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2   %% http://bibdesk.sourceforge.net/
3  
4  
5 < %% Created for Dan Gezelter at 2008-01-11 16:20:18 -0500
5 > %% Created for Dan Gezelter at 2008-03-13 17:04:26 -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{jml = {J. Mol. Liq.}}
30 +
31 + @string{jmb = {J. Mol. Bio.}}
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{Peters:1999uq,
61 +        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.},
62 +        Author = {Peters, MH},
63 +        Date-Added = {2008-03-13 16:54:59 -0400},
64 +        Date-Modified = {2008-03-13 16:56:54 -0400},
65 +        Journal = {Journal of Statistical Physics},
66 +        Keywords = {Brownian particle; Fokker Planck equation; adsorption; molecular friction; force autocorrelation function; molecular dynamics},
67 +        Pages = {557-586},
68 +        Timescited = {0},
69 +        Title = {Fokker-Planck equation, molecular friction, and molecular dynamics for Brownian particle transport near external solid surfaces},
70 +        Volume = {94},
71 +        Year = {1999}}
72 +
73 + @article{Peters:1999qy,
74 +        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].},
75 +        Author = {Peters, MH},
76 +        Date-Added = {2008-03-13 16:54:59 -0400},
77 +        Date-Modified = {2008-03-13 16:56:44 -0400},
78 +        Journal = jcp,
79 +        Pages = {528-538},
80 +        Timescited = {0},
81 +        Title = {Fokker-Planck equation and the grand molecular friction tensor for coupled rotational and translational motions of structured Brownian particles near structured surfaces},
82 +        Volume = {110},
83 +        Year = {1999}}
84 +
85 + @article{Peters:2000fk,
86 +        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].},
87 +        Author = {Peters, MH},
88 +        Date-Added = {2008-03-13 16:54:59 -0400},
89 +        Date-Modified = {2008-03-13 16:56:20 -0400},
90 +        Journal = jcp,
91 +        Pages = {5488-5498},
92 +        Timescited = {0},
93 +        Title = {The Smoluchowski diffusion equation for structured macromolecules near structured surfaces},
94 +        Volume = {112},
95 +        Year = {2000}}
96 +
97 + @article{Nienhuis:1970lr,
98 +        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.},
99 +        Author = {Nienhuis, G. },
100 +        Date-Added = {2008-03-13 16:53:44 -0400},
101 +        Date-Modified = {2008-03-13 16:53:44 -0400},
102 +        Journal = {Physica},
103 +        Number = {1},
104 +        Pages = {26--48},
105 +        Title = {On the microscopic theory of Brownian motion with a rotational degree of freedom},
106 +        Ty = {JOUR},
107 +        Url = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413},
108 +        Volume = {49},
109 +        Year = {1970},
110 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}}
111 +
112 + @article{SunX._jp0762020,
113 +        Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556},
114 +        Author = {Sun, X. and Gezelter, J.D.},
115 +        Date-Added = {2008-02-15 13:48:18 -0500},
116 +        Date-Modified = {2008-02-15 13:48:18 -0500},
117 +        Issn = {1520-6106},
118 +        Journal = jpcb,
119 +        Number = {7},
120 +        Pages = {1968-1975},
121 +        Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes},
122 +        Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020},
123 +        Volume = {112},
124 +        Year = {2008},
125 +        Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}}
126 +
127 + @book{Schlick2002,
128 +        Address = {Secaucus, NJ, USA},
129 +        Author = {Tamar Schlick},
130 +        Date-Added = {2008-02-12 16:52:19 -0500},
131 +        Date-Modified = {2008-02-12 16:53:15 -0500},
132 +        Isbn = {038795404X},
133 +        Publisher = {Springer-Verlag New York, Inc.},
134 +        Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
135 +        Year = {2002}}
136 +
137 + @article{Chun:2000fj,
138 +        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.},
139 +        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},
140 +        Date-Added = {2008-01-22 10:38:33 -0500},
141 +        Date-Modified = {2008-01-22 10:38:49 -0500},
142 +        Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
143 +        Journal = jcc,
144 +        Pages = {159--184},
145 +        Timescited = 0,
146 +        Title = {{MBO(N)D:} A multibody method for long-time molecular dynamics simulations},
147 +        Volume = 21,
148 +        Year = 2000}
149 +
150 + @article{Fogolari:1996lr,
151 +        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.},
152 +        Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.},
153 +        Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
154 +        Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
155 +        Da = {19960924},
156 +        Date-Added = {2008-01-22 10:19:04 -0500},
157 +        Date-Modified = {2008-01-22 10:19:09 -0500},
158 +        Dcom = {19960924},
159 +        Edat = {1996/03/01},
160 +        Issn = {0006-3495 (Print)},
161 +        Jid = {0370626},
162 +        Journal = {Biophys J},
163 +        Jt = {Biophysical journal},
164 +        Language = {eng},
165 +        Lr = {20071115},
166 +        Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; *Models, Molecular; Molecular Structure; Peptides/*chemistry; *Protein Conformation; Software; Thermodynamics},
167 +        Mhda = {1996/03/01 00:01},
168 +        Number = {3},
169 +        Own = {NLM},
170 +        Pages = {1183--1197},
171 +        Pl = {UNITED STATES},
172 +        Pmid = {8785277},
173 +        Pst = {ppublish},
174 +        Pt = {Journal Article},
175 +        Pubm = {Print},
176 +        Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)},
177 +        Sb = {IM},
178 +        So = {Biophys J. 1996 Mar;70(3):1183-97. },
179 +        Stat = {MEDLINE},
180 +        Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.},
181 +        Volume = {70},
182 +        Year = {1996}}
183 +
184 + @inbook{Ramachandran1996,
185 +        Address = {Providence, Rhode Island},
186 +        author = {Gomathi Ramachandran and Tamar Schlick},
187 +        Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
188 +        Date-Added = {2008-01-22 10:03:42 -0500},
189 +        Date-Modified = {2008-01-22 10:06:57 -0500},
190 +        Editor = {P. M. Pardalos and D. Shalloway and G. Xue},
191 +        Pages = {215-231},
192 +        Publisher = {American Mathematical Society},
193 +        Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
194 +        Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
195 +        Volume = {23},
196 +        Year = {1996}}
197 +
198 + @article{FIXMAN:1986lr,
199 +        Author = {Fixman, M},
200 +        Date-Added = {2008-01-22 09:59:29 -0500},
201 +        Date-Modified = {2008-01-22 09:59:35 -0500},
202 +        Journal = {Macromolecules},
203 +        Pages = {1204-1207},
204 +        Timescited = {0},
205 +        Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION},
206 +        Volume = {19},
207 +        Year = {1986}}
208 +
209 + @article{Berendsen87,
210 +        Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
211 +        Date-Added = {2008-01-22 09:53:15 -0500},
212 +        Date-Modified = {2008-01-22 09:53:15 -0500},
213 +        Journal = jpc,
214 +        Pages = {6269-6271},
215 +        Title = {The Missing Term in Effective Pair Potentials},
216 +        Volume = 91,
217 +        Year = 1987}
218 +
219 + @incollection{Berendsen81,
220 +        Address = {Dordrecht},
221 +        Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
222 +        Booktitle = {Intermolecular Forces},
223 +        Date-Added = {2008-01-22 09:52:49 -0500},
224 +        Date-Modified = {2008-01-22 09:52:49 -0500},
225 +        Editor = {B. Pullman},
226 +        Pages = {331-342},
227 +        Publisher = {Reidel},
228 +        Title = {Simple Point Charge Water},
229 +        Year = 1981}
230 +
231 + @article{Stillinger74,
232 +        Author = {F.~H. Stillinger and A. Rahman},
233 +        Date-Added = {2008-01-22 09:51:43 -0500},
234 +        Date-Modified = {2008-01-22 09:51:43 -0500},
235 +        Journal = jcp,
236 +        Number = 4,
237 +        Pages = {1545-1557},
238 +        Title = {Improved simulation of liquid water by molecular dynamics},
239 +        Volume = 60,
240 +        Year = 1974}
241 +
242   @article{Torre:1983lr,
243 <        Author = {de la Torre, Jose Garcia and Rodes, Vicente},
243 >        Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
244          Date-Added = {2008-01-11 16:16:43 -0500},
245          Date-Modified = {2008-01-11 16:16:43 -0500},
246 <        Journal = {The Journal of Chemical Physics},
246 >        Journal = jcp,
247          Journal1 = {The Journal of Chemical Physics},
248          Journal2 = {J. Chem. Phys.},
249          Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
250 <        Number = {5},
250 >        Number = 5,
251          Pages = {2454--2460},
252          Publisher = {AIP},
253          Title = {Effects from bead size and hydrodynamic interactions on the translational and rotational coefficients of macromolecular bead models},
254          Ty = {JOUR},
255          Url = {http://link.aip.org/link/?JCP/79/2454/1},
256 <        Volume = {79},
257 <        Year = {1983}}
256 >        Volume = 79,
257 >        Year = 1983,
258 >        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}}
259  
260   @article{PhysRev.119.53,
261          Author = {Favro, L. Dale},
# Line 33 | Line 264
264          Doi = {10.1103/PhysRev.119.53},
265          Journal = {Phys. Rev.},
266          Month = {Jul},
267 <        Number = {1},
268 <        Numpages = {9},
267 >        Number = 1,
268 >        Numpages = 9,
269          Pages = {53--62},
270          Publisher = {American Physical Society},
271          Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body},
272 <        Volume = {119},
273 <        Year = {1960}}
272 >        Volume = 119,
273 >        Year = 1960,
274 >        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}}
275  
276   @article{hess:209,
277          Author = {Berk Hess},
278          Date-Added = {2008-01-08 16:41:06 -0500},
279          Date-Modified = {2008-01-08 16:41:06 -0500},
280          Doi = {10.1063/1.1421362},
281 <        Journal = {The Journal of Chemical Physics},
281 >        Journal = jcp,
282          Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
283 <        Number = {1},
283 >        Number = 1,
284          Pages = {209-217},
285          Publisher = {AIP},
286          Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
287          Url = {http://link.aip.org/link/?JCP/116/209/1},
288 <        Volume = {116},
289 <        Year = {2002}}
288 >        Volume = 116,
289 >        Year = 2002,
290 >        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
291 >        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}}
292  
293   @article{Garcia-de-la-Torre:1997qy,
294          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.},
295          Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es},
296 <        Au = {Garcia de la Torre, J and Carrasco, B and Harding, SE},
297 <        Author = {Garcia de la Torre, J and Carrasco, B and Harding, S E},
298 <        Da = {19970709},
296 >        Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE},
297 >        Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E},
298 >        Da = 19970709,
299          Date-Added = {2008-01-08 15:45:31 -0500},
300          Date-Modified = {2008-01-08 15:46:57 -0500},
301 <        Dcom = {19970709},
301 >        Dcom = 19970709,
302          Edat = {1997/01/01},
303          Issn = {0175-7571 (Print)},
304 <        Jid = {8409413},
304 >        Jid = 8409413,
305          Journal = {Eur Biophys J},
306          Jt = {European biophysics journal : EBJ},
307          Keywords = {Birefringence; Fluorescence Polarization; Humans; Immunoglobulin G/chemistry; Models, Structural; *Protein Conformation; Proteins/*chemistry; Scattering, Radiation; *Software; Ultracentrifugation/methods},
308          Language = {eng},
309 <        Lr = {20061115},
309 >        Lr = 20061115,
310          Mhda = {1997/01/01 00:01},
311          Number = {5-6},
312          Own = {NLM},
313          Pages = {361--372},
314          Pl = {GERMANY},
315 <        Pmid = {9213556},
315 >        Pmid = 9213556,
316          Pst = {ppublish},
317          Pt = {Journal Article; Research Support, Non-U.S. Gov't},
318          Pubm = {Print},
# Line 87 | Line 321
321          So = {Eur Biophys J. 1997;25(5-6):361-72.},
322          Stat = {MEDLINE},
323          Title = {SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.},
324 <        Volume = {25},
325 <        Year = {1997}}
324 >        Volume = 25,
325 >        Year = 1997}
326  
327   @article{Ravichandran:1999fk,
328          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].},
329          Author = {Ravichandran, S and Bagchi, B},
330          Date-Added = {2008-01-08 15:24:48 -0500},
331          Date-Modified = {2008-01-08 15:25:41 -0500},
332 <        Journal = {Journal of Chemical Physics},
332 >        Journal = jcp,
333          Pages = {7505-7511},
334          Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
335 <        Volume = {111},
336 <        Year = {1999}}
335 >        Volume = 111,
336 >        Year = 1999}
337  
338   @article{TANG:1993lr,
339          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.},
340          Author = {TANG, SA and EVANS, GT},
341          Date-Added = {2008-01-08 15:23:42 -0500},
342          Date-Modified = {2008-01-08 15:24:09 -0500},
343 <        Journal = {Molecular Physics},
343 >        Journal = mp,
344          Pages = {1443-1457},
345          Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
346 <        Volume = {80},
347 <        Year = {1993}}
346 >        Volume = 80,
347 >        Year = 1993}
348  
349   @article{Schmidt:2003kx,
350          Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a spherical solute in a dense fluid of spherical solvent particles. The size and mass of the solute particle are related in such a way that we can naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that as long as the solute radius is interpreted as an effective hydrodynamic radius, the Stokes-Einstein law with slip boundary conditions is satisfied as the Brownian limit is approached (specifically, when the solute is roughly 100 times more massive than the solvent particles). In contrast, the Stokes-Einstein law is not satisfied for a tagged particle of the neat solvent. We also find that in the Brownian limit the amplitude of the long-time tail of the solute's velocity autocorrelation function is in good agreement with theoretical hydrodynamic predictions. When the solvent density is substantially lower than the triple density, the Stokes-Einstein law is no longer satisfied, and the amplitude of the long-time tail is not in good agreement with theoretical predictions, signaling the breakdown of hydrodynamics. (C) 2003 American Institute of Physics.},
# Line 118 | Line 352
352          Date-Added = {2008-01-08 15:12:53 -0500},
353          Date-Modified = {2008-01-08 15:13:21 -0500},
354          Doi = {DOI 10.1063/1.1610442},
355 <        Journal = {Journal of Chemical Physics},
355 >        Journal = jcp,
356          Pages = {8062-8068},
357          Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
358 <        Volume = {119},
359 <        Year = {2003}}
358 >        Volume = 119,
359 >        Year = 2003,
360 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}
361  
362   @article{Schmidt:2004fj,
363          Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a variety of solutes in a dense fluid of spherical solvent particles. We explore the effects of surface roughness of the solute on the resulting hydrodynamic boundary condition as we naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that when the solute and solvent interact through a purely repulsive isotropic potential, in the Brownian limit the Stokes-Einstein law is satisfied with slip boundary conditions. However, when surface roughness is introduced through an anisotropic solute-solvent interaction potential, we find that the Stokes-Einstein law is satisfied with stick boundary conditions. In addition, when the attractive strength of a short-range isotropic solute-solvent potential is increased, the solute becomes dressed with solvent particles, making it effectively rough, and so stick boundary conditions are again recovered.},
# Line 130 | Line 365
365          Date-Added = {2008-01-08 15:12:53 -0500},
366          Date-Modified = {2008-01-08 15:13:20 -0500},
367          Doi = {DOI 10.1021/jp037185r},
368 <        Journal = {Journal of Physical Chemistry B},
368 >        Journal = jpcb,
369          Pages = {6767-6771},
