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9
10
11	+	@string{acp = {Adv. Chem. Phys.}}
12
13	+	@string{bj = {Biophys. J.}}
14	+
15	+	@string{ccp5 = {CCP5 Information Quarterly}}
16	+
17	+	@string{cp = {Chem. Phys.}}
18	+
19	+	@string{cpl = {Chem. Phys. Lett.}}
20	+
21	+	@string{jacs = {J. Am. Chem. Soc.}}
22	+
23	+	@string{jcc = {J. Comp. Chem.}}
24	+
25	+	@string{jcop = {J. Comp. Phys.}}
26	+
27	+	@string{jcp = {J. Chem. Phys.}}
28	+
29	+	@string{jmb = {J. Mol. Bio.}}
30	+
31	+	@string{jml = {J. Mol. Liq.}}
32	+
33	+	@string{jpc = {J. Phys. Chem.}}
34	+
35	+	@string{jpca = {J. Phys. Chem. A}}
36	+
37	+	@string{jpcb = {J. Phys. Chem. B}}
38	+
39	+	@string{mp = {Mol. Phys.}}
40	+
41	+	@string{pams = {Proc. Am. Math Soc.}}
42	+
43	+	@string{pccp = {Phys. Chem. Chem. Phys.}}
44	+
45	+	@string{pnas = {Proc. Natl. Acad. Sci. USA}}
46	+
47	+	@string{pr = {Phys. Rev.}}
48	+
49	+	@string{pra = {Phys. Rev. A}}
50	+
51	+	@string{prb = {Phys. Rev. B}}
52	+
53	+	@string{pre = {Phys. Rev. E}}
54	+
55	+	@string{prl = {Phys. Rev. Lett.}}
56	+
57	+	@string{rmp = {Rev. Mod. Phys.}}
58	+
59	+
60	+	@article{Jeffrey:2006dk,
61	+	Author = {Jeffrey,D. J. and Onishi,Y.},
62	+	Date-Added = {2008-04-30 12:15:31 -0400},
63	+	Date-Modified = {2008-04-30 12:15:31 -0400},
64	+	Journal = {Journal of Fluid Mechanics Digital Archive},
65	+	M3 = {10.1017/S0022112084000355},
66	+	Number = {-1},
67	+	Pages = {261--290},
68	+	Title = {Calculation of the resistance and mobility functions for two unequal rigid spheres in low-Reynolds-number flow},
69	+	Ty = {JOUR},
70	+	Volume = {139},
71	+	Year = {2006}}
72	+
73	+	@article{Goldman:1966ph,
74	+	Abstract = { Bipolar coordinates are employed to determine the terminal settling motion of two, identical, homogeneous, unconstrained spheres in an unbounded fluid at small Reynolds numbers. Exact numerical values are obtained for the linear and angular velocities of the spheres as a function of their relative separation and of the orientation of their line-of-centers relative to the direction of gravity. Comparison with published experimental data indicates good agreement, especially when wall effects are taken into account.},
75	+	Author = {Goldman, A. J. and Cox, R. G. and Brenner, H.},
76	+	Date-Added = {2008-04-30 12:12:54 -0400},
77	+	Date-Modified = {2008-04-30 12:12:54 -0400},
78	+	Journal = {Chemical Engineering Science},
79	+	Number = {12},
80	+	Pages = {1151--1170},
81	+	Title = {The slow motion of two identical arbitrarily oriented spheres through a viscous fluid},
82	+	Ty = {JOUR},
83	+	Url = {http://www.sciencedirect.com/science/article/B6TFK-44360XJ-D0/1/c14cf5c48fab65f0aaa096e60d15fa87},
84	+	Volume = {21},
85	+	Year = {1966},
86	+	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-44360XJ-D0/1/c14cf5c48fab65f0aaa096e60d15fa87}}
87	+
88	+	@article{Brenner:1972th,
89	+	Abstract = { A general theory is presented for determining the quasistatic Stokes resistance of a particle or an aggregate of particles of arbitrary shape which move with arbitrary translational and rotational velocities in an infinite viscous fluid subjected to a general linear shear flow in the absence of the particles. It is shown that the hydrodynamic resistance of the particles may be characterized by two intrinsic matrices-the grand resistance matrix and the shear resistance matrix, the elements of each matrix being dependent only upon the instantaneous geometrical configuration of the multiparticle system. Explicit expressions for these matrix elements are given for a single ellipsoidal particle and for two spheres. Analytical, closed-form expressions are given for the case where the spheres are widely spaced compared with their radii. When the separation between the spheres is arbitrary, the matrix elements are only determinate numerically for specified ratios of sphere radii and center-to-center separation distances. These numerical values are derived from available bipolar-coordinate system solutions for two spheres. Besides providing a compact and systematic representation of the intrinsic Stokes resistance of multiparticle systems subjected to shear, which does not depend upon the precise velocities of the particles or on the nature of the shear flow, it is demonstrated (by way of example) that the matrix representation permits an immediate determination of the translational and rotational velocities of the individual particles in a neutrally buoyant multiparticle system.},
90	+	Author = {Brenner, Howard and O'Neill, Michael E.},
91	+	Date-Added = {2008-04-30 12:12:49 -0400},
92	+	Date-Modified = {2008-04-30 12:12:49 -0400},
93	+	Journal = {Chemical Engineering Science},
94	+	Number = {7},
95	+	Pages = {1421--1439},
96	+	Title = {On the Stokes resistance of multiparticle systems in a linear shear field},
97	+	Ty = {JOUR},
98	+	Url = {http://www.sciencedirect.com/science/article/B6TFK-444GW12-16J/1/ba6bda9d1e50c88fea6cd92aac2f6bd7},
99	+	Volume = {27},
100	+	Year = {1972},
101	+	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-444GW12-16J/1/ba6bda9d1e50c88fea6cd92aac2f6bd7}}
102	+
103	+	@article{GarciadelaTorreJjp0647941,
104	+	Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain},
105	+	Author = {{Garc\'{i}a de la Torre}, Jose and del Rio Echenique, G. and Ortega, A.},
106	+	Date-Added = {2008-04-30 10:14:50 -0400},
107	+	Date-Modified = {2008-04-30 10:14:50 -0400},
108	+	Issn = {1520-6106},
109	+	Journal = jpcb,
110	+	Number = {5},
111	+	Pages = {955-961},
112	+	Title = {Improved Calculation of Rotational Diffusion and Intrinsic Viscosity of Bead Models for Macromolecules and Nanoparticles},
113	+	Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0647941},
114	+	Volume = {111},
115	+	Year = {2007},
116	+	Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0647941}}
117	+
118	+	@article{Garcia-de-la-Torre:2001wd,
119	+	Abstract = { The calculation of hydrodynamic and other solution properties of rigid macromolecules, using bead-shell model methodologies, requires the specification of the macromolecular shape in a format that can be interfaced with existing programs for hydrodynamic computations. Here, a procedure is presented for such a structural specification that is applicable to arbitrarily shaped particles. A computer program (), in which the user inserts the code needed to determine the structure, produces an structural file that is interpreted by another program () which is in charge of the computation of properties. As simple and yet illustrative examples we consider two cases: (1) dimeric structures composed of ellipsoidal subunits; and (2) toroidal structures, presenting simple equations that predict the properties of toroids with varying radial ratios.},
120	+	Author = {{Garc\'{i}a de la Torre}, Jose },
121	+	Date-Added = {2008-04-29 15:11:32 -0400},
122	+	Date-Modified = {2008-04-29 15:11:32 -0400},
123	+	Journal = {Biophysical Chemistry},
124	+	Keywords = {Rigid macromolecules; Hydrodynamic properties; Bead-shell model; Three-dimensional structure},
125	+	Number = {3},
126	+	Pages = {265--274},
127	+	Title = {Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape},
128	+	Ty = {JOUR},
129	+	Url = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953},
130	+	Volume = {94},
131	+	Year = {2001},
132	+	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953}}
133	+
134	+	@article{Peters:1999uq,
135	+	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.},
136	+	Author = {Peters, MH},
137	+	Date-Added = {2008-03-13 16:54:59 -0400},
138	+	Date-Modified = {2008-03-13 16:56:54 -0400},
139	+	Journal = {Journal of Statistical Physics},
140	+	Keywords = {Brownian particle; Fokker Planck equation; adsorption; molecular friction; force autocorrelation function; molecular dynamics},
141	+	Pages = {557-586},
142	+	Timescited = {0},
143	+	Title = {Fokker-Planck equation, molecular friction, and molecular dynamics for Brownian particle transport near external solid surfaces},
144	+	Volume = {94},
145	+	Year = {1999}}
146	+
147	+	@article{Peters:1999qy,
148	+	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].},
149	+	Author = {Peters, MH},
150	+	Date-Added = {2008-03-13 16:54:59 -0400},
151	+	Date-Modified = {2008-03-13 16:56:44 -0400},
152	+	Journal = jcp,
153	+	Pages = {528-538},
154	+	Timescited = {0},
155	+	Title = {Fokker-Planck equation and the grand molecular friction tensor for coupled rotational and translational motions of structured Brownian particles near structured surfaces},
156	+	Volume = {110},
157	+	Year = {1999}}
158	+
159	+	@article{Peters:2000fk,
160	+	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].},
161	+	Author = {Peters, MH},
162	+	Date-Added = {2008-03-13 16:54:59 -0400},
163	+	Date-Modified = {2008-03-13 16:56:20 -0400},
164	+	Journal = jcp,
165	+	Pages = {5488-5498},
166	+	Timescited = {0},
167	+	Title = {The Smoluchowski diffusion equation for structured macromolecules near structured surfaces},
168	+	Volume = {112},
169	+	Year = {2000}}
170	+
171	+	@article{Nienhuis:1970lr,
172	+	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.},
173	+	Author = {Nienhuis, G. },
174	+	Date-Added = {2008-03-13 16:53:44 -0400},
175	+	Date-Modified = {2008-03-13 16:53:44 -0400},
176	+	Journal = {Physica},
177	+	Number = {1},
178	+	Pages = {26--48},
179	+	Title = {On the microscopic theory of Brownian motion with a rotational degree of freedom},
180	+	Ty = {JOUR},
181	+	Url = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413},
