volume = {110},
1488 <        Year = {1999}}
1487 >        Volume = 110,
1488 >        Year = 1999}
1489  
1490   @article{Rhee89,
1491          Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
# Line 1223 | Line 1493
1493          Date-Modified = {2008-01-08 14:58:59 -0500},
1494          Journal = {Phys. Rev. B},
1495          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
1496 <        Number = {1},
1496 >        Number = 1,
1497          Pages = {36-42},
1498          Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions},
1499 <        Volume = {40},
1500 <        Year = {1989}}
1499 >        Volume = 40,
1500 >        Year = 1989}
1501  
1502   @article{Yeh99,
1503          Author = {I.-C. Yeh and M.~L. Berkowitz},
# Line 1235 | Line 1505
1505          Date-Modified = {2008-01-08 14:58:59 -0500},
1506          Journal = {J. Chem. Phys.},
1507          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
1508 <        Number = {7},
1508 >        Number = 7,
1509          Pages = {3155-3162},
1510          Title = {Ewald summation for systems with slab geometry},
1511 <        Volume = {111},
1512 <        Year = {1999}}
1511 >        Volume = 111,
1512 >        Year = 1999}
1513  
1514   @article{Brodka04,
1515          Author = {A. Br\'{o}dka},
1516 +        Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086},
1517          Date-Added = {2008-01-08 14:58:56 -0500},
1518          Date-Modified = {2008-01-08 14:58:59 -0500},
1519          Doi = {10.1016/j.cplett.2004.10.086},
# Line 1250 | Line 1521
1521          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf},
1522          Pages = {62-67},
1523          Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
1524 <        Volume = {400},
1525 <        Year = {2004}}
1524 >        Volume = 400,
1525 >        Year = 2004}
1526  
1527   @article{Chuang98,
1528          Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
# Line 1319 | Line 1590
1590          Abstract = {The plasma membrane of cells is an ordered environment, giving rise to anisotropic orientation and restricted motion of molecules and proteins residing in the membrane. At the same time as being an organized matrix of defined structure, the cell membrane is heterogeneous and dynamic. Here we present a method where we use fluorescence imaging of linear dichroism to measure the orientation of molecules relative to the cell membrane. By detecting linear dichroism as well as fluorescence anisotropy, the orientation parameters are separated from dynamic properties such as rotational diffusion and homo energy transfer (energy migration). The sensitivity of the technique is enhanced by using two-photon excitation for higher photo-selection compared to single photon excitation. We show here that we can accurately image lipid organization in whole cell membranes and in delicate structures such as membrane nanotubes connecting two cells. The speed of our wide-field imaging system makes it possible to image changes in orientation and anisotropy occurring on a subsecond timescale. This is demonstrated by time-lapse studies showing that cholesterol depletion rapidly disrupts the orientation of a fluorophore located within the hydrophobic region of the cell membrane but not of a surface bound probe. This is consistent with cholesterol having an important role in stabilizing and ordering the lipid tails within the plasma membrane. },
1591          Annote = {10.1529/biophysj.104.050096},
1592          Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.},
1593 +        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
1594          Date-Added = {2008-01-08 14:58:56 -0500},
1595          Date-Modified = {2008-01-08 14:58:59 -0500},
1596 <        Journal = {Biophysical Journal},
1596 >        Journal = bj,
1597          Journal1 = {Biophys. J.},
1598 <        Number = {1},
1598 >        Number = 1,
1599          Pages = {609--622},
1600          Title = {Fluorescence Imaging of Two-Photon Linear Dichroism: Cholesterol Depletion Disrupts Molecular Orientation in Cell Membranes},
1601          Ty = {JOUR},
1602          Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
1603 <        Volume = {88},
1604 <        Year = {2005}}
1603 >        Volume = 88,
1604 >        Year = 2005}
1605  
1606   @inbook{Blumen86,
1607          Address = {Amsterdam},
# Line 1380 | Line 1652
1652          Date-Added = {2008-01-08 14:58:56 -0500},
1653          Date-Modified = {2008-01-08 14:58:59 -0500},
1654          Eid = 157802,
1655 <        Journal = {Physical Review Letters},
1655 >        Journal = prl,
1656          Number = 15,
1657          Numpages = 4,
1658          Pages = 157802,
# Line 1447 | Line 1719
1719          Date-Modified = {2008-01-08 14:58:59 -0500},
1720          Journal = {J. Chem. Phys.},
1721          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
1722 <        Number = {6},
1722 >        Number = 6,
1723          Pages = {5024-5031},
1724          Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
1725 <        Volume = {101},
1726 <        Year = {1994}}
1725 >        Volume = 101,
1726 >        Year = 1994}
1727  
1728   @article{Stillinger85,
1729          Author = {F.~H. Stillinger and T.~A. Weber},
# Line 1472 | Line 1744
1744          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
1745          Pages = {398-404},
1746          Title = {Integral equation theory for correcting truncation errors in molecular simulations},
1747 <        Volume = {367},
1748 <        Year = {2003}}
1747 >        Volume = 367,
1748 >        Year = 2003}
1749  
1750   @article{Ayton01,
1751          Author = {Gary Ayton and Scott G. Bardenhagen and Patrick McMurty and Deborah Sulsky and Gregory A. Voth},
# Line 1532 | Line 1804
1804          Date-Modified = {2008-01-08 14:58:59 -0500},
1805          Journal = {J. Chem. Phys.},
1806          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
1807 <        Number = {8},
1807 >        Number = 8,
1808          Pages = {3014-3021},
1809          Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
1810 <        Volume = {103},
1811 <        Year = {1995}}
1810 >        Volume = 103,
1811 >        Year = 1995}
1812  
1813   @article{Wan94,
1814          Author = {Yi. Wan and R.~M. Stratt},
# Line 1572 | Line 1844
1844          Author = {E. Lindahl and O. Edholm},
1845          Date-Added = {2008-01-08 14:58:56 -0500},
1846          Date-Modified = {2008-01-08 14:58:59 -0500},
1847 <        Journal = {Biophysical Journal},
1847 >        Journal = bj,
1848          Month = {July},
1849          Pages = {426-433},
1850          Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
# Line 1600 | Line 1872
1872  
1873   @article{Goldstein88,
1874          Author = {Raymond E. Goldstein and Stanislas Leibler},
1875 +        Bdsk-File-1 = {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},
1876          Date-Added = {2008-01-08 14:58:56 -0500},
1877          Date-Modified = {2008-01-08 14:58:59 -0500},
1878          Journal = prl,
# Line 1624 | Line 1897
1897          Date-Added = {2008-01-08 14:58:56 -0500},
1898          Date-Modified = {2008-01-08 14:58:59 -0500},
1899          Journal = {J. Chem. Soc., Faraday Trans. II},
1900 <        Number = {7},
1900 >        Number = 7,
1901          Pages = {1485-1496},
1902          Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride},
1903 <        Volume = {73},
1904 <        Year = {1977}}
1903 >        Volume = 73,
1904 >        Year = 1977}
1905  
1906   @article{Vuilleumier97,
1907          Author = {Rodolphe Vuilleumier and Daniel Borgis},
# Line 1663 | Line 1936
1936          Author = {A.~M. Smondyrev and M.~L. Berkowitz},
1937          Date-Added = {2008-01-08 14:58:56 -0500},
1938          Date-Modified = {2008-01-08 14:59:00 -0500},
1939 <        Journal = {Biophysical Journal},
1939 >        Journal = bj,
1940          Pages = {2472-2478},
1941          Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1942          Volume = 76,
# Line 1673 | Line 1946
1946          Author = {S.~J. Marrink and D.~P. Teileman},
1947          Date-Added = {2008-01-08 14:58:56 -0500},
1948          Date-Modified = {2008-01-08 14:59:00 -0500},
1949 <        Journal = {Biophysical Journal},
1949 >        Journal = bj,
1950          Pages = {2386-2392},
1951          Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1952          Volume = 83,
# Line 1712 | Line 1985
1985  
1986   @article{Weber00,
1987          Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
1988 +        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757},
1989          Date-Added = {2008-01-08 14:58:56 -0500},
1990          Date-Modified = {2008-01-08 14:59:00 -0500},
1991          Doi = {10.1021/jp9937757},
1992          Journal = {J. Phys. Chem. B},
1993          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
1994 <        Number = {15},
1994 >        Number = 15,
1995          Pages = {3668-3675},
1996          Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
1997 <        Volume = {104},
1998 <        Year = {2000}}
1997 >        Volume = 104,
1998 >        Year = 2000}
1999  
2000   @article{Venable00,
2001          Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
# Line 1738 | Line 2012
2012          Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
2013          Date-Added = {2008-01-08 14:58:56 -0500},
2014          Date-Modified = {2008-01-08 14:59:00 -0500},
2015 <        Journal = {Biophysical Journal},
2015 >        Journal = bj,
2016          Pages = {3636-3645},
2017          Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
2018          Volume = 84,
# Line 1761 | Line 2035
2035          Journal = {J. Chem. Phys.},
2036          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
2037          Month = {October},
2038 <        Number = {7},
2038 >        Number = 7,
2039          Pages = {3336-3359},
2040          Title = {Molecular Dynamics Study of Liquid Water},
2041 <        Volume = {55},
2042 <        Year = {1971}}
2041 >        Volume = 55,
2042 >        Year = 1971}
2043  
2044   @article{Sum03,
2045          Author = {A.~K. Sum and J.~J. de~Pablo},
2046          Date-Added = {2008-01-08 14:58:56 -0500},
2047          Date-Modified = {2008-01-08 14:59:00 -0500},
2048 <        Journal = {Biophysical Journal},
2048 >        Journal = bj,
2049          Pages = {3636-3645},
2050          Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
2051          Volume = 85,
# Line 1826 | Line 2100
2100          Journal = {Mol. Phys.},
2101          Pages = {789-792},
2102          Title = {Monte Carlo studies of the dielectric properties of water-like models},
2103 <        Volume = {26},
2104 <        Year = {1973}}
2103 >        Volume = 26,
2104 >        Year = 1973}
2105  
2106   @article{Brush66,
2107          Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
# Line 1836 | Line 2110
2110          Journal = {J. Chem. Phys.},
2111          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
2112          Month = {September},
2113 <        Number = {6},
2113 >        Number = 6,
2114          Pages = {2102-2118},
2115          Title = {Monte Carlo Study of a One-Component Plasma. I},
2116 <        Volume = {45},
2117 <        Year = {1966}}
2116 >        Volume = 45,
2117 >        Year = 1966}
2118  
2119   @article{Tenchov2001,
2120          Author = {Boris Tenchov and Rumiana Koynova and Gert Rapp},
# Line 1854 | Line 2128
2128  
2129   @article{Steinbach94,
2130          Author = {P.~J. Steinbach and B.~R. Brooks},
2131 +        Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150702},
2132          Date-Added = {2008-01-08 14:58:56 -0500},
2133          Date-Modified = {2008-01-08 14:59:00 -0500},
2134          Doi = {10.1002/jcc.540150702},
2135          Journal = {J. Comput. Chem.},
2136 <        Number = {7},
2136 >        Number = 7,
2137          Pages = {667-683},
2138          Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
2139 <        Volume = {15},
2140 <        Year = {1994}}
2139 >        Volume = 15,
2140 >        Year = 1994}
2141  
2142   @article{McKinnon92,
2143          Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
# Line 1959 | Line 2234
2234          Author = {J. Norberg and L. Nilsson},
2235          Date-Added = {2008-01-08 14:58:56 -0500},
2236          Date-Modified = {2008-01-08 14:59:00 -0500},
2237 <        Journal = {Biophysical Journal},
2237 >        Journal = bj,
2238          Pages = {1537-1553},
2239          Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
2240          Volume = 79,
# Line 1994 | Line 2269
2269          Date-Modified = {2008-01-08 14:59:00 -0500},
2270          Journal = {J. Chem. Phys.},
2271          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
2272 <        Number = {5},
2272 >        Number = 5,
2273          Pages = {1062-1063},
2274          Title = {Optimum Atomic Shape for Bertaut Series},
2275 <        Volume = {25},
2276 <        Year = {1956}}
2275 >        Volume = 25,
2276 >        Year = 1956}
2277  
2278   @article{Renard1966,
2279          Author = {R\'emi Renard and Carl W. Garland},
# Line 2136 | Line 2411
2411          Volume = 51,
2412          Year = 1995}
2413  
2414 < @book{Cevc87,
2414 > @book{Cevc80,
2415          Address = {New York},
2416          Author = {Gregor Cevc and Derek Marsh},
2417          Date-Added = {2008-01-08 14:58:56 -0500},
2418 <        Date-Modified = {2008-01-08 14:59:01 -0500},
2418 >        Date-Modified = {2008-03-20 12:27:15 -0400},
2419          Publisher = {Wiley-Interscience},
2420          Title = {Phospholipid Bilayers},
2421          Year = 1980}
# Line 2263 | Line 2538
2538          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Kawata_Rapid2DEwald_01.pdf},
2539          Pages = {157-164},
2540          Title = {Rapid calculation of two-dimensional Ewald summation},
2541 <        Volume = {340},
2542 <        Year = {2001}}
2541 >        Volume = 340,
2542 >        Year = 2001}
2543  
2544   @inproceedings{Barker80,
2545          Author = {J.~A. Barker},
# Line 2467 | Line 2742
2742          Date-Modified = {2008-01-08 14:59:01 -0500},
2743          Journal = {Proc. R. Soc. London Ser. A},
2744          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
2745 <        Number = {1752},
2745 >        Number = 1752,
2746          Pages = {27-56},
2747          Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
2748 <        Volume = {373},
2749 <        Year = {1980}}
2748 >        Volume = 373,
2749 >        Year = 1980}
2750  
2751   @article{Ercolessi88,
2752          Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
# Line 2579 | Line 2854
2854          Abstract = {Quantitative structures of the fully hydrated fluid phases of dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) were obtained at 30{degrees}C. Data for the relative form factors F(qz) for DMPC were obtained using a combination of four methods. 1), Volumetric data provided F(0). 2), Diffuse x-ray scattering from oriented stacks of bilayers provided relative form factors |F(qz)| for high qz, 0.22 < qz < 0.8 A-1. 3), X-ray scattering from extruded unilamellar vesicles with diameter 600 A provided |F(qz)| for low qz, 0.1 < qz < 0.3 A-1. 4), Previous measurements using a liquid crystallographic x-ray method provided |F(2{pi}h/D)| for h = 1 and 2 for a range of nearly fully hydrated D-spacings. The data from method 4 overlap and validate the new unilamellar vesicles data for DMPC, so method 4 is not required for DLPC or future studies. We used hybrid electron density models to obtain structural results from these form factors. Comparison of the model electron density profiles with that of gel phase DMPC provides areas per lipid A, 60.6 {+/-} 0.5 A2 for DMPC and 63.2 {+/-} 0.5 A2 for DLPC. Constraints on the model provided by volume measurements and component volumes obtained from simulations put the electron density profiles {rho}(z) and the corresponding form factors F(qz) on absolute scales. Various thicknesses, such as the hydrophobic thickness and the steric thickness, are obtained and compared to literature values.