370          Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
371 <        Volume = {108},
372 <        Year = {2004}}
371 >        Volume = 108,
372 >        Year = 2004,
373 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}}
374  
375   @article{Klein01,
376          Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
# Line 274 | Line 510
510          Date-Modified = {2008-01-08 14:58:56 -0500},
511          Journal = {J. Chem. Phys.},
512          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf},
513 <        Number = {19},
513 >        Number = 19,
514          Pages = {8577-8593},
515          Title = {A smooth particle mesh Ewald method},
516 <        Volume = {103},
517 <        Year = {1995}}
516 >        Volume = 103,
517 >        Year = 1995}
518  
519   @article{Ricci94,
520          Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
# Line 328 | Line 564
564          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf},
565          Pages = {7320-7327},
566          Title = {Acceleration of Convergence for Lattice Sums},
567 <        Volume = {93},
568 <        Year = {1989}}
567 >        Volume = 93,
568 >        Year = 1989}
569  
570   @article{Petersen95,
571          Author = {H.~G. Petersen},
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574          Journal = {J. Chem. Phys.},
575          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
576          Month = {September},
577 <        Number = {9},
577 >        Number = 9,
578          Pages = {3668-3679},
579          Title = {Accuracy and efficiency of the particle mesh Ewald method},
580 <        Volume = {103},
581 <        Year = {1995}}
580 >        Volume = 103,
581 >        Year = 1995}
582  
583   @article{Duncan06,
584          Author = {Peter D. Duncan and Philip J. Camp},
# Line 428 | Line 664
664          Year = 2003}
665  
666   @article{Cascales98,
667 <        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
667 >        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and {Garc\'{i}a de la Torre}, Jose},
668          Date-Added = {2008-01-08 14:58:56 -0500},
669          Date-Modified = {2008-01-08 14:58:57 -0500},
670          Journal = {J. Phys. Chem. B},
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711          Journal = {Phil. Mag. A},
712          Pages = {1057-1066},
713          Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
714 <        Volume = {75},
715 <        Year = {1997}}
714 >        Volume = 75,
715 >        Year = 1997}
716  
717   @inproceedings{Gotze89,
718          Address = {Amsterdam},
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765          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
766          Pages = {1322-1331},
767          Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
768 <        Volume = {99},
769 <        Year = {1995}}
768 >        Volume = 99,
769 >        Year = 1995}
770  
771   @article{Ayton02,
772          Author = {G. Ayton and G.~A. Voth},
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848          Doi = {10.1529/biophysj.106.086017},
849          Eprint = {http://www.biophysj.org/cgi/reprint/90/11/L83.pdf},
850          Journal = {Biophys. J.},
851 <        Number = {11},
851 >        Number = 11,
852          Pages = {L83-85},
853          Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}},
854          Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
855 <        Volume = {90},
856 <        Year = {2006}}
855 >        Volume = 90,
856 >        Year = 2006,
857 >        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
858 >        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017}}
859  
860   @article{deJoannis06,
861          Author = {J. de~Joannis and F.~Y. Jiang and J.~T. Kindt},
# Line 747 | Line 985
985          Journal = {Mol. Simul.},
986          Pages = {351-368},
987          Title = {Cutoff Errors in the Ewald. Summation Formulae for Point Charge Systems},
988 <        Volume = {9},
989 <        Year = {1992}}
988 >        Volume = 9,
989 >        Year = 1992}
990  
991   @article{Tlusty00,
992          Author = {T. Tlusty and S.~A. Safran},
# Line 767 | Line 1005
1005          Doi = {10.1103/PhysRevA.38.1005},
1006          Journal = {Phys. Rev. A},
1007          Month = {Jul},
1008 <        Number = {2},
1009 <        Numpages = {13},
1008 >        Number = 2,
1009 >        Numpages = 13,
1010          Pages = {1005--1018},
1011          Publisher = {American Physical Society},
1012          Title = {Defects in flexible membranes with crystalline order},
1013 <        Volume = {38},
1014 <        Year = {1988}}
1013 >        Volume = 38,
1014 >        Year = 1988,
1015 >        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005}}
1016  
1017   @article{Monroe95,
1018          Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
# Line 834 | Line 1073
1073          Journal = {Ann. Physik},
1074          Pages = {253-287},
1075          Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
1076 <        Volume = {64},
1077 <        Year = {1921}}
1076 >        Volume = 64,
1077 >        Year = 1921}
1078  
1079   @article{Zwanzig88,
1080          Author = {R. Zwanzig},
# Line 882 | Line 1121
1121          Date-Added = {2008-01-08 14:58:56 -0500},
1122          Date-Modified = {2008-01-08 14:58:58 -0500},
1123          Journal = prl,
1124 <        Pages = {3649},
1124 >        Pages = 3649,
1125          Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
1126          Volume = 82,
1127 <        Year = {1999}}
1127 >        Year = 1999}
1128  
1129   @article{Ngai81,
1130          Author = {K.~L. Ngai and F.-S. Liu},
# Line 935 | Line 1174
1174          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
1175          Pages = {69-88},
1176          Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
1177 <        Volume = {78},
1178 <        Year = {1999}}
1177 >        Volume = 78,
1178 >        Year = 1999}
1179  
1180   @article{Spohr97,
1181          Author = {E. Spohr},
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1183          Date-Modified = {2008-01-08 14:58:58 -0500},
1184          Journal = {J. Chem. Phys.},
1185          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
1186 <        Number = {16},
1186 >        Number = 16,
1187          Pages = {6342-6348},
1188          Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
1189 <        Volume = {107},
1190 <        Year = {1997}}
1189 >        Volume = 107,
1190 >        Year = 1997}
1191  
1192   @article{Marrink01b,
1193          Author = {S.~J. Marrink and A.~E. Mark},
1194          Date-Added = {2008-01-08 14:58:56 -0500},
1195          Date-Modified = {2008-01-08 14:58:58 -0500},
1196 <        Journal = {Journal of Physical Chemistry B},
1196 >        Journal = jpcb,
1197          Pages = {6122-6127},
1198          Title = {Effect of undulations on surface tension in simulated bilayers},
1199          Volume = 105,
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1286          Journal = {Mol. Phys.},
1287          Pages = {1313-1327},
1288          Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices},
1289 <        Volume = {37},
1290 <        Year = {1979}}
1289 >        Volume = 37,
1290 >        Year = 1979}
1291  
1292   @article{Heyes81,
1293          Author = {D.~M. Heyes},
# Line 1057 | Line 1296
1296          Journal = {J. Chem. Phys.},
1297          Keywords = {Empty Keywords},
1298          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
1299 <        Number = {3},
1299 >        Number = 3,
1300          Pages = {1924-1929},
1301          Title = {Electrostatic potentials and fields in infinite point charge lattices},
1302 <        Volume = {74},
1303 <        Year = {1981}}
1302 >        Volume = 74,
1303 >        Year = 1981}
1304  
1305   @article{Tsonchev04,
1306          Author = {Stefan Tsonchev and George C. Schatz and Mark A. Ratner},
# Line 1081 | Line 1320
1320          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
1321          Pages = {253-261},
1322          Title = {Electrostatics calculations: recent methodological advances and applications to membranes},
1323 <        Volume = {11},
1324 <        Year = {2001}}
1323 >        Volume = 11,
1324 >        Year = 2001}
1325  
1326   @article{Arnold02,
1327          Author = {A. Arnold and J. {de Joannis} and C. Holm},
# Line 1091 | Line 1330
1330          Doi = {10.1063/1.149195},
1331          Journal = {J. Chem. Phys.},
1332          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Arnold_SlabElectrostatics_02.pdf},
1333 <        Number = {6},
1333 >        Number = 6,
1334          Pages = {2496-2502},
1335          Title = {Electrostatics in periodic slab geometries. I},
1336 <        Volume = {117},
1337 <        Year = {2002}}
1336 >        Volume = 117,
1337 >        Year = 2002,
1338 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1339  
1340   @article{deJoannis02,
1341          Author = {J. {de Joannis} and A. Arnold and C. Holm},
# Line 1104 | Line 1344
1344          Doi = {10.1063/1.149195},
1345          Journal = {J. Chem. Phys.},
1346          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf},
1347 <        Number = {6},
1347 >        Number = 6,
1348          Pages = {2503-2512},
1349          Title = {Electrostatics in periodic slab geometries. II},
1350 <        Volume = {117},
1351 <        Year = {2002}}
1350 >        Volume = 117,
1351 >        Year = 2002,
1352 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1353  
1354   @article{Barenco95,
1355          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},
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1399          Date-Modified = {2008-01-08 14:58:58 -0500},
1400          Journal = {J. Phys. Chem. B},
1401          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
1402 <        Number = {41},
1402 >        Number = 41,
1403          Pages = {10725-10732},
1404          Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
1405 <        Volume = {106},
1406 <        Year = {2002}}
1405 >        Volume = 106,
1406 >        Year = 2002}
1407  
1408   @article{Metropolis53,
1409          Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
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1421          Date-Added = {2008-01-08 14:58:56 -0500},
1422          Date-Modified = {2008-01-08 14:58:58 -0500},
1423          Journal = {Surf. Sci.},
1424 <        Pages = {195},
1424 >        Pages = 195,
1425          Title = {Errata: The electrostatic potential in the surface region of an ionic crystal},
1426 <        Volume = {54},
1427 <        Year = {1976}}
1426 >        Volume = 54,
1427 >        Year = 1976}
1428  
1429   @article{Steane96,
1430          Author = {A.~M. Steane},
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1452          Date-Modified = {2008-01-08 14:58:59 -0500},
1453          Journal = {J. Chem. Phys.},
1454          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
1455 <        Number = {4},
1455 >        Number = 4,
1456          Pages = {1856-1872},
1457          Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study},
1458 <        Volume = {110},
1459 <        Year = {1999}}
1458 >        Volume = 110,
1459 >        Year = 1999}
1460  
1461   @article{Rhee89,
1462          Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
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1464          Date-Modified = {2008-01-08 14:58:59 -0500},
1465          Journal = {Phys. Rev. B},
1466          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
1467 <        Number = {1},
1467 >        Number = 1,
1468          Pages = {36-42},
1469          Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions},
1470 <        Volume = {40},
1471 <        Year = {1989}}
1470 >        Volume = 40,
1471 >        Year = 1989}
1472  
1473   @article{Yeh99,
1474          Author = {I.-C. Yeh and M.~L. Berkowitz},
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1476          Date-Modified = {2008-01-08 14:58:59 -0500},
1477          Journal = {J. Chem. Phys.},
1478          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
1479 <        Number = {7},
1479 >        Number = 7,
1480          Pages = {3155-3162},
1481          Title = {Ewald summation for systems with slab geometry},
1482 <        Volume = {111},
1483 <        Year = {1999}}
1482 >        Volume = 111,
1483 >        Year = 1999}
1484  
1485   @article{Brodka04,
1486          Author = {A. Br\'{o}dka},
# Line 1250 | Line 1491
1491          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf},
1492          Pages = {62-67},
1493          Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
1494 <        Volume = {400},
1495 <        Year = {2004}}
1494 >        Volume = 400,
1495 >        Year = 2004,
1496 >        Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086}}
1497  
1498   @article{Chuang98,
1499          Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
# Line 1321 | Line 1563
1563          Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.},
1564          Date-Added = {2008-01-08 14:58:56 -0500},
1565          Date-Modified = {2008-01-08 14:58:59 -0500},
1566 <        Journal = {Biophysical Journal},
1566 >        Journal = bj,
1567          Journal1 = {Biophys. J.},
1568 <        Number = {1},
1568 >        Number = 1,
1569          Pages = {609--622},
1570          Title = {Fluorescence Imaging of Two-Photon Linear Dichroism: Cholesterol Depletion Disrupts Molecular Orientation in Cell Membranes},
1571          Ty = {JOUR},
1572          Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
1573 <        Volume = {88},
1574 <        Year = {2005}}
1573 >        Volume = 88,
1574 >        Year = 2005,
1575 >        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609}}
1576  
1577   @inbook{Blumen86,
1578          Address = {Amsterdam},
# Line 1380 | Line 1623
1623          Date-Added = {2008-01-08 14:58:56 -0500},
1624          Date-Modified = {2008-01-08 14:58:59 -0500},
1625          Eid = 157802,
1626 <        Journal = {Physical Review Letters},
1626 >        Journal = prl,
1627          Number = 15,
1628          Numpages = 4,
1629          Pages = 157802,
# Line 1447 | Line 1690
1690          Date-Modified = {2008-01-08 14:58:59 -0500},
1691          Journal = {J. Chem. Phys.},
1692          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
1693 <        Number = {6},
1693 >        Number = 6,
1694          Pages = {5024-5031},
1695          Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
1696 <        Volume = {101},
1697 <        Year = {1994}}
1696 >        Volume = 101,
1697 >        Year = 1994}
1698  
1699   @article{Stillinger85,
1700          Author = {F.~H. Stillinger and T.~A. Weber},
# Line 1472 | Line 1715
1715          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
1716          Pages = {398-404},
1717          Title = {Integral equation theory for correcting truncation errors in molecular simulations},
1718 <        Volume = {367},
1719 <        Year = {2003}}
1718 >        Volume = 367,
1719 >        Year = 2003}
1720  
1721   @article{Ayton01,
1722          Author = {Gary Ayton and Scott G. Bardenhagen and Patrick McMurty and Deborah Sulsky and Gregory A. Voth},
# Line 1532 | Line 1775
1775          Date-Modified = {2008-01-08 14:58:59 -0500},
1776          Journal = {J. Chem. Phys.},
1777          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
1778 <        Number = {8},
1778 >        Number = 8,
1779          Pages = {3014-3021},
1780          Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
1781 <        Volume = {103},
1782 <        Year = {1995}}
1781 >        Volume = 103,
1782 >        Year = 1995}
1783  
1784   @article{Wan94,
1785          Author = {Yi. Wan and R.~M. Stratt},
# Line 1572 | Line 1815
1815          Author = {E. Lindahl and O. Edholm},
1816          Date-Added = {2008-01-08 14:58:56 -0500},
1817          Date-Modified = {2008-01-08 14:58:59 -0500},
1818 <        Journal = {Biophysical Journal},
1818 >        Journal = bj,
1819          Month = {July},
1820          Pages = {426-433},
1821          Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
# Line 1607 | Line 1850
1850          Pages = {2213-2216},
1851          Title = {Model for Lamellar Phases of Interacting Lipid Membranes},
1852          Volume = 61,
1853 <        Year = 1988}
1853 >        Year = 1988,
1854 >        Bdsk-File-1 = {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}}
1855  
1856   @article{Daw89,
1857          Author = {Murray~S. Daw},
# Line 1624 | Line 1868
1868          Date-Added = {2008-01-08 14:58:56 -0500},
1869          Date-Modified = {2008-01-08 14:58:59 -0500},
1870          Journal = {J. Chem. Soc., Faraday Trans. II},
1871 <        Number = {7},
1871 >        Number = 7,
1872          Pages = {1485-1496},
1873          Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride},