182	+	Volume = {49},
183	+	Year = {1970},
184	+	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}}
185	+
186	+	@article{SunX._jp0762020,
187	+	Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556},
188	+	Author = {Sun, X. and Gezelter, J.D.},
189	+	Date-Added = {2008-02-15 13:48:18 -0500},
190	+	Date-Modified = {2008-02-15 13:48:18 -0500},
191	+	Issn = {1520-6106},
192	+	Journal = jpcb,
193	+	Number = {7},
194	+	Pages = {1968-1975},
195	+	Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes},
196	+	Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020},
197	+	Volume = {112},
198	+	Year = {2008},
199	+	Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}}
200	+
201	+	@book{Schlick2002,
202	+	Address = {Secaucus, NJ, USA},
203	+	Author = {Tamar Schlick},
204	+	Date-Added = {2008-02-12 16:52:19 -0500},
205	+	Date-Modified = {2008-02-12 16:53:15 -0500},
206	+	Isbn = {038795404X},
207	+	Publisher = {Springer-Verlag New York, Inc.},
208	+	Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
209	+	Year = {2002}}
210	+
211	+	@article{Chun:2000fj,
212	+	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.},
213	+	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},
214	+	Date-Added = {2008-01-22 10:38:33 -0500},
215	+	Date-Modified = {2008-01-22 10:38:49 -0500},
216	+	Journal = jcc,
217	+	Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
218	+	Pages = {159--184},
219	+	Timescited = 0,
220	+	Title = {{MBO(N)D:} A multibody method for long-time molecular dynamics simulations},
221	+	Volume = 21,
222	+	Year = 2000}
223	+
224	+	@article{Fogolari:1996lr,
225	+	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.},
226	+	Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.},
227	+	Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
228	+	Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
229	+	Da = {19960924},
230	+	Date-Added = {2008-01-22 10:19:04 -0500},
231	+	Date-Modified = {2008-01-22 10:19:09 -0500},
232	+	Dcom = {19960924},
233	+	Edat = {1996/03/01},
234	+	Issn = {0006-3495 (Print)},
235	+	Jid = {0370626},
236	+	Journal = {Biophys J},
237	+	Jt = {Biophysical journal},
238	+	Language = {eng},
239	+	Lr = {20071115},
240	+	Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; Models, Molecular; Molecular Structure; Peptides/chemistry; *Protein Conformation; Software; Thermodynamics},
241	+	Mhda = {1996/03/01 00:01},
242	+	Number = {3},
243	+	Own = {NLM},
244	+	Pages = {1183--1197},
245	+	Pl = {UNITED STATES},
246	+	Pmid = {8785277},
247	+	Pst = {ppublish},
248	+	Pt = {Journal Article},
249	+	Pubm = {Print},
250	+	Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)},
251	+	Sb = {IM},
252	+	So = {Biophys J. 1996 Mar;70(3):1183-97. },
253	+	Stat = {MEDLINE},
254	+	Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.},
255	+	Volume = {70},
256	+	Year = {1996}}
257	+
258	+	@inbook{Ramachandran1996,
259	+	Address = {Providence, Rhode Island},
260	+	Author = {Gomathi Ramachandran and Tamar Schlick},
261	+	Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
262	+	Date-Added = {2008-01-22 10:03:42 -0500},
263	+	Date-Modified = {2008-01-22 10:06:57 -0500},
264	+	Editor = {P. M. Pardalos and D. Shalloway and G. Xue},
265	+	Pages = {215-231},
266	+	Publisher = {American Mathematical Society},
267	+	Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
268	+	Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
269	+	Volume = {23},
270	+	Year = {1996}}
271	+
272	+	@article{FIXMAN:1986lr,
273	+	Author = {Fixman, M},
274	+	Date-Added = {2008-01-22 09:59:29 -0500},
275	+	Date-Modified = {2008-01-22 09:59:35 -0500},
276	+	Journal = {Macromolecules},
277	+	Pages = {1204-1207},
278	+	Timescited = {0},
279	+	Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION},
280	+	Volume = {19},
281	+	Year = {1986}}
282	+
283	+	@article{Berendsen87,
284	+	Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
285	+	Date-Added = {2008-01-22 09:53:15 -0500},
286	+	Date-Modified = {2008-01-22 09:53:15 -0500},
287	+	Journal = jpc,
288	+	Pages = {6269-6271},
289	+	Title = {The Missing Term in Effective Pair Potentials},
290	+	Volume = 91,
291	+	Year = 1987}
292	+
293	+	@incollection{Berendsen81,
294	+	Address = {Dordrecht},
295	+	Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
296	+	Booktitle = {Intermolecular Forces},
297	+	Date-Added = {2008-01-22 09:52:49 -0500},
298	+	Date-Modified = {2008-01-22 09:52:49 -0500},
299	+	Editor = {B. Pullman},
300	+	Pages = {331-342},
301	+	Publisher = {Reidel},
302	+	Title = {Simple Point Charge Water},
303	+	Year = 1981}
304	+
305	+	@article{Stillinger74,
306	+	Author = {F.~H. Stillinger and A. Rahman},
307	+	Date-Added = {2008-01-22 09:51:43 -0500},
308	+	Date-Modified = {2008-01-22 09:51:43 -0500},
309	+	Journal = jcp,
310	+	Number = 4,
311	+	Pages = {1545-1557},
312	+	Title = {Improved simulation of liquid water by molecular dynamics},
313	+	Volume = 60,
314	+	Year = 1974}
315	+
316		@article{Torre:1983lr,
317	<	Author = {de la Torre, Jose Garcia and Rodes, Vicente},
317	>	Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
318		Date-Added = {2008-01-11 16:16:43 -0500},
319		Date-Modified = {2008-01-11 16:16:43 -0500},
320	<	Journal = {The Journal of Chemical Physics},
320	>	Journal = jcp,
321		Journal1 = {The Journal of Chemical Physics},
322		Journal2 = {J. Chem. Phys.},
323		Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
324	<	Number = {5},
324	>	Number = 5,
325		Pages = {2454--2460},
326		Publisher = {AIP},
327		Title = {Effects from bead size and hydrodynamic interactions on the translational and rotational coefficients of macromolecular bead models},
328		Ty = {JOUR},
329		Url = {http://link.aip.org/link/?JCP/79/2454/1},
330	<	Volume = {79},
331	<	Year = {1983}}
330	>	Volume = 79,
331	>	Year = 1983,
332	>	Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}}
333
334		@article{PhysRev.119.53,
335		Author = {Favro, L. Dale},
#	Line 33 \| Line 338
338		Doi = {10.1103/PhysRev.119.53},
339		Journal = {Phys. Rev.},
340		Month = {Jul},
341	<	Number = {1},
342	<	Numpages = {9},
341	>	Number = 1,
342	>	Numpages = 9,
343		Pages = {53--62},
344		Publisher = {American Physical Society},
345		Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body},
346	<	Volume = {119},
347	<	Year = {1960}}
346	>	Volume = 119,
347	>	Year = 1960,
348	>	Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}}
349
350		@article{hess:209,
351		Author = {Berk Hess},
352		Date-Added = {2008-01-08 16:41:06 -0500},
353		Date-Modified = {2008-01-08 16:41:06 -0500},
354		Doi = {10.1063/1.1421362},
355	<	Journal = {The Journal of Chemical Physics},
355	>	Journal = jcp,
356		Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
357	<	Number = {1},
357	>	Number = 1,
358		Pages = {209-217},
359		Publisher = {AIP},
360		Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
361		Url = {http://link.aip.org/link/?JCP/116/209/1},
362	<	Volume = {116},
363	<	Year = {2002}}
362	>	Volume = 116,
363	>	Year = 2002,
364	>	Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
365	>	Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}}
366
367		@article{Garcia-de-la-Torre:1997qy,
368		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.},
369		Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es},
370	<	Au = {Garcia de la Torre, J and Carrasco, B and Harding, SE},
371	<	Author = {Garcia de la Torre, J and Carrasco, B and Harding, S E},
372	<	Da = {19970709},
370	>	Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE},
371	>	Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E},
372	>	Da = 19970709,
373		Date-Added = {2008-01-08 15:45:31 -0500},
374		Date-Modified = {2008-01-08 15:46:57 -0500},
375	<	Dcom = {19970709},
375	>	Dcom = 19970709,
376		Edat = {1997/01/01},
377		Issn = {0175-7571 (Print)},
378	<	Jid = {8409413},
378	>	Jid = 8409413,
379		Journal = {Eur Biophys J},
380		Jt = {European biophysics journal : EBJ},
381		Keywords = {Birefringence; Fluorescence Polarization; Humans; Immunoglobulin G/chemistry; Models, Structural; Protein Conformation; Proteins/chemistry; Scattering, Radiation; *Software; Ultracentrifugation/methods},
382		Language = {eng},
383	<	Lr = {20061115},
383	>	Lr = 20061115,
384		Mhda = {1997/01/01 00:01},
385		Number = {5-6},
386		Own = {NLM},
387		Pages = {361--372},
388		Pl = {GERMANY},
389	<	Pmid = {9213556},
389	>	Pmid = 9213556,
390		Pst = {ppublish},
391		Pt = {Journal Article; Research Support, Non-U.S. Gov't},
392		Pubm = {Print},
#	Line 87 \| Line 395
395		So = {Eur Biophys J. 1997;25(5-6):361-72.},
396		Stat = {MEDLINE},
397		Title = {SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.},
398	<	Volume = {25},
399	<	Year = {1997}}
398	>	Volume = 25,
399	>	Year = 1997}
400
401		@article{Ravichandran:1999fk,
402		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].},
403		Author = {Ravichandran, S and Bagchi, B},
404		Date-Added = {2008-01-08 15:24:48 -0500},
405		Date-Modified = {2008-01-08 15:25:41 -0500},
406	<	Journal = {Journal of Chemical Physics},
406	>	Journal = jcp,
407		Pages = {7505-7511},
408		Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
409	<	Volume = {111},
410	<	Year = {1999}}
409	>	Volume = 111,
410	>	Year = 1999}
411
412		@article{TANG:1993lr,
413		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.},
414		Author = {TANG, SA and EVANS, GT},
415		Date-Added = {2008-01-08 15:23:42 -0500},
416		Date-Modified = {2008-01-08 15:24:09 -0500},
417	<	Journal = {Molecular Physics},