2855   },
2856          Author = {Kucerka, Norbert and Liu, Yufeng and Chu, Nanjun and Petrache, Horia I. and Tristram-Nagle, Stephanie and Nagle, John F.},
2857 +        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2858 +        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606},
2859          Date-Added = {2008-01-08 14:58:56 -0500},
2860          Date-Modified = {2008-01-08 14:59:02 -0500},
2861          Doi = {10.1529/biophysj.104.056606},
2862          Eprint = {http://www.biophysj.org/cgi/reprint/88/4/2626.pdf},
2863          Journal = {Biophys. J.},
2864 <        Number = {4},
2864 >        Number = 4,
2865          Pages = {2626-2637},
2866          Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}},
2867          Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2868 <        Volume = {88},
2869 <        Year = {2005}}
2868 >        Volume = 88,
2869 >        Year = 2005}
2870  
2871   @article{Lenz07,
2872          Author = {Olaf Lenz and Friederike Schmid},
# Line 2699 | Line 2976
2976          Date-Added = {2008-01-08 14:58:56 -0500},
2977          Date-Modified = {2008-01-08 14:59:02 -0500},
2978          Journal = {Mol. Phys.},
2979 <        Number = {2},
2979 >        Number = 2,
2980          Pages = {387-400},
2981          Title = {The computer simulation of polar liquids},
2982 <        Volume = {38},
2983 <        Year = {1979}}
2982 >        Volume = 38,
2983 >        Year = 1979}
2984  
2985   @article{Pense92,
2986          Author = {A. W. Pense},
# Line 2743 | Line 3020
3020          Journal = {Surf. Sci.},
3021          Pages = {433-440},
3022          Title = {The electrostatic potential in the surface region of an ionic crystal},
3023 <        Volume = {49},
3024 <        Year = {1975}}
3023 >        Volume = 49,
3024 >        Year = 1975}
3025  
3026   @article{Daw93,
3027          Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes},
# Line 2792 | Line 3069
3069          Date-Modified = {2008-01-08 14:59:02 -0500},
3070          Journal = {J. Chem. Phys.},
3071          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
3072 <        Number = {9},
3072 >        Number = 9,
3073          Pages = {4576-4584},
3074          Title = {The role of long ranged forces in determining the structure and properties of liquid water},
3075 <        Volume = {79},
3076 <        Year = {1983}}
3075 >        Volume = 79,
3076 >        Year = 1983}
3077  
3078   @article{Brannigan04b,
3079          Author = {G. Brannigan and A.~C. Tamboli and F.~L.~H. Brown},
# Line 3000 | Line 3277
3277  
3278   @article{Mutz1991,
3279          Author = {Mutz, M. and Bensimon, D. and Brienne, M. J.},
3280 +        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923},
3281          Date-Added = {2008-01-08 14:58:56 -0500},
3282          Date-Modified = {2008-01-08 14:59:03 -0500},
3283          Doi = {10.1103/PhysRevLett.67.923},
3284          Journal = {Phys. Rev. Lett.},
3285          Month = {Aug},
3286 <        Number = {7},
3287 <        Numpages = {3},
3286 >        Number = 7,
3287 >        Numpages = 3,
3288          Pages = {923--926},
3289          Publisher = {American Physical Society},
3290          Title = {Wrinkling transition in partially polymerized vesicles},
3291 <        Volume = {67},
3292 <        Year = {1991}}
3291 >        Volume = 67,
3292 >        Year = 1991}
3293  
3294   @article{Wendt78,
3295          Author = {H. Wendt and F.~F. Abraham},
# Line 3027 | Line 3305
3305          Date-Added = {2008-01-08 14:58:56 -0500},
3306          Date-Modified = {2008-01-08 14:59:03 -0500},
3307          Note = {private correspondence},
3308 <        Year = {2000}}
3308 >        Year = 2000}
3309  
3310   @article{Dwyer1977,
3311          Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
# Line 3086 | Line 3364
3364   @article{Davis:1969uq,
3365          Abstract = { Exact solutions of the Stokes equations are derived for the case of two unequal spheres slowly rotating or translating perpendicular to their line of centers in a quiescent, unbounded viscous fluid, following Wakiya[16]. Numerical results are presented for the force and torque coefficients for size ratios from 1[middle dot]0 to 10[middle dot]0, and separations down to 0[middle dot]001 times the radius of the smaller.},
3366          Author = {Davis, M. H.},
3367 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
3368          Date-Added = {2008-01-08 14:57:14 -0500},
3369          Date-Modified = {2008-01-08 14:57:14 -0500},
3370          Journal = {Chemical Engineering Science},
3371 <        Number = {12},
3371 >        Number = 12,
3372          Pages = {1769--1776},
3373          Title = {The slow translation and rotation of two unequal spheres in a viscous fluid},
3374          Ty = {JOUR},
3375          Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
3376 <        Volume = {24},
3377 <        Year = {1969}}
3376 >        Volume = 24,
3377 >        Year = 1969}
3378  
3379   @article{Stimson:1926qy,
3380          Author = {Stimson, M and Jeffery, GB},
# Line 3104 | Line 3383
3383          Journal = {Proceedings of the Royal Society of London Series A-Containing Papers of a Mathematical and Physical Character},
3384          Pages = {110-116},
3385          Title = {The motion of two spheres in a viscous fluid},
3386 <        Volume = {111},
3387 <        Year = {1926}}
3386 >        Volume = 111,
3387 >        Year = 1926}
3388  
3389   @article{Orlandi:2006fk,
3390          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.},
3391          Address = {Dipartimento di Chimica Fisica e Inorganica, and INSTM, Universita di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.},
3392          Au = {Orlandi, S and Berardi, R and Steltzer, J and Zannoni, C},
3393          Author = {Orlandi, Silvia and Berardi, Roberto and Steltzer, Joachim and Zannoni, Claudio},
3394 <        Da = {20060407},
3394 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622},
3395 >        Da = 20060407,
3396          Date-Added = {2008-01-08 14:47:56 -0500},
3397          Date-Modified = {2008-01-08 14:48:06 -0500},
3398 <        Dcom = {20070727},
3398 >        Dcom = 20070727,
3399          Doi = {10.1063/1.2176622},
3400          Edat = {2006/04/08 09:00},
3401          Issn = {0021-9606 (Print)},
3402 <        Jid = {0375360},
3402 >        Jid = 0375360,
3403          Journal = {J Chem Phys},
3404          Jt = {The Journal of chemical physics},
3405          Language = {eng},
3406          Mhda = {2006/04/08 09:01},
3407 <        Number = {12},
3407 >        Number = 12,
3408          Own = {NLM},
3409 <        Pages = {124907},
3409 >        Pages = 124907,
3410          Pl = {United States},
3411 <        Pmid = {16599725},
3411 >        Pmid = 16599725,
3412          Pst = {ppublish},
3413          Pt = {Journal Article},
3414          Pubm = {Print},
3415          So = {J Chem Phys. 2006 Mar 28;124(12):124907.},
3416          Stat = {PubMed-not-MEDLINE},
3417          Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.},
3418 <        Volume = {124},
3419 <        Year = {2006}}
3418 >        Volume = 124,
3419 >        Year = 2006}
3420  
3421   @article{sun:031602,
3422          Author = {Xiuquan Sun and J. Daniel Gezelter},
3423 +        Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602},
3424 +        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602},
3425          Date-Added = {2008-01-08 14:42:33 -0500},
3426          Date-Modified = {2008-01-08 14:42:33 -0500},
3427          Doi = {10.1103/PhysRevE.75.031602},
3428 <        Eid = {031602},
3428 >        Eid = 031602,
3429          Journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)},
3430          Keywords = {lattice theory; membranes},
3431 <        Number = {3},
3432 <        Numpages = {7},
3433 <        Pages = {031602},
3431 >        Number = 3,
3432 >        Numpages = 7,
3433 >        Pages = 031602,
3434          Publisher = {APS},
3435          Title = {Spontaneous corrugation of dipolar membranes},
3436          Url = {http://link.aps.org/abstract/PRE/v75/e031602},
3437 <        Volume = {75},
3438 <        Year = {2007}}
3437 >        Volume = 75,
3438 >        Year = 2007}
3439  
3440   @article{Ortega:2007lr,
3441          Abstract = {The equivalent radius for any solution property is the radius of a spherical particle having the same value of solution property as that of the macromolecule under consideration. Equivalent radii for different properties present a dependence on size and shape that are more similar than the values of the properties themselves. Furthermore, the ratios of equivalent radii of two properties depend on the conformation (shape or flexibility), but not on the absolute sizes. We define equivalent radii and their ratios, and describe their evaluation for some common models of rigid and flexible macromolecules. Using radii and ratios, we have devised procedures to fit macromolecular models to experimental properties, allowing the determination of the model parameters. Using these quantities, we can construct target functions for an equilibrated, unbiased optimization. The procedures, which have been implemented in public-domain computer programs, are illustrated for rigid, globular proteins, and the rodlike tobacco mosaic virus, and for semiflexible, wormlike heparin molecules.},
3442          Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.},
3443 <        Au = {Ortega, A and Garcia de la Torre, J},
3444 <        Author = {Ortega, A and Garcia de la Torre, J},
3445 <        Da = {20070813},
3443 >        Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3444 >        Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3445 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f},
3446 >        Da = 20070813,
3447          Date-Added = {2008-01-08 14:38:03 -0500},
3448          Date-Modified = {2008-01-08 14:38:49 -0500},
3449 <        Dcom = {20071017},
3450 <        Dep = {20070724},
3449 >        Dcom = 20071017,
3450 >        Dep = 20070724,
3451          Doi = {10.1021/bm700473f},
3452          Edat = {2007/07/25 09:00},
3453          Issn = {1525-7797 (Print)},
3454 <        Jid = {100892849},
3454 >        Jid = 100892849,
3455          Journal = {Biomacromolecules},
3456          Jt = {Biomacromolecules},
3457          Keywords = {Computer Simulation; Heparin/chemistry; Macromolecular Substances/*chemistry; *Models, Chemical; *Models, Molecular; Molecular Conformation; Particle Size; Protein Conformation; Proteins/chemistry; Software; Solutions},
3458          Language = {eng},
3459          Mhda = {2007/10/18 09:00},
3460 <        Number = {8},
3460 >        Number = 8,
3461          Own = {NLM},
3462          Pages = {2464--2475},
3463          Phst = {2007/07/24 {$[$}aheadofprint{$]$}},
3464          Pl = {United States},
3465 <        Pmid = {17645309},
3465 >        Pmid = 17645309,
3466          Pst = {ppublish},
3467          Pt = {Journal Article; Research Support, Non-U.S. Gov't},
3468          Pubm = {Print-Electronic},
# Line 3188 | Line 3471
3471          So = {Biomacromolecules. 2007 Aug;8(8):2464-75. Epub 2007 Jul 24.},
3472          Stat = {MEDLINE},
3473          Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.},
3474 <        Volume = {8},
3475 <        Year = {2007}}
3474 >        Volume = 8,
3475 >        Year = 2007}
3476  
3477   @article{Torre2003,
3478          Abstract = {While the prediction of hydrodynamic properties of rigid particles
# Line 3215 | Line 3498
3498      We provide an example of the application of this methodology to
3499      the dynamics of a semiflexible, wormlike DNA.},
3500          Annote = {724XK Times Cited:6 Cited References Count:64},
3501 <        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},
3501 >        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},
3502          Issn = {0175-7571},
3503          Journal = {European Biophysics Journal with Biophysics Letters},
3504          Month = {Aug},
3505 <        Number = {5},
3505 >        Number = 5,
3506          Pages = {477-486},
3507          Title = {Calculation of the solution properties of flexible macromolecules: methods and applications},
3508          Uri = {<Go to ISI>://000185513400011},
3509 <        Volume = {32},
3510 <        Year = {2003}}
3509 >        Volume = 32,
3510 >        Year = 2003}
3511  
3512   @article{Alakent2005,
3513          Abstract = {Time series analysis tools are employed on the principal modes obtained
# Line 3264 | Line 3547
3547          Annote = {973OH Times Cited:1 Cited References Count:33},
3548          Author = {B. Alakent and M. C. Camurdan and P. Doruker},
3549          Issn = {0021-9606},
3550 <        Journal = {Journal of Chemical Physics},
3550 >        Journal = jcp,
3551          Month = {Oct 8},
3552 <        Number = {14},
3552 >        Number = 14,
3553          Pages = {-},
3554          Title = {Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects},
3555          Uri = {<Go to ISI>://000232532000064},
3556 <        Volume = {123},
3557 <        Year = {2005}}
3556 >        Volume = 123,
3557 >        Year = 2005}
3558  
3559   @book{Alexander1987,
3560          Address = {New York},
3561          Author = {C. Alexander},
3562          Publisher = {Oxford University Press},
3563          Title = {A Pattern Language: Towns, Buildings, Construction},
3564 <        Year = {1987}}
3564 >        Year = 1987}
3565  
3566   @book{Allen1987,
3567          Address = {New York},
3568          Author = {M.~P. Allen and D.~J. Tildesley},
3569          Publisher = {Oxford University Press},
3570          Title = {Computer Simulations of Liquids},
3571 <        Year = {1987}}
3571 >        Year = 1987}
3572  
3573   @article{Allison1991,
3574          Abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