1874 <        Volume = {73},
1875 <        Year = {1977}}
1874 >        Volume = 73,
1875 >        Year = 1977}
1876  
1877   @article{Vuilleumier97,
1878          Author = {Rodolphe Vuilleumier and Daniel Borgis},
# Line 1663 | Line 1907
1907          Author = {A.~M. Smondyrev and M.~L. Berkowitz},
1908          Date-Added = {2008-01-08 14:58:56 -0500},
1909          Date-Modified = {2008-01-08 14:59:00 -0500},
1910 <        Journal = {Biophysical Journal},
1910 >        Journal = bj,
1911          Pages = {2472-2478},
1912          Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1913          Volume = 76,
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1917          Author = {S.~J. Marrink and D.~P. Teileman},
1918          Date-Added = {2008-01-08 14:58:56 -0500},
1919          Date-Modified = {2008-01-08 14:59:00 -0500},
1920 <        Journal = {Biophysical Journal},
1920 >        Journal = bj,
1921          Pages = {2386-2392},
1922          Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1923          Volume = 83,
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1961          Doi = {10.1021/jp9937757},
1962          Journal = {J. Phys. Chem. B},
1963          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
1964 <        Number = {15},
1964 >        Number = 15,
1965          Pages = {3668-3675},
1966          Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
1967 <        Volume = {104},
1968 <        Year = {2000}}
1967 >        Volume = 104,
1968 >        Year = 2000,
1969 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757}}
1970  
1971   @article{Venable00,
1972          Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
# Line 1738 | Line 1983
1983          Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
1984          Date-Added = {2008-01-08 14:58:56 -0500},
1985          Date-Modified = {2008-01-08 14:59:00 -0500},
1986 <        Journal = {Biophysical Journal},
1986 >        Journal = bj,
1987          Pages = {3636-3645},
1988          Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
1989          Volume = 84,
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2006          Journal = {J. Chem. Phys.},
2007          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
2008          Month = {October},
2009 <        Number = {7},
2009 >        Number = 7,
2010          Pages = {3336-3359},
2011          Title = {Molecular Dynamics Study of Liquid Water},
2012 <        Volume = {55},
2013 <        Year = {1971}}
2012 >        Volume = 55,
2013 >        Year = 1971}
2014  
2015   @article{Sum03,
2016          Author = {A.~K. Sum and J.~J. de~Pablo},
2017          Date-Added = {2008-01-08 14:58:56 -0500},
2018          Date-Modified = {2008-01-08 14:59:00 -0500},
2019 <        Journal = {Biophysical Journal},
2019 >        Journal = bj,
2020          Pages = {3636-3645},
2021          Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
2022          Volume = 85,
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2071          Journal = {Mol. Phys.},
2072          Pages = {789-792},
2073          Title = {Monte Carlo studies of the dielectric properties of water-like models},
2074 <        Volume = {26},
2075 <        Year = {1973}}
2074 >        Volume = 26,
2075 >        Year = 1973}
2076  
2077   @article{Brush66,
2078          Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
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2081          Journal = {J. Chem. Phys.},
2082          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
2083          Month = {September},
2084 <        Number = {6},
2084 >        Number = 6,
2085          Pages = {2102-2118},
2086          Title = {Monte Carlo Study of a One-Component Plasma. I},
2087 <        Volume = {45},
2088 <        Year = {1966}}
2087 >        Volume = 45,
2088 >        Year = 1966}
2089  
2090   @article{Tenchov2001,
2091          Author = {Boris Tenchov and Rumiana Koynova and Gert Rapp},
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2103          Date-Modified = {2008-01-08 14:59:00 -0500},
2104          Doi = {10.1002/jcc.540150702},
2105          Journal = {J. Comput. Chem.},
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2106 >        Number = 7,
2107          Pages = {667-683},
2108          Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
2109 <        Volume = {15},
2110 <        Year = {1994}}
2109 >        Volume = 15,
2110 >        Year = 1994,
2111 >        Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150702}}
2112  
2113   @article{McKinnon92,
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2206          Date-Added = {2008-01-08 14:58:56 -0500},
2207          Date-Modified = {2008-01-08 14:59:00 -0500},
2208 <        Journal = {Biophysical Journal},
2208 >        Journal = bj,
2209          Pages = {1537-1553},
2210          Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
2211          Volume = 79,
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2240          Date-Modified = {2008-01-08 14:59:00 -0500},
2241          Journal = {J. Chem. Phys.},
2242          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
2243 <        Number = {5},
2243 >        Number = 5,
2244          Pages = {1062-1063},
2245          Title = {Optimum Atomic Shape for Bertaut Series},
2246 <        Volume = {25},
2247 <        Year = {1956}}
2246 >        Volume = 25,
2247 >        Year = 1956}
2248  
2249   @article{Renard1966,
2250          Author = {R\'emi Renard and Carl W. Garland},
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2509          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Kawata_Rapid2DEwald_01.pdf},
2510          Pages = {157-164},
2511          Title = {Rapid calculation of two-dimensional Ewald summation},
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2516          Author = {J.~A. Barker},
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2713          Date-Modified = {2008-01-08 14:59:01 -0500},
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2715          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
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2716 >        Number = 1752,
2717          Pages = {27-56},
2718          Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
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2720 >        Year = 1980}
2721  
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2723          Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
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2830          Doi = {10.1529/biophysj.104.056606},
2831          Eprint = {http://www.biophysj.org/cgi/reprint/88/4/2626.pdf},
2832          Journal = {Biophys. J.},
2833 <        Number = {4},
2833 >        Number = 4,
2834          Pages = {2626-2637},
2835          Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}},
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2837 <        Volume = {88},
2838 <        Year = {2005}}
2837 >        Volume = 88,
2838 >        Year = 2005,
2839 >        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2840 >        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606}}
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2947          Date-Added = {2008-01-08 14:58:56 -0500},
2948          Date-Modified = {2008-01-08 14:59:02 -0500},
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2950 <        Number = {2},
2950 >        Number = 2,
2951          Pages = {387-400},
2952          Title = {The computer simulation of polar liquids},
2953 <        Volume = {38},
2954 <        Year = {1979}}
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2954 >        Year = 1979}
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2994 >        Volume = 49,
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3041          Journal = {J. Chem. Phys.},
3042          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
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3048  
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3050          Author = {G. Brannigan and A.~C. Tamboli and F.~L.~H. Brown},
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3257 <        Numpages = {3},
3256 >        Number = 7,
3257 >        Numpages = 3,
3258          Pages = {923--926},
3259          Publisher = {American Physical Society},
3260          Title = {Wrinkling transition in partially polymerized vesicles},
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3264  
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3266          Author = {H. Wendt and F.~F. Abraham},
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3276          Date-Added = {2008-01-08 14:58:56 -0500},
3277          Date-Modified = {2008-01-08 14:59:03 -0500},
3278          Note = {private correspondence},
3279 <        Year = {2000}}
3279 >        Year = 2000}
3280  
3281   @article{Dwyer1977,
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3338          Date-Added = {2008-01-08 14:57:14 -0500},
3339          Date-Modified = {2008-01-08 14:57:14 -0500},
3340          Journal = {Chemical Engineering Science},
3341 <        Number = {12},
3341 >        Number = 12,
3342          Pages = {1769--1776},
3343          Title = {The slow translation and rotation of two unequal spheres in a viscous fluid},
3344          Ty = {JOUR},
3345          Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
3346 <        Volume = {24},
3347 <        Year = {1969}}
3346 >        Volume = 24,
3347 >        Year = 1969,
3348 >        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}}
3349  
3350   @article{Stimson:1926qy,
3351          Author = {Stimson, M and Jeffery, GB},
# Line 3104 | Line 3354
3354          Journal = {Proceedings of the Royal Society of London Series A-Containing Papers of a Mathematical and Physical Character},
3355          Pages = {110-116},
3356          Title = {The motion of two spheres in a viscous fluid},
3357 <        Volume = {111},
3358 <        Year = {1926}}
3357 >        Volume = 111,
3358 >        Year = 1926}
3359  
3360   @article{Orlandi:2006fk,
3361          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.},
3362          Address = {Dipartimento di Chimica Fisica e Inorganica, and INSTM, Universita di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.},
3363          Au = {Orlandi, S and Berardi, R and Steltzer, J and Zannoni, C},
3364          Author = {Orlandi, Silvia and Berardi, Roberto and Steltzer, Joachim and Zannoni, Claudio},
3365 <        Da = {20060407},
3365 >        Da = 20060407,
3366          Date-Added = {2008-01-08 14:47:56 -0500},
3367          Date-Modified = {2008-01-08 14:48:06 -0500},
3368 <        Dcom = {20070727},
3368 >        Dcom = 20070727,
3369          Doi = {10.1063/1.2176622},
3370          Edat = {2006/04/08 09:00},
3371          Issn = {0021-9606 (Print)},
3372 <        Jid = {0375360},
3372 >        Jid = 0375360,
3373          Journal = {J Chem Phys},
3374          Jt = {The Journal of chemical physics},
3375          Language = {eng},
3376          Mhda = {2006/04/08 09:01},
3377 <        Number = {12},
3377 >        Number = 12,
3378          Own = {NLM},
3379 <        Pages = {124907},
3379 >        Pages = 124907,
3380          Pl = {United States},
3381 <        Pmid = {16599725},
3381 >        Pmid = 16599725,
3382          Pst = {ppublish},
3383          Pt = {Journal Article},
3384          Pubm = {Print},
3385          So = {J Chem Phys. 2006 Mar 28;124(12):124907.},
3386          Stat = {PubMed-not-MEDLINE},
3387          Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.},
3388 <        Volume = {124},
3389 <        Year = {2006}}
3388 >        Volume = 124,
3389 >        Year = 2006,
3390 >        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}}
3391  
3392   @article{sun:031602,
3393          Author = {Xiuquan Sun and J. Daniel Gezelter},
3394          Date-Added = {2008-01-08 14:42:33 -0500},
3395          Date-Modified = {2008-01-08 14:42:33 -0500},
3396          Doi = {10.1103/PhysRevE.75.031602},
3397 <        Eid = {031602},
3397 >        Eid = 031602,
3398          Journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)},
3399          Keywords = {lattice theory; membranes},
3400 <        Number = {3},
3401 <        Numpages = {7},
3402 <        Pages = {031602},
3400 >        Number = 3,
3401 >        Numpages = 7,
3402 >        Pages = 031602,
3403          Publisher = {APS},
3404          Title = {Spontaneous corrugation of dipolar membranes},
3405          Url = {http://link.aps.org/abstract/PRE/v75/e031602},
3406 <        Volume = {75},
3407 <        Year = {2007}}
3406 >        Volume = 75,
3407 >        Year = 2007,
3408 >        Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602},
3409 >        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}}
3410  
3411   @article{Ortega:2007lr,
3412          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.},
3413          Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.},
3414 <        Au = {Ortega, A and Garcia de la Torre, J},
3415 <        Author = {Ortega, A and Garcia de la Torre, J},
3416 <        Da = {20070813},
3414 >        Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3415 >        Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3416 >        Da = 20070813,
3417          Date-Added = {2008-01-08 14:38:03 -0500},
3418          Date-Modified = {2008-01-08 14:38:49 -0500},
3419 <        Dcom = {20071017},
3420 <        Dep = {20070724},
3419 >        Dcom = 20071017,
3420 >        Dep = 20070724,
3421          Doi = {10.1021/bm700473f},
3422          Edat = {2007/07/25 09:00},
3423          Issn = {1525-7797 (Print)},
3424 <        Jid = {100892849},
3424 >        Jid = 100892849,
3425          Journal = {Biomacromolecules},
3426          Jt = {Biomacromolecules},
3427          Keywords = {Computer Simulation; Heparin/chemistry; Macromolecular Substances/*chemistry; *Models, Chemical; *Models, Molecular; Molecular Conformation; Particle Size; Protein Conformation; Proteins/chemistry; Software; Solutions},
3428          Language = {eng},
3429          Mhda = {2007/10/18 09:00},
3430 <        Number = {8},
3430 >        Number = 8,
3431          Own = {NLM},
3432          Pages = {2464--2475},
3433          Phst = {2007/07/24 {$[$}aheadofprint{$]$}},
3434          Pl = {United States},
3435 <        Pmid = {17645309},
3435 >        Pmid = 17645309,
3436          Pst = {ppublish},
3437          Pt = {Journal Article; Research Support, Non-U.S. Gov't},
3438          Pubm = {Print-Electronic},
# Line 3188 | Line 3441
3441          So = {Biomacromolecules. 2007 Aug;8(8):2464-75. Epub 2007 Jul 24.},
3442          Stat = {MEDLINE},
3443          Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.},
3444 <        Volume = {8},
3445 <        Year = {2007}}
3444 >        Volume = 8,
3445 >        Year = 2007,
3446 >        Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}}
3447  
3448   @article{Torre2003,
3449          Abstract = {While the prediction of hydrodynamic properties of rigid particles
# Line 3215 | Line 3469
3469      We provide an example of the application of this methodology to
3470      the dynamics of a semiflexible, wormlike DNA.},
3471          Annote = {724XK Times Cited:6 Cited References Count:64},
3472 <        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},
3472 >        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},
3473          Issn = {0175-7571},
3474          Journal = {European Biophysics Journal with Biophysics Letters},
3475          Month = {Aug},
3476 <        Number = {5},
3476 >        Number = 5,
3477          Pages = {477-486},
3478          Title = {Calculation of the solution properties of flexible macromolecules: methods and applications},
3479          Uri = {<Go to ISI>://000185513400011},
3480 <        Volume = {32},
3481 <        Year = {2003}}
3480 >        Volume = 32,
3481 >        Year = 2003}
3482  
3483   @article{Alakent2005,
3484          Abstract = {Time series analysis tools are employed on the principal modes obtained
# Line 3264 | Line 3518
3518          Annote = {973OH Times Cited:1 Cited References Count:33},
3519          Author = {B. Alakent and M. C. Camurdan and P. Doruker},
3520          Issn = {0021-9606},
3521 <        Journal = {Journal of Chemical Physics},
3521 >        Journal = jcp,
3522          Month = {Oct 8},
3523 <        Number = {14},
3523 >        Number = 14,
3524          Pages = {-},
3525          Title = {Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects},
3526          Uri = {<Go to ISI>://000232532000064},
3527 <        Volume = {123},
3528 <        Year = {2005}}
3527 >        Volume = 123,
3528 >        Year = 2005}
3529  
3530   @book{Alexander1987,
3531          Address = {New York},
3532          Author = {C. Alexander},
3533          Publisher = {Oxford University Press},