417	>	Journal = mp,
418		Pages = {1443-1457},
419		Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
420	<	Volume = {80},
421	<	Year = {1993}}
420	>	Volume = 80,
421	>	Year = 1993}
422
423		@article{Schmidt:2003kx,
424		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 426
426		Date-Added = {2008-01-08 15:12:53 -0500},
427		Date-Modified = {2008-01-08 15:13:21 -0500},
428		Doi = {DOI 10.1063/1.1610442},
429	<	Journal = {Journal of Chemical Physics},
429	>	Journal = jcp,
430		Pages = {8062-8068},
431		Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
432	<	Volume = {119},
433	<	Year = {2003}}
432	>	Volume = 119,
433	>	Year = 2003,
434	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}
435
436		@article{Schmidt:2004fj,
437		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 439
439		Date-Added = {2008-01-08 15:12:53 -0500},
440		Date-Modified = {2008-01-08 15:13:20 -0500},
441		Doi = {DOI 10.1021/jp037185r},
442	<	Journal = {Journal of Physical Chemistry B},
442	>	Journal = jpcb,
443		Pages = {6767-6771},
444		Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
445	<	Volume = {108},
446	<	Year = {2004}}
445	>	Volume = 108,
446	>	Year = 2004,
447	>	Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}}
448
449		@article{Klein01,
450		Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
#	Line 274 \| Line 584
584		Date-Modified = {2008-01-08 14:58:56 -0500},
585		Journal = {J. Chem. Phys.},
586		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf},
587	<	Number = {19},
587	>	Number = 19,
588		Pages = {8577-8593},
589		Title = {A smooth particle mesh Ewald method},
590	<	Volume = {103},
591	<	Year = {1995}}
590	>	Volume = 103,
591	>	Year = 1995}
592
593		@article{Ricci94,
594		Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
#	Line 328 \| Line 638
638		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf},
639		Pages = {7320-7327},
640		Title = {Acceleration of Convergence for Lattice Sums},
641	<	Volume = {93},
642	<	Year = {1989}}
641	>	Volume = 93,
642	>	Year = 1989}
643
644		@article{Petersen95,
645		Author = {H.~G. Petersen},
#	Line 338 \| Line 648
648		Journal = {J. Chem. Phys.},
649		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
650		Month = {September},
651	<	Number = {9},
651	>	Number = 9,
652		Pages = {3668-3679},
653		Title = {Accuracy and efficiency of the particle mesh Ewald method},
654	<	Volume = {103},
655	<	Year = {1995}}
654	>	Volume = 103,
655	>	Year = 1995}
656
657		@article{Duncan06,
658		Author = {Peter D. Duncan and Philip J. Camp},
#	Line 428 \| Line 738
738		Year = 2003}
739
740		@article{Cascales98,
741	<	Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
741	>	Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and {Garc\'{i}a de la Torre}, Jose},
742		Date-Added = {2008-01-08 14:58:56 -0500},
743		Date-Modified = {2008-01-08 14:58:57 -0500},
744		Journal = {J. Phys. Chem. B},
#	Line 475 \| Line 785
785		Journal = {Phil. Mag. A},
786		Pages = {1057-1066},
787		Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
788	<	Volume = {75},
789	<	Year = {1997}}
788	>	Volume = 75,
789	>	Year = 1997}
790
791		@inproceedings{Gotze89,
792		Address = {Amsterdam},
#	Line 529 \| Line 839
839		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
840		Pages = {1322-1331},
841		Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
842	<	Volume = {99},
843	<	Year = {1995}}
842	>	Volume = 99,
843	>	Year = 1995}
844
845		@article{Ayton02,
846		Author = {G. Ayton and G.~A. Voth},
#	Line 612 \| Line 922
922		Doi = {10.1529/biophysj.106.086017},
923		Eprint = {http://www.biophysj.org/cgi/reprint/90/11/L83.pdf},
924		Journal = {Biophys. J.},
925	<	Number = {11},
925	>	Number = 11,
926		Pages = {L83-85},
927		Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}},
928		Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
929	<	Volume = {90},
930	<	Year = {2006}}
929	>	Volume = 90,
930	>	Year = 2006,
931	>	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
932	>	Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017}}
933
934		@article{deJoannis06,
935		Author = {J. de~Joannis and F.~Y. Jiang and J.~T. Kindt},
#	Line 747 \| Line 1059
1059		Journal = {Mol. Simul.},
1060		Pages = {351-368},
1061		Title = {Cutoff Errors in the Ewald. Summation Formulae for Point Charge Systems},
1062	<	Volume = {9},
1063	<	Year = {1992}}
1062	>	Volume = 9,
1063	>	Year = 1992}
1064
1065		@article{Tlusty00,
1066		Author = {T. Tlusty and S.~A. Safran},
#	Line 767 \| Line 1079
1079		Doi = {10.1103/PhysRevA.38.1005},
1080		Journal = {Phys. Rev. A},
1081		Month = {Jul},
1082	<	Number = {2},
1083	<	Numpages = {13},
1082	>	Number = 2,
1083	>	Numpages = 13,
1084		Pages = {1005--1018},
1085		Publisher = {American Physical Society},
1086		Title = {Defects in flexible membranes with crystalline order},
1087	<	Volume = {38},
1088	<	Year = {1988}}
1087	>	Volume = 38,
1088	>	Year = 1988,
1089	>	Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005}}
1090
1091		@article{Monroe95,
1092		Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
#	Line 834 \| Line 1147
1147		Journal = {Ann. Physik},
1148		Pages = {253-287},
1149		Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
1150	<	Volume = {64},
1151	<	Year = {1921}}
1150	>	Volume = 64,
1151	>	Year = 1921}
1152
1153		@article{Zwanzig88,
1154		Author = {R. Zwanzig},
#	Line 882 \| Line 1195
1195		Date-Added = {2008-01-08 14:58:56 -0500},
1196		Date-Modified = {2008-01-08 14:58:58 -0500},
1197		Journal = prl,
1198	<	Pages = {3649},
1198	>	Pages = 3649,
1199		Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
1200		Volume = 82,
1201	<	Year = {1999}}
1201	>	Year = 1999}
1202
1203		@article{Ngai81,
1204		Author = {K.~L. Ngai and F.-S. Liu},
#	Line 935 \| Line 1248
1248		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
1249		Pages = {69-88},
1250		Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
1251	<	Volume = {78},
1252	<	Year = {1999}}
1251	>	Volume = 78,
1252	>	Year = 1999}
1253
1254		@article{Spohr97,
1255		Author = {E. Spohr},
#	Line 944 \| Line 1257
1257		Date-Modified = {2008-01-08 14:58:58 -0500},
1258		Journal = {J. Chem. Phys.},
1259		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
1260	<	Number = {16},
1260	>	Number = 16,
1261		Pages = {6342-6348},
1262		Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
1263	<	Volume = {107},
1264	<	Year = {1997}}
1263	>	Volume = 107,
1264	>	Year = 1997}
1265
1266		@article{Marrink01b,
1267		Author = {S.~J. Marrink and A.~E. Mark},
1268		Date-Added = {2008-01-08 14:58:56 -0500},
1269		Date-Modified = {2008-01-08 14:58:58 -0500},
1270	<	Journal = {Journal of Physical Chemistry B},
1270	>	Journal = jpcb,
1271		Pages = {6122-6127},
1272		Title = {Effect of undulations on surface tension in simulated bilayers},
1273		Volume = 105,
#	Line 1047 \| Line 1360
1360		Journal = {Mol. Phys.},
1361		Pages = {1313-1327},
1362		Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices},
1363	<	Volume = {37},
1364	<	Year = {1979}}
1363	>	Volume = 37,
1364	>	Year = 1979}
1365
1366		@article{Heyes81,
1367		Author = {D.~M. Heyes},
#	Line 1057 \| Line 1370
1370		Journal = {J. Chem. Phys.},
1371		Keywords = {Empty Keywords},
1372		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
1373	<	Number = {3},
1373	>	Number = 3,
1374		Pages = {1924-1929},
1375		Title = {Electrostatic potentials and fields in infinite point charge lattices},
1376	<	Volume = {74},
1377	<	Year = {1981}}
1376	>	Volume = 74,
1377	>	Year = 1981}
1378
1379		@article{Tsonchev04,
1380		Author = {Stefan Tsonchev and George C. Schatz and Mark A. Ratner},
#	Line 1081 \| Line 1394
1394		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
1395		Pages = {253-261},
1396		Title = {Electrostatics calculations: recent methodological advances and applications to membranes},
1397	<	Volume = {11},
1398	<	Year = {2001}}
1397	>	Volume = 11,
1398	>	Year = 2001}
1399
1400		@article{Arnold02,
1401		Author = {A. Arnold and J. {de Joannis} and C. Holm},
#	Line 1091 \| Line 1404
1404		Doi = {10.1063/1.149195},
1405		Journal = {J. Chem. Phys.},
1406		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Arnold_SlabElectrostatics_02.pdf},
1407	<	Number = {6},
1407	>	Number = 6,
1408		Pages = {2496-2502},
1409		Title = {Electrostatics in periodic slab geometries. I},
1410	<	Volume = {117},
1411	<	Year = {2002}}
1410	>	Volume = 117,
1411	>	Year = 2002,
1412	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1413
1414		@article{deJoannis02,
1415		Author = {J. {de Joannis} and A. Arnold and C. Holm},
#	Line 1104 \| Line 1418
1418		Doi = {10.1063/1.149195},
1419		Journal = {J. Chem. Phys.},
1420		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf},
1421	<	Number = {6},
1421	>	Number = 6,
1422		Pages = {2503-2512},
1423		Title = {Electrostatics in periodic slab geometries. II},
1424	<	Volume = {117},
1425	<	Year = {2002}}
1424	>	Volume = 117,
1425	>	Year = 2002,
1426	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1427
1428		@article{Barenco95,
1429		Author = {A. Barenco and C.~H. Bennett and R. Cleve and D.~P. DiVincenzo and N. Margolus and P. Shor and T. Sleator and J.~A. Smolin and H. Weinfurter},
#	Line 1158 \| Line 1473
1473		Date-Modified = {2008-01-08 14:58:58 -0500},
1474		Journal = {J. Phys. Chem. B},
1475		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
1476	<	Number = {41},
1476	>	Number = 41,
1477		Pages = {10725-10732},
1478		Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