# Line 3307 | Line 3590
3590          Issn = {0024-9297},
3591          Journal = {Macromolecules},
3592          Month = {Jan 21},
3593 <        Number = {2},
3593 >        Number = 2,
3594          Pages = {530-536},
3595          Title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application to Polarized Dynamic Light-Scattering},
3596          Uri = {<Go to ISI>://A1991EU81400029},
3597 <        Volume = {24},
3598 <        Year = {1991}}
3597 >        Volume = 24,
3598 >        Year = 1991}
3599  
3600   @article{Andersen1983,
3601          Annote = {Rq238 Times Cited:559 Cited References Count:14},
3602          Author = {H. C. Andersen},
3603          Issn = {0021-9991},
3604 <        Journal = {Journal of Computational Physics},
3605 <        Number = {1},
3604 >        Journal = jcop,
3605 >        Number = 1,
3606          Pages = {24-34},
3607          Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
3608          Uri = {<Go to ISI>://A1983RQ23800002},
3609 <        Volume = {52},
3610 <        Year = {1983}}
3609 >        Volume = 52,
3610 >        Year = 1983}
3611  
3612   @article{Auerbach2005,
3613          Abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
# Line 3349 | Line 3632
3632          Annote = {895QF Times Cited:9 Cited References Count:33},
3633          Author = {A. Auerbach},
3634          Issn = {0027-8424},
3635 <        Journal = {Proceedings of the National Academy of Sciences of the United States of America},
3635 >        Journal = pnas,
3636          Month = {Feb 1},
3637 <        Number = {5},
3637 >        Number = 5,
3638          Pages = {1408-1412},
3639          Title = {Gating of acetylcholine receptor channels: Brownian motion across a broad transition state},
3640          Uri = {<Go to ISI>://000226877300030},
3641 <        Volume = {102},
3642 <        Year = {2005}}
3641 >        Volume = 102,
3642 >        Year = 2005}
3643  
3644   @article{Baber1995,
3645          Abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
# Line 3385 | Line 3668
3668          Issn = {0006-2960},
3669          Journal = {Biochemistry},
3670          Month = {May 16},
3671 <        Number = {19},
3671 >        Number = 19,
3672          Pages = {6533-6539},
3673          Title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
3674          Uri = {<Go to ISI>://A1995QZ71600035},
3675 <        Volume = {34},
3676 <        Year = {1995}}
3675 >        Volume = 34,
3676 >        Year = 1995}
3677  
3678   @article{Banerjee2004,
3679          Abstract = {Based on a coherent state representation of noise operator and an
# Line 3410 | Line 3693
3693          Annote = {816YY Times Cited:8 Cited References Count:35},
3694          Author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
3695          Issn = {0021-9606},
3696 <        Journal = {Journal of Chemical Physics},
3696 >        Journal = jcp,
3697          Month = {May 15},
3698 <        Number = {19},
3698 >        Number = 19,
3699          Pages = {8960-8972},
3700          Title = {Solution of quantum Langevin equation: Approximations, theoretical and numerical aspects},
3701          Uri = {<Go to ISI>://000221146400009},
3702 <        Volume = {120},
3703 <        Year = {2004}}
3702 >        Volume = 120,
3703 >        Year = 2004}
3704  
3705   @article{Barojas1973,
3706          Author = {J. Barojas and D. Levesque},
3707          Journal = {Phys. Rev. A},
3708          Pages = {1092-1105},
3709          Title = {Simulation of Diatomic Homonuclear Liquids},
3710 <        Volume = {7},
3711 <        Year = {1973}}
3710 >        Volume = 7,
3711 >        Year = 1973}
3712  
3713   @article{Barth1998,
3714          Abstract = {We present an efficient new method termed LN for propagating biomolecular
# Line 3457 | Line 3740
3740          Annote = {105HH Times Cited:29 Cited References Count:49},
3741          Author = {E. Barth and T. Schlick},
3742          Issn = {0021-9606},
3743 <        Journal = {Journal of Chemical Physics},
3743 >        Journal = jcp,
3744          Month = {Aug 1},
3745 <        Number = {5},
3745 >        Number = 5,
3746          Pages = {1617-1632},
3747          Title = {Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN},
3748          Uri = {<Go to ISI>://000075066300006},
3749 <        Volume = {109},
3750 <        Year = {1998}}
3749 >        Volume = 109,
3750 >        Year = 1998}
3751  
3752   @article{Batcho2001,
3753          Abstract = {We present an analysis for a simple two-component harmonic oscillator
# Line 3481 | Line 3764
3764          Annote = {469KV Times Cited:6 Cited References Count:30},
3765          Author = {P. F. Batcho and T. Schlick},
3766          Issn = {0021-9606},
3767 <        Journal = {Journal of Chemical Physics},
3767 >        Journal = jcp,
3768          Month = {Sep 1},
3769 <        Number = {9},
3769 >        Number = 9,
3770          Pages = {4019-4029},
3771          Title = {Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration},
3772          Uri = {<Go to ISI>://000170813800005},
3773 <        Volume = {115},
3774 <        Year = {2001}}
3773 >        Volume = 115,
3774 >        Year = 2001}
3775  
3776   @article{Bates2005,
3777          Abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
# Line 3514 | Line 3797
3797          Issn = {1539-3755},
3798          Journal = {Physical Review E},
3799          Month = {Nov},
3800 <        Number = {5},
3800 >        Number = 5,
3801          Pages = {-},
3802          Title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation study},
3803          Uri = {<Go to ISI>://000233603100030},
3804 <        Volume = {72},
3805 <        Year = {2005}}
3804 >        Volume = 72,
3805 >        Year = 2005}
3806  
3807   @article{Beard2003,
3808          Abstract = {We introduce an unbiased protocol for performing rotational moves
# Line 3534 | Line 3817
3817          Annote = {736UA Times Cited:0 Cited References Count:11},
3818          Author = {D. A. Beard and T. Schlick},
3819          Issn = {0006-3495},
3820 <        Journal = {Biophysical Journal},
3820 >        Journal = bj,
3821          Month = {Nov 1},
3822 <        Number = {5},
3822 >        Number = 5,
3823          Pages = {2973-2976},
3824          Title = {Unbiased rotational moves for rigid-body dynamics},
3825          Uri = {<Go to ISI>://000186190500018},
3826 <        Volume = {85},
3827 <        Year = {2003}}
3826 >        Volume = 85,
3827 >        Year = 2003}
3828  
3829   @article{Beloborodov1998,
3830          Abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
# Line 3558 | Line 3841
3841          Issn = {1090-7807},
3842          Journal = {Journal of Magnetic Resonance},
3843          Month = {Jun},
3844 <        Number = {2},
3844 >        Number = 2,
3845          Pages = {328-329},
3846          Title = {Effect of coupling between rotational and translational Brownian motions on NMR spin relaxation: Consideration using green function of rigid body diffusion},
3847          Uri = {<Go to ISI>://000074214800017},
3848 <        Volume = {132},
3849 <        Year = {1998}}
3848 >        Volume = 132,
3849 >        Year = 1998}
3850  
3851   @article{Berardi1996,
3852          Abstract = {We demonstrate that the overall molecular dipole organization in a
# Line 3580 | Line 3863
3863          Issn = {0009-2614},
3864          Journal = {Chemical Physics Letters},
3865          Month = {Oct 18},
3866 <        Number = {3},
3866 >        Number = 3,
3867          Pages = {357-362},
3868          Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
3869          Uri = {<Go to ISI>://A1996VN63700023},
3870 <        Volume = {261},
3871 <        Year = {1996}}
3870 >        Volume = 261,
3871 >        Year = 1996}
3872  
3873   @article{Berkov2005,
3874          Abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
# Line 3610 | Line 3893
3893          Issn = {1098-0121},
3894          Journal = {Physical Review B},
3895          Month = {Sep},
3896 <        Number = {9},
3896 >        Number = 9,
3897          Pages = {-},
3898          Title = {Magnetization precession due to a spin-polarized current in a thin nanoelement: Numerical simulation study},
3899          Uri = {<Go to ISI>://000232228500058},
3900 <        Volume = {72},
3901 <        Year = {2005}}
3900 >        Volume = 72,
3901 >        Year = 2005}
3902  
3903   @article{Berkov2005a,
3904          Abstract = {Numerical simulations of fast remagnetization processes using stochastic
# Line 3641 | Line 3924
3924          Pages = {442-448},
3925          Title = {Stochastic dynamic simulations of fast remagnetization processes: recent advances and applications},
3926          Uri = {<Go to ISI>://000228837600109},
3927 <        Volume = {290},
3928 <        Year = {2005}}
3927 >        Volume = 290,
3928 >        Year = 2005}
3929  
3930   @article{Berkov2002,
3931          Abstract = {We report on recent progress achieved by the development of numerical
# Line 3664 | Line 3947
3947          Issn = {0031-8965},
3948          Journal = {Physica Status Solidi a-Applied Research},
3949          Month = {Feb 16},
3950 <        Number = {2},
3950 >        Number = 2,
3951          Pages = {409-421},
3952          Title = {Magnetization dynamics in nanoparticle systems: Numerical simulation using Langevin dynamics},
3953          Uri = {<Go to ISI>://000174145200026},
3954 <        Volume = {189},
3955 <        Year = {2002}}
3954 >        Volume = 189,
3955 >        Year = 2002}
3956  
3957   @article{Bernal1980,
3958 <        Author = {J.M. Bernal and J. G. {de la Torre}},
3958 >        Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose},
3959          Journal = {Biopolymers},
3960          Pages = {751-766},
3961          Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape},
3962 <        Volume = {19},
3963 <        Year = {1980}}
3962 >        Volume = 19,
3963 >        Year = 1980}
3964  
3965   @article{Brenner1967,
3966          Author = {H. Brenner},
3967          Journal = {J. Collid. Int. Sci.},
3968          Pages = {407-436},
3969          Title = {Coupling between the Translational and Rotational Brownian Motions of Rigid Particles of Arbitrary shape},
3970 <        Volume = {23},
3971 <        Year = {1967}}
3970 >        Volume = 23,
3971 >        Year = 1967}
3972  
3973   @article{Brooks1983,
3974          Annote = {Qp423 Times Cited:6414 Cited References Count:96},
3975          Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus},
3976          Issn = {0192-8651},
3977 <        Journal = {Journal of Computational Chemistry},
3978 <        Number = {2},
3977 >        Journal = jcc,
3978 >        Number = 2,
3979          Pages = {187-217},
3980          Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
3981          Uri = {<Go to ISI>://A1983QP42300010},
3982 <        Volume = {4},
3983 <        Year = {1983}}
3982 >        Volume = 4,
3983 >        Year = 1983}
3984  
3985   @article{Brunger1984,
3986          Annote = {Sm173 Times Cited:143 Cited References Count:22},
3987          Author = {A. Brunger and C. L. Brooks and M. Karplus},
3988          Issn = {0009-2614},
3989          Journal = {Chemical Physics Letters},
3990 <        Number = {5},
3990 >        Number = 5,
3991          Pages = {495-500},
3992          Title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations of St2 Water},
3993          Uri = {<Go to ISI>://A1984SM17300007},
3994 <        Volume = {105},
3995 <        Year = {1984}}
3994 >        Volume = 105,
3995 >        Year = 1984}
3996  
3997   @article{Budd1999,
3998          Abstract = {This paper examines a synthesis of adaptive mesh methods with the
# Line 3723 | Line 4006
4006          Issn = {1364-503X},
4007          Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
4008          Month = {Apr 15},
4009 <        Number = {1754},
4009 >        Number = 1754,
4010          Pages = {1047-1077},
4011          Title = {Self-similar numerical solutions of the porous-medium equation using moving mesh methods},
4012          Uri = {<Go to ISI>://000080466800005},
4013 <        Volume = {357},
4014 <        Year = {1999}}
4013 >        Volume = 357,
4014 >        Year = 1999}
4015  
4016   @article{Camp1999,
4017          Abstract = {Fluids of hard bent-core molecules have been studied using theory
# Line 3764 | Line 4047
4047          Annote = {255TC Times Cited:24 Cited References Count:38},
4048          Author = {P. J. Camp and M. P. Allen and A. J. Masters},
4049          Issn = {0021-9606},
4050 <        Journal = {Journal of Chemical Physics},
4050 >        Journal = jcp,
4051          Month = {Dec 1},
4052 <        Number = {21},
4052 >        Number = 21,
4053          Pages = {9871-9881},
4054          Title = {Theory and computer simulation of bent-core molecules},
4055          Uri = {<Go to ISI>://000083685400056},
4056 <        Volume = {111},
4057 <        Year = {1999}}
4056 >        Volume = 111,
4057 >        Year = 1999}
4058  
4059   @article{Care2005,
4060          Abstract = {A review is presented of molecular and mesoscopic computer simulations
# Line 3786 | Line 4069
4069          Issn = {0034-4885},
4070          Journal = {Reports on Progress in Physics},
4071          Month = {Nov},
4072 <        Number = {11},
4072 >        Number = 11,
4073          Pages = {2665-2700},
4074          Title = {Computer simulation of liquid crystals},
4075          Uri = {<Go to ISI>://000233697600004},
4076 <        Volume = {68},
4077 <        Year = {2005}}
4076 >        Volume = 68,
4077 >        Year = 2005}
4078  
4079   @article{Carrasco1999,
4080          Abstract = {The hydrodynamic properties of rigid particles are calculated from
# Line 3813 | Line 4096
4096      them to some test cases, for which the properties are known a priori.