3534          Title = {A Pattern Language: Towns, Buildings, Construction},
3535 <        Year = {1987}}
3535 >        Year = 1987}
3536  
3537   @book{Allen1987,
3538          Address = {New York},
3539          Author = {M.~P. Allen and D.~J. Tildesley},
3540          Publisher = {Oxford University Press},
3541          Title = {Computer Simulations of Liquids},
3542 <        Year = {1987}}
3542 >        Year = 1987}
3543  
3544   @article{Allison1991,
3545          Abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
# Line 3307 | Line 3561
3561          Issn = {0024-9297},
3562          Journal = {Macromolecules},
3563          Month = {Jan 21},
3564 <        Number = {2},
3564 >        Number = 2,
3565          Pages = {530-536},
3566          Title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application to Polarized Dynamic Light-Scattering},
3567          Uri = {<Go to ISI>://A1991EU81400029},
3568 <        Volume = {24},
3569 <        Year = {1991}}
3568 >        Volume = 24,
3569 >        Year = 1991}
3570  
3571   @article{Andersen1983,
3572          Annote = {Rq238 Times Cited:559 Cited References Count:14},
3573          Author = {H. C. Andersen},
3574          Issn = {0021-9991},
3575 <        Journal = {Journal of Computational Physics},
3576 <        Number = {1},
3575 >        Journal = jcop,
3576 >        Number = 1,
3577          Pages = {24-34},
3578          Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
3579          Uri = {<Go to ISI>://A1983RQ23800002},
3580 <        Volume = {52},
3581 <        Year = {1983}}
3580 >        Volume = 52,
3581 >        Year = 1983}
3582  
3583   @article{Auerbach2005,
3584          Abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
# Line 3349 | Line 3603
3603          Annote = {895QF Times Cited:9 Cited References Count:33},
3604          Author = {A. Auerbach},
3605          Issn = {0027-8424},
3606 <        Journal = {Proceedings of the National Academy of Sciences of the United States of America},
3606 >        Journal = pnas,
3607          Month = {Feb 1},
3608 <        Number = {5},
3608 >        Number = 5,
3609          Pages = {1408-1412},
3610          Title = {Gating of acetylcholine receptor channels: Brownian motion across a broad transition state},
3611          Uri = {<Go to ISI>://000226877300030},
3612 <        Volume = {102},
3613 <        Year = {2005}}
3612 >        Volume = 102,
3613 >        Year = 2005}
3614  
3615   @article{Baber1995,
3616          Abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
# Line 3385 | Line 3639
3639          Issn = {0006-2960},
3640          Journal = {Biochemistry},
3641          Month = {May 16},
3642 <        Number = {19},
3642 >        Number = 19,
3643          Pages = {6533-6539},
3644          Title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
3645          Uri = {<Go to ISI>://A1995QZ71600035},
3646 <        Volume = {34},
3647 <        Year = {1995}}
3646 >        Volume = 34,
3647 >        Year = 1995}
3648  
3649   @article{Banerjee2004,
3650          Abstract = {Based on a coherent state representation of noise operator and an
# Line 3410 | Line 3664
3664          Annote = {816YY Times Cited:8 Cited References Count:35},
3665          Author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
3666          Issn = {0021-9606},
3667 <        Journal = {Journal of Chemical Physics},
3667 >        Journal = jcp,
3668          Month = {May 15},
3669 <        Number = {19},
3669 >        Number = 19,
3670          Pages = {8960-8972},
3671          Title = {Solution of quantum Langevin equation: Approximations, theoretical and numerical aspects},
3672          Uri = {<Go to ISI>://000221146400009},
3673 <        Volume = {120},
3674 <        Year = {2004}}
3673 >        Volume = 120,
3674 >        Year = 2004}
3675  
3676   @article{Barojas1973,
3677          Author = {J. Barojas and D. Levesque},
3678          Journal = {Phys. Rev. A},
3679          Pages = {1092-1105},
3680          Title = {Simulation of Diatomic Homonuclear Liquids},
3681 <        Volume = {7},
3682 <        Year = {1973}}
3681 >        Volume = 7,
3682 >        Year = 1973}
3683  
3684   @article{Barth1998,
3685          Abstract = {We present an efficient new method termed LN for propagating biomolecular
# Line 3457 | Line 3711
3711          Annote = {105HH Times Cited:29 Cited References Count:49},
3712          Author = {E. Barth and T. Schlick},
3713          Issn = {0021-9606},
3714 <        Journal = {Journal of Chemical Physics},
3714 >        Journal = jcp,
3715          Month = {Aug 1},
3716 <        Number = {5},
3716 >        Number = 5,
3717          Pages = {1617-1632},
3718          Title = {Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN},
3719          Uri = {<Go to ISI>://000075066300006},
3720 <        Volume = {109},
3721 <        Year = {1998}}
3720 >        Volume = 109,
3721 >        Year = 1998}
3722  
3723   @article{Batcho2001,
3724          Abstract = {We present an analysis for a simple two-component harmonic oscillator
# Line 3481 | Line 3735
3735          Annote = {469KV Times Cited:6 Cited References Count:30},
3736          Author = {P. F. Batcho and T. Schlick},
3737          Issn = {0021-9606},
3738 <        Journal = {Journal of Chemical Physics},
3738 >        Journal = jcp,
3739          Month = {Sep 1},
3740 <        Number = {9},
3740 >        Number = 9,
3741          Pages = {4019-4029},
3742          Title = {Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration},
3743          Uri = {<Go to ISI>://000170813800005},
3744 <        Volume = {115},
3745 <        Year = {2001}}
3744 >        Volume = 115,
3745 >        Year = 2001}
3746  
3747   @article{Bates2005,
3748          Abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
# Line 3514 | Line 3768
3768          Issn = {1539-3755},
3769          Journal = {Physical Review E},
3770          Month = {Nov},
3771 <        Number = {5},
3771 >        Number = 5,
3772          Pages = {-},
3773          Title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation study},
3774          Uri = {<Go to ISI>://000233603100030},
3775 <        Volume = {72},
3776 <        Year = {2005}}
3775 >        Volume = 72,
3776 >        Year = 2005}
3777  
3778   @article{Beard2003,
3779          Abstract = {We introduce an unbiased protocol for performing rotational moves
# Line 3534 | Line 3788
3788          Annote = {736UA Times Cited:0 Cited References Count:11},
3789          Author = {D. A. Beard and T. Schlick},
3790          Issn = {0006-3495},
3791 <        Journal = {Biophysical Journal},
3791 >        Journal = bj,
3792          Month = {Nov 1},
3793 <        Number = {5},
3793 >        Number = 5,
3794          Pages = {2973-2976},
3795          Title = {Unbiased rotational moves for rigid-body dynamics},
3796          Uri = {<Go to ISI>://000186190500018},
3797 <        Volume = {85},
3798 <        Year = {2003}}
3797 >        Volume = 85,
3798 >        Year = 2003}
3799  
3800   @article{Beloborodov1998,
3801          Abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
# Line 3558 | Line 3812
3812          Issn = {1090-7807},
3813          Journal = {Journal of Magnetic Resonance},
3814          Month = {Jun},
3815 <        Number = {2},
3815 >        Number = 2,
3816          Pages = {328-329},
3817          Title = {Effect of coupling between rotational and translational Brownian motions on NMR spin relaxation: Consideration using green function of rigid body diffusion},
3818          Uri = {<Go to ISI>://000074214800017},
3819 <        Volume = {132},
3820 <        Year = {1998}}
3819 >        Volume = 132,
3820 >        Year = 1998}
3821  
3822   @article{Berardi1996,
3823          Abstract = {We demonstrate that the overall molecular dipole organization in a
# Line 3580 | Line 3834
3834          Issn = {0009-2614},
3835          Journal = {Chemical Physics Letters},
3836          Month = {Oct 18},
3837 <        Number = {3},
3837 >        Number = 3,
3838          Pages = {357-362},
3839          Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
3840          Uri = {<Go to ISI>://A1996VN63700023},
3841 <        Volume = {261},
3842 <        Year = {1996}}
3841 >        Volume = 261,
3842 >        Year = 1996}
3843  
3844   @article{Berkov2005,
3845          Abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
# Line 3610 | Line 3864
3864          Issn = {1098-0121},
3865          Journal = {Physical Review B},
3866          Month = {Sep},
3867 <        Number = {9},
3867 >        Number = 9,
3868          Pages = {-},
3869          Title = {Magnetization precession due to a spin-polarized current in a thin nanoelement: Numerical simulation study},
3870          Uri = {<Go to ISI>://000232228500058},
3871 <        Volume = {72},
3872 <        Year = {2005}}
3871 >        Volume = 72,
3872 >        Year = 2005}
3873  
3874   @article{Berkov2005a,
3875          Abstract = {Numerical simulations of fast remagnetization processes using stochastic
# Line 3641 | Line 3895
3895          Pages = {442-448},
3896          Title = {Stochastic dynamic simulations of fast remagnetization processes: recent advances and applications},
3897          Uri = {<Go to ISI>://000228837600109},
3898 <        Volume = {290},
3899 <        Year = {2005}}
3898 >        Volume = 290,
3899 >        Year = 2005}
3900  
3901   @article{Berkov2002,
3902          Abstract = {We report on recent progress achieved by the development of numerical
# Line 3664 | Line 3918
3918          Issn = {0031-8965},
3919          Journal = {Physica Status Solidi a-Applied Research},
3920          Month = {Feb 16},
3921 <        Number = {2},
3921 >        Number = 2,
3922          Pages = {409-421},
3923          Title = {Magnetization dynamics in nanoparticle systems: Numerical simulation using Langevin dynamics},
3924          Uri = {<Go to ISI>://000174145200026},
3925 <        Volume = {189},
3926 <        Year = {2002}}
3925 >        Volume = 189,
3926 >        Year = 2002}
3927  
3928   @article{Bernal1980,
3929 <        Author = {J.M. Bernal and J. G. {de la Torre}},
3929 >        Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose},
3930          Journal = {Biopolymers},
3931          Pages = {751-766},
3932          Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape},
3933 <        Volume = {19},
3934 <        Year = {1980}}
3933 >        Volume = 19,
3934 >        Year = 1980}
3935  
3936   @article{Brenner1967,
3937          Author = {H. Brenner},
3938          Journal = {J. Collid. Int. Sci.},
3939          Pages = {407-436},
3940          Title = {Coupling between the Translational and Rotational Brownian Motions of Rigid Particles of Arbitrary shape},
3941 <        Volume = {23},
3942 <        Year = {1967}}
3941 >        Volume = 23,
3942 >        Year = 1967}
3943  
3944   @article{Brooks1983,
3945          Annote = {Qp423 Times Cited:6414 Cited References Count:96},
3946          Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus},
3947          Issn = {0192-8651},
3948 <        Journal = {Journal of Computational Chemistry},
3949 <        Number = {2},
3948 >        Journal = jcc,
3949 >        Number = 2,
3950          Pages = {187-217},
3951          Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
3952          Uri = {<Go to ISI>://A1983QP42300010},
3953 <        Volume = {4},
3954 <        Year = {1983}}
3953 >        Volume = 4,
3954 >        Year = 1983}
3955  
3956   @article{Brunger1984,
3957          Annote = {Sm173 Times Cited:143 Cited References Count:22},
3958          Author = {A. Brunger and C. L. Brooks and M. Karplus},
3959          Issn = {0009-2614},
3960          Journal = {Chemical Physics Letters},
3961 <        Number = {5},
3961 >        Number = 5,
3962          Pages = {495-500},
3963          Title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations of St2 Water},
3964          Uri = {<Go to ISI>://A1984SM17300007},
3965 <        Volume = {105},
3966 <        Year = {1984}}
3965 >        Volume = 105,
3966 >        Year = 1984}
3967  
3968   @article{Budd1999,
3969          Abstract = {This paper examines a synthesis of adaptive mesh methods with the
# Line 3723 | Line 3977
3977          Issn = {1364-503X},
3978          Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
3979          Month = {Apr 15},
3980 <        Number = {1754},
3980 >        Number = 1754,
3981          Pages = {1047-1077},
3982          Title = {Self-similar numerical solutions of the porous-medium equation using moving mesh methods},
3983          Uri = {<Go to ISI>://000080466800005},
3984 <        Volume = {357},
3985 <        Year = {1999}}
3984 >        Volume = 357,
3985 >        Year = 1999}
3986  
3987   @article{Camp1999,
3988          Abstract = {Fluids of hard bent-core molecules have been studied using theory
# Line 3764 | Line 4018
4018          Annote = {255TC Times Cited:24 Cited References Count:38},
4019          Author = {P. J. Camp and M. P. Allen and A. J. Masters},
4020          Issn = {0021-9606},
4021 <        Journal = {Journal of Chemical Physics},
4021 >        Journal = jcp,
4022          Month = {Dec 1},
4023 <        Number = {21},
4023 >        Number = 21,
4024          Pages = {9871-9881},
4025          Title = {Theory and computer simulation of bent-core molecules},
4026          Uri = {<Go to ISI>://000083685400056},
4027 <        Volume = {111},
4028 <        Year = {1999}}
4027 >        Volume = 111,
4028 >        Year = 1999}
4029  
4030   @article{Care2005,
4031          Abstract = {A review is presented of molecular and mesoscopic computer simulations
# Line 3786 | Line 4040
4040          Issn = {0034-4885},
4041          Journal = {Reports on Progress in Physics},
4042          Month = {Nov},
4043 <        Number = {11},
4043 >        Number = 11,
4044          Pages = {2665-2700},
4045          Title = {Computer simulation of liquid crystals},
4046          Uri = {<Go to ISI>://000233697600004},
4047 <        Volume = {68},
4048 <        Year = {2005}}
4047 >        Volume = 68,
4048 >        Year = 2005}
4049  
4050   @article{Carrasco1999,
4051          Abstract = {The hydrodynamic properties of rigid particles are calculated from
# Line 3813 | Line 4067
4067      them to some test cases, for which the properties are known a priori.
4068      We provide guidelines and computational tools for bead modeling.},
4069          Annote = {200TT Times Cited:46 Cited References Count:57},
4070 <        Author = {B. Carrasco and J. G. {de la Torre}},
4071 <        Issn = {0006-3495},
4072 <        Journal = {Biophysical Journal},
4070 >        Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
4071 >        Issn = {0006-3495},
4072 >        Journal = bj,
4073          Month = {Jun},
4074 <        Number = {6},
4074 >        Number = 6,
4075          Pages = {3044-3057},
4076          Title = {Hydrodynamic properties of rigid particles: Comparison of different modeling and computational procedures},
4077          Uri = {<Go to ISI>://000080556700016},
4078 <        Volume = {76},
4079 <        Year = {1999}}
4078 >        Volume = 76,
4079 >        Year = 1999}
4080  
4081   @article{Chandra1999,
4082          Abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
# Line 3846 | Line 4100
4100          Annote = {221EN Times Cited:14 Cited References Count:66},
4101          Author = {A. Chandra and T. Ichiye},
4102          Issn = {0021-9606},
4103 <        Journal = {Journal of Chemical Physics},
4103 >        Journal = jcp,
4104          Month = {Aug 8},
4105 <        Number = {6},
4105 >        Number = 6,
4106          Pages = {2701-2709},
4107          Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations},
4108          Uri = {<Go to ISI>://000081711200038},
4109 <        Volume = {111},
4110 <        Year = {1999}}
4109 >        Volume = 111,
4110 >        Year = 1999}
4111  
4112   @article{Channell1990,
4113          Annote = {Dk631 Times Cited:152 Cited References Count:34},
# Line 3861 | Line 4115
4115          Issn = {0951-7715},
4116          Journal = {Nonlinearity},
4117          Month = {may},
4118 <        Number = {2},
4118 >        Number = 2,
4119          Pages = {231-259},
4120          Title = {Symplectic Integration of Hamiltonian-Systems},
4121          Uri = {<Go to ISI>://A1990DK63100001},
4122 <        Volume = {3},
4123 <        Year = {1990}}
4122 >        Volume = 3,
4123 >        Year = 1990}
4124  
4125   @article{Chen2003,
4126          Abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
# Line 3887 | Line 4141
4141          Pages = {21-30},
4142          Title = {Explicit mixed finite order Runge-Kutta methods},
4143          Uri = {<Go to ISI>://000180314200002},
4144 <        Volume = {44},
4145 <        Year = {2003}}
4144 >        Volume = 44,
4145 >        Year = 2003}
4146  
4147   @article{Cheung2004,
4148          Abstract = {Equilibrium molecular dynamics calculations have been performed for