1479	<	Volume = {106},
1480	<	Year = {2002}}
1479	>	Volume = 106,
1480	>	Year = 2002}
1481
1482		@article{Metropolis53,
1483		Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
#	Line 1180 \| Line 1495
1495		Date-Added = {2008-01-08 14:58:56 -0500},
1496		Date-Modified = {2008-01-08 14:58:58 -0500},
1497		Journal = {Surf. Sci.},
1498	<	Pages = {195},
1498	>	Pages = 195,
1499		Title = {Errata: The electrostatic potential in the surface region of an ionic crystal},
1500	<	Volume = {54},
1501	<	Year = {1976}}
1500	>	Volume = 54,
1501	>	Year = 1976}
1502
1503		@article{Steane96,
1504		Author = {A.~M. Steane},
#	Line 1211 \| Line 1526
1526		Date-Modified = {2008-01-08 14:58:59 -0500},
1527		Journal = {J. Chem. Phys.},
1528		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
1529	<	Number = {4},
1529	>	Number = 4,
1530		Pages = {1856-1872},
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1890		Date-Added = {2008-01-08 14:58:56 -0500},
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3433
3434		@article{Orlandi:2006fk,
3435		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.},
3436		Address = {Dipartimento di Chimica Fisica e Inorganica, and INSTM, Universita di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.},
3437		Au = {Orlandi, S and Berardi, R and Steltzer, J and Zannoni, C},
3438		Author = {Orlandi, Silvia and Berardi, Roberto and Steltzer, Joachim and Zannoni, Claudio},
3439	<	Da = {20060407},
3439	>	Da = 20060407,
3440		Date-Added = {2008-01-08 14:47:56 -0500},
3441		Date-Modified = {2008-01-08 14:48:06 -0500},
3442	<	Dcom = {20070727},
3442	>	Dcom = 20070727,
3443		Doi = {10.1063/1.2176622},
3444		Edat = {2006/04/08 09:00},
3445		Issn = {0021-9606 (Print)},
3446	<	Jid = {0375360},
3446	>	Jid = 0375360,
3447		Journal = {J Chem Phys},
3448		Jt = {The Journal of chemical physics},
3449		Language = {eng},
3450		Mhda = {2006/04/08 09:01},
3451	<	Number = {12},
3451	>	Number = 12,
3452		Own = {NLM},
3453	<	Pages = {124907},
3453	>	Pages = 124907,
3454		Pl = {United States},
3455	<	Pmid = {16599725},
3455	>	Pmid = 16599725,
3456		Pst = {ppublish},
3457		Pt = {Journal Article},
3458		Pubm = {Print},
3459		So = {J Chem Phys. 2006 Mar 28;124(12):124907.},
3460		Stat = {PubMed-not-MEDLINE},
3461		Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.},
3462	<	Volume = {124},
3463	<	Year = {2006}}
3462	>	Volume = 124,
3463	>	Year = 2006,
3464	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}}
3465
3466		@article{sun:031602,
3467		Author = {Xiuquan Sun and J. Daniel Gezelter},
3468		Date-Added = {2008-01-08 14:42:33 -0500},
3469		Date-Modified = {2008-01-08 14:42:33 -0500},
3470		Doi = {10.1103/PhysRevE.75.031602},
3471	<	Eid = {031602},
3471	>	Eid = 031602,
3472		Journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)},
3473		Keywords = {lattice theory; membranes},
3474	<	Number = {3},
3475	<	Numpages = {7},
3476	<	Pages = {031602},
3474	>	Number = 3,
3475	>	Numpages = 7,
3476	>	Pages = 031602,
3477		Publisher = {APS},
3478		Title = {Spontaneous corrugation of dipolar membranes},
3479		Url = {http://link.aps.org/abstract/PRE/v75/e031602},
3480	<	Volume = {75},
3481	<	Year = {2007}}
3480	>	Volume = 75,
3481	>	Year = 2007,
3482	>	Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602},
3483	>	Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}}
3484
3485		@article{Ortega:2007lr,
3486		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.},
3487		Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.},
3488	<	Au = {Ortega, A and Garcia de la Torre, J},
3489	<	Author = {Ortega, A and Garcia de la Torre, J},
3490	<	Da = {20070813},
3488	>	Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3489	>	Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3490	>	Da = 20070813,
3491		Date-Added = {2008-01-08 14:38:03 -0500},
3492		Date-Modified = {2008-01-08 14:38:49 -0500},
3493	<	Dcom = {20071017},
3494	<	Dep = {20070724},
3493	>	Dcom = 20071017,
3494	>	Dep = 20070724,
3495		Doi = {10.1021/bm700473f},
3496		Edat = {2007/07/25 09:00},
3497		Issn = {1525-7797 (Print)},
3498	<	Jid = {100892849},
3498	>	Jid = 100892849,
3499		Journal = {Biomacromolecules},
3500		Jt = {Biomacromolecules},
3501		Keywords = {Computer Simulation; Heparin/chemistry; Macromolecular Substances/chemistry; Models, Chemical; *Models, Molecular; Molecular Conformation; Particle Size; Protein Conformation; Proteins/chemistry; Software; Solutions},
3502		Language = {eng},
3503		Mhda = {2007/10/18 09:00},
3504	<	Number = {8},
3504	>	Number = 8,
3505		Own = {NLM},
3506		Pages = {2464--2475},
3507		Phst = {2007/07/24 {$[$}aheadofprint{$]$}},
3508		Pl = {United States},
3509	<	Pmid = {17645309},
3509	>	Pmid = 17645309,
3510		Pst = {ppublish},
3511		Pt = {Journal Article; Research Support, Non-U.S. Gov't},
3512		Pubm = {Print-Electronic},
#	Line 3188 \| Line 3515
3515		So = {Biomacromolecules. 2007 Aug;8(8):2464-75. Epub 2007 Jul 24.},
3516		Stat = {MEDLINE},
3517		Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.},
3518	<	Volume = {8},
3519	<	Year = {2007}}
3518	>	Volume = 8,
3519	>	Year = 2007,
3520	>	Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}}
3521
3522		@article{Torre2003,
3523		Abstract = {While the prediction of hydrodynamic properties of rigid particles
#	Line 3215 \| Line 3543
3543		We provide an example of the application of this methodology to
3544		the dynamics of a semiflexible, wormlike DNA.},
3545		Annote = {724XK Times Cited:6 Cited References Count:64},
3546	<	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},
3546	>	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},
3547		Issn = {0175-7571},
3548		Journal = {European Biophysics Journal with Biophysics Letters},
3549		Month = {Aug},
3550	<	Number = {5},
3550	>	Number = 5,
3551		Pages = {477-486},
3552		Title = {Calculation of the solution properties of flexible macromolecules: methods and applications},
3553		Uri = {<Go to ISI>://000185513400011},
3554	<	Volume = {32},
3555	<	Year = {2003}}
3554	>	Volume = 32,
3555	>	Year = 2003}
3556
3557		@article{Alakent2005,
3558		Abstract = {Time series analysis tools are employed on the principal modes obtained
#	Line 3264 \| Line 3592
3592		Annote = {973OH Times Cited:1 Cited References Count:33},
3593		Author = {B. Alakent and M. C. Camurdan and P. Doruker},
3594		Issn = {0021-9606},
3595	<	Journal = {Journal of Chemical Physics},
3595	>	Journal = jcp,
3596		Month = {Oct 8},
3597	<	Number = {14},
3597	>	Number = 14,
3598		Pages = {-},
3599		Title = {Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects},
3600		Uri = {<Go to ISI>://000232532000064},
3601	<	Volume = {123},
3602	<	Year = {2005}}
3601	>	Volume = 123,
3602	>	Year = 2005}
3603
3604		@book{Alexander1987,
3605		Address = {New York},
3606		Author = {C. Alexander},
3607		Publisher = {Oxford University Press},
3608		Title = {A Pattern Language: Towns, Buildings, Construction},
3609	<	Year = {1987}}
3609	>	Year = 1987}
3610
3611		@book{Allen1987,
3612		Address = {New York},
3613		Author = {M.~P. Allen and D.~J. Tildesley},
3614		Publisher = {Oxford University Press},
3615		Title = {Computer Simulations of Liquids},
3616	<	Year = {1987}}
3616	>	Year = 1987}
3617
3618		@article{Allison1991,
3619		Abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
#	Line 3307 \| Line 3635
3635		Issn = {0024-9297},
3636		Journal = {Macromolecules},
3637		Month = {Jan 21},
3638	<	Number = {2},
3638	>	Number = 2,
3639		Pages = {530-536},
3640		Title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application to Polarized Dynamic Light-Scattering},
3641		Uri = {<Go to ISI>://A1991EU81400029},
3642	<	Volume = {24},
3643	<	Year = {1991}}
3642	>	Volume = 24,
3643	>	Year = 1991}
3644
3645		@article{Andersen1983,
3646		Annote = {Rq238 Times Cited:559 Cited References Count:14},
3647		Author = {H. C. Andersen},
3648		Issn = {0021-9991},
3649	<	Journal = {Journal of Computational Physics},
3650	<	Number = {1},
3649	>	Journal = jcop,
3650	>	Number = 1,
3651		Pages = {24-34},
3652		Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
3653		Uri = {<Go to ISI>://A1983RQ23800002},
3654	<	Volume = {52},
3655	<	Year = {1983}}
3654	>	Volume = 52,
3655	>	Year = 1983}
3656
3657		@article{Auerbach2005,
3658		Abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
#	Line 3349 \| Line 3677
3677		Annote = {895QF Times Cited:9 Cited References Count:33},
3678		Author = {A. Auerbach},
3679		Issn = {0027-8424},
3680	<	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
3680	>	Journal = pnas,
3681		Month = {Feb 1},
3682	<	Number = {5},
3682	>	Number = 5,
3683		Pages = {1408-1412},
3684		Title = {Gating of acetylcholine receptor channels: Brownian motion across a broad transition state},
3685		Uri = {<Go to ISI>://000226877300030},
3686	<	Volume = {102},
3687	<	Year = {2005}}
3686	>	Volume = 102,
3687	>	Year = 2005}
3688
3689		@article{Baber1995,
3690		Abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
#	Line 3385 \| Line 3713
3713		Issn = {0006-2960},
3714		Journal = {Biochemistry},
3715		Month = {May 16},
3716	<	Number = {19},
3716	>	Number = 19,
3717		Pages = {6533-6539},
3718		Title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
3719		Uri = {<Go to ISI>://A1995QZ71600035},
3720	<	Volume = {34},
3721	<	Year = {1995}}
3720	>	Volume = 34,
3721	>	Year = 1995}
3722
3723		@article{Banerjee2004,
3724		Abstract = {Based on a coherent state representation of noise operator and an