4097      We provide guidelines and computational tools for bead modeling.},
4098          Annote = {200TT Times Cited:46 Cited References Count:57},
4099 <        Author = {B. Carrasco and J. G. {de la Torre}},
4099 >        Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
4100          Issn = {0006-3495},
4101 <        Journal = {Biophysical Journal},
4101 >        Journal = bj,
4102          Month = {Jun},
4103 <        Number = {6},
4103 >        Number = 6,
4104          Pages = {3044-3057},
4105          Title = {Hydrodynamic properties of rigid particles: Comparison of different modeling and computational procedures},
4106          Uri = {<Go to ISI>://000080556700016},
4107 <        Volume = {76},
4108 <        Year = {1999}}
4107 >        Volume = 76,
4108 >        Year = 1999}
4109  
4110   @article{Chandra1999,
4111          Abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
# Line 3846 | Line 4129
4129          Annote = {221EN Times Cited:14 Cited References Count:66},
4130          Author = {A. Chandra and T. Ichiye},
4131          Issn = {0021-9606},
4132 <        Journal = {Journal of Chemical Physics},
4132 >        Journal = jcp,
4133          Month = {Aug 8},
4134 <        Number = {6},
4134 >        Number = 6,
4135          Pages = {2701-2709},
4136          Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations},
4137          Uri = {<Go to ISI>://000081711200038},
4138 <        Volume = {111},
4139 <        Year = {1999}}
4138 >        Volume = 111,
4139 >        Year = 1999}
4140  
4141   @article{Channell1990,
4142          Annote = {Dk631 Times Cited:152 Cited References Count:34},
# Line 3861 | Line 4144
4144          Issn = {0951-7715},
4145          Journal = {Nonlinearity},
4146          Month = {may},
4147 <        Number = {2},
4147 >        Number = 2,
4148          Pages = {231-259},
4149          Title = {Symplectic Integration of Hamiltonian-Systems},
4150          Uri = {<Go to ISI>://A1990DK63100001},
4151 <        Volume = {3},
4152 <        Year = {1990}}
4151 >        Volume = 3,
4152 >        Year = 1990}
4153  
4154   @article{Chen2003,
4155          Abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
# Line 3887 | Line 4170
4170          Pages = {21-30},
4171          Title = {Explicit mixed finite order Runge-Kutta methods},
4172          Uri = {<Go to ISI>://000180314200002},
4173 <        Volume = {44},
4174 <        Year = {2003}}
4173 >        Volume = 44,
4174 >        Year = 2003}
4175  
4176   @article{Cheung2004,
4177          Abstract = {Equilibrium molecular dynamics calculations have been performed for
# Line 3906 | Line 4189
4189          Annote = {866UM Times Cited:4 Cited References Count:61},
4190          Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
4191          Issn = {0021-9606},
4192 <        Journal = {Journal of Chemical Physics},
4192 >        Journal = jcp,
4193          Month = {Nov 8},
4194 <        Number = {18},
4194 >        Number = 18,
4195          Pages = {9131-9139},
4196          Title = {Calculation of flexoelectric coefficients for a nematic liquid crystal by atomistic simulation},
4197          Uri = {<Go to ISI>://000224798900053},
4198 <        Volume = {121},
4199 <        Year = {2004}}
4198 >        Volume = 121,
4199 >        Year = 2004}
4200  
4201   @article{Cheung2002,
4202          Abstract = {Equilibrium molecular dynamics calculations have been performed for
# Line 3935 | Line 4218
4218          Pages = {140-146},
4219          Title = {Calculation of the rotational viscosity of a nematic liquid crystal},
4220          Uri = {<Go to ISI>://000175331000020},
4221 <        Volume = {356},
4222 <        Year = {2002}}
4221 >        Volume = 356,
4222 >        Year = 2002}
4223  
4224   @article{Chin2004,
4225          Abstract = {Current molecular dynamics simulations of biomolecules using multiple
# Line 3957 | Line 4240
4240          Annote = {757TK Times Cited:1 Cited References Count:22},
4241          Author = {S. A. Chin},
4242          Issn = {0021-9606},
4243 <        Journal = {Journal of Chemical Physics},
4243 >        Journal = jcp,
4244          Month = {Jan 1},
4245 <        Number = {1},
4245 >        Number = 1,
4246          Pages = {8-13},
4247          Title = {Dynamical multiple-time stepping methods for overcoming resonance instabilities},
4248          Uri = {<Go to ISI>://000187577400003},
4249 <        Volume = {120},
4250 <        Year = {2004}}
4249 >        Volume = 120,
4250 >        Year = 2004}
4251  
4252   @article{Cook2000,
4253          Abstract = {The Kirkwood correlation factor g(1) determines the preference for
# Line 3988 | Line 4271
4271          Issn = {0267-8292},
4272          Journal = {Liquid Crystals},
4273          Month = {Dec},
4274 <        Number = {12},
4274 >        Number = 12,
4275          Pages = {1573-1583},
4276          Title = {Simulation studies of dipole correlation in the isotropic liquid phase},
4277          Uri = {<Go to ISI>://000165437800002},
4278 <        Volume = {27},
4279 <        Year = {2000}}
4278 >        Volume = 27,
4279 >        Year = 2000}
4280  
4281   @article{Cui2003,
4282          Abstract = {All-atom Langevin dynamics simulations have been performed to study
# Line 4016 | Line 4299
4299          Annote = {689LC Times Cited:3 Cited References Count:48},
4300          Author = {B. X. Cui and M. Y. Shen and K. F. Freed},
4301          Issn = {0027-8424},
4302 <        Journal = {Proceedings of the National Academy of Sciences of the United States of America},
4302 >        Journal = pnas,
4303          Month = {Jun 10},
4304 <        Number = {12},
4304 >        Number = 12,
4305          Pages = {7087-7092},
4306          Title = {Folding and misfolding of the papillomavirus E6 interacting peptide E6ap},
4307          Uri = {<Go to ISI>://000183493500037},
4308 <        Volume = {100},
4309 <        Year = {2003}}
4308 >        Volume = 100,
4309 >        Year = 2003}
4310  
4311   @article{Denisov2003,
4312          Abstract = {We study the slow phase of thermally activated magnetic relaxation
# Line 4041 | Line 4324
4324          Issn = {1098-0121},
4325          Journal = {Physical Review B},
4326          Month = {Jan 1},
4327 <        Number = {1},
4327 >        Number = 1,
4328          Pages = {-},
4329          Title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
4330          Uri = {<Go to ISI>://000180830400056},
4331 <        Volume = {67},
4332 <        Year = {2003}}
4331 >        Volume = 67,
4332 >        Year = 2003}
4333  
4334   @article{Derreumaux1998,
4335          Abstract = {To explore the origin of the large-scale motion of triosephosphate
# Line 4076 | Line 4359
4359          Annote = {Zl046 Times Cited:30 Cited References Count:29},
4360          Author = {P. Derreumaux and T. Schlick},
4361          Issn = {0006-3495},
4362 <        Journal = {Biophysical Journal},
4362 >        Journal = bj,
4363          Month = {Jan},
4364 <        Number = {1},
4364 >        Number = 1,
4365          Pages = {72-81},
4366          Title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
4367          Uri = {<Go to ISI>://000073393400009},
4368 <        Volume = {74},
4369 <        Year = {1998}}
4368 >        Volume = 74,
4369 >        Year = 1998}
4370  
4371   @article{Dullweber1997,
4372          Abstract = {Rigid body molecular models possess symplectic structure and time-reversal
# Line 4108 | Line 4391
4391          Annote = {Ya587 Times Cited:35 Cited References Count:32},
4392          Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
4393          Issn = {0021-9606},
4394 <        Journal = {Journal of Chemical Physics},
4394 >        Journal = jcp,
4395          Month = {Oct 15},
4396 <        Number = {15},
4396 >        Number = 15,
4397          Pages = {5840-5851},
4398          Title = {Symplectic splitting methods for rigid body molecular dynamics},
4399          Uri = {<Go to ISI>://A1997YA58700024},
4400 <        Volume = {107},
4401 <        Year = {1997}}
4400 >        Volume = 107,
4401 >        Year = 1997}
4402  
4403   @book{Gamma1994,
4404          Address = {London},
4405          Author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
4406 <        Chapter = {7},
4406 >        Chapter = 7,
4407          Publisher = {Perason Education},
4408          Title = {Design Patterns: Elements of Reusable Object-Oriented Software},
4409 <        Year = {1994}}
4409 >        Year = 1994}
4410  
4411   @article{Edwards2005,
4412          Abstract = {Using the Langevin dynamics technique, we have carried out simulations
# Line 4141 | Line 4424
4424          Issn = {0024-9297},
4425          Journal = {Macromolecules},
4426          Month = {Dec 13},
4427 <        Number = {25},
4427 >        Number = 25,
4428          Pages = {10590-10595},
4429          Title = {Stretching a single diblock copolymer in a selective solvent: Langevin dynamics simulations},
4430          Uri = {<Go to ISI>://000233866200035},
4431 <        Volume = {38},
4432 <        Year = {2005}}
4431 >        Volume = 38,
4432 >        Year = 2005}
4433  
4434   @article{Egberts1988,
4435          Annote = {Q0188 Times Cited:219 Cited References Count:43},
4436          Author = {E. Egberts and H. J. C. Berendsen},
4437          Issn = {0021-9606},
4438 <        Journal = {Journal of Chemical Physics},
4438 >        Journal = jcp,
4439          Month = {Sep 15},
4440 <        Number = {6},
4440 >        Number = 6,
4441          Pages = {3718-3732},
4442          Title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic Detail},
4443          Uri = {<Go to ISI>://A1988Q018800036},
4444 <        Volume = {89},
4445 <        Year = {1988}}
4444 >        Volume = 89,
4445 >        Year = 1988}
4446  
4447   @article{Ermak1978,
4448          Annote = {Fp216 Times Cited:785 Cited References Count:42},
4449          Author = {D. L. Ermak and J. A. Mccammon},
4450          Issn = {0021-9606},
4451 <        Journal = {Journal of Chemical Physics},
4452 <        Number = {4},
4451 >        Journal = jcp,
4452 >        Number = 4,
4453          Pages = {1352-1360},
4454          Title = {Brownian Dynamics with Hydrodynamic Interactions},
4455          Uri = {<Go to ISI>://A1978FP21600004},
4456 <        Volume = {69},
4457 <        Year = {1978}}
4456 >        Volume = 69,
4457 >        Year = 1978}
4458  
4459   @article{Evans1977,
4460          Annote = {Ds757 Times Cited:271 Cited References Count:18},
4461          Author = {D. J. Evans},
4462          Issn = {0026-8976},
4463 <        Journal = {Molecular Physics},
4464 <        Number = {2},
4463 >        Journal = mp,
4464 >        Number = 2,
4465          Pages = {317-325},
4466          Title = {Representation of Orientation Space},
4467          Uri = {<Go to ISI>://A1977DS75700002},
4468 <        Volume = {34},
4469 <        Year = {1977}}
4468 >        Volume = 34,
4469 >        Year = 1977}
4470  
4471   @article{Fennell2004,
4472          Abstract = {The density maximum and temperature dependence of the self-diffusion
# Line 4212 | Line 4495
4495          Annote = {816YY Times Cited:5 Cited References Count:39},
4496          Author = {C. J. Fennell and J. D. Gezelter},
4497          Issn = {0021-9606},
4498 <        Journal = {Journal of Chemical Physics},
4498 >        Journal = jcp,
4499          Month = {May 15},
4500 <        Number = {19},
4500 >        Number = 19,
4501          Pages = {9175-9184},
4502          Title = {On the structural and transport properties of the soft sticky dipole and related single-point water models},
4503          Uri = {<Go to ISI>://000221146400032},
4504 <        Volume = {120},
4505 <        Year = {2004}}
4504 >        Volume = 120,
4505 >        Year = 2004}
4506  
4507   @article{Fernandes2002,
4508          Abstract = {We have developed a Brownian dynamics simulation algorithm to generate
# Line 4234 | Line 4517
4517      its applicability. Examples include free diffusion, transport in
4518      an electric field, and diffusion in a restricting environment.},
4519          Annote = {633AD Times Cited:2 Cited References Count:43},
4520 <        Author = {M. X. Fernandes and J. G. {de la Torre}},
4520 >        Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4521          Issn = {0006-3495},
4522 <        Journal = {Biophysical Journal},
4522 >        Journal = bj,
4523          Month = {Dec},
4524 <        Number = {6},
4524 >        Number = 6,
4525          Pages = {3039-3048},
4526          Title = {Brownian dynamics simulation of rigid particles of arbitrary shape in external fields},
4527          Uri = {<Go to ISI>://000180256300012},
4528 <        Volume = {83},
4529 <        Year = {2002}}
4528 >        Volume = 83,
4529 >        Year = 2002}
4530  
4531   @book{Frenkel1996,
4532          Address = {New York},
4533          Author = {D. Frenkel and B. Smit},
4534          Publisher = {Academic Press},
4535          Title = {Understanding Molecular Simulation : From Algorithms to Applications},
4536 <        Year = {1996}}
4536 >        Year = 1996}
4537  
4538   @article{Gay1981,
4539          Annote = {Lj347 Times Cited:482 Cited References Count:13},
4540          Author = {J. G. Gay and B. J. Berne},
4541          Issn = {0021-9606},
4542 <        Journal = {Journal of Chemical Physics},
4543 <        Number = {6},
4542 >        Journal = jcp,
4543 >        Number = 6,
4544          Pages = {3316-3319},
4545          Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
4546          Uri = {<Go to ISI>://A1981LJ34700029},
4547 <        Volume = {74},
4548 <        Year = {1981}}
4547 >        Volume = 74,
4548 >        Year = 1981}
4549  
4550   @article{Gelin1999,
4551          Abstract = {To investigate the influence of inertial effects on the dynamics of
# Line 4288 | Line 4571
4571          Issn = {1022-1344},
4572          Journal = {Macromolecular Theory and Simulations},
4573          Month = {Nov},
4574 <        Number = {6},
4574 >        Number = 6,
4575          Pages = {529-543},
4576          Title = {Inertial effects in the Brownian dynamics with rigid constraints},
4577          Uri = {<Go to ISI>://000083785700002},
4578 <        Volume = {8},
4579 <        Year = {1999}}
4578 >        Volume = 8,
4579 >        Year = 1999}
4580  
4581   @article{Goetz1998,
4582          Author = {R. Goetz and R. Lipowsky},
4583 <        Journal = {Journal of Chemical Physics},
4584 <        Number = {17},
4585 <        Pages = {7397},
4583 >        Journal = jcp,
4584 >        Number = 17,
4585 >        Pages = 7397,
4586          Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
4587 <        Volume = {108},
4588 <        Year = {1998}}
4587 >        Volume = 108,