# Line 3906 | Line 4160
4160          Annote = {866UM Times Cited:4 Cited References Count:61},
4161          Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
4162          Issn = {0021-9606},
4163 <        Journal = {Journal of Chemical Physics},
4163 >        Journal = jcp,
4164          Month = {Nov 8},
4165 <        Number = {18},
4165 >        Number = 18,
4166          Pages = {9131-9139},
4167          Title = {Calculation of flexoelectric coefficients for a nematic liquid crystal by atomistic simulation},
4168          Uri = {<Go to ISI>://000224798900053},
4169 <        Volume = {121},
4170 <        Year = {2004}}
4169 >        Volume = 121,
4170 >        Year = 2004}
4171  
4172   @article{Cheung2002,
4173          Abstract = {Equilibrium molecular dynamics calculations have been performed for
# Line 3935 | Line 4189
4189          Pages = {140-146},
4190          Title = {Calculation of the rotational viscosity of a nematic liquid crystal},
4191          Uri = {<Go to ISI>://000175331000020},
4192 <        Volume = {356},
4193 <        Year = {2002}}
4192 >        Volume = 356,
4193 >        Year = 2002}
4194  
4195   @article{Chin2004,
4196          Abstract = {Current molecular dynamics simulations of biomolecules using multiple
# Line 3957 | Line 4211
4211          Annote = {757TK Times Cited:1 Cited References Count:22},
4212          Author = {S. A. Chin},
4213          Issn = {0021-9606},
4214 <        Journal = {Journal of Chemical Physics},
4214 >        Journal = jcp,
4215          Month = {Jan 1},
4216 <        Number = {1},
4216 >        Number = 1,
4217          Pages = {8-13},
4218          Title = {Dynamical multiple-time stepping methods for overcoming resonance instabilities},
4219          Uri = {<Go to ISI>://000187577400003},
4220 <        Volume = {120},
4221 <        Year = {2004}}
4220 >        Volume = 120,
4221 >        Year = 2004}
4222  
4223   @article{Cook2000,
4224          Abstract = {The Kirkwood correlation factor g(1) determines the preference for
# Line 3988 | Line 4242
4242          Issn = {0267-8292},
4243          Journal = {Liquid Crystals},
4244          Month = {Dec},
4245 <        Number = {12},
4245 >        Number = 12,
4246          Pages = {1573-1583},
4247          Title = {Simulation studies of dipole correlation in the isotropic liquid phase},
4248          Uri = {<Go to ISI>://000165437800002},
4249 <        Volume = {27},
4250 <        Year = {2000}}
4249 >        Volume = 27,
4250 >        Year = 2000}
4251  
4252   @article{Cui2003,
4253          Abstract = {All-atom Langevin dynamics simulations have been performed to study
# Line 4016 | Line 4270
4270          Annote = {689LC Times Cited:3 Cited References Count:48},
4271          Author = {B. X. Cui and M. Y. Shen and K. F. Freed},
4272          Issn = {0027-8424},
4273 <        Journal = {Proceedings of the National Academy of Sciences of the United States of America},
4273 >        Journal = pnas,
4274          Month = {Jun 10},
4275 <        Number = {12},
4275 >        Number = 12,
4276          Pages = {7087-7092},
4277          Title = {Folding and misfolding of the papillomavirus E6 interacting peptide E6ap},
4278          Uri = {<Go to ISI>://000183493500037},
4279 <        Volume = {100},
4280 <        Year = {2003}}
4279 >        Volume = 100,
4280 >        Year = 2003}
4281  
4282   @article{Denisov2003,
4283          Abstract = {We study the slow phase of thermally activated magnetic relaxation
# Line 4041 | Line 4295
4295          Issn = {1098-0121},
4296          Journal = {Physical Review B},
4297          Month = {Jan 1},
4298 <        Number = {1},
4298 >        Number = 1,
4299          Pages = {-},
4300          Title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
4301          Uri = {<Go to ISI>://000180830400056},
4302 <        Volume = {67},
4303 <        Year = {2003}}
4302 >        Volume = 67,
4303 >        Year = 2003}
4304  
4305   @article{Derreumaux1998,
4306          Abstract = {To explore the origin of the large-scale motion of triosephosphate
# Line 4076 | Line 4330
4330          Annote = {Zl046 Times Cited:30 Cited References Count:29},
4331          Author = {P. Derreumaux and T. Schlick},
4332          Issn = {0006-3495},
4333 <        Journal = {Biophysical Journal},
4333 >        Journal = bj,
4334          Month = {Jan},
4335 <        Number = {1},
4335 >        Number = 1,
4336          Pages = {72-81},
4337          Title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
4338          Uri = {<Go to ISI>://000073393400009},
4339 <        Volume = {74},
4340 <        Year = {1998}}
4339 >        Volume = 74,
4340 >        Year = 1998}
4341  
4342   @article{Dullweber1997,
4343          Abstract = {Rigid body molecular models possess symplectic structure and time-reversal
# Line 4108 | Line 4362
4362          Annote = {Ya587 Times Cited:35 Cited References Count:32},
4363          Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
4364          Issn = {0021-9606},
4365 <        Journal = {Journal of Chemical Physics},
4365 >        Journal = jcp,
4366          Month = {Oct 15},
4367 <        Number = {15},
4367 >        Number = 15,
4368          Pages = {5840-5851},
4369          Title = {Symplectic splitting methods for rigid body molecular dynamics},
4370          Uri = {<Go to ISI>://A1997YA58700024},
4371 <        Volume = {107},
4372 <        Year = {1997}}
4371 >        Volume = 107,
4372 >        Year = 1997}
4373  
4374   @book{Gamma1994,
4375          Address = {London},
4376          Author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
4377 <        Chapter = {7},
4377 >        Chapter = 7,
4378          Publisher = {Perason Education},
4379          Title = {Design Patterns: Elements of Reusable Object-Oriented Software},
4380 <        Year = {1994}}
4380 >        Year = 1994}
4381  
4382   @article{Edwards2005,
4383          Abstract = {Using the Langevin dynamics technique, we have carried out simulations
# Line 4141 | Line 4395
4395          Issn = {0024-9297},
4396          Journal = {Macromolecules},
4397          Month = {Dec 13},
4398 <        Number = {25},
4398 >        Number = 25,
4399          Pages = {10590-10595},
4400          Title = {Stretching a single diblock copolymer in a selective solvent: Langevin dynamics simulations},
4401          Uri = {<Go to ISI>://000233866200035},
4402 <        Volume = {38},
4403 <        Year = {2005}}
4402 >        Volume = 38,
4403 >        Year = 2005}
4404  
4405   @article{Egberts1988,
4406          Annote = {Q0188 Times Cited:219 Cited References Count:43},
4407          Author = {E. Egberts and H. J. C. Berendsen},
4408          Issn = {0021-9606},
4409 <        Journal = {Journal of Chemical Physics},
4409 >        Journal = jcp,
4410          Month = {Sep 15},
4411 <        Number = {6},
4411 >        Number = 6,
4412          Pages = {3718-3732},
4413          Title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic Detail},
4414          Uri = {<Go to ISI>://A1988Q018800036},
4415 <        Volume = {89},
4416 <        Year = {1988}}
4415 >        Volume = 89,
4416 >        Year = 1988}
4417  
4418   @article{Ermak1978,
4419          Annote = {Fp216 Times Cited:785 Cited References Count:42},
4420          Author = {D. L. Ermak and J. A. Mccammon},
4421          Issn = {0021-9606},
4422 <        Journal = {Journal of Chemical Physics},
4423 <        Number = {4},
4422 >        Journal = jcp,
4423 >        Number = 4,
4424          Pages = {1352-1360},
4425          Title = {Brownian Dynamics with Hydrodynamic Interactions},
4426          Uri = {<Go to ISI>://A1978FP21600004},
4427 <        Volume = {69},
4428 <        Year = {1978}}
4427 >        Volume = 69,
4428 >        Year = 1978}
4429  
4430   @article{Evans1977,
4431          Annote = {Ds757 Times Cited:271 Cited References Count:18},
4432          Author = {D. J. Evans},
4433          Issn = {0026-8976},
4434 <        Journal = {Molecular Physics},
4435 <        Number = {2},
4434 >        Journal = mp,
4435 >        Number = 2,
4436          Pages = {317-325},
4437          Title = {Representation of Orientation Space},
4438          Uri = {<Go to ISI>://A1977DS75700002},
4439 <        Volume = {34},
4440 <        Year = {1977}}
4439 >        Volume = 34,
4440 >        Year = 1977}
4441  
4442   @article{Fennell2004,
4443          Abstract = {The density maximum and temperature dependence of the self-diffusion
# Line 4212 | Line 4466
4466          Annote = {816YY Times Cited:5 Cited References Count:39},
4467          Author = {C. J. Fennell and J. D. Gezelter},
4468          Issn = {0021-9606},
4469 <        Journal = {Journal of Chemical Physics},
4469 >        Journal = jcp,
4470          Month = {May 15},
4471 <        Number = {19},
4471 >        Number = 19,
4472          Pages = {9175-9184},
4473          Title = {On the structural and transport properties of the soft sticky dipole and related single-point water models},
4474          Uri = {<Go to ISI>://000221146400032},
4475 <        Volume = {120},
4476 <        Year = {2004}}
4475 >        Volume = 120,
4476 >        Year = 2004}
4477  
4478   @article{Fernandes2002,
4479          Abstract = {We have developed a Brownian dynamics simulation algorithm to generate
# Line 4234 | Line 4488
4488      its applicability. Examples include free diffusion, transport in
4489      an electric field, and diffusion in a restricting environment.},
4490          Annote = {633AD Times Cited:2 Cited References Count:43},
4491 <        Author = {M. X. Fernandes and J. G. {de la Torre}},
4491 >        Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4492          Issn = {0006-3495},
4493 <        Journal = {Biophysical Journal},
4493 >        Journal = bj,
4494          Month = {Dec},
4495 <        Number = {6},
4495 >        Number = 6,
4496          Pages = {3039-3048},
4497          Title = {Brownian dynamics simulation of rigid particles of arbitrary shape in external fields},
4498          Uri = {<Go to ISI>://000180256300012},
4499 <        Volume = {83},
4500 <        Year = {2002}}
4499 >        Volume = 83,
4500 >        Year = 2002}
4501  
4502   @book{Frenkel1996,
4503          Address = {New York},
4504          Author = {D. Frenkel and B. Smit},
4505          Publisher = {Academic Press},
4506          Title = {Understanding Molecular Simulation : From Algorithms to Applications},
4507 <        Year = {1996}}
4507 >        Year = 1996}
4508  
4509   @article{Gay1981,
4510          Annote = {Lj347 Times Cited:482 Cited References Count:13},
4511          Author = {J. G. Gay and B. J. Berne},
4512          Issn = {0021-9606},
4513 <        Journal = {Journal of Chemical Physics},
4514 <        Number = {6},
4513 >        Journal = jcp,
4514 >        Number = 6,
4515          Pages = {3316-3319},
4516          Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
4517          Uri = {<Go to ISI>://A1981LJ34700029},
4518 <        Volume = {74},
4519 <        Year = {1981}}
4518 >        Volume = 74,
4519 >        Year = 1981}
4520  
4521   @article{Gelin1999,
4522          Abstract = {To investigate the influence of inertial effects on the dynamics of
# Line 4288 | Line 4542
4542          Issn = {1022-1344},
4543          Journal = {Macromolecular Theory and Simulations},
4544          Month = {Nov},
4545 <        Number = {6},
4545 >        Number = 6,
4546          Pages = {529-543},
4547          Title = {Inertial effects in the Brownian dynamics with rigid constraints},
4548          Uri = {<Go to ISI>://000083785700002},
4549 <        Volume = {8},
4550 <        Year = {1999}}
4549 >        Volume = 8,
4550 >        Year = 1999}
4551  
4552   @article{Goetz1998,
4553          Author = {R. Goetz and R. Lipowsky},
4554 <        Journal = {Journal of Chemical Physics},
4555 <        Number = {17},
4556 <        Pages = {7397},
4554 >        Journal = jcp,
4555 >        Number = 17,
4556 >        Pages = 7397,
4557          Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
4558 <        Volume = {108},
4559 <        Year = {1998}}
4558 >        Volume = 108,
4559 >        Year = 1998}
4560  
4561   @book{Goldstein2001,
4562          Address = {San Francisco},
# Line 4310 | Line 4564
4564          Edition = {3rd},
4565          Publisher = {Addison Wesley},
4566          Title = {Classical Mechanics},
4567 <        Year = {2001}}
4567 >        Year = 2001}
4568  
4569   @article{Gray2003,
4570          Abstract = {Protein-protein docking algorithms provide a means to elucidate structural
# Line 4340 | Line 4594
4594          Annote = {704QL Times Cited:48 Cited References Count:60},
4595          Author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and B. Kuhlman and C. A. Rohl and D. Baker},
4596          Issn = {0022-2836},
4597 <        Journal = {Journal of Molecular Biology},
4597 >        Journal = jmb,
4598          Month = {Aug 1},
4599 <        Number = {1},
4599 >        Number = 1,
4600          Pages = {281-299},
4601          Title = {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations},
4602          Uri = {<Go to ISI>://000184351300022},
4603 <        Volume = {331},
4604 <        Year = {2003}}
4603 >        Volume = 331,
4604 >        Year = 2003}
4605  
4606   @article{Greengard1994,
4607          Abstract = {Some of the recently developed fast summation methods that have arisen
# Line 4364 | Line 4618
4618          Issn = {0036-8075},
4619          Journal = {Science},
4620          Month = {Aug 12},
4621 <        Number = {5174},
4621 >        Number = 5174,
4622          Pages = {909-914},
4623          Title = {Fast Algorithms for Classical Physics},
4624          Uri = {<Go to ISI>://A1994PB49900031},
4625 <        Volume = {265},
4626 <        Year = {1994}}
4625 >        Volume = 265,
4626 >        Year = 1994}
4627  
4628   @article{Greengard1987,
4629          Annote = {L0498 Times Cited:899 Cited References Count:7},
4630          Author = {L. Greengard and V. Rokhlin},
4631          Issn = {0021-9991},
4632 <        Journal = {Journal of Computational Physics},
4632 >        Journal = jcop,
4633          Month = {Dec},
4634 <        Number = {2},
4634 >        Number = 2,
4635          Pages = {325-348},
4636          Title = {A Fast Algorithm for Particle Simulations},
4637          Uri = {<Go to ISI>://A1987L049800006},
4638 <        Volume = {73},
4639 <        Year = {1987}}
4638 >        Volume = 73,
4639 >        Year = 1987}
4640  
4641   @article{Hairer1997,
4642          Abstract = {Backward error analysis is a useful tool for the study of numerical
# Line 4403 | Line 4657
4657          Issn = {0029-599X},
4658          Journal = {Numerische Mathematik},
4659          Month = {Jun},
4660 <        Number = {4},
4660 >        Number = 4,
4661          Pages = {441-462},
4662          Title = {The life-span of backward error analysis for numerical integrators},
4663          Uri = {<Go to ISI>://A1997XJ48800002},
4664 <        Volume = {76},
4665 <        Year = {1997}}
4664 >        Volume = 76,
4665 >        Year = 1997}
4666  
4667   @article{Hao1993,
4668          Abstract = {A new procedure for studying the folding and unfolding of proteins,
# Line 4450 | Line 4704
4704          Issn = {0006-2960},
4705          Journal = {Biochemistry},
4706          Month = {Sep 21},
4707 <        Number = {37},
4707 >        Number = 37,
4708          Pages = {9614-9631},
4709          Title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic Trypsin-Inhibitor Studied by Computer-Simulations},
4710          Uri = {<Go to ISI>://A1993LY29400014},
4711 <        Volume = {32},
4712 <        Year = {1993}}
4711 >        Volume = 32,
4712 >        Year = 1993}
4713  
4714   @article{Hinsen2000,
4715          Abstract = {The slow dynamics of proteins around its native folded state is usually
# Line 4494 | Line 4748
4748          Pages = {25-37},
4749          Title = {Harmonicity in slow protein dynamics},
4750          Uri = {<Go to ISI>://000090121700003},
4751 <        Volume = {261},
4752 <        Year = {2000}}
4751 >        Volume = 261,
4752 >        Year = 2000}
4753  
4754   @article{Ho1992,
4755          Abstract = {Evidence has been found for the existence water at the protein-lipid
# Line 4528 | Line 4782
4782          Annote = {Ju251 Times Cited:55 Cited References Count:44},
4783          Author = {C. Ho and C. D. Stubbs},
4784          Issn = {0006-3495},
4785 <        Journal = {Biophysical Journal},
4785 >        Journal = bj,
4786          Month = {Oct},
4787 <        Number = {4},
4787 >        Number = 4,
4788          Pages = {897-902},
4789          Title = {Hydration at the Membrane Protein-Lipid Interface},
4790          Uri = {<Go to ISI>://A1992JU25100002},
4791 <        Volume = {63},
4792 <        Year = {1992}}
4791 >        Volume = 63,
4792 >        Year = 1992}
4793  
4794   @book{Hockney1981,
4795          Address = {New York},
4796          Author = {R.W. Hockney and J.W. Eastwood},