#	Line 3410 \| Line 3738
3738		Annote = {816YY Times Cited:8 Cited References Count:35},
3739		Author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
3740		Issn = {0021-9606},
3741	<	Journal = {Journal of Chemical Physics},
3741	>	Journal = jcp,
3742		Month = {May 15},
3743	<	Number = {19},
3743	>	Number = 19,
3744		Pages = {8960-8972},
3745		Title = {Solution of quantum Langevin equation: Approximations, theoretical and numerical aspects},
3746		Uri = {<Go to ISI>://000221146400009},
3747	<	Volume = {120},
3748	<	Year = {2004}}
3747	>	Volume = 120,
3748	>	Year = 2004}
3749
3750		@article{Barojas1973,
3751		Author = {J. Barojas and D. Levesque},
3752		Journal = {Phys. Rev. A},
3753		Pages = {1092-1105},
3754		Title = {Simulation of Diatomic Homonuclear Liquids},
3755	<	Volume = {7},
3756	<	Year = {1973}}
3755	>	Volume = 7,
3756	>	Year = 1973}
3757
3758		@article{Barth1998,
3759		Abstract = {We present an efficient new method termed LN for propagating biomolecular
#	Line 3457 \| Line 3785
3785		Annote = {105HH Times Cited:29 Cited References Count:49},
3786		Author = {E. Barth and T. Schlick},
3787		Issn = {0021-9606},
3788	<	Journal = {Journal of Chemical Physics},
3788	>	Journal = jcp,
3789		Month = {Aug 1},
3790	<	Number = {5},
3790	>	Number = 5,
3791		Pages = {1617-1632},
3792		Title = {Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN},
3793		Uri = {<Go to ISI>://000075066300006},
3794	<	Volume = {109},
3795	<	Year = {1998}}
3794	>	Volume = 109,
3795	>	Year = 1998}
3796
3797		@article{Batcho2001,
3798		Abstract = {We present an analysis for a simple two-component harmonic oscillator
#	Line 3481 \| Line 3809
3809		Annote = {469KV Times Cited:6 Cited References Count:30},
3810		Author = {P. F. Batcho and T. Schlick},
3811		Issn = {0021-9606},
3812	<	Journal = {Journal of Chemical Physics},
3812	>	Journal = jcp,
3813		Month = {Sep 1},
3814	<	Number = {9},
3814	>	Number = 9,
3815		Pages = {4019-4029},
3816		Title = {Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration},
3817		Uri = {<Go to ISI>://000170813800005},
3818	<	Volume = {115},
3819	<	Year = {2001}}
3818	>	Volume = 115,
3819	>	Year = 2001}
3820
3821		@article{Bates2005,
3822		Abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
#	Line 3514 \| Line 3842
3842		Issn = {1539-3755},
3843		Journal = {Physical Review E},
3844		Month = {Nov},
3845	<	Number = {5},
3845	>	Number = 5,
3846		Pages = {-},
3847		Title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation study},
3848		Uri = {<Go to ISI>://000233603100030},
3849	<	Volume = {72},
3850	<	Year = {2005}}
3849	>	Volume = 72,
3850	>	Year = 2005}
3851
3852		@article{Beard2003,
3853		Abstract = {We introduce an unbiased protocol for performing rotational moves
#	Line 3534 \| Line 3862
3862		Annote = {736UA Times Cited:0 Cited References Count:11},
3863		Author = {D. A. Beard and T. Schlick},
3864		Issn = {0006-3495},
3865	<	Journal = {Biophysical Journal},
3865	>	Journal = bj,
3866		Month = {Nov 1},
3867	<	Number = {5},
3867	>	Number = 5,
3868		Pages = {2973-2976},
3869		Title = {Unbiased rotational moves for rigid-body dynamics},
3870		Uri = {<Go to ISI>://000186190500018},
3871	<	Volume = {85},
3872	<	Year = {2003}}
3871	>	Volume = 85,
3872	>	Year = 2003}
3873
3874		@article{Beloborodov1998,
3875		Abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
#	Line 3558 \| Line 3886
3886		Issn = {1090-7807},
3887		Journal = {Journal of Magnetic Resonance},
3888		Month = {Jun},
3889	<	Number = {2},
3889	>	Number = 2,
3890		Pages = {328-329},
3891		Title = {Effect of coupling between rotational and translational Brownian motions on NMR spin relaxation: Consideration using green function of rigid body diffusion},
3892		Uri = {<Go to ISI>://000074214800017},
3893	<	Volume = {132},
3894	<	Year = {1998}}
3893	>	Volume = 132,
3894	>	Year = 1998}
3895
3896		@article{Berardi1996,
3897		Abstract = {We demonstrate that the overall molecular dipole organization in a
#	Line 3580 \| Line 3908
3908		Issn = {0009-2614},
3909		Journal = {Chemical Physics Letters},
3910		Month = {Oct 18},
3911	<	Number = {3},
3911	>	Number = 3,
3912		Pages = {357-362},
3913		Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
3914		Uri = {<Go to ISI>://A1996VN63700023},
3915	<	Volume = {261},
3916	<	Year = {1996}}
3915	>	Volume = 261,
3916	>	Year = 1996}
3917
3918		@article{Berkov2005,
3919		Abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
#	Line 3610 \| Line 3938
3938		Issn = {1098-0121},
3939		Journal = {Physical Review B},
3940		Month = {Sep},
3941	<	Number = {9},
3941	>	Number = 9,
3942		Pages = {-},
3943		Title = {Magnetization precession due to a spin-polarized current in a thin nanoelement: Numerical simulation study},
3944		Uri = {<Go to ISI>://000232228500058},
3945	<	Volume = {72},
3946	<	Year = {2005}}
3945	>	Volume = 72,
3946	>	Year = 2005}
3947
3948		@article{Berkov2005a,
3949		Abstract = {Numerical simulations of fast remagnetization processes using stochastic
#	Line 3641 \| Line 3969
3969		Pages = {442-448},
3970		Title = {Stochastic dynamic simulations of fast remagnetization processes: recent advances and applications},
3971		Uri = {<Go to ISI>://000228837600109},
3972	<	Volume = {290},
3973	<	Year = {2005}}
3972	>	Volume = 290,
3973	>	Year = 2005}
3974
3975		@article{Berkov2002,
3976		Abstract = {We report on recent progress achieved by the development of numerical
#	Line 3664 \| Line 3992
3992		Issn = {0031-8965},
3993		Journal = {Physica Status Solidi a-Applied Research},
3994		Month = {Feb 16},
3995	<	Number = {2},
3995	>	Number = 2,
3996		Pages = {409-421},
3997		Title = {Magnetization dynamics in nanoparticle systems: Numerical simulation using Langevin dynamics},
3998		Uri = {<Go to ISI>://000174145200026},
3999	<	Volume = {189},
4000	<	Year = {2002}}
3999	>	Volume = 189,
4000	>	Year = 2002}
4001
4002		@article{Bernal1980,
4003	<	Author = {J.M. Bernal and J. G. {de la Torre}},
4003	>	Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose},
4004		Journal = {Biopolymers},
4005		Pages = {751-766},
4006		Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape},
4007	<	Volume = {19},
4008	<	Year = {1980}}
4007	>	Volume = 19,
4008	>	Year = 1980}
4009
4010		@article{Brenner1967,
4011		Author = {H. Brenner},
4012		Journal = {J. Collid. Int. Sci.},
4013		Pages = {407-436},
4014		Title = {Coupling between the Translational and Rotational Brownian Motions of Rigid Particles of Arbitrary shape},
4015	<	Volume = {23},
4016	<	Year = {1967}}
4015	>	Volume = 23,
4016	>	Year = 1967}
4017
4018		@article{Brooks1983,
4019		Annote = {Qp423 Times Cited:6414 Cited References Count:96},
4020		Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus},
4021		Issn = {0192-8651},
4022	<	Journal = {Journal of Computational Chemistry},
4023	<	Number = {2},
4022	>	Journal = jcc,
4023	>	Number = 2,
4024		Pages = {187-217},
4025		Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
4026		Uri = {<Go to ISI>://A1983QP42300010},
4027	<	Volume = {4},
4028	<	Year = {1983}}
4027	>	Volume = 4,
4028	>	Year = 1983}
4029
4030		@article{Brunger1984,
4031		Annote = {Sm173 Times Cited:143 Cited References Count:22},
4032		Author = {A. Brunger and C. L. Brooks and M. Karplus},
4033		Issn = {0009-2614},
4034		Journal = {Chemical Physics Letters},
4035	<	Number = {5},
4035	>	Number = 5,
4036		Pages = {495-500},
4037		Title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations of St2 Water},
4038		Uri = {<Go to ISI>://A1984SM17300007},
4039	<	Volume = {105},
4040	<	Year = {1984}}
4039	>	Volume = 105,
4040	>	Year = 1984}
4041
4042		@article{Budd1999,
4043		Abstract = {This paper examines a synthesis of adaptive mesh methods with the
#	Line 3723 \| Line 4051
4051		Issn = {1364-503X},
4052		Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
4053		Month = {Apr 15},
4054	<	Number = {1754},
4054	>	Number = 1754,
4055		Pages = {1047-1077},
4056		Title = {Self-similar numerical solutions of the porous-medium equation using moving mesh methods},
4057		Uri = {<Go to ISI>://000080466800005},
4058	<	Volume = {357},
4059	<	Year = {1999}}
4058	>	Volume = 357,
4059	>	Year = 1999}
4060
4061		@article{Camp1999,
4062		Abstract = {Fluids of hard bent-core molecules have been studied using theory
#	Line 3764 \| Line 4092
4092		Annote = {255TC Times Cited:24 Cited References Count:38},
4093		Author = {P. J. Camp and M. P. Allen and A. J. Masters},
4094		Issn = {0021-9606},
4095	<	Journal = {Journal of Chemical Physics},
4095	>	Journal = jcp,
4096		Month = {Dec 1},
4097	<	Number = {21},
4097	>	Number = 21,
4098		Pages = {9871-9881},
4099		Title = {Theory and computer simulation of bent-core molecules},
4100		Uri = {<Go to ISI>://000083685400056},
4101	<	Volume = {111},
4102	<	Year = {1999}}
4101	>	Volume = 111,
4102	>	Year = 1999}
4103
4104		@article{Care2005,
4105		Abstract = {A review is presented of molecular and mesoscopic computer simulations
#	Line 3786 \| Line 4114
4114		Issn = {0034-4885},
4115		Journal = {Reports on Progress in Physics},
4116		Month = {Nov},
4117	<	Number = {11},
4117	>	Number = 11,
4118		Pages = {2665-2700},
4119		Title = {Computer simulation of liquid crystals},
4120		Uri = {<Go to ISI>://000233697600004},
4121	<	Volume = {68},
4122	<	Year = {2005}}
4121	>	Volume = 68,
4122	>	Year = 2005}
4123
4124		@article{Carrasco1999,
4125		Abstract = {The hydrodynamic properties of rigid particles are calculated from
#	Line 3813 \| Line 4141
4141		them to some test cases, for which the properties are known a priori.