4588 >        Year = 1998}
4589  
4590   @book{Goldstein2001,
4591          Address = {San Francisco},
# Line 4310 | Line 4593
4593          Edition = {3rd},
4594          Publisher = {Addison Wesley},
4595          Title = {Classical Mechanics},
4596 <        Year = {2001}}
4596 >        Year = 2001}
4597  
4598   @article{Gray2003,
4599          Abstract = {Protein-protein docking algorithms provide a means to elucidate structural
# Line 4340 | Line 4623
4623          Annote = {704QL Times Cited:48 Cited References Count:60},
4624          Author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and B. Kuhlman and C. A. Rohl and D. Baker},
4625          Issn = {0022-2836},
4626 <        Journal = {Journal of Molecular Biology},
4626 >        Journal = jmb,
4627          Month = {Aug 1},
4628 <        Number = {1},
4628 >        Number = 1,
4629          Pages = {281-299},
4630          Title = {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations},
4631          Uri = {<Go to ISI>://000184351300022},
4632 <        Volume = {331},
4633 <        Year = {2003}}
4632 >        Volume = 331,
4633 >        Year = 2003}
4634  
4635   @article{Greengard1994,
4636          Abstract = {Some of the recently developed fast summation methods that have arisen
# Line 4364 | Line 4647
4647          Issn = {0036-8075},
4648          Journal = {Science},
4649          Month = {Aug 12},
4650 <        Number = {5174},
4650 >        Number = 5174,
4651          Pages = {909-914},
4652          Title = {Fast Algorithms for Classical Physics},
4653          Uri = {<Go to ISI>://A1994PB49900031},
4654 <        Volume = {265},
4655 <        Year = {1994}}
4654 >        Volume = 265,
4655 >        Year = 1994}
4656  
4657   @article{Greengard1987,
4658          Annote = {L0498 Times Cited:899 Cited References Count:7},
4659          Author = {L. Greengard and V. Rokhlin},
4660          Issn = {0021-9991},
4661 <        Journal = {Journal of Computational Physics},
4661 >        Journal = jcop,
4662          Month = {Dec},
4663 <        Number = {2},
4663 >        Number = 2,
4664          Pages = {325-348},
4665          Title = {A Fast Algorithm for Particle Simulations},
4666          Uri = {<Go to ISI>://A1987L049800006},
4667 <        Volume = {73},
4668 <        Year = {1987}}
4667 >        Volume = 73,
4668 >        Year = 1987}
4669  
4670   @article{Hairer1997,
4671          Abstract = {Backward error analysis is a useful tool for the study of numerical
# Line 4403 | Line 4686
4686          Issn = {0029-599X},
4687          Journal = {Numerische Mathematik},
4688          Month = {Jun},
4689 <        Number = {4},
4689 >        Number = 4,
4690          Pages = {441-462},
4691          Title = {The life-span of backward error analysis for numerical integrators},
4692          Uri = {<Go to ISI>://A1997XJ48800002},
4693 <        Volume = {76},
4694 <        Year = {1997}}
4693 >        Volume = 76,
4694 >        Year = 1997}
4695  
4696   @article{Hao1993,
4697          Abstract = {A new procedure for studying the folding and unfolding of proteins,
# Line 4450 | Line 4733
4733          Issn = {0006-2960},
4734          Journal = {Biochemistry},
4735          Month = {Sep 21},
4736 <        Number = {37},
4736 >        Number = 37,
4737          Pages = {9614-9631},
4738          Title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic Trypsin-Inhibitor Studied by Computer-Simulations},
4739          Uri = {<Go to ISI>://A1993LY29400014},
4740 <        Volume = {32},
4741 <        Year = {1993}}
4740 >        Volume = 32,
4741 >        Year = 1993}
4742  
4743   @article{Hinsen2000,
4744          Abstract = {The slow dynamics of proteins around its native folded state is usually
# Line 4494 | Line 4777
4777          Pages = {25-37},
4778          Title = {Harmonicity in slow protein dynamics},
4779          Uri = {<Go to ISI>://000090121700003},
4780 <        Volume = {261},
4781 <        Year = {2000}}
4780 >        Volume = 261,
4781 >        Year = 2000}
4782  
4783   @article{Ho1992,
4784          Abstract = {Evidence has been found for the existence water at the protein-lipid
# Line 4528 | Line 4811
4811          Annote = {Ju251 Times Cited:55 Cited References Count:44},
4812          Author = {C. Ho and C. D. Stubbs},
4813          Issn = {0006-3495},
4814 <        Journal = {Biophysical Journal},
4814 >        Journal = bj,
4815          Month = {Oct},
4816 <        Number = {4},
4816 >        Number = 4,
4817          Pages = {897-902},
4818          Title = {Hydration at the Membrane Protein-Lipid Interface},
4819          Uri = {<Go to ISI>://A1992JU25100002},
4820 <        Volume = {63},
4821 <        Year = {1992}}
4820 >        Volume = 63,
4821 >        Year = 1992}
4822  
4823   @book{Hockney1981,
4824          Address = {New York},
4825          Author = {R.W. Hockney and J.W. Eastwood},
4826          Publisher = {McGraw-Hill},
4827          Title = {Computer Simulation Using Particles},
4828 <        Year = {1981}}
4828 >        Year = 1981}
4829  
4830   @article{Hoover1985,
4831          Annote = {Acr30 Times Cited:1809 Cited References Count:11},
4832          Author = {W. G. Hoover},
4833          Issn = {1050-2947},
4834          Journal = {Physical Review A},
4835 <        Number = {3},
4835 >        Number = 3,
4836          Pages = {1695-1697},
4837          Title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
4838          Uri = {<Go to ISI>://A1985ACR3000056},
4839 <        Volume = {31},
4840 <        Year = {1985}}
4839 >        Volume = 31,
4840 >        Year = 1985}
4841  
4842   @article{Huh2004,
4843          Abstract = {Racemic fluids of chiral calamitic molecules are investigated with
# Line 4570 | Line 4853
4853          Annote = {870FJ Times Cited:0 Cited References Count:63},
4854          Author = {Y. Huh and N. M. Cann},
4855          Issn = {0021-9606},
4856 <        Journal = {Journal of Chemical Physics},
4856 >        Journal = jcp,
4857          Month = {Nov 22},
4858 <        Number = {20},
4858 >        Number = 20,
4859          Pages = {10299-10308},
4860          Title = {Discrimination in isotropic, nematic, and smectic phases of chiral calamitic molecules: A computer simulation study},
4861          Uri = {<Go to ISI>://000225042700059},
4862 <        Volume = {121},
4863 <        Year = {2004}}
4862 >        Volume = 121,
4863 >        Year = 2004}
4864  
4865   @article{Humphrey1996,
4866          Abstract = {VMD is a molecular graphics program designed for the display and analysis
# Line 4611 | Line 4894
4894          Issn = {0263-7855},
4895          Journal = {Journal of Molecular Graphics},
4896          Month = {Feb},
4897 <        Number = {1},
4897 >        Number = 1,
4898          Pages = {33-\&},
4899          Title = {VMD: Visual molecular dynamics},
4900          Uri = {<Go to ISI>://A1996UH51500005},
4901 <        Volume = {14},
4902 <        Year = {1996}}
4901 >        Volume = 14,
4902 >        Year = 1996}
4903  
4904   @article{Izaguirre2001,
4905          Abstract = {In this paper we show the possibility of using very mild stochastic
# Line 4649 | Line 4932
4932          Annote = {397CQ Times Cited:14 Cited References Count:36},
4933          Author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
4934          Issn = {0021-9606},
4935 <        Journal = {Journal of Chemical Physics},
4935 >        Journal = jcp,
4936          Month = {Feb 1},
4937 <        Number = {5},
4937 >        Number = 5,
4938          Pages = {2090-2098},
4939          Title = {Langevin stabilization of molecular dynamics},
4940          Uri = {<Go to ISI>://000166676100020},
4941 <        Volume = {114},
4942 <        Year = {2001}}
4941 >        Volume = 114,
4942 >        Year = 2001}
4943  
4944   @article{Torre1977,
4945 <        Author = {Jose Garcia De La Torre, V.A. Bloomfield},
4945 >        Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield},
4946          Journal = {Biopolymers},
4947          Pages = {1747-1763},
4948          Title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
4949 <        Volume = {16},
4950 <        Year = {1977}}
4949 >        Volume = 16,
4950 >        Year = 1977}
4951  
4952   @article{Kale1999,
4953          Abstract = {Molecular dynamics programs simulate the behavior of biomolecular
# Line 4692 | Line 4975
4975          Annote = {194FM Times Cited:373 Cited References Count:51},
4976          Author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan and K. Schulten},
4977          Issn = {0021-9991},
4978 <        Journal = {Journal of Computational Physics},
4978 >        Journal = jcop,
4979          Month = {May 1},
4980 <        Number = {1},
4980 >        Number = 1,
4981          Pages = {283-312},
4982          Title = {NAMD2: Greater scalability for parallel molecular dynamics},
4983          Uri = {<Go to ISI>://000080181500013},
4984 <        Volume = {151},
4985 <        Year = {1999}}
4984 >        Volume = 151,
4985 >        Year = 1999}
4986  
4987   @article{Kane2000,
4988          Abstract = {The purpose of this work is twofold. First, we demonstrate analytically
# Line 4723 | Line 5006
5006          Issn = {0029-5981},
5007          Journal = {International Journal for Numerical Methods in Engineering},
5008          Month = {Dec 10},
5009 <        Number = {10},
5009 >        Number = 10,
5010          Pages = {1295-1325},
5011          Title = {Variational integrators and the Newmark algorithm for conservative and dissipative mechanical systems},
5012          Uri = {<Go to ISI>://000165270600004},
5013 <        Volume = {49},
5014 <        Year = {2000}}
5013 >        Volume = 49,
5014 >        Year = 2000}
5015  
5016   @article{Klimov1997,
5017          Abstract = {The viscosity (eta) dependence of the folding rates for four sequences
# Line 4745 | Line 5028
5028          Annote = {Xk293 Times Cited:77 Cited References Count:17},
5029          Author = {D. K. Klimov and D. Thirumalai},
5030          Issn = {0031-9007},
5031 <        Journal = {Physical Review Letters},
5031 >        Journal = prl,
5032          Month = {Jul 14},
5033 <        Number = {2},
5033 >        Number = 2,
5034          Pages = {317-320},
5035          Title = {Viscosity dependence of the folding rates of proteins},
5036          Uri = {<Go to ISI>://A1997XK29300035},
5037 <        Volume = {79},
5038 <        Year = {1997}}
5037 >        Volume = 79,
5038 >        Year = 1997}
5039  
5040   @article{Kol1997,
5041          Abstract = {Rigid-body molecular dynamics simulations typically are performed
# Line 4778 | Line 5061
5061          Annote = {Xq332 Times Cited:11 Cited References Count:18},
5062          Author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
5063          Issn = {0021-9606},
5064 <        Journal = {Journal of Chemical Physics},
5064 >        Journal = jcp,
5065          Month = {Aug 15},
5066 <        Number = {7},
5066 >        Number = 7,
5067          Pages = {2580-2588},
5068          Title = {A symplectic method for rigid-body molecular simulation},
5069          Uri = {<Go to ISI>://A1997XQ33200046},
5070 <        Volume = {107},
5071 <        Year = {1997}}
5070 >        Volume = 107,
5071 >        Year = 1997}
5072  
5073   @article{Lansac2001,
5074          Abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
# Line 4814 | Line 5097
5097          Issn = {1063-651X},
5098          Journal = {Physical Review E},
5099          Month = {Nov},
5100 <        Number = {5},
5100 >        Number = 5,
5101          Pages = {-},
5102          Title = {Microscopic structure and dynamics of a partial bilayer smectic liquid crystal},
5103          Uri = {<Go to ISI>://000172406900063},
5104 <        Volume = {6405},
5105 <        Year = {2001}}
5104 >        Volume = 6405,
5105 >        Year = 2001}
5106  
5107   @article{Lansac2003,
5108          Abstract = {Recently, a new class of smectic liquid crystal phases characterized
# Line 4842 | Line 5125
5125          Issn = {1063-651X},
5126          Journal = {Physical Review E},
5127          Month = {Jan},
5128 <        Number = {1},
5128 >        Number = 1,
5129          Pages = {-},
5130          Title = {Phase behavior of bent-core molecules},
5131          Uri = {<Go to ISI>://000181017300042},
5132 <        Volume = {67},
5133 <        Year = {2003}}
5132 >        Volume = 67,
5133 >        Year = 2003}
5134  
5135   @book{Leach2001,
5136          Address = {Harlow, England},
# Line 4855 | Line 5138
5138          Edition = {2nd},
5139          Publisher = {Pearson Educated Limited},
5140          Title = {Molecular Modeling: Principles and Applications},
5141 <        Year = {2001}}
5141 >        Year = 2001}
5142  
5143   @article{Leimkuhler1999,
5144          Abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
# Line 4875 | Line 5158
5158          Issn = {1364-503X},
5159          Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
5160          Month = {Apr 15},
5161 <        Number = {1754},
5161 >        Number = 1754,
5162          Pages = {1101-1133},
5163          Title = {Reversible adaptive regularization: perturbed Kepler motion and classical atomic trajectories},
5164          Uri = {<Go to ISI>://000080466800007},
5165 <        Volume = {357},
5166 <        Year = {1999}}
5165 >        Volume = 357,
5166 >        Year = 1999}
5167  
5168   @book{Leimkuhler2004,
5169          Address = {Cambridge},
5170          Author = {B. Leimkuhler and S. Reich},
5171          Publisher = {Cambridge University Press},
5172          Title = {Simulating Hamiltonian Dynamics},
5173 <        Year = {2004}}
5173 >        Year = 2004}
5174  
5175   @article{Levelut1981,
5176          Annote = {Ml751 Times Cited:96 Cited References Count:16},
5177          Author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard and G. Sigaud},
5178          Issn = {1050-2947},
5179          Journal = {Physical Review A},
5180 <        Number = {4},
5180 >        Number = 4,
5181          Pages = {2180-2186},
5182          Title = {Number of Sa Phases},
5183          Uri = {<Go to ISI>://A1981ML75100057},
5184 <        Volume = {24},
5185 <        Year = {1981}}
5184 >        Volume = 24,
5185 >        Year = 1981}
5186  
5187   @article{Lieb1982,
5188          Annote = {Nu461 Times Cited:40 Cited References Count:28},
5189          Author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
5190          Issn = {0006-3002},
5191          Journal = {Biochimica Et Biophysica Acta},
5192 <        Number = {2},
5192 >        Number = 2,
5193          Pages = {388-398},
5194          Title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - Evidence from Raman-Scattering},
5195          Uri = {<Go to ISI>://A1982NU46100012},