4797          Publisher = {McGraw-Hill},
4798          Title = {Computer Simulation Using Particles},
4799 <        Year = {1981}}
4799 >        Year = 1981}
4800  
4801   @article{Hoover1985,
4802          Annote = {Acr30 Times Cited:1809 Cited References Count:11},
4803          Author = {W. G. Hoover},
4804          Issn = {1050-2947},
4805          Journal = {Physical Review A},
4806 <        Number = {3},
4806 >        Number = 3,
4807          Pages = {1695-1697},
4808          Title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
4809          Uri = {<Go to ISI>://A1985ACR3000056},
4810 <        Volume = {31},
4811 <        Year = {1985}}
4810 >        Volume = 31,
4811 >        Year = 1985}
4812  
4813   @article{Huh2004,
4814          Abstract = {Racemic fluids of chiral calamitic molecules are investigated with
# Line 4570 | Line 4824
4824          Annote = {870FJ Times Cited:0 Cited References Count:63},
4825          Author = {Y. Huh and N. M. Cann},
4826          Issn = {0021-9606},
4827 <        Journal = {Journal of Chemical Physics},
4827 >        Journal = jcp,
4828          Month = {Nov 22},
4829 <        Number = {20},
4829 >        Number = 20,
4830          Pages = {10299-10308},
4831          Title = {Discrimination in isotropic, nematic, and smectic phases of chiral calamitic molecules: A computer simulation study},
4832          Uri = {<Go to ISI>://000225042700059},
4833 <        Volume = {121},
4834 <        Year = {2004}}
4833 >        Volume = 121,
4834 >        Year = 2004}
4835  
4836   @article{Humphrey1996,
4837          Abstract = {VMD is a molecular graphics program designed for the display and analysis
# Line 4611 | Line 4865
4865          Issn = {0263-7855},
4866          Journal = {Journal of Molecular Graphics},
4867          Month = {Feb},
4868 <        Number = {1},
4868 >        Number = 1,
4869          Pages = {33-\&},
4870          Title = {VMD: Visual molecular dynamics},
4871          Uri = {<Go to ISI>://A1996UH51500005},
4872 <        Volume = {14},
4873 <        Year = {1996}}
4872 >        Volume = 14,
4873 >        Year = 1996}
4874  
4875   @article{Izaguirre2001,
4876          Abstract = {In this paper we show the possibility of using very mild stochastic
# Line 4649 | Line 4903
4903          Annote = {397CQ Times Cited:14 Cited References Count:36},
4904          Author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
4905          Issn = {0021-9606},
4906 <        Journal = {Journal of Chemical Physics},
4906 >        Journal = jcp,
4907          Month = {Feb 1},
4908 <        Number = {5},
4908 >        Number = 5,
4909          Pages = {2090-2098},
4910          Title = {Langevin stabilization of molecular dynamics},
4911          Uri = {<Go to ISI>://000166676100020},
4912 <        Volume = {114},
4913 <        Year = {2001}}
4912 >        Volume = 114,
4913 >        Year = 2001}
4914  
4915   @article{Torre1977,
4916 <        Author = {Jose Garcia De La Torre, V.A. Bloomfield},
4916 >        Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield},
4917          Journal = {Biopolymers},
4918          Pages = {1747-1763},
4919          Title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
4920 <        Volume = {16},
4921 <        Year = {1977}}
4920 >        Volume = 16,
4921 >        Year = 1977}
4922  
4923   @article{Kale1999,
4924          Abstract = {Molecular dynamics programs simulate the behavior of biomolecular
# Line 4692 | Line 4946
4946          Annote = {194FM Times Cited:373 Cited References Count:51},
4947          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},
4948          Issn = {0021-9991},
4949 <        Journal = {Journal of Computational Physics},
4949 >        Journal = jcop,
4950          Month = {May 1},
4951 <        Number = {1},
4951 >        Number = 1,
4952          Pages = {283-312},
4953          Title = {NAMD2: Greater scalability for parallel molecular dynamics},
4954          Uri = {<Go to ISI>://000080181500013},
4955 <        Volume = {151},
4956 <        Year = {1999}}
4955 >        Volume = 151,
4956 >        Year = 1999}
4957  
4958   @article{Kane2000,
4959          Abstract = {The purpose of this work is twofold. First, we demonstrate analytically
# Line 4723 | Line 4977
4977          Issn = {0029-5981},
4978          Journal = {International Journal for Numerical Methods in Engineering},
4979          Month = {Dec 10},
4980 <        Number = {10},
4980 >        Number = 10,
4981          Pages = {1295-1325},
4982          Title = {Variational integrators and the Newmark algorithm for conservative and dissipative mechanical systems},
4983          Uri = {<Go to ISI>://000165270600004},
4984 <        Volume = {49},
4985 <        Year = {2000}}
4984 >        Volume = 49,
4985 >        Year = 2000}
4986  
4987   @article{Klimov1997,
4988          Abstract = {The viscosity (eta) dependence of the folding rates for four sequences
# Line 4745 | Line 4999
4999          Annote = {Xk293 Times Cited:77 Cited References Count:17},
5000          Author = {D. K. Klimov and D. Thirumalai},
5001          Issn = {0031-9007},
5002 <        Journal = {Physical Review Letters},
5002 >        Journal = prl,
5003          Month = {Jul 14},
5004 <        Number = {2},
5004 >        Number = 2,
5005          Pages = {317-320},
5006          Title = {Viscosity dependence of the folding rates of proteins},
5007          Uri = {<Go to ISI>://A1997XK29300035},
5008 <        Volume = {79},
5009 <        Year = {1997}}
5008 >        Volume = 79,
5009 >        Year = 1997}
5010  
5011   @article{Kol1997,
5012          Abstract = {Rigid-body molecular dynamics simulations typically are performed
# Line 4778 | Line 5032
5032          Annote = {Xq332 Times Cited:11 Cited References Count:18},
5033          Author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
5034          Issn = {0021-9606},
5035 <        Journal = {Journal of Chemical Physics},
5035 >        Journal = jcp,
5036          Month = {Aug 15},
5037 <        Number = {7},
5037 >        Number = 7,
5038          Pages = {2580-2588},
5039          Title = {A symplectic method for rigid-body molecular simulation},
5040          Uri = {<Go to ISI>://A1997XQ33200046},
5041 <        Volume = {107},
5042 <        Year = {1997}}
5041 >        Volume = 107,
5042 >        Year = 1997}
5043  
5044   @article{Lansac2001,
5045          Abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
# Line 4814 | Line 5068
5068          Issn = {1063-651X},
5069          Journal = {Physical Review E},
5070          Month = {Nov},
5071 <        Number = {5},
5071 >        Number = 5,
5072          Pages = {-},
5073          Title = {Microscopic structure and dynamics of a partial bilayer smectic liquid crystal},
5074          Uri = {<Go to ISI>://000172406900063},
5075 <        Volume = {6405},
5076 <        Year = {2001}}
5075 >        Volume = 6405,
5076 >        Year = 2001}
5077  
5078   @article{Lansac2003,
5079          Abstract = {Recently, a new class of smectic liquid crystal phases characterized
# Line 4842 | Line 5096
5096          Issn = {1063-651X},
5097          Journal = {Physical Review E},
5098          Month = {Jan},
5099 <        Number = {1},
5099 >        Number = 1,
5100          Pages = {-},
5101          Title = {Phase behavior of bent-core molecules},
5102          Uri = {<Go to ISI>://000181017300042},
5103 <        Volume = {67},
5104 <        Year = {2003}}
5103 >        Volume = 67,
5104 >        Year = 2003}
5105  
5106   @book{Leach2001,
5107          Address = {Harlow, England},
# Line 4855 | Line 5109
5109          Edition = {2nd},
5110          Publisher = {Pearson Educated Limited},
5111          Title = {Molecular Modeling: Principles and Applications},
5112 <        Year = {2001}}
5112 >        Year = 2001}
5113  
5114   @article{Leimkuhler1999,
5115          Abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
# Line 4875 | Line 5129
5129          Issn = {1364-503X},
5130          Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
5131          Month = {Apr 15},
5132 <        Number = {1754},
5132 >        Number = 1754,
5133          Pages = {1101-1133},
5134          Title = {Reversible adaptive regularization: perturbed Kepler motion and classical atomic trajectories},
5135          Uri = {<Go to ISI>://000080466800007},
5136 <        Volume = {357},
5137 <        Year = {1999}}
5136 >        Volume = 357,
5137 >        Year = 1999}
5138  
5139   @book{Leimkuhler2004,
5140          Address = {Cambridge},
5141          Author = {B. Leimkuhler and S. Reich},
5142          Publisher = {Cambridge University Press},
5143          Title = {Simulating Hamiltonian Dynamics},
5144 <        Year = {2004}}
5144 >        Year = 2004}
5145  
5146   @article{Levelut1981,
5147          Annote = {Ml751 Times Cited:96 Cited References Count:16},
5148          Author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard and G. Sigaud},
5149          Issn = {1050-2947},
5150          Journal = {Physical Review A},
5151 <        Number = {4},
5151 >        Number = 4,
5152          Pages = {2180-2186},
5153          Title = {Number of Sa Phases},
5154          Uri = {<Go to ISI>://A1981ML75100057},
5155 <        Volume = {24},
5156 <        Year = {1981}}
5155 >        Volume = 24,
5156 >        Year = 1981}
5157  
5158   @article{Lieb1982,
5159          Annote = {Nu461 Times Cited:40 Cited References Count:28},
5160          Author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
5161          Issn = {0006-3002},
5162          Journal = {Biochimica Et Biophysica Acta},
5163 <        Number = {2},
5163 >        Number = 2,
5164          Pages = {388-398},
5165          Title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - Evidence from Raman-Scattering},
5166          Uri = {<Go to ISI>://A1982NU46100012},
5167 <        Volume = {688},
5168 <        Year = {1982}}
5167 >        Volume = 688,
5168 >        Year = 1982}
5169  
5170   @article{Link1997,
5171          Abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
# Line 4929 | Line 5183
5183          Issn = {0036-8075},
5184          Journal = {Science},
5185          Month = {Dec 12},
5186 <        Number = {5345},
5186 >        Number = 5345,
5187          Pages = {1924-1927},
5188          Title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic phase of achiral molecules},
5189          Uri = {<Go to ISI>://A1997YL00200028},
5190 <        Volume = {278},
5191 <        Year = {1997}}
5190 >        Volume = 278,
5191 >        Year = 1997}
5192  
5193   @article{Liwo2005,
5194          Annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
# Line 4945 | Line 5199
5199          Pages = {359-360},
5200          Title = {Ab initio simulations of protein folding pathways by molecular dynamics with the united-residue (UNRES) model of polypeptide chains},
5201          Uri = {<Go to ISI>://000234826102043},
5202 <        Volume = {272},
5203 <        Year = {2005}}
5202 >        Volume = 272,
5203 >        Year = 2005}
5204  
5205   @article{Luty1994,
5206          Abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
# Line 4961 | Line 5215
5215          Author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
5216          Issn = {0892-7022},
5217          Journal = {Molecular Simulation},
5218 <        Number = {1},
5218 >        Number = 1,
5219          Pages = {11-20},
5220          Title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
5221          Uri = {<Go to ISI>://A1994QF46400002},
5222 <        Volume = {14},
5223 <        Year = {1994}}
5222 >        Volume = 14,
5223 >        Year = 1994}
5224  
5225   @book{Marion1990,
5226          Address = {New York},
# Line 4974 | Line 5228
5228          Edition = {2rd},
5229          Publisher = {Academic Press},
5230          Title = {Classical Dynamics of Particles and Systems},
5231 <        Year = {1990}}
5231 >        Year = 1990}
5232  
5233   @article{Marrink1994,
5234          Abstract = {To obtain insight in the process of water permeation through a lipid
# Line 5006 | Line 5260
5260          Issn = {0022-3654},
5261          Journal = {Journal of Physical Chemistry},
5262          Month = {Apr 14},
5263 <        Number = {15},
5263 >        Number = 15,
5264          Pages = {4155-4168},
5265          Title = {Simulation of Water Transport through a Lipid-Membrane},
5266          Uri = {<Go to ISI>://A1994NG21900040},
5267 <        Volume = {98},
5268 <        Year = {1994}}
5267 >        Volume = 98,
5268 >        Year = 1994}
5269  
5270   @article{Marrink2004,
5271          Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
5272          Journal = {J. Phys. Chem. B},
5273          Pages = {750-760},
5274          Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
5275 <        Volume = {108},
5276 <        Year = {2004}}
5275 >        Volume = 108,
5276 >        Year = 2004}
5277  
5278   @article{Marsden1998,
5279          Abstract = {This paper presents a geometric-variational approach to continuous
# Line 5047 | Line 5301
5301          Issn = {0010-3616},
5302          Journal = {Communications in Mathematical Physics},
5303          Month = {Dec},
5304 <        Number = {2},
5304 >        Number = 2,
5305          Pages = {351-395},
5306          Title = {Multisymplectic geometry, variational integrators, and nonlinear PDEs},
5307          Uri = {<Go to ISI>://000077902200006},
5308 <        Volume = {199},
5309 <        Year = {1998}}
5308 >        Volume = 199,
5309 >        Year = 1998}
5310  
5311   @article{Matthey2004,
5312          Abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
# Line 5077 | Line 5331
5331          Issn = {0098-3500},
5332          Journal = {Acm Transactions on Mathematical Software},
5333          Month = {Sep},
5334 <        Number = {3},
5334 >        Number = 3,
5335          Pages = {237-265},
5336          Title = {ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics},
5337          Uri = {<Go to ISI>://000224325600001},
5338 <        Volume = {30},
5339 <        Year = {2004}}
5338 >        Volume = 30,
5339 >        Year = 2004}
5340  
5341   @article{McLachlan1993,
5342          Author = {R.~I McLachlan},
5343          Journal = {prl},
5344          Pages = {3043-3046},
5345          Title = {Explicit Lie-Poisson integration and the Euler equations},
5346 <        Volume = {71},
5347 <        Year = {1993}}
5346 >        Volume = 71,
5347 >        Year = 1993}
5348  
5349   @article{McLachlan1998,
5350          Abstract = {We give a survey and some new examples of generating functions for
# Line 5108 | Line 5362
5362          Pages = {298-309},
5363          Title = {Generating functions for dynamical systems with symmetries, integrals, and differential invariants},
5364          Uri = {<Go to ISI>://000071558900021},
5365 <        Volume = {112},
5366 <        Year = {1998}}
5365 >        Volume = 112,
5366 >        Year = 1998}
5367  
5368   @article{McLachlan1998a,
5369          Abstract = {We consider properties of flows, the relationships between them, and
# Line 5126 | Line 5380
5380          Issn = {0036-1429},
5381          Journal = {Siam Journal on Numerical Analysis},
5382          Month = {Apr},
5383 <        Number = {2},
5383 >        Number = 2,
5384          Pages = {586-599},
5385          Title = {Numerical integrators that preserve symmetries and reversing symmetries},
5386          Uri = {<Go to ISI>://000072580500010},
5387 <        Volume = {35},
5388 <        Year = {1998}}
5387 >        Volume = 35,
5388 >        Year = 1998}
5389  
5390   @article{McLachlan2005,
5391          Abstract = {In this paper we revisit the Moser-Veselov description of the free
# Line 5152 | Line 5406
5406          Issn = {1615-3375},
5407          Journal = {Foundations of Computational Mathematics},
5408          Month = {Feb},
5409 <        Number = {1},
5409 >        Number = 1,
5410          Pages = {87-123},
5411          Title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
5412          Uri = {<Go to ISI>://000228011900003},
5413 <        Volume = {5},
5414 <        Year = {2005}}
5413 >        Volume = 5,
5414 >        Year = 2005}
5415  
5416   @article{Meineke2005,
5417          Abstract = {OOPSE is a new molecular dynamics simulation program that is capable
# Line 5173 | Line 5427
5427          Annote = {891CF Times Cited:1 Cited References Count:56},
5428          Author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and J. D. Gezelter},
5429          Issn = {0192-8651},
5430 <        Journal = {Journal of Computational Chemistry},
5430 >        Journal = jcc,
5431          Month = {Feb},
5432 <        Number = {3},
5432 >        Number = 3,
5433          Pages = {252-271},
5434          Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
5435          Uri = {<Go to ISI>://000226558200006},
5436 <        Volume = {26},
5437 <        Year = {2005}}
5436 >        Volume = 26,