4142		We provide guidelines and computational tools for bead modeling.},
4143		Annote = {200TT Times Cited:46 Cited References Count:57},
4144	<	Author = {B. Carrasco and J. G. {de la Torre}},
4144	>	Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
4145		Issn = {0006-3495},
4146	<	Journal = {Biophysical Journal},
4146	>	Journal = bj,
4147		Month = {Jun},
4148	<	Number = {6},
4148	>	Number = 6,
4149		Pages = {3044-3057},
4150		Title = {Hydrodynamic properties of rigid particles: Comparison of different modeling and computational procedures},
4151		Uri = {<Go to ISI>://000080556700016},
4152	<	Volume = {76},
4153	<	Year = {1999}}
4152	>	Volume = 76,
4153	>	Year = 1999}
4154
4155		@article{Chandra1999,
4156		Abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
#	Line 3846 \| Line 4174
4174		Annote = {221EN Times Cited:14 Cited References Count:66},
4175		Author = {A. Chandra and T. Ichiye},
4176		Issn = {0021-9606},
4177	<	Journal = {Journal of Chemical Physics},
4177	>	Journal = jcp,
4178		Month = {Aug 8},
4179	<	Number = {6},
4179	>	Number = 6,
4180		Pages = {2701-2709},
4181		Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations},
4182		Uri = {<Go to ISI>://000081711200038},
4183	<	Volume = {111},
4184	<	Year = {1999}}
4183	>	Volume = 111,
4184	>	Year = 1999}
4185
4186		@article{Channell1990,
4187		Annote = {Dk631 Times Cited:152 Cited References Count:34},
#	Line 3861 \| Line 4189
4189		Issn = {0951-7715},
4190		Journal = {Nonlinearity},
4191		Month = {may},
4192	<	Number = {2},
4192	>	Number = 2,
4193		Pages = {231-259},
4194		Title = {Symplectic Integration of Hamiltonian-Systems},
4195		Uri = {<Go to ISI>://A1990DK63100001},
4196	<	Volume = {3},
4197	<	Year = {1990}}
4196	>	Volume = 3,
4197	>	Year = 1990}
4198
4199		@article{Chen2003,
4200		Abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
#	Line 3887 \| Line 4215
4215		Pages = {21-30},
4216		Title = {Explicit mixed finite order Runge-Kutta methods},
4217		Uri = {<Go to ISI>://000180314200002},
4218	<	Volume = {44},
4219	<	Year = {2003}}
4218	>	Volume = 44,
4219	>	Year = 2003}
4220
4221		@article{Cheung2004,
4222		Abstract = {Equilibrium molecular dynamics calculations have been performed for
#	Line 3906 \| Line 4234
4234		Annote = {866UM Times Cited:4 Cited References Count:61},
4235		Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
4236		Issn = {0021-9606},
4237	<	Journal = {Journal of Chemical Physics},
4237	>	Journal = jcp,
4238		Month = {Nov 8},
4239	<	Number = {18},
4239	>	Number = 18,
4240		Pages = {9131-9139},
4241		Title = {Calculation of flexoelectric coefficients for a nematic liquid crystal by atomistic simulation},
4242		Uri = {<Go to ISI>://000224798900053},
4243	<	Volume = {121},
4244	<	Year = {2004}}
4243	>	Volume = 121,
4244	>	Year = 2004}
4245
4246		@article{Cheung2002,
4247		Abstract = {Equilibrium molecular dynamics calculations have been performed for
#	Line 3935 \| Line 4263
4263		Pages = {140-146},
4264		Title = {Calculation of the rotational viscosity of a nematic liquid crystal},
4265		Uri = {<Go to ISI>://000175331000020},
4266	<	Volume = {356},
4267	<	Year = {2002}}
4266	>	Volume = 356,
4267	>	Year = 2002}
4268
4269		@article{Chin2004,
4270		Abstract = {Current molecular dynamics simulations of biomolecules using multiple
#	Line 3957 \| Line 4285
4285		Annote = {757TK Times Cited:1 Cited References Count:22},
4286		Author = {S. A. Chin},
4287		Issn = {0021-9606},
4288	<	Journal = {Journal of Chemical Physics},
4288	>	Journal = jcp,
4289		Month = {Jan 1},
4290	<	Number = {1},
4290	>	Number = 1,
4291		Pages = {8-13},
4292		Title = {Dynamical multiple-time stepping methods for overcoming resonance instabilities},
4293		Uri = {<Go to ISI>://000187577400003},
4294	<	Volume = {120},
4295	<	Year = {2004}}
4294	>	Volume = 120,
4295	>	Year = 2004}
4296
4297		@article{Cook2000,
4298		Abstract = {The Kirkwood correlation factor g(1) determines the preference for
#	Line 3988 \| Line 4316
4316		Issn = {0267-8292},
4317		Journal = {Liquid Crystals},
4318		Month = {Dec},
4319	<	Number = {12},
4319	>	Number = 12,
4320		Pages = {1573-1583},
4321		Title = {Simulation studies of dipole correlation in the isotropic liquid phase},
4322		Uri = {<Go to ISI>://000165437800002},
4323	<	Volume = {27},
4324	<	Year = {2000}}
4323	>	Volume = 27,
4324	>	Year = 2000}
4325
4326		@article{Cui2003,
4327		Abstract = {All-atom Langevin dynamics simulations have been performed to study
#	Line 4016 \| Line 4344
4344		Annote = {689LC Times Cited:3 Cited References Count:48},
4345		Author = {B. X. Cui and M. Y. Shen and K. F. Freed},
4346		Issn = {0027-8424},
4347	<	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
4347	>	Journal = pnas,
4348		Month = {Jun 10},
4349	<	Number = {12},
4349	>	Number = 12,
4350		Pages = {7087-7092},
4351		Title = {Folding and misfolding of the papillomavirus E6 interacting peptide E6ap},
4352		Uri = {<Go to ISI>://000183493500037},
4353	<	Volume = {100},
4354	<	Year = {2003}}
4353	>	Volume = 100,
4354	>	Year = 2003}
4355
4356		@article{Denisov2003,
4357		Abstract = {We study the slow phase of thermally activated magnetic relaxation
#	Line 4041 \| Line 4369
4369		Issn = {1098-0121},
4370		Journal = {Physical Review B},
4371		Month = {Jan 1},
4372	<	Number = {1},
4372	>	Number = 1,
4373		Pages = {-},
4374		Title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
4375		Uri = {<Go to ISI>://000180830400056},
4376	<	Volume = {67},
4377	<	Year = {2003}}
4376	>	Volume = 67,
4377	>	Year = 2003}
4378
4379		@article{Derreumaux1998,
4380		Abstract = {To explore the origin of the large-scale motion of triosephosphate
#	Line 4076 \| Line 4404
4404		Annote = {Zl046 Times Cited:30 Cited References Count:29},
4405		Author = {P. Derreumaux and T. Schlick},
4406		Issn = {0006-3495},
4407	<	Journal = {Biophysical Journal},
4407	>	Journal = bj,
4408		Month = {Jan},
4409	<	Number = {1},
4409	>	Number = 1,
4410		Pages = {72-81},
4411		Title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
4412		Uri = {<Go to ISI>://000073393400009},
4413	<	Volume = {74},
4414	<	Year = {1998}}
4413	>	Volume = 74,
4414	>	Year = 1998}
4415
4416		@article{Dullweber1997,
4417		Abstract = {Rigid body molecular models possess symplectic structure and time-reversal
#	Line 4108 \| Line 4436
4436		Annote = {Ya587 Times Cited:35 Cited References Count:32},
4437		Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
4438		Issn = {0021-9606},
4439	<	Journal = {Journal of Chemical Physics},
4439	>	Journal = jcp,
4440		Month = {Oct 15},
4441	<	Number = {15},
4441	>	Number = 15,
4442		Pages = {5840-5851},
4443		Title = {Symplectic splitting methods for rigid body molecular dynamics},
4444		Uri = {<Go to ISI>://A1997YA58700024},
4445	<	Volume = {107},
4446	<	Year = {1997}}
4445	>	Volume = 107,
4446	>	Year = 1997}
4447
4448		@book{Gamma1994,
4449		Address = {London},
4450		Author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
4451	<	Chapter = {7},
4451	>	Chapter = 7,
4452		Publisher = {Perason Education},
4453		Title = {Design Patterns: Elements of Reusable Object-Oriented Software},
4454	<	Year = {1994}}
4454	>	Year = 1994}
4455
4456		@article{Edwards2005,
4457		Abstract = {Using the Langevin dynamics technique, we have carried out simulations
#	Line 4141 \| Line 4469
4469		Issn = {0024-9297},
4470		Journal = {Macromolecules},
4471		Month = {Dec 13},
4472	<	Number = {25},
4472	>	Number = 25,
4473		Pages = {10590-10595},
4474		Title = {Stretching a single diblock copolymer in a selective solvent: Langevin dynamics simulations},
4475		Uri = {<Go to ISI>://000233866200035},
4476	<	Volume = {38},