5196 <        Volume = {688},
5197 <        Year = {1982}}
5196 >        Volume = 688,
5197 >        Year = 1982}
5198  
5199   @article{Link1997,
5200          Abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
# Line 4929 | Line 5212
5212          Issn = {0036-8075},
5213          Journal = {Science},
5214          Month = {Dec 12},
5215 <        Number = {5345},
5215 >        Number = 5345,
5216          Pages = {1924-1927},
5217          Title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic phase of achiral molecules},
5218          Uri = {<Go to ISI>://A1997YL00200028},
5219 <        Volume = {278},
5220 <        Year = {1997}}
5219 >        Volume = 278,
5220 >        Year = 1997}
5221  
5222   @article{Liwo2005,
5223          Annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
# Line 4945 | Line 5228
5228          Pages = {359-360},
5229          Title = {Ab initio simulations of protein folding pathways by molecular dynamics with the united-residue (UNRES) model of polypeptide chains},
5230          Uri = {<Go to ISI>://000234826102043},
5231 <        Volume = {272},
5232 <        Year = {2005}}
5231 >        Volume = 272,
5232 >        Year = 2005}
5233  
5234   @article{Luty1994,
5235          Abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
# Line 4961 | Line 5244
5244          Author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
5245          Issn = {0892-7022},
5246          Journal = {Molecular Simulation},
5247 <        Number = {1},
5247 >        Number = 1,
5248          Pages = {11-20},
5249          Title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
5250          Uri = {<Go to ISI>://A1994QF46400002},
5251 <        Volume = {14},
5252 <        Year = {1994}}
5251 >        Volume = 14,
5252 >        Year = 1994}
5253  
5254   @book{Marion1990,
5255          Address = {New York},
# Line 4974 | Line 5257
5257          Edition = {2rd},
5258          Publisher = {Academic Press},
5259          Title = {Classical Dynamics of Particles and Systems},
5260 <        Year = {1990}}
5260 >        Year = 1990}
5261  
5262   @article{Marrink1994,
5263          Abstract = {To obtain insight in the process of water permeation through a lipid
# Line 5006 | Line 5289
5289          Issn = {0022-3654},
5290          Journal = {Journal of Physical Chemistry},
5291          Month = {Apr 14},
5292 <        Number = {15},
5292 >        Number = 15,
5293          Pages = {4155-4168},
5294          Title = {Simulation of Water Transport through a Lipid-Membrane},
5295          Uri = {<Go to ISI>://A1994NG21900040},
5296 <        Volume = {98},
5297 <        Year = {1994}}
5296 >        Volume = 98,
5297 >        Year = 1994}
5298  
5299   @article{Marrink2004,
5300          Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
5301          Journal = {J. Phys. Chem. B},
5302          Pages = {750-760},
5303          Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
5304 <        Volume = {108},
5305 <        Year = {2004}}
5304 >        Volume = 108,
5305 >        Year = 2004}
5306  
5307   @article{Marsden1998,
5308          Abstract = {This paper presents a geometric-variational approach to continuous
# Line 5047 | Line 5330
5330          Issn = {0010-3616},
5331          Journal = {Communications in Mathematical Physics},
5332          Month = {Dec},
5333 <        Number = {2},
5333 >        Number = 2,
5334          Pages = {351-395},
5335          Title = {Multisymplectic geometry, variational integrators, and nonlinear PDEs},
5336          Uri = {<Go to ISI>://000077902200006},
5337 <        Volume = {199},
5338 <        Year = {1998}}
5337 >        Volume = 199,
5338 >        Year = 1998}
5339  
5340   @article{Matthey2004,
5341          Abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
# Line 5077 | Line 5360
5360          Issn = {0098-3500},
5361          Journal = {Acm Transactions on Mathematical Software},
5362          Month = {Sep},
5363 <        Number = {3},
5363 >        Number = 3,
5364          Pages = {237-265},
5365          Title = {ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics},
5366          Uri = {<Go to ISI>://000224325600001},
5367 <        Volume = {30},
5368 <        Year = {2004}}
5367 >        Volume = 30,
5368 >        Year = 2004}
5369  
5370   @article{McLachlan1993,
5371          Author = {R.~I McLachlan},
5372          Journal = {prl},
5373          Pages = {3043-3046},
5374          Title = {Explicit Lie-Poisson integration and the Euler equations},
5375 <        Volume = {71},
5376 <        Year = {1993}}
5375 >        Volume = 71,
5376 >        Year = 1993}
5377  
5378   @article{McLachlan1998,
5379          Abstract = {We give a survey and some new examples of generating functions for
# Line 5108 | Line 5391
5391          Pages = {298-309},
5392          Title = {Generating functions for dynamical systems with symmetries, integrals, and differential invariants},
5393          Uri = {<Go to ISI>://000071558900021},
5394 <        Volume = {112},
5395 <        Year = {1998}}
5394 >        Volume = 112,
5395 >        Year = 1998}
5396  
5397   @article{McLachlan1998a,
5398          Abstract = {We consider properties of flows, the relationships between them, and
# Line 5126 | Line 5409
5409          Issn = {0036-1429},
5410          Journal = {Siam Journal on Numerical Analysis},
5411          Month = {Apr},
5412 <        Number = {2},
5412 >        Number = 2,
5413          Pages = {586-599},
5414          Title = {Numerical integrators that preserve symmetries and reversing symmetries},
5415          Uri = {<Go to ISI>://000072580500010},
5416 <        Volume = {35},
5417 <        Year = {1998}}
5416 >        Volume = 35,
5417 >        Year = 1998}
5418  
5419   @article{McLachlan2005,
5420          Abstract = {In this paper we revisit the Moser-Veselov description of the free
# Line 5152 | Line 5435
5435          Issn = {1615-3375},
5436          Journal = {Foundations of Computational Mathematics},
5437          Month = {Feb},
5438 <        Number = {1},
5438 >        Number = 1,
5439          Pages = {87-123},
5440          Title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
5441          Uri = {<Go to ISI>://000228011900003},
5442 <        Volume = {5},
5443 <        Year = {2005}}
5442 >        Volume = 5,
5443 >        Year = 2005}
5444  
5445   @article{Meineke2005,
5446          Abstract = {OOPSE is a new molecular dynamics simulation program that is capable
# Line 5173 | Line 5456
5456          Annote = {891CF Times Cited:1 Cited References Count:56},
5457          Author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and J. D. Gezelter},
5458          Issn = {0192-8651},
5459 <        Journal = {Journal of Computational Chemistry},
5459 >        Journal = jcc,
5460          Month = {Feb},
5461 <        Number = {3},
5461 >        Number = 3,
5462          Pages = {252-271},
5463          Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
5464          Uri = {<Go to ISI>://000226558200006},
5465 <        Volume = {26},
5466 <        Year = {2005}}
5465 >        Volume = 26,
5466 >        Year = 2005}
5467  
5468   @article{Melchionna1993,
5469          Abstract = {In this paper we write down equations of motion (following the approach
# Line 5192 | Line 5475
5475          Annote = {Kq355 Times Cited:172 Cited References Count:17},
5476          Author = {S. Melchionna and G. Ciccotti and B. L. Holian},
5477          Issn = {0026-8976},
5478 <        Journal = {Molecular Physics},
5478 >        Journal = mp,
5479          Month = {Feb 20},
5480 <        Number = {3},
5480 >        Number = 3,
5481          Pages = {533-544},
5482          Title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
5483          Uri = {<Go to ISI>://A1993KQ35500002},
5484 <        Volume = {78},
5485 <        Year = {1993}}
5484 >        Volume = 78,
5485 >        Year = 1993}
5486  
5487   @article{Memmer2002,
5488          Abstract = {The phase behaviour of achiral banana-shaped molecules was studied
# Line 5232 | Line 5515
5515          Issn = {0267-8292},
5516          Journal = {Liquid Crystals},
5517          Month = {Apr},
5518 <        Number = {4},
5518 >        Number = 4,
5519          Pages = {483-496},
5520          Title = {Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study},
5521          Uri = {<Go to ISI>://000174410500001},
5522 <        Volume = {29},
5523 <        Year = {2002}}
5522 >        Volume = 29,
5523 >        Year = 2002}
5524  
5525   @article{Metropolis1949,
5526          Author = {N. Metropolis and S. Ulam},
5527          Journal = {J. Am. Stat. Ass.},
5528          Pages = {335-341},
5529          Title = {The $\mbox{Monte Carlo}$ Method},
5530 <        Volume = {44},
5531 <        Year = {1949}}
5530 >        Volume = 44,
5531 >        Year = 1949}
5532  
5533   @article{Mielke2004,
5534          Abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
# Line 5276 | Line 5559
5559          Annote = {861ZF Times Cited:3 Cited References Count:34},
5560          Author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen and C. J. Benham},
5561          Issn = {0021-9606},
5562 <        Journal = {Journal of Chemical Physics},
5562 >        Journal = jcp,
5563          Month = {Oct 22},
5564 <        Number = {16},
5564 >        Number = 16,
5565          Pages = {8104-8112},
5566          Title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study},
5567          Uri = {<Go to ISI>://000224456500064},
5568 <        Volume = {121},
5569 <        Year = {2004}}
5568 >        Volume = 121,
5569 >        Year = 2004}
5570  
5571   @article{Naess2001,
5572          Abstract = {The three Eulerian angles constitute the classical choice of generalized
# Line 5308 | Line 5591
5591          Pages = {323-339},
5592          Title = {Brownian dynamics simulation of rigid bodies and segmented polymer chains. Use of Cartesian rotation vectors as the generalized coordinates describing angular orientations},
5593          Uri = {<Go to ISI>://000168774800005},
5594 <        Volume = {294},
5595 <        Year = {2001}}
5594 >        Volume = 294,
5595 >        Year = 2001}
5596  
5597   @article{Niori1996,
5598          Abstract = {The synthesis of a banana-shaped molecule is reported and it is found
# Line 5324 | Line 5607
5607          Issn = {0959-9428},
5608          Journal = {Journal of Materials Chemistry},
5609          Month = {Jul},
5610 <        Number = {7},
5610 >        Number = 7,
5611          Pages = {1231-1233},
5612          Title = {Distinct ferroelectric smectic liquid crystals consisting of banana shaped achiral molecules},
5613          Uri = {<Go to ISI>://A1996UX85500025},
5614 <        Volume = {6},
5615 <        Year = {1996}}
5614 >        Volume = 6,
5615 >        Year = 1996}
5616  
5617   @article{Noguchi2002,
5618          Abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
# Line 5349 | Line 5632
5632          Issn = {1063-651X},
5633          Journal = {Physical Review E},
5634          Month = {may},
5635 <        Number = {5},
5635 >        Number = 5,
5636          Pages = {-},
5637          Title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
5638          Uri = {<Go to ISI>://000176552300084},
5639 <        Volume = {65},
5640 <        Year = {2002}}
5639 >        Volume = 65,
5640 >        Year = 2002}
5641  
5642   @article{Noguchi2001,
5643          Abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
# Line 5371 | Line 5654
5654          Annote = {491UW Times Cited:48 Cited References Count:25},
5655          Author = {H. Noguchi and M. Takasu},
5656          Issn = {0021-9606},
5657 <        Journal = {Journal of Chemical Physics},
5657 >        Journal = jcp,
5658          Month = {Nov 22},
5659 <        Number = {20},
5659 >        Number = 20,
5660          Pages = {9547-9551},
5661          Title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
5662          Uri = {<Go to ISI>://000172129300049},
5663 <        Volume = {115},
5664 <        Year = {2001}}
5663 >        Volume = 115,
5664 >        Year = 2001}
5665  
5666   @book{Olver1986,
5667          Address = {New York},
5668          Author = {P.J. Olver},
5669          Publisher = {Springer},
5670          Title = {Applications of Lie groups to differential equatitons},
5671 <        Year = {1986}}
5671 >        Year = 1986}
5672  
5673   @article{Omelyan1998,
5674          Abstract = {A revised version of the quaternion approach for numerical integration
# Line 5404 | Line 5687
5687          Issn = {0894-1866},
5688          Journal = {Computers in Physics},
5689          Month = {Jan-Feb},
5690 <        Number = {1},
5690 >        Number = 1,
5691          Pages = {97-103},
5692          Title = {On the numerical integration of motion for rigid polyatomics: The modified quaternion approach},
5693          Uri = {<Go to ISI>://000072024300025},
5694 <        Volume = {12},
5695 <        Year = {1998}}
5694 >        Volume = 12,
5695 >        Year = 1998}
5696  
5697   @article{Omelyan1998a,
5698          Abstract = {An algorithm for numerical integration of the rigid-body equations
# Line 5426 | Line 5709
5709          Issn = {1063-651X},
5710          Journal = {Physical Review E},
5711          Month = {Jul},
5712 <        Number = {1},
5712 >        Number = 1,
5713          Pages = {1169-1172},
5714          Title = {Algorithm for numerical integration of the rigid-body equations of motion},
5715          Uri = {<Go to ISI>://000074893400151},
5716 <        Volume = {58},
5717 <        Year = {1998}}
5716 >        Volume = 58,
5717 >        Year = 1998}
5718  
5719   @article{Owren1992,
5720          Abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
# Line 5452 | Line 5735
5735          Issn = {0196-5204},
5736          Journal = {Siam Journal on Scientific and Statistical Computing},
5737          Month = {Nov},
5738 <        Number = {6},
5738 >        Number = 6,
5739          Pages = {1488-1501},
5740          Title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
5741          Uri = {<Go to ISI>://A1992JU93600013},
5742 <        Volume = {13},
5743 <        Year = {1992}}
5742 >        Volume = 13,
5743 >        Year = 1992}
5744  
5745   @article{Palacios1998,
5746          Abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
# Line 5495 | Line 5778
5778          Issn = {0163-1829},
5779          Journal = {Physical Review B},
5780          Month = {Dec 1},
5781 <        Number = {22},
5781 >        Number = 22,
5782          Pages = {14937-14958},
5783          Title = {Langevin-dynamics study of the dynamical properties of small magnetic particles},
5784          Uri = {<Go to ISI>://000077460000052},
5785 <        Volume = {58},
5786 <        Year = {1998}}