5437 >        Year = 2005}
5438  
5439   @article{Melchionna1993,
5440          Abstract = {In this paper we write down equations of motion (following the approach
# Line 5192 | Line 5446
5446          Annote = {Kq355 Times Cited:172 Cited References Count:17},
5447          Author = {S. Melchionna and G. Ciccotti and B. L. Holian},
5448          Issn = {0026-8976},
5449 <        Journal = {Molecular Physics},
5449 >        Journal = mp,
5450          Month = {Feb 20},
5451 <        Number = {3},
5451 >        Number = 3,
5452          Pages = {533-544},
5453          Title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
5454          Uri = {<Go to ISI>://A1993KQ35500002},
5455 <        Volume = {78},
5456 <        Year = {1993}}
5455 >        Volume = 78,
5456 >        Year = 1993}
5457  
5458   @article{Memmer2002,
5459          Abstract = {The phase behaviour of achiral banana-shaped molecules was studied
# Line 5232 | Line 5486
5486          Issn = {0267-8292},
5487          Journal = {Liquid Crystals},
5488          Month = {Apr},
5489 <        Number = {4},
5489 >        Number = 4,
5490          Pages = {483-496},
5491          Title = {Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study},
5492          Uri = {<Go to ISI>://000174410500001},
5493 <        Volume = {29},
5494 <        Year = {2002}}
5493 >        Volume = 29,
5494 >        Year = 2002}
5495  
5496   @article{Metropolis1949,
5497          Author = {N. Metropolis and S. Ulam},
5498          Journal = {J. Am. Stat. Ass.},
5499          Pages = {335-341},
5500          Title = {The $\mbox{Monte Carlo}$ Method},
5501 <        Volume = {44},
5502 <        Year = {1949}}
5501 >        Volume = 44,
5502 >        Year = 1949}
5503  
5504   @article{Mielke2004,
5505          Abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
# Line 5276 | Line 5530
5530          Annote = {861ZF Times Cited:3 Cited References Count:34},
5531          Author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen and C. J. Benham},
5532          Issn = {0021-9606},
5533 <        Journal = {Journal of Chemical Physics},
5533 >        Journal = jcp,
5534          Month = {Oct 22},
5535 <        Number = {16},
5535 >        Number = 16,
5536          Pages = {8104-8112},
5537          Title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study},
5538          Uri = {<Go to ISI>://000224456500064},
5539 <        Volume = {121},
5540 <        Year = {2004}}
5539 >        Volume = 121,
5540 >        Year = 2004}
5541  
5542   @article{Naess2001,
5543          Abstract = {The three Eulerian angles constitute the classical choice of generalized
# Line 5308 | Line 5562
5562          Pages = {323-339},
5563          Title = {Brownian dynamics simulation of rigid bodies and segmented polymer chains. Use of Cartesian rotation vectors as the generalized coordinates describing angular orientations},
5564          Uri = {<Go to ISI>://000168774800005},
5565 <        Volume = {294},
5566 <        Year = {2001}}
5565 >        Volume = 294,
5566 >        Year = 2001}
5567  
5568   @article{Niori1996,
5569          Abstract = {The synthesis of a banana-shaped molecule is reported and it is found
# Line 5324 | Line 5578
5578          Issn = {0959-9428},
5579          Journal = {Journal of Materials Chemistry},
5580          Month = {Jul},
5581 <        Number = {7},
5581 >        Number = 7,
5582          Pages = {1231-1233},
5583          Title = {Distinct ferroelectric smectic liquid crystals consisting of banana shaped achiral molecules},
5584          Uri = {<Go to ISI>://A1996UX85500025},
5585 <        Volume = {6},
5586 <        Year = {1996}}
5585 >        Volume = 6,
5586 >        Year = 1996}
5587  
5588   @article{Noguchi2002,
5589          Abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
# Line 5349 | Line 5603
5603          Issn = {1063-651X},
5604          Journal = {Physical Review E},
5605          Month = {may},
5606 <        Number = {5},
5606 >        Number = 5,
5607          Pages = {-},
5608          Title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
5609          Uri = {<Go to ISI>://000176552300084},
5610 <        Volume = {65},
5611 <        Year = {2002}}
5610 >        Volume = 65,
5611 >        Year = 2002}
5612  
5613   @article{Noguchi2001,
5614          Abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
# Line 5371 | Line 5625
5625          Annote = {491UW Times Cited:48 Cited References Count:25},
5626          Author = {H. Noguchi and M. Takasu},
5627          Issn = {0021-9606},
5628 <        Journal = {Journal of Chemical Physics},
5628 >        Journal = jcp,
5629          Month = {Nov 22},
5630 <        Number = {20},
5630 >        Number = 20,
5631          Pages = {9547-9551},
5632          Title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
5633          Uri = {<Go to ISI>://000172129300049},
5634 <        Volume = {115},
5635 <        Year = {2001}}
5634 >        Volume = 115,
5635 >        Year = 2001}
5636  
5637   @book{Olver1986,
5638          Address = {New York},
5639          Author = {P.J. Olver},
5640          Publisher = {Springer},
5641          Title = {Applications of Lie groups to differential equatitons},
5642 <        Year = {1986}}
5642 >        Year = 1986}
5643  
5644   @article{Omelyan1998,
5645          Abstract = {A revised version of the quaternion approach for numerical integration
# Line 5404 | Line 5658
5658          Issn = {0894-1866},
5659          Journal = {Computers in Physics},
5660          Month = {Jan-Feb},
5661 <        Number = {1},
5661 >        Number = 1,
5662          Pages = {97-103},
5663          Title = {On the numerical integration of motion for rigid polyatomics: The modified quaternion approach},
5664          Uri = {<Go to ISI>://000072024300025},
5665 <        Volume = {12},
5666 <        Year = {1998}}
5665 >        Volume = 12,
5666 >        Year = 1998}
5667  
5668   @article{Omelyan1998a,
5669          Abstract = {An algorithm for numerical integration of the rigid-body equations
# Line 5426 | Line 5680
5680          Issn = {1063-651X},
5681          Journal = {Physical Review E},
5682          Month = {Jul},
5683 <        Number = {1},
5683 >        Number = 1,
5684          Pages = {1169-1172},
5685          Title = {Algorithm for numerical integration of the rigid-body equations of motion},
5686          Uri = {<Go to ISI>://000074893400151},
5687 <        Volume = {58},
5688 <        Year = {1998}}
5687 >        Volume = 58,
5688 >        Year = 1998}
5689  
5690   @article{Owren1992,
5691          Abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
# Line 5452 | Line 5706
5706          Issn = {0196-5204},
5707          Journal = {Siam Journal on Scientific and Statistical Computing},
5708          Month = {Nov},
5709 <        Number = {6},
5709 >        Number = 6,
5710          Pages = {1488-1501},
5711          Title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
5712          Uri = {<Go to ISI>://A1992JU93600013},
5713 <        Volume = {13},
5714 <        Year = {1992}}
5713 >        Volume = 13,
5714 >        Year = 1992}
5715  
5716   @article{Palacios1998,
5717          Abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
# Line 5495 | Line 5749
5749          Issn = {0163-1829},
5750          Journal = {Physical Review B},
5751          Month = {Dec 1},
5752 <        Number = {22},
5752 >        Number = 22,
5753          Pages = {14937-14958},
5754          Title = {Langevin-dynamics study of the dynamical properties of small magnetic particles},
5755          Uri = {<Go to ISI>://000077460000052},
5756 <        Volume = {58},
5757 <        Year = {1998}}
5756 >        Volume = 58,
5757 >        Year = 1998}
5758  
5759   @article{Parr1995,
5760          Abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
# Line 5527 | Line 5781
5781          Issn = {0038-0644},
5782          Journal = {Software-Practice \& Experience},
5783          Month = {Jul},
5784 <        Number = {7},
5784 >        Number = 7,
5785          Pages = {789-810},
5786          Title = {Antlr - a Predicated-Ll(K) Parser Generator},
5787          Uri = {<Go to ISI>://A1995RK10400004},
5788 <        Volume = {25},
5789 <        Year = {1995}}
5788 >        Volume = 25,
5789 >        Year = 1995}
5790  
5791   @article{Pastor1988,
5792          Annote = {T1302 Times Cited:61 Cited References Count:26},
5793          Author = {R. W. Pastor and B. R. Brooks and A. Szabo},
5794          Issn = {0026-8976},
5795 <        Journal = {Molecular Physics},
5795 >        Journal = mp,
5796          Month = {Dec 20},
5797 <        Number = {6},
5797 >        Number = 6,
5798          Pages = {1409-1419},
5799          Title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
5800          Uri = {<Go to ISI>://A1988T130200011},
5801 <        Volume = {65},
5802 <        Year = {1988}}
5801 >        Volume = 65,
5802 >        Year = 1988}
5803  
5804   @article{Pelzl1999,
5805          Annote = {220RC Times Cited:313 Cited References Count:49},
# Line 5553 | Line 5807
5807          Issn = {0935-9648},
5808          Journal = {Advanced Materials},
5809          Month = {Jul 5},
5810 <        Number = {9},
5810 >        Number = 9,
5811          Pages = {707-724},
5812          Title = {Banana-shaped compounds - A new field of liquid crystals},
5813          Uri = {<Go to ISI>://000081680400007},
5814 <        Volume = {11},
5815 <        Year = {1999}}
5814 >        Volume = 11,
5815 >        Year = 1999}
5816  
5817   @article{Perram1985,
5818          Annote = {Akb93 Times Cited:71 Cited References Count:12},
5819          Author = {J. W. Perram and M. S. Wertheim},
5820          Issn = {0021-9991},
5821 <        Journal = {Journal of Computational Physics},
5822 <        Number = {3},
5821 >        Journal = jcop,
5822 >        Number = 3,
5823          Pages = {409-416},
5824          Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function},
5825          Uri = {<Go to ISI>://A1985AKB9300008},
5826 <        Volume = {58},
5827 <        Year = {1985}}
5826 >        Volume = 58,
5827 >        Year = 1985}
5828  
5829   @article{Rotne1969,
5830          Author = {F. Perrin},
5831          Journal = {J. Chem. Phys.},
5832          Pages = {4831-4837},
5833          Title = {Variational treatment of hydrodynamic interaction in polymers},
5834 <        Volume = {50},
5835 <        Year = {1969}}
5834 >        Volume = 50,
5835 >        Year = 1969}
5836  
5837   @article{Perrin1936,
5838          Author = {F. Perrin},
5839          Journal = {J. Phys. Radium},
5840          Pages = {1-11},
5841          Title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation des fluorescences. Translation et diffusion de moleculese ellipsoidales},
5842 <        Volume = {7},
5843 <        Year = {1936}}
5842 >        Volume = 7,
5843 >        Year = 1936}
5844  
5845   @article{Perrin1934,
5846          Author = {F. Perrin},
5847          Journal = {J. Phys. Radium},
5848          Pages = {497-511},
5849          Title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour des molecules ellipsoidales},
5850 <        Volume = {5},
5851 <        Year = {1934}}
5850 >        Volume = 5,
5851 >        Year = 1934}
5852  
5853   @article{Petrache2000,
5854          Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
5855 <        Journal = {Biophysical Journal},
5855 >        Journal = bj,
5856          Pages = {3172-3192},
5857          Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
5858 <        Volume = {79},
5859 <        Year = {2000}}
5858 >        Volume = 79,
5859 >        Year = 2000}
5860  
5861   @article{Petrache1998,
5862          Abstract = {X-ray diffraction data taken at high instrumental resolution were
# Line 5627 | Line 5881
5881          Issn = {0009-3084},
5882          Journal = {Chemistry and Physics of Lipids},
5883          Month = {Sep},
5884 <        Number = {1},
5884 >        Number = 1,
5885          Pages = {83-94},
5886          Title = {Fluid phase structure of EPC and DMPC bilayers},
5887          Uri = {<Go to ISI>://000076497600007},
5888 <        Volume = {95},
5889 <        Year = {1998}}
5888 >        Volume = 95,
5889 >        Year = 1998}
5890  
5891   @article{Powles1973,
5892          Author = {J.~G. Powles},
5893          Journal = {Advan. Phys.},
5894          Pages = {1-56},
5895          Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
5896 <        Volume = {22},
5897 <        Year = {1973}}
5896 >        Volume = 22,
5897 >        Year = 1973}
5898  
5899   @article{Recio2004,
5900          Abstract = {Protein recognition is one of the most challenging and intriguing
# Line 5669 | Line 5923
5923          Annote = {763GQ Times Cited:21 Cited References Count:59},
5924          Author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
5925          Issn = {0022-2836},
5926 <        Journal = {Journal of Molecular Biology},
5926 >        Journal = jmb,
5927          Month = {Jan 16},
5928 <        Number = {3},
5928 >        Number = 3,
5929          Pages = {843-865},
5930          Title = {Identification of protein-protein interaction sites from docking energy landscapes},
5931          Uri = {<Go to ISI>://000188066900016},
5932 <        Volume = {335},
5933 <        Year = {2004}}
5932 >        Volume = 335,
5933 >        Year = 2004}
5934  
5935   @article{Reddy2006,
5936          Abstract = {An overview on the recent developments in the field of liquid crystalline
# Line 5694 | Line 5948
5948          Author = {R. A. Reddy and C. Tschierske},
5949          Issn = {0959-9428},
5950          Journal = {Journal of Materials Chemistry},
5951 <        Number = {10},
5951 >        Number = 10,
5952          Pages = {907-961},
5953          Title = {Bent-core liquid crystals: polar order, superstructural chirality and spontaneous desymmetrisation in soft matter systems},
5954          Uri = {<Go to ISI>://000235990500001},
5955 <        Volume = {16},
5956 <        Year = {2006}}
5955 >        Volume = 16,
5956 >        Year = 2006}
5957  
5958   @article{Reich1999,
5959          Abstract = {Backward error analysis has become an important tool for understanding
# Line 5729 | Line 5983
5983          Issn = {0036-1429},
5984          Journal = {Siam Journal on Numerical Analysis},
5985          Month = {Sep 8},
5986 <        Number = {5},
5986 >        Number = 5,
5987          Pages = {1549-1570},
5988          Title = {Backward error analysis for numerical integrators},
5989          Uri = {<Go to ISI>://000082650600010},
5990 <        Volume = {36},
5991 <        Year = {1999}}
5990 >        Volume = 36,
5991 >        Year = 1999}
5992  
5993   @article{Ros2005,
5994          Abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
# Line 5749 | Line 6003
6003          Author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
6004          Issn = {0959-9428},
6005          Journal = {Journal of Materials Chemistry},
6006 <        Number = {48},
6006 >        Number = 48,
6007          Pages = {5093-5098},
6008          Title = {Banana-shaped liquid crystals: a new field to explore},
6009          Uri = {<Go to ISI>://000233775500001},
6010 <        Volume = {15},
6011 <        Year = {2005}}
6010 >        Volume = 15,
6011 >        Year = 2005}
6012  
6013   @article{Roux1991,
6014          Abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
# Line 5782 | Line 6036
6036          Issn = {0022-3654},
6037          Journal = {Journal of Physical Chemistry},
6038          Month = {Jun 13},
6039 <        Number = {12},
6039 >        Number = 12,
6040          Pages = {4856-4868},
6041          Title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
6042          Uri = {<Go to ISI>://A1991FR75600049},
6043 <        Volume = {95},
6044 <        Year = {1991}}
6043 >        Volume = 95,
6044 >        Year = 1991}
6045  
6046   @article{Roy2005,
6047          Abstract = {A vast majority of compounds with bent core or banana shaped molecules
# Line 5806 | Line 6060
6060          Issn = {1292-8941},
6061          Journal = {European Physical Journal E},
6062          Month = {Nov},
6063 <        Number = {3},
6063 >        Number = 3,
6064          Pages = {253-258},
6065          Title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases in banana shaped molecules},
6066          Uri = {<Go to ISI>://000233363300002},
6067 <        Volume = {18},
6068 <        Year = {2005}}
6067 >        Volume = 18,
6068 >        Year = 2005}
6069  
6070   @article{Ryckaert1977,
6071          Annote = {Cz253 Times Cited:3680 Cited References Count:7},
6072          Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
6073          Issn = {0021-9991},
6074 <        Journal = {Journal of Computational Physics},
6075 <        Number = {3},
6074 >        Journal = jcop,
6075 >        Number = 3,
6076          Pages = {327-341},
6077          Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes},