4477	<	Year = {2005}}
4476	>	Volume = 38,
4477	>	Year = 2005}
4478
4479		@article{Egberts1988,
4480		Annote = {Q0188 Times Cited:219 Cited References Count:43},
4481		Author = {E. Egberts and H. J. C. Berendsen},
4482		Issn = {0021-9606},
4483	<	Journal = {Journal of Chemical Physics},
4483	>	Journal = jcp,
4484		Month = {Sep 15},
4485	<	Number = {6},
4485	>	Number = 6,
4486		Pages = {3718-3732},
4487		Title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic Detail},
4488		Uri = {<Go to ISI>://A1988Q018800036},
4489	<	Volume = {89},
4490	<	Year = {1988}}
4489	>	Volume = 89,
4490	>	Year = 1988}
4491
4492		@article{Ermak1978,
4493		Annote = {Fp216 Times Cited:785 Cited References Count:42},
4494		Author = {D. L. Ermak and J. A. Mccammon},
4495		Issn = {0021-9606},
4496	<	Journal = {Journal of Chemical Physics},
4497	<	Number = {4},
4496	>	Journal = jcp,
4497	>	Number = 4,
4498		Pages = {1352-1360},
4499		Title = {Brownian Dynamics with Hydrodynamic Interactions},
4500		Uri = {<Go to ISI>://A1978FP21600004},
4501	<	Volume = {69},
4502	<	Year = {1978}}
4501	>	Volume = 69,
4502	>	Year = 1978}
4503
4504		@article{Evans1977,
4505		Annote = {Ds757 Times Cited:271 Cited References Count:18},
4506		Author = {D. J. Evans},
4507		Issn = {0026-8976},
4508	<	Journal = {Molecular Physics},
4509	<	Number = {2},
4508	>	Journal = mp,
4509	>	Number = 2,
4510		Pages = {317-325},
4511		Title = {Representation of Orientation Space},
4512		Uri = {<Go to ISI>://A1977DS75700002},
4513	<	Volume = {34},
4514	<	Year = {1977}}
4513	>	Volume = 34,
4514	>	Year = 1977}
4515
4516		@article{Fennell2004,
4517		Abstract = {The density maximum and temperature dependence of the self-diffusion
#	Line 4212 \| Line 4540
4540		Annote = {816YY Times Cited:5 Cited References Count:39},
4541		Author = {C. J. Fennell and J. D. Gezelter},
4542		Issn = {0021-9606},
4543	<	Journal = {Journal of Chemical Physics},
4543	>	Journal = jcp,
4544		Month = {May 15},
4545	<	Number = {19},
4545	>	Number = 19,
4546		Pages = {9175-9184},
4547		Title = {On the structural and transport properties of the soft sticky dipole and related single-point water models},
4548		Uri = {<Go to ISI>://000221146400032},
4549	<	Volume = {120},
4550	<	Year = {2004}}
4549	>	Volume = 120,
4550	>	Year = 2004}
4551
4552		@article{Fernandes2002,
4553		Abstract = {We have developed a Brownian dynamics simulation algorithm to generate
#	Line 4234 \| Line 4562
4562		its applicability. Examples include free diffusion, transport in
4563		an electric field, and diffusion in a restricting environment.},
4564		Annote = {633AD Times Cited:2 Cited References Count:43},
4565	<	Author = {M. X. Fernandes and J. G. {de la Torre}},
4565	>	Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4566		Issn = {0006-3495},
4567	<	Journal = {Biophysical Journal},
4567	>	Journal = bj,
4568		Month = {Dec},
4569	<	Number = {6},
4569	>	Number = 6,
4570		Pages = {3039-3048},
4571		Title = {Brownian dynamics simulation of rigid particles of arbitrary shape in external fields},
4572		Uri = {<Go to ISI>://000180256300012},
4573	<	Volume = {83},
4574	<	Year = {2002}}
4573	>	Volume = 83,
4574	>	Year = 2002}
4575
4576		@book{Frenkel1996,
4577		Address = {New York},
4578		Author = {D. Frenkel and B. Smit},
4579		Publisher = {Academic Press},
4580		Title = {Understanding Molecular Simulation : From Algorithms to Applications},
4581	<	Year = {1996}}
4581	>	Year = 1996}
4582
4583		@article{Gay1981,
4584		Annote = {Lj347 Times Cited:482 Cited References Count:13},
4585		Author = {J. G. Gay and B. J. Berne},
4586		Issn = {0021-9606},
4587	<	Journal = {Journal of Chemical Physics},
4588	<	Number = {6},
4587	>	Journal = jcp,
4588	>	Number = 6,
4589		Pages = {3316-3319},
4590		Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
4591		Uri = {<Go to ISI>://A1981LJ34700029},
4592	<	Volume = {74},
4593	<	Year = {1981}}
4592	>	Volume = 74,
4593	>	Year = 1981}
4594
4595		@article{Gelin1999,
4596		Abstract = {To investigate the influence of inertial effects on the dynamics of
#	Line 4288 \| Line 4616
4616		Issn = {1022-1344},
4617		Journal = {Macromolecular Theory and Simulations},
4618		Month = {Nov},
4619	<	Number = {6},
4619	>	Number = 6,
4620		Pages = {529-543},
4621		Title = {Inertial effects in the Brownian dynamics with rigid constraints},
4622		Uri = {<Go to ISI>://000083785700002},
4623	<	Volume = {8},
4624	<	Year = {1999}}
4623	>	Volume = 8,
4624	>	Year = 1999}
4625
4626		@article{Goetz1998,
4627		Author = {R. Goetz and R. Lipowsky},
4628	<	Journal = {Journal of Chemical Physics},
4629	<	Number = {17},
4630	<	Pages = {7397},
4628	>	Journal = jcp,
4629	>	Number = 17,
4630	>	Pages = 7397,
4631		Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
4632	<	Volume = {108},
4633	<	Year = {1998}}
4632	>	Volume = 108,
4633	>	Year = 1998}
4634
4635		@book{Goldstein2001,
4636		Address = {San Francisco},
#	Line 4310 \| Line 4638
4638		Edition = {3rd},
4639		Publisher = {Addison Wesley},
4640		Title = {Classical Mechanics},
4641	<	Year = {2001}}
4641	>	Year = 2001}
4642
4643		@article{Gray2003,
4644		Abstract = {Protein-protein docking algorithms provide a means to elucidate structural
#	Line 4340 \| Line 4668
4668		Annote = {704QL Times Cited:48 Cited References Count:60},
4669		Author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and B. Kuhlman and C. A. Rohl and D. Baker},
4670		Issn = {0022-2836},
4671	<	Journal = {Journal of Molecular Biology},
4671	>	Journal = jmb,
4672		Month = {Aug 1},
4673	<	Number = {1},
4673	>	Number = 1,
4674		Pages = {281-299},
4675		Title = {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations},
4676		Uri = {<Go to ISI>://000184351300022},
4677	<	Volume = {331},
4678	<	Year = {2003}}
4677	>	Volume = 331,
4678	>	Year = 2003}
4679
4680		@article{Greengard1994,
4681		Abstract = {Some of the recently developed fast summation methods that have arisen
#	Line 4364 \| Line 4692
4692		Issn = {0036-8075},
4693		Journal = {Science},
4694		Month = {Aug 12},
4695	<	Number = {5174},
4695	>	Number = 5174,
4696		Pages = {909-914},
4697		Title = {Fast Algorithms for Classical Physics},
4698		Uri = {<Go to ISI>://A1994PB49900031},
4699	<	Volume = {265},
4700	<	Year = {1994}}
4699	>	Volume = 265,
4700	>	Year = 1994}
4701
4702		@article{Greengard1987,
4703		Annote = {L0498 Times Cited:899 Cited References Count:7},
4704		Author = {L. Greengard and V. Rokhlin},
4705		Issn = {0021-9991},
4706	<	Journal = {Journal of Computational Physics},
4706	>	Journal = jcop,
4707		Month = {Dec},
4708	<	Number = {2},
4708	>	Number = 2,
4709		Pages = {325-348},
4710		Title = {A Fast Algorithm for Particle Simulations},
4711		Uri = {<Go to ISI>://A1987L049800006},
4712	<	Volume = {73},
4713	<	Year = {1987}}
4712	>	Volume = 73,
4713	>	Year = 1987}
4714
4715		@article{Hairer1997,
4716		Abstract = {Backward error analysis is a useful tool for the study of numerical
#	Line 4403 \| Line 4731
4731		Issn = {0029-599X},
4732		Journal = {Numerische Mathematik},
4733		Month = {Jun},
4734	<	Number = {4},
4734	>	Number = 4,
4735		Pages = {441-462},
4736		Title = {The life-span of backward error analysis for numerical integrators},
4737		Uri = {<Go to ISI>://A1997XJ48800002},
4738	<	Volume = {76},
4739	<	Year = {1997}}
4738	>	Volume = 76,
4739	>	Year = 1997}
4740
4741		@article{Hao1993,
4742		Abstract = {A new procedure for studying the folding and unfolding of proteins,
#	Line 4450 \| Line 4778
4778		Issn = {0006-2960},
4779		Journal = {Biochemistry},
4780		Month = {Sep 21},
4781	<	Number = {37},
4781	>	Number = 37,
4782		Pages = {9614-9631},