5785 >        Volume = 58,
5786 >        Year = 1998}
5787  
5788   @article{Parr1995,
5789          Abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
# Line 5527 | Line 5810
5810          Issn = {0038-0644},
5811          Journal = {Software-Practice \& Experience},
5812          Month = {Jul},
5813 <        Number = {7},
5813 >        Number = 7,
5814          Pages = {789-810},
5815          Title = {Antlr - a Predicated-Ll(K) Parser Generator},
5816          Uri = {<Go to ISI>://A1995RK10400004},
5817 <        Volume = {25},
5818 <        Year = {1995}}
5817 >        Volume = 25,
5818 >        Year = 1995}
5819  
5820   @article{Pastor1988,
5821          Annote = {T1302 Times Cited:61 Cited References Count:26},
5822          Author = {R. W. Pastor and B. R. Brooks and A. Szabo},
5823          Issn = {0026-8976},
5824 <        Journal = {Molecular Physics},
5824 >        Journal = mp,
5825          Month = {Dec 20},
5826 <        Number = {6},
5826 >        Number = 6,
5827          Pages = {1409-1419},
5828          Title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
5829          Uri = {<Go to ISI>://A1988T130200011},
5830 <        Volume = {65},
5831 <        Year = {1988}}
5830 >        Volume = 65,
5831 >        Year = 1988}
5832  
5833   @article{Pelzl1999,
5834          Annote = {220RC Times Cited:313 Cited References Count:49},
# Line 5553 | Line 5836
5836          Issn = {0935-9648},
5837          Journal = {Advanced Materials},
5838          Month = {Jul 5},
5839 <        Number = {9},
5839 >        Number = 9,
5840          Pages = {707-724},
5841          Title = {Banana-shaped compounds - A new field of liquid crystals},
5842          Uri = {<Go to ISI>://000081680400007},
5843 <        Volume = {11},
5844 <        Year = {1999}}
5843 >        Volume = 11,
5844 >        Year = 1999}
5845  
5846   @article{Perram1985,
5847          Annote = {Akb93 Times Cited:71 Cited References Count:12},
5848          Author = {J. W. Perram and M. S. Wertheim},
5849          Issn = {0021-9991},
5850 <        Journal = {Journal of Computational Physics},
5851 <        Number = {3},
5850 >        Journal = jcop,
5851 >        Number = 3,
5852          Pages = {409-416},
5853          Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function},
5854          Uri = {<Go to ISI>://A1985AKB9300008},
5855 <        Volume = {58},
5856 <        Year = {1985}}
5855 >        Volume = 58,
5856 >        Year = 1985}
5857  
5858   @article{Rotne1969,
5859          Author = {F. Perrin},
5860          Journal = {J. Chem. Phys.},
5861          Pages = {4831-4837},
5862          Title = {Variational treatment of hydrodynamic interaction in polymers},
5863 <        Volume = {50},
5864 <        Year = {1969}}
5863 >        Volume = 50,
5864 >        Year = 1969}
5865  
5866   @article{Perrin1936,
5867          Author = {F. Perrin},
5868          Journal = {J. Phys. Radium},
5869          Pages = {1-11},
5870          Title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation des fluorescences. Translation et diffusion de moleculese ellipsoidales},
5871 <        Volume = {7},
5872 <        Year = {1936}}
5871 >        Volume = 7,
5872 >        Year = 1936}
5873  
5874   @article{Perrin1934,
5875          Author = {F. Perrin},
5876          Journal = {J. Phys. Radium},
5877          Pages = {497-511},
5878          Title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour des molecules ellipsoidales},
5879 <        Volume = {5},
5880 <        Year = {1934}}
5879 >        Volume = 5,
5880 >        Year = 1934}
5881  
5882   @article{Petrache2000,
5883          Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
5884 <        Journal = {Biophysical Journal},
5884 >        Journal = bj,
5885          Pages = {3172-3192},
5886          Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
5887 <        Volume = {79},
5888 <        Year = {2000}}
5887 >        Volume = 79,
5888 >        Year = 2000}
5889  
5890   @article{Petrache1998,
5891          Abstract = {X-ray diffraction data taken at high instrumental resolution were
# Line 5627 | Line 5910
5910          Issn = {0009-3084},
5911          Journal = {Chemistry and Physics of Lipids},
5912          Month = {Sep},
5913 <        Number = {1},
5913 >        Number = 1,
5914          Pages = {83-94},
5915          Title = {Fluid phase structure of EPC and DMPC bilayers},
5916          Uri = {<Go to ISI>://000076497600007},
5917 <        Volume = {95},
5918 <        Year = {1998}}
5917 >        Volume = 95,
5918 >        Year = 1998}
5919  
5920   @article{Powles1973,
5921          Author = {J.~G. Powles},
5922          Journal = {Advan. Phys.},
5923          Pages = {1-56},
5924          Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
5925 <        Volume = {22},
5926 <        Year = {1973}}
5925 >        Volume = 22,
5926 >        Year = 1973}
5927  
5928   @article{Recio2004,
5929          Abstract = {Protein recognition is one of the most challenging and intriguing
# Line 5669 | Line 5952
5952          Annote = {763GQ Times Cited:21 Cited References Count:59},
5953          Author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
5954          Issn = {0022-2836},
5955 <        Journal = {Journal of Molecular Biology},
5955 >        Journal = jmb,
5956          Month = {Jan 16},
5957 <        Number = {3},
5957 >        Number = 3,
5958          Pages = {843-865},
5959          Title = {Identification of protein-protein interaction sites from docking energy landscapes},
5960          Uri = {<Go to ISI>://000188066900016},
5961 <        Volume = {335},
5962 <        Year = {2004}}
5961 >        Volume = 335,
5962 >        Year = 2004}
5963  
5964   @article{Reddy2006,
5965          Abstract = {An overview on the recent developments in the field of liquid crystalline
# Line 5694 | Line 5977
5977          Author = {R. A. Reddy and C. Tschierske},
5978          Issn = {0959-9428},
5979          Journal = {Journal of Materials Chemistry},
5980 <        Number = {10},
5980 >        Number = 10,
5981          Pages = {907-961},
5982          Title = {Bent-core liquid crystals: polar order, superstructural chirality and spontaneous desymmetrisation in soft matter systems},
5983          Uri = {<Go to ISI>://000235990500001},
5984 <        Volume = {16},
5985 <        Year = {2006}}
5984 >        Volume = 16,
5985 >        Year = 2006}
5986  
5987   @article{Reich1999,
5988          Abstract = {Backward error analysis has become an important tool for understanding
# Line 5729 | Line 6012
6012          Issn = {0036-1429},
6013          Journal = {Siam Journal on Numerical Analysis},
6014          Month = {Sep 8},
6015 <        Number = {5},
6015 >        Number = 5,
6016          Pages = {1549-1570},
6017          Title = {Backward error analysis for numerical integrators},
6018          Uri = {<Go to ISI>://000082650600010},
6019 <        Volume = {36},
6020 <        Year = {1999}}
6019 >        Volume = 36,
6020 >        Year = 1999}
6021  
6022   @article{Ros2005,
6023          Abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
# Line 5749 | Line 6032
6032          Author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
6033          Issn = {0959-9428},
6034          Journal = {Journal of Materials Chemistry},
6035 <        Number = {48},
6035 >        Number = 48,
6036          Pages = {5093-5098},
6037          Title = {Banana-shaped liquid crystals: a new field to explore},
6038          Uri = {<Go to ISI>://000233775500001},
6039 <        Volume = {15},
6040 <        Year = {2005}}
6039 >        Volume = 15,
6040 >        Year = 2005}
6041  
6042   @article{Roux1991,
6043          Abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
# Line 5782 | Line 6065
6065          Issn = {0022-3654},
6066          Journal = {Journal of Physical Chemistry},
6067          Month = {Jun 13},
6068 <        Number = {12},
6068 >        Number = 12,
6069          Pages = {4856-4868},
6070          Title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
6071          Uri = {<Go to ISI>://A1991FR75600049},
6072 <        Volume = {95},
6073 <        Year = {1991}}
6072 >        Volume = 95,
6073 >        Year = 1991}
6074  
6075   @article{Roy2005,
6076          Abstract = {A vast majority of compounds with bent core or banana shaped molecules
# Line 5806 | Line 6089
6089          Issn = {1292-8941},
6090          Journal = {European Physical Journal E},
6091          Month = {Nov},
6092 <        Number = {3},
6092 >        Number = 3,
6093          Pages = {253-258},
6094          Title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases in banana shaped molecules},
6095          Uri = {<Go to ISI>://000233363300002},
6096 <        Volume = {18},
6097 <        Year = {2005}}
6096 >        Volume = 18,
6097 >        Year = 2005}
6098  
6099   @article{Ryckaert1977,
6100          Annote = {Cz253 Times Cited:3680 Cited References Count:7},
6101          Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
6102          Issn = {0021-9991},
6103 <        Journal = {Journal of Computational Physics},
6104 <        Number = {3},
6103 >        Journal = jcop,
6104 >        Number = 3,
6105          Pages = {327-341},
6106          Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes},
6107          Uri = {<Go to ISI>://A1977CZ25300007},
6108 <        Volume = {23},
6109 <        Year = {1977}}
6108 >        Volume = 23,
6109 >        Year = 1977}
6110  
6111   @article{Sagui1999,
6112          Abstract = {Current computer simulations of biomolecules typically make use of
# Line 5848 | Line 6131
6131          Pages = {155-179},
6132          Title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic effects},
6133          Uri = {<Go to ISI>://000081271400008},
6134 <        Volume = {28},
6135 <        Year = {1999}}
6134 >        Volume = 28,
6135 >        Year = 1999}
6136  
6137   @article{Sandu1999,
6138          Abstract = {Numerical resonance artifacts have become recognized recently as a
# Line 5892 | Line 6175
6175          Annote = {194FM Times Cited:14 Cited References Count:32},
6176          Author = {A. Sandu and T. Schlick},
6177          Issn = {0021-9991},
6178 <        Journal = {Journal of Computational Physics},
6178 >        Journal = jcop,
6179          Month = {May 1},
6180 <        Number = {1},
6180 >        Number = 1,
6181          Pages = {74-113},
6182          Title = {Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics},
6183          Uri = {<Go to ISI>://000080181500004},
6184 <        Volume = {151},
6185 <        Year = {1999}}
6184 >        Volume = 151,
6185 >        Year = 1999}
6186  
6187   @article{Sasaki2004,
6188          Abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
# Line 5913 | Line 6196
6196          Author = {Y. Sasaki and R. Shukla and B. D. Smith},
6197          Issn = {1477-0520},
6198          Journal = {Organic \& Biomolecular Chemistry},
6199 <        Number = {2},
6199 >        Number = 2,
6200          Pages = {214-219},
6201          Title = {Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases},
6202          Uri = {<Go to ISI>://000187843800012},
6203 <        Volume = {2},
6204 <        Year = {2004}}
6203 >        Volume = 2,
6204 >        Year = 2004}
6205  
6206   @article{Satoh1996,
6207          Abstract = {The effects of dipole-dipole interaction on mesophase formation are
# Line 5937 | Line 6220
6220          Pages = {99-104},
6221          Title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect of terminal dipole moment on mesophase formation},
6222          Uri = {<Go to ISI>://A1996UQ97500017},
6223 <        Volume = {255},
6224 <        Year = {1996}}
6223 >        Volume = 255,
6224 >        Year = 1996}
6225  
6226   @article{Schaps1999,
6227          Annote = {163EC Times Cited:0 Cited References Count:0},
# Line 5946 | Line 6229
6229          Issn = {1044-789X},
6230          Journal = {Dr Dobbs Journal},
6231          Month = {Mar},
6232 <        Number = {3},
6232 >        Number = 3,
6233          Pages = {84-+},
6234          Title = {Compiler construction with ANTLR and Java - Tools for building tools},
6235          Uri = {<Go to ISI>://000078389200023},
6236 <        Volume = {24},
6237 <        Year = {1999}}
6236 >        Volume = 24,
6237 >        Year = 1999}
6238  
6239   @article{Shen2002,
6240          Abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
# Line 5976 | Line 6259
6259          Annote = {540MH Times Cited:36 Cited References Count:45},
6260          Author = {M. Y. Shen and K. F. Freed},
6261          Issn = {0006-3495},
6262 <        Journal = {Biophysical Journal},
6262 >        Journal = bj,
6263          Month = {Apr},
6264 <        Number = {4},
6264 >        Number = 4,
6265          Pages = {1791-1808},
6266          Title = {Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models},
6267          Uri = {<Go to ISI>://000174932400010},
6268 <        Volume = {82},
6269 <        Year = {2002}}
6268 >        Volume = 82,
6269 >        Year = 2002}
6270  
6271   @article{Shillcock2005,
6272          Annote = {901QJ Times Cited:9 Cited References Count:23},
# Line 5991 | Line 6274
6274          Issn = {1476-1122},
6275          Journal = {Nature Materials},
6276          Month = {Mar},
6277 <        Number = {3},
6277 >        Number = 3,
6278          Pages = {225-228},
6279          Title = {Tension-induced fusion of bilayer membranes and vesicles},
6280          Uri = {<Go to ISI>://000227296700019},
6281 <        Volume = {4},
6282 <        Year = {2005}}
6281 >        Volume = 4,
6282 >        Year = 2005}
6283  
6284   @article{Shimada1993,
6285          Abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
# Line 6019 | Line 6302
6302          Annote = {Lh164 Times Cited:27 Cited References Count:47},
6303          Author = {J. Shimada and H. Kaneko and T. Takada},
6304          Issn = {0192-8651},
6305 <        Journal = {Journal of Computational Chemistry},
6305 >        Journal = jcc,
6306          Month = {Jul},
6307 <        Number = {7},
6307 >        Number = 7,
6308          Pages = {867-878},
6309          Title = {Efficient Calculations of Coulombic Interactions in Biomolecular Simulations with Periodic Boundary-Conditions},
6310          Uri = {<Go to ISI>://A1993LH16400011},
6311 <        Volume = {14},
6312 <        Year = {1993}}
6311 >        Volume = 14,
6312 >        Year = 1993}
6313  
6314   @article{Skeel2002,
6315          Abstract = {The best simple method for Newtonian molecular dynamics is indisputably
# Line 6042 | Line 6325
6325          Annote = {633RX Times Cited:8 Cited References Count:22},
6326          Author = {R. D. Skeel and J. A. Izaguirre},
6327          Issn = {0026-8976},