6078          Uri = {<Go to ISI>://A1977CZ25300007},
6079 <        Volume = {23},
6080 <        Year = {1977}}
6079 >        Volume = 23,
6080 >        Year = 1977}
6081  
6082   @article{Sagui1999,
6083          Abstract = {Current computer simulations of biomolecules typically make use of
# Line 5848 | Line 6102
6102          Pages = {155-179},
6103          Title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic effects},
6104          Uri = {<Go to ISI>://000081271400008},
6105 <        Volume = {28},
6106 <        Year = {1999}}
6105 >        Volume = 28,
6106 >        Year = 1999}
6107  
6108   @article{Sandu1999,
6109          Abstract = {Numerical resonance artifacts have become recognized recently as a
# Line 5892 | Line 6146
6146          Annote = {194FM Times Cited:14 Cited References Count:32},
6147          Author = {A. Sandu and T. Schlick},
6148          Issn = {0021-9991},
6149 <        Journal = {Journal of Computational Physics},
6149 >        Journal = jcop,
6150          Month = {May 1},
6151 <        Number = {1},
6151 >        Number = 1,
6152          Pages = {74-113},
6153          Title = {Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics},
6154          Uri = {<Go to ISI>://000080181500004},
6155 <        Volume = {151},
6156 <        Year = {1999}}
6155 >        Volume = 151,
6156 >        Year = 1999}
6157  
6158   @article{Sasaki2004,
6159          Abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
# Line 5913 | Line 6167
6167          Author = {Y. Sasaki and R. Shukla and B. D. Smith},
6168          Issn = {1477-0520},
6169          Journal = {Organic \& Biomolecular Chemistry},
6170 <        Number = {2},
6170 >        Number = 2,
6171          Pages = {214-219},
6172          Title = {Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases},
6173          Uri = {<Go to ISI>://000187843800012},
6174 <        Volume = {2},
6175 <        Year = {2004}}
6174 >        Volume = 2,
6175 >        Year = 2004}
6176  
6177   @article{Satoh1996,
6178          Abstract = {The effects of dipole-dipole interaction on mesophase formation are
# Line 5937 | Line 6191
6191          Pages = {99-104},
6192          Title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect of terminal dipole moment on mesophase formation},
6193          Uri = {<Go to ISI>://A1996UQ97500017},
6194 <        Volume = {255},
6195 <        Year = {1996}}
6194 >        Volume = 255,
6195 >        Year = 1996}
6196  
6197   @article{Schaps1999,
6198          Annote = {163EC Times Cited:0 Cited References Count:0},
# Line 5946 | Line 6200
6200          Issn = {1044-789X},
6201          Journal = {Dr Dobbs Journal},
6202          Month = {Mar},
6203 <        Number = {3},
6203 >        Number = 3,
6204          Pages = {84-+},
6205          Title = {Compiler construction with ANTLR and Java - Tools for building tools},
6206          Uri = {<Go to ISI>://000078389200023},
6207 <        Volume = {24},
6208 <        Year = {1999}}
6207 >        Volume = 24,
6208 >        Year = 1999}
6209  
6210   @article{Shen2002,
6211          Abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
# Line 5976 | Line 6230
6230          Annote = {540MH Times Cited:36 Cited References Count:45},
6231          Author = {M. Y. Shen and K. F. Freed},
6232          Issn = {0006-3495},
6233 <        Journal = {Biophysical Journal},
6233 >        Journal = bj,
6234          Month = {Apr},
6235 <        Number = {4},
6235 >        Number = 4,
6236          Pages = {1791-1808},
6237          Title = {Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models},
6238          Uri = {<Go to ISI>://000174932400010},
6239 <        Volume = {82},
6240 <        Year = {2002}}
6239 >        Volume = 82,
6240 >        Year = 2002}
6241  
6242   @article{Shillcock2005,
6243          Annote = {901QJ Times Cited:9 Cited References Count:23},
# Line 5991 | Line 6245
6245          Issn = {1476-1122},
6246          Journal = {Nature Materials},
6247          Month = {Mar},
6248 <        Number = {3},
6248 >        Number = 3,
6249          Pages = {225-228},
6250          Title = {Tension-induced fusion of bilayer membranes and vesicles},
6251          Uri = {<Go to ISI>://000227296700019},
6252 <        Volume = {4},
6253 <        Year = {2005}}
6252 >        Volume = 4,
6253 >        Year = 2005}
6254  
6255   @article{Shimada1993,
6256          Abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
# Line 6019 | Line 6273
6273          Annote = {Lh164 Times Cited:27 Cited References Count:47},
6274          Author = {J. Shimada and H. Kaneko and T. Takada},
6275          Issn = {0192-8651},
6276 <        Journal = {Journal of Computational Chemistry},
6276 >        Journal = jcc,
6277          Month = {Jul},
6278 <        Number = {7},
6278 >        Number = 7,
6279          Pages = {867-878},
6280          Title = {Efficient Calculations of Coulombic Interactions in Biomolecular Simulations with Periodic Boundary-Conditions},
6281          Uri = {<Go to ISI>://A1993LH16400011},
6282 <        Volume = {14},
6283 <        Year = {1993}}
6282 >        Volume = 14,
6283 >        Year = 1993}
6284  
6285   @article{Skeel2002,
6286          Abstract = {The best simple method for Newtonian molecular dynamics is indisputably
# Line 6042 | Line 6296
6296          Annote = {633RX Times Cited:8 Cited References Count:22},
6297          Author = {R. D. Skeel and J. A. Izaguirre},
6298          Issn = {0026-8976},
6299 <        Journal = {Molecular Physics},
6299 >        Journal = mp,
6300          Month = {Dec 20},
6301 <        Number = {24},
6301 >        Number = 24,
6302          Pages = {3885-3891},
6303          Title = {An impulse integrator for Langevin dynamics},
6304          Uri = {<Go to ISI>://000180297200014},
6305 <        Volume = {100},
6306 <        Year = {2002}}
6305 >        Volume = 100,
6306 >        Year = 2002}
6307  
6308   @article{Skeel1997,
6309          Abstract = {The following integration methods for special second-order ordinary
# Line 6070 | Line 6324
6324          Issn = {1064-8275},
6325          Journal = {Siam Journal on Scientific Computing},
6326          Month = {Jan},
6327 <        Number = {1},
6327 >        Number = 1,
6328          Pages = {203-222},
6329          Title = {A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications},
6330          Uri = {<Go to ISI>://A1997WE98100012},
6331 <        Volume = {18},
6332 <        Year = {1997}}
6331 >        Volume = 18,
6332 >        Year = 1997}
6333  
6334   @article{Tao2005,
6335          Abstract = {Recently a microscopic theory for the dynamics of suspensions of long
# Line 6101 | Line 6355
6355          Annote = {943DN Times Cited:3 Cited References Count:26},
6356          Author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont and W. J. Briels},
6357          Issn = {0021-9606},
6358 <        Journal = {Journal of Chemical Physics},
6358 >        Journal = jcp,
6359          Month = {Jun 22},
6360 <        Number = {24},
6360 >        Number = 24,
6361          Pages = {-},
6362          Title = {Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods},
6363          Uri = {<Go to ISI>://000230332400077},
6364 <        Volume = {122},
6365 <        Year = {2005}}
6364 >        Volume = 122,
6365 >        Year = 2005}
6366  
6367   @book{Tolman1979,
6368          Address = {New York},
6369          Author = {R.~C. Tolman},
6370 <        Chapter = {2},
6370 >        Chapter = 2,
6371          Pages = {19-22},
6372          Publisher = {Dover Publications, Inc.},
6373          Title = {The Principles of Statistical Mechanics},
6374 <        Year = {1979}}
6374 >        Year = 1979}
6375  
6376   @article{Tu1995,
6377          Abstract = {We report a constant pressure and temperature molecular dynamics simulation
# Line 6142 | Line 6396
6396          Annote = {Tv018 Times Cited:108 Cited References Count:34},
6397          Author = {K. Tu and D. J. Tobias and M. L. Klein},
6398          Issn = {0006-3495},
6399 <        Journal = {Biophysical Journal},
6399 >        Journal = bj,
6400          Month = {Dec},
6401 <        Number = {6},
6401 >        Number = 6,
6402          Pages = {2558-2562},
6403          Title = {Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer},
6404          Uri = {<Go to ISI>://A1995TV01800037},
6405 <        Volume = {69},
6406 <        Year = {1995}}
6405 >        Volume = 69,
6406 >        Year = 1995}
6407  
6408   @article{Tuckerman1992,
6409          Abstract = {The Trotter factorization of the Liouville propagator is used to generate
# Line 6167 | Line 6421
6421          Annote = {Je891 Times Cited:680 Cited References Count:19},
6422          Author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
6423          Issn = {0021-9606},
6424 <        Journal = {Journal of Chemical Physics},
6424 >        Journal = jcp,
6425          Month = {Aug 1},
6426 <        Number = {3},
6426 >        Number = 3,
6427          Pages = {1990-2001},
6428          Title = {Reversible Multiple Time Scale Molecular-Dynamics},
6429          Uri = {<Go to ISI>://A1992JE89100044},
6430 <        Volume = {97},
6431 <        Year = {1992}}
6430 >        Volume = 97,
6431 >        Year = 1992}
6432  
6433   @book{Varadarajan1974,
6434          Address = {New York},
6435          Author = {V.S. Varadarajan},
6436          Publisher = {Prentice-Hall},
6437          Title = {Lie groups, Lie algebras, and their representations},
6438 <        Year = {1974}}
6438 >        Year = 1974}
6439  
6440   @article{Vincent1995,
6441          Abstract = {We have implemented a portable parallel version of the macromolecular
# Line 6201 | Line 6455
6455          Annote = {Ta403 Times Cited:16 Cited References Count:23},
6456          Author = {J. J. Vincent and K. M. Merz},
6457          Issn = {0192-8651},
6458 <        Journal = {Journal of Computational Chemistry},
6458 >        Journal = jcc,
6459          Month = {Nov},
6460 <        Number = {11},
6460 >        Number = 11,
6461          Pages = {1420-1427},
6462          Title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing Interface Standard},
6463          Uri = {<Go to ISI>://A1995TA40300009},
6464 <        Volume = {16},
6465 <        Year = {1995}}
6464 >        Volume = 16,
6465 >        Year = 1995}
6466  
6467   @article{Wegener1979,
6468          Author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
6469          Journal = {Proc. Natl. Acad. Sci.},
6470 <        Number = {12},
6470 >        Number = 12,
6471          Pages = {6356-6360},
6472          Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
6473 <        Volume = {76},
6474 <        Year = {1979}}
6473 >        Volume = 76,
6474 >        Year = 1979}
6475  
6476   @article{Wilson2006,
6477          Author = {G.~V. Wilson},
6478          Journal = {American Scientist},
6479          Title = {Where's the Real Bottleneck in Scientific Computing?},
6480 <        Volume = {94},
6481 <        Year = {2006}}
6480 >        Volume = 94,
6481 >        Year = 2006}
6482  
6483   @article{Withers2003,
6484          Abstract = {The effects of longitudinal quadrupole moments on the formation of
# Line 6257 | Line 6511
6511          Annote = {738EF Times Cited:3 Cited References Count:43},
6512          Author = {I. M. Withers},
6513          Issn = {0021-9606},
6514 <        Journal = {Journal of Chemical Physics},
6514 >        Journal = jcp,
6515          Month = {Nov 15},
6516 <        Number = {19},
6516 >        Number = 19,
6517          Pages = {10209-10223},
6518          Title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne fluid},
6519          Uri = {<Go to ISI>://000186273200027},
6520 <        Volume = {119},
6521 <        Year = {2003}}
6520 >        Volume = 119,
6521 >        Year = 2003}
6522  
6523   @article{Wolf1999,
6524          Abstract = {Based on a recent result showing that the net Coulomb potential in
# Line 6291 | Line 6545
6545          Annote = {189PD Times Cited:70 Cited References Count:34},
6546          Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
6547          Issn = {0021-9606},
6548 <        Journal = {Journal of Chemical Physics},
6548 >        Journal = jcp,
6549          Month = {May 1},
6550 <        Number = {17},
6550 >        Number = 17,
6551          Pages = {8254-8282},
6552          Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r(-1) summation},
6553          Uri = {<Go to ISI>://000079913000008},
6554 <        Volume = {110},
6555 <        Year = {1999}}
6554 >        Volume = 110,
6555 >        Year = 1999}
6556  
6557   @article{Yoshida1990,
6558          Annote = {Ej798 Times Cited:492 Cited References Count:9},
# Line 6310 | Line 6564
6564          Pages = {262-268},
6565          Title = {Construction of Higher-Order Symplectic Integrators},
6566          Uri = {<Go to ISI>://A1990EJ79800009},
6567 <        Volume = {150},
6568 <        Year = {1990}}
6567 >        Volume = 150,
6568 >        Year = 1990}
6569  
6570   @article{Blum1972,
6571          Author = {L. Blum and A.~J. Torruella},
6572 <        Journal = {Journal of Chemical Physics},
6572 >        Journal = jcp,
6573          Number = 1,
6574          Pages = {303-309},
6575          Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
# Line 6324 | Line 6578
6578  
6579   @article{Stone1978,
6580          Author = {A.~J. Stone},
6581 <        Journal = {Molecular Physics},
6581 >        Journal = mp,
6582          Number = 1,
6583          Pages = {241-256},
6584          Title = {The description of bimolecular potentials, forces and torques: the S and V function expansions},
# Line 6333 | Line 6587
6587  
6588   @article{Berardi2003,
6589          Author = {R. Berardi, M. Cecchini and C. Zannoni},
6590 <        Journal = {Journal of Chemical Physics},
6590 >        Journal = jcp,
6591          Number = 18,
6592          Pages = {9933-9946},
6593          Title = {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
# Line 6342 | Line 6596
6596  
6597   @article{Beard2000,
6598          Author = {D. A. Beard and T. Schlick},
6599 <        Journal = {Journal of Chemical Physics},
6599 >        Journal = jcp,
6600          Number = 17,
6601          Pages = {7313-7322},
6602          Title = {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
# Line 6354 | Line 6608
6608          Author = {M.W. Hirsch},
6609          Publisher = {Springer},
6610          Title = {Differential Topology},
6611 <        Year = {1997}}
6611 >        Year = 1997}
6612  
6613   @book{Jost2002,
6614          Address = {Berlin},
6615          Author = {J. Jost},
6616          Publisher = {Springer-Verlag},
6617          Title = {Riemannian Geometry and Geometric Analysis},
6618 <        Year = {2002}}
6618 >        Year = 2002}
6619  
6620   @book{McDuff1998,
6621          Address = {Oxford},
6622          Author = {D. McDuff and D. Salamon},
6623          Publisher = {Oxford Mathematical Monographs},
6624          Title = {Introduction to Symplectic Topology},
6625 <        Year = {1998}}
6625 >        Year = 1998}
6626  
6627   @article{Matubayasi1999,
6628          Author = {N. Matubayasi and M. Nakahara},
6629 <        Journal = {Journal of Chemical Physics},
6629 >        Journal = jcp,
6630          Number = 7,
6631          Pages = {3291-3301},
6632          Title = {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
# Line 6381 | Line 6635
6635  
6636   @article{Miller2002,
6637          Author = {T.F. Miller III, M. Eleftheriou},
6638 <        Journal = {Journal of Chemical Physics},
6638 >        Journal = jcp,
6639          Number = 20,
6640          Pages = {8649-8659},
6641          Title = {Symplectic quaternion scheme for biophysical molecular dynamics},
# Line 6390 | Line 6644
6644  
6645   @article{McMillan1971,
6646          Author = {W.L. McMillan},
6647 <        Journal = {Journal of Chemical Physics},
6647 >        Journal = jcp,
6648          Number = 3,
6649          Pages = {1238-1246},
6650          Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},
# Line 6432 | Line 6686
6686          Title = {The Dynamics of Runge-Kutta Methods},
6687          Volume = 2,
6688          Year = 1992}
6689 +
6690 + @article{HuseyinKaya07012005,
6691 +        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.
6692 + },
6693 +        Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun},
6694 +        Doi = {10.1529/biophysj.104.057471},
6695 +        Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf},
6696 +        Journal = {Biophys. J.},
6697 +        Number = 1,
6698 +        Pages = {520-535},
6699 +        Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}},
6700 +        Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6701 +        Volume = 89,
6702 +        Year = 2005,
6703 +        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6704 +        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}}

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