6328 <        Journal = {Molecular Physics},
6328 >        Journal = mp,
6329          Month = {Dec 20},
6330 <        Number = {24},
6330 >        Number = 24,
6331          Pages = {3885-3891},
6332          Title = {An impulse integrator for Langevin dynamics},
6333          Uri = {<Go to ISI>://000180297200014},
6334 <        Volume = {100},
6335 <        Year = {2002}}
6334 >        Volume = 100,
6335 >        Year = 2002}
6336  
6337   @article{Skeel1997,
6338          Abstract = {The following integration methods for special second-order ordinary
# Line 6070 | Line 6353
6353          Issn = {1064-8275},
6354          Journal = {Siam Journal on Scientific Computing},
6355          Month = {Jan},
6356 <        Number = {1},
6356 >        Number = 1,
6357          Pages = {203-222},
6358          Title = {A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications},
6359          Uri = {<Go to ISI>://A1997WE98100012},
6360 <        Volume = {18},
6361 <        Year = {1997}}
6360 >        Volume = 18,
6361 >        Year = 1997}
6362  
6363   @article{Tao2005,
6364          Abstract = {Recently a microscopic theory for the dynamics of suspensions of long
# Line 6101 | Line 6384
6384          Annote = {943DN Times Cited:3 Cited References Count:26},
6385          Author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont and W. J. Briels},
6386          Issn = {0021-9606},
6387 <        Journal = {Journal of Chemical Physics},
6387 >        Journal = jcp,
6388          Month = {Jun 22},
6389 <        Number = {24},
6389 >        Number = 24,
6390          Pages = {-},
6391          Title = {Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods},
6392          Uri = {<Go to ISI>://000230332400077},
6393 <        Volume = {122},
6394 <        Year = {2005}}
6393 >        Volume = 122,
6394 >        Year = 2005}
6395  
6396   @book{Tolman1979,
6397          Address = {New York},
6398          Author = {R.~C. Tolman},
6399 <        Chapter = {2},
6399 >        Chapter = 2,
6400          Pages = {19-22},
6401          Publisher = {Dover Publications, Inc.},
6402          Title = {The Principles of Statistical Mechanics},
6403 <        Year = {1979}}
6403 >        Year = 1979}
6404  
6405   @article{Tu1995,
6406          Abstract = {We report a constant pressure and temperature molecular dynamics simulation
# Line 6142 | Line 6425
6425          Annote = {Tv018 Times Cited:108 Cited References Count:34},
6426          Author = {K. Tu and D. J. Tobias and M. L. Klein},
6427          Issn = {0006-3495},
6428 <        Journal = {Biophysical Journal},
6428 >        Journal = bj,
6429          Month = {Dec},
6430 <        Number = {6},
6430 >        Number = 6,
6431          Pages = {2558-2562},
6432          Title = {Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer},
6433          Uri = {<Go to ISI>://A1995TV01800037},
6434 <        Volume = {69},
6435 <        Year = {1995}}
6434 >        Volume = 69,
6435 >        Year = 1995}
6436  
6437   @article{Tuckerman1992,
6438          Abstract = {The Trotter factorization of the Liouville propagator is used to generate
# Line 6167 | Line 6450
6450          Annote = {Je891 Times Cited:680 Cited References Count:19},
6451          Author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
6452          Issn = {0021-9606},
6453 <        Journal = {Journal of Chemical Physics},
6453 >        Journal = jcp,
6454          Month = {Aug 1},
6455 <        Number = {3},
6455 >        Number = 3,
6456          Pages = {1990-2001},
6457          Title = {Reversible Multiple Time Scale Molecular-Dynamics},
6458          Uri = {<Go to ISI>://A1992JE89100044},
6459 <        Volume = {97},
6460 <        Year = {1992}}
6459 >        Volume = 97,
6460 >        Year = 1992}
6461  
6462   @book{Varadarajan1974,
6463          Address = {New York},
6464          Author = {V.S. Varadarajan},
6465          Publisher = {Prentice-Hall},
6466          Title = {Lie groups, Lie algebras, and their representations},
6467 <        Year = {1974}}
6467 >        Year = 1974}
6468  
6469   @article{Vincent1995,
6470          Abstract = {We have implemented a portable parallel version of the macromolecular
# Line 6201 | Line 6484
6484          Annote = {Ta403 Times Cited:16 Cited References Count:23},
6485          Author = {J. J. Vincent and K. M. Merz},
6486          Issn = {0192-8651},
6487 <        Journal = {Journal of Computational Chemistry},
6487 >        Journal = jcc,
6488          Month = {Nov},
6489 <        Number = {11},
6489 >        Number = 11,
6490          Pages = {1420-1427},
6491          Title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing Interface Standard},
6492          Uri = {<Go to ISI>://A1995TA40300009},
6493 <        Volume = {16},
6494 <        Year = {1995}}
6493 >        Volume = 16,
6494 >        Year = 1995}
6495  
6496   @article{Wegener1979,
6497          Author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
6498          Journal = {Proc. Natl. Acad. Sci.},
6499 <        Number = {12},
6499 >        Number = 12,
6500          Pages = {6356-6360},
6501          Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
6502 <        Volume = {76},
6503 <        Year = {1979}}
6502 >        Volume = 76,
6503 >        Year = 1979}
6504  
6505   @article{Wilson2006,
6506          Author = {G.~V. Wilson},
6507          Journal = {American Scientist},
6508          Title = {Where's the Real Bottleneck in Scientific Computing?},
6509 <        Volume = {94},
6510 <        Year = {2006}}
6509 >        Volume = 94,
6510 >        Year = 2006}
6511  
6512   @article{Withers2003,
6513          Abstract = {The effects of longitudinal quadrupole moments on the formation of
# Line 6257 | Line 6540
6540          Annote = {738EF Times Cited:3 Cited References Count:43},
6541          Author = {I. M. Withers},
6542          Issn = {0021-9606},
6543 <        Journal = {Journal of Chemical Physics},
6543 >        Journal = jcp,
6544          Month = {Nov 15},
6545 <        Number = {19},
6545 >        Number = 19,
6546          Pages = {10209-10223},
6547          Title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne fluid},
6548          Uri = {<Go to ISI>://000186273200027},
6549 <        Volume = {119},
6550 <        Year = {2003}}
6549 >        Volume = 119,
6550 >        Year = 2003}
6551  
6552   @article{Wolf1999,
6553          Abstract = {Based on a recent result showing that the net Coulomb potential in
# Line 6291 | Line 6574
6574          Annote = {189PD Times Cited:70 Cited References Count:34},
6575          Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
6576          Issn = {0021-9606},
6577 <        Journal = {Journal of Chemical Physics},
6577 >        Journal = jcp,
6578          Month = {May 1},
6579 <        Number = {17},
6579 >        Number = 17,
6580          Pages = {8254-8282},
6581          Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r(-1) summation},
6582          Uri = {<Go to ISI>://000079913000008},
6583 <        Volume = {110},
6584 <        Year = {1999}}
6583 >        Volume = 110,
6584 >        Year = 1999}
6585  
6586   @article{Yoshida1990,
6587          Annote = {Ej798 Times Cited:492 Cited References Count:9},
# Line 6310 | Line 6593
6593          Pages = {262-268},
6594          Title = {Construction of Higher-Order Symplectic Integrators},
6595          Uri = {<Go to ISI>://A1990EJ79800009},
6596 <        Volume = {150},
6597 <        Year = {1990}}
6596 >        Volume = 150,
6597 >        Year = 1990}
6598  
6599   @article{Blum1972,
6600          Author = {L. Blum and A.~J. Torruella},
6601 <        Journal = {Journal of Chemical Physics},
6601 >        Journal = jcp,
6602          Number = 1,
6603          Pages = {303-309},
6604          Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
# Line 6324 | Line 6607
6607  
6608   @article{Stone1978,
6609          Author = {A.~J. Stone},
6610 <        Journal = {Molecular Physics},
6610 >        Journal = mp,
6611          Number = 1,
6612          Pages = {241-256},
6613          Title = {The description of bimolecular potentials, forces and torques: the S and V function expansions},
# Line 6333 | Line 6616
6616  
6617   @article{Berardi2003,
6618          Author = {R. Berardi, M. Cecchini and C. Zannoni},
6619 <        Journal = {Journal of Chemical Physics},
6619 >        Journal = jcp,
6620          Number = 18,
6621          Pages = {9933-9946},
6622          Title = {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
# Line 6342 | Line 6625
6625  
6626   @article{Beard2000,
6627          Author = {D. A. Beard and T. Schlick},
6628 <        Journal = {Journal of Chemical Physics},
6628 >        Journal = jcp,
6629          Number = 17,
6630          Pages = {7313-7322},
6631          Title = {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
# Line 6354 | Line 6637
6637          Author = {M.W. Hirsch},
6638          Publisher = {Springer},
6639          Title = {Differential Topology},
6640 <        Year = {1997}}
6640 >        Year = 1997}
6641  
6642   @book{Jost2002,
6643          Address = {Berlin},
6644          Author = {J. Jost},
6645          Publisher = {Springer-Verlag},
6646          Title = {Riemannian Geometry and Geometric Analysis},
6647 <        Year = {2002}}
6647 >        Year = 2002}
6648  
6649   @book{McDuff1998,
6650          Address = {Oxford},
6651          Author = {D. McDuff and D. Salamon},
6652          Publisher = {Oxford Mathematical Monographs},
6653          Title = {Introduction to Symplectic Topology},
6654 <        Year = {1998}}
6654 >        Year = 1998}
6655  
6656   @article{Matubayasi1999,
6657          Author = {N. Matubayasi and M. Nakahara},
6658 <        Journal = {Journal of Chemical Physics},
6658 >        Journal = jcp,
6659          Number = 7,
6660          Pages = {3291-3301},
6661          Title = {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
# Line 6381 | Line 6664
6664  
6665   @article{Miller2002,
6666          Author = {T.F. Miller III, M. Eleftheriou},
6667 <        Journal = {Journal of Chemical Physics},
6667 >        Journal = jcp,
6668          Number = 20,
6669          Pages = {8649-8659},
6670          Title = {Symplectic quaternion scheme for biophysical molecular dynamics},
# Line 6390 | Line 6673
6673  
6674   @article{McMillan1971,
6675          Author = {W.L. McMillan},
6676 <        Journal = {Journal of Chemical Physics},
6676 >        Journal = jcp,
6677          Number = 3,
6678          Pages = {1238-1246},
6679          Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},
# Line 6432 | Line 6715
6715          Title = {The Dynamics of Runge-Kutta Methods},
6716          Volume = 2,
6717          Year = 1992}
6718 +
6719 + @article{HuseyinKaya07012005,
6720 +        Abstract = {It has been demonstrated that a "near-Levinthal" cooperative mechanism, whereby the common G[o] interaction scheme is augmented by an extra favorability for the native state as a whole, can lead to apparent two-state folding/unfolding kinetics over a broad range of native stabilities in lattice models of proteins. Here such a mechanism is shown to be generalizable to a simplified continuum (off-lattice) Langevin dynamics model with a C{alpha} protein chain representation, with the resulting chevron plots exhibiting an extended quasilinear regime reminiscent of that of apparent two-state real proteins. Similarly high degrees of cooperativity are possible in G[o]-like continuum models with rudimentary pairwise desolvation barriers as well. In these models, cooperativity increases with increasing desolvation barrier height, suggesting strongly that two-state-like folding/unfolding kinetics would be achievable when the pairwise desolvation barrier becomes sufficiently high. Besides cooperativity, another generic folding property of interest that has emerged from published experiments on several apparent two-state proteins is that their folding relaxation under constant native stability (isostability) conditions is essentially Arrhenius, entailing high intrinsic enthalpic folding barriers of [~]17-30 kcal/mol. Based on a new analysis of published data on barnase, here we propose that a similar property should also apply to a certain class of non-two-state proteins that fold with chevron rollovers. However, several continuum G[o]-like constructs considered here fail to predict any significant intrinsic enthalpic folding barrier under isostability conditions; thus the physical origin of such barriers in real proteins remains to be elucidated.
6721 + },
6722 +        Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun},
6723 +        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6724 +        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471},
6725 +        Doi = {10.1529/biophysj.104.057471},
6726 +        Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf},
6727 +        Journal = {Biophys. J.},
6728 +        Number = 1,
6729 +        Pages = {520-535},
6730 +        Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}},
6731 +        Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6732 +        Volume = 89,
6733 +        Year = 2005}
6734 +
6735 + @article{JoseGarciadelaTorre02012000,
6736 +        Abstract = {The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (Carrasco and Garcia de la Torre, 1999, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overlapping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 proteins. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 A, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A computational shortcut makes the procedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer program.
6737 + },
6738 +        Author = {{Garc\'{i}a de la Torre}, Jose and Huertas, Maria L. and Carrasco, Beatriz},
6739 +        Eprint = {http://www.biophysj.org/cgi/reprint/78/2/719.pdf},
6740 +        Journal = bj,
6741 +        Number = {2},
6742 +        Pages = {719-730},
6743 +        Title = {{Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure}},
6744 +        Url = {http://www.biophysj.org/cgi/content/abstract/78/2/719},
6745 +        Volume = {78},
6746 +        Year = {2000}}
6747 +
6748 + @article{GarciadelaTorreJ2002,
6749 +        Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain},
6750 +        Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B.},
6751 +        Journal = {Biopolymers},
6752 +        Number = {3},
6753 +        Pages = {163-167},
6754 +        Title = {Hydrodynamic Properties of Rigid Macromolecules Composed of Ellipsoidal and Cylindrical Subunits},
6755 +        Volume = {63},
6756 +        Year = {2002}}

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