4783		Title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic Trypsin-Inhibitor Studied by Computer-Simulations},
4784		Uri = {<Go to ISI>://A1993LY29400014},
4785	<	Volume = {32},
4786	<	Year = {1993}}
4785	>	Volume = 32,
4786	>	Year = 1993}
4787
4788		@article{Hinsen2000,
4789		Abstract = {The slow dynamics of proteins around its native folded state is usually
#	Line 4494 \| Line 4822
4822		Pages = {25-37},
4823		Title = {Harmonicity in slow protein dynamics},
4824		Uri = {<Go to ISI>://000090121700003},
4825	<	Volume = {261},
4826	<	Year = {2000}}
4825	>	Volume = 261,
4826	>	Year = 2000}
4827
4828		@article{Ho1992,
4829		Abstract = {Evidence has been found for the existence water at the protein-lipid
#	Line 4528 \| Line 4856
4856		Annote = {Ju251 Times Cited:55 Cited References Count:44},
4857		Author = {C. Ho and C. D. Stubbs},
4858		Issn = {0006-3495},
4859	<	Journal = {Biophysical Journal},
4859	>	Journal = bj,
4860		Month = {Oct},
4861	<	Number = {4},
4861	>	Number = 4,
4862		Pages = {897-902},
4863		Title = {Hydration at the Membrane Protein-Lipid Interface},
4864		Uri = {<Go to ISI>://A1992JU25100002},
4865	<	Volume = {63},
4866	<	Year = {1992}}
4865	>	Volume = 63,
4866	>	Year = 1992}
4867
4868		@book{Hockney1981,
4869		Address = {New York},
4870		Author = {R.W. Hockney and J.W. Eastwood},
4871		Publisher = {McGraw-Hill},
4872		Title = {Computer Simulation Using Particles},
4873	<	Year = {1981}}
4873	>	Year = 1981}
4874
4875		@article{Hoover1985,
4876		Annote = {Acr30 Times Cited:1809 Cited References Count:11},
4877		Author = {W. G. Hoover},
4878		Issn = {1050-2947},
4879		Journal = {Physical Review A},
4880	<	Number = {3},
4880	>	Number = 3,
4881		Pages = {1695-1697},
4882		Title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
4883		Uri = {<Go to ISI>://A1985ACR3000056},
4884	<	Volume = {31},
4885	<	Year = {1985}}
4884	>	Volume = 31,
4885	>	Year = 1985}
4886
4887		@article{Huh2004,
4888		Abstract = {Racemic fluids of chiral calamitic molecules are investigated with
#	Line 4570 \| Line 4898
4898		Annote = {870FJ Times Cited:0 Cited References Count:63},
4899		Author = {Y. Huh and N. M. Cann},
4900		Issn = {0021-9606},
4901	<	Journal = {Journal of Chemical Physics},
4901	>	Journal = jcp,
4902		Month = {Nov 22},
4903	<	Number = {20},
4903	>	Number = 20,
4904		Pages = {10299-10308},
4905		Title = {Discrimination in isotropic, nematic, and smectic phases of chiral calamitic molecules: A computer simulation study},
4906		Uri = {<Go to ISI>://000225042700059},
4907	<	Volume = {121},
4908	<	Year = {2004}}
4907	>	Volume = 121,
4908	>	Year = 2004}
4909
4910		@article{Humphrey1996,
4911		Abstract = {VMD is a molecular graphics program designed for the display and analysis
#	Line 4611 \| Line 4939
4939		Issn = {0263-7855},
4940		Journal = {Journal of Molecular Graphics},
4941		Month = {Feb},
4942	<	Number = {1},
4942	>	Number = 1,
4943		Pages = {33-\&},
4944		Title = {VMD: Visual molecular dynamics},
4945		Uri = {<Go to ISI>://A1996UH51500005},
4946	<	Volume = {14},
4947	<	Year = {1996}}
4946	>	Volume = 14,
4947	>	Year = 1996}
4948
4949		@article{Izaguirre2001,
4950		Abstract = {In this paper we show the possibility of using very mild stochastic
#	Line 4649 \| Line 4977
4977		Annote = {397CQ Times Cited:14 Cited References Count:36},
4978		Author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
4979		Issn = {0021-9606},
4980	<	Journal = {Journal of Chemical Physics},
4980	>	Journal = jcp,
4981		Month = {Feb 1},
4982	<	Number = {5},
4982	>	Number = 5,
4983		Pages = {2090-2098},
4984		Title = {Langevin stabilization of molecular dynamics},
4985		Uri = {<Go to ISI>://000166676100020},
4986	<	Volume = {114},
4987	<	Year = {2001}}
4986	>	Volume = 114,
4987	>	Year = 2001}
4988
4989		@article{Torre1977,
4990	<	Author = {Jose Garcia De La Torre, V.A. Bloomfield},
4990	>	Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield},
4991		Journal = {Biopolymers},
4992		Pages = {1747-1763},
4993		Title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
4994	<	Volume = {16},
4995	<	Year = {1977}}
4994	>	Volume = 16,
4995	>	Year = 1977}
4996
4997		@article{Kale1999,
4998		Abstract = {Molecular dynamics programs simulate the behavior of biomolecular
#	Line 4692 \| Line 5020
5020		Annote = {194FM Times Cited:373 Cited References Count:51},
5021		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},
5022		Issn = {0021-9991},
5023	<	Journal = {Journal of Computational Physics},
5023	>	Journal = jcop,
5024		Month = {May 1},
5025	<	Number = {1},
5025	>	Number = 1,
5026		Pages = {283-312},
5027		Title = {NAMD2: Greater scalability for parallel molecular dynamics},
5028		Uri = {<Go to ISI>://000080181500013},
5029	<	Volume = {151},
5030	<	Year = {1999}}
5029	>	Volume = 151,
5030	>	Year = 1999}
5031
5032		@article{Kane2000,
5033		Abstract = {The purpose of this work is twofold. First, we demonstrate analytically
#	Line 4723 \| Line 5051
5051		Issn = {0029-5981},
5052		Journal = {International Journal for Numerical Methods in Engineering},
5053		Month = {Dec 10},
5054	<	Number = {10},
5054	>	Number = 10,
5055		Pages = {1295-1325},
5056		Title = {Variational integrators and the Newmark algorithm for conservative and dissipative mechanical systems},
5057		Uri = {<Go to ISI>://000165270600004},
5058	<	Volume = {49},
5059	<	Year = {2000}}
5058	>	Volume = 49,
5059	>	Year = 2000}
5060
5061		@article{Klimov1997,
5062		Abstract = {The viscosity (eta) dependence of the folding rates for four sequences
#	Line 4745 \| Line 5073
5073		Annote = {Xk293 Times Cited:77 Cited References Count:17},
5074		Author = {D. K. Klimov and D. Thirumalai},
5075		Issn = {0031-9007},
5076	<	Journal = {Physical Review Letters},
5076	>	Journal = prl,
5077		Month = {Jul 14},
5078	<	Number = {2},
5078	>	Number = 2,
5079		Pages = {317-320},
5080		Title = {Viscosity dependence of the folding rates of proteins},
5081		Uri = {<Go to ISI>://A1997XK29300035},
5082	<	Volume = {79},
5083	<	Year = {1997}}
5082	>	Volume = 79,
5083	>	Year = 1997}
5084
5085		@article{Kol1997,
5086		Abstract = {Rigid-body molecular dynamics simulations typically are performed
#	Line 4778 \| Line 5106
5106		Annote = {Xq332 Times Cited:11 Cited References Count:18},
5107		Author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
5108		Issn = {0021-9606},
5109	<	Journal = {Journal of Chemical Physics},
5109	>	Journal = jcp,
5110		Month = {Aug 15},
5111	<	Number = {7},
5111	>	Number = 7,
5112		Pages = {2580-2588},
5113		Title = {A symplectic method for rigid-body molecular simulation},
5114		Uri = {<Go to ISI>://A1997XQ33200046},
5115	<	Volume = {107},
5116	<	Year = {1997}}
5115	>	Volume = 107,
5116	>	Year = 1997}
5117
5118		@article{Lansac2001,
5119		Abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
#	Line 4814 \| Line 5142
5142		Issn = {1063-651X},
5143		Journal = {Physical Review E},
5144		Month = {Nov},
5145	<	Number = {5},
5145	>	Number = 5,
5146		Pages = {-},
5147		Title = {Microscopic structure and dynamics of a partial bilayer smectic liquid crystal},
5148		Uri = {<Go to ISI>://000172406900063},
5149	<	Volume = {6405},
5150	<	Year = {2001}}
5149	>	Volume = 6405,
5150	>	Year = 2001}
5151
5152		@article{Lansac2003,
5153		Abstract = {Recently, a new class of smectic liquid crystal phases characterized
#	Line 4842 \| Line 5170
5170		Issn = {1063-651X},
5171		Journal = {Physical Review E},
5172		Month = {Jan},
5173	<	Number = {1},
5173	>	Number = 1,
5174		Pages = {-},
5175		Title = {Phase behavior of bent-core molecules},
5176		Uri = {<Go to ISI>://000181017300042},
5177	<	Volume = {67},
5178	<	Year = {2003}}
5177	>	Volume = 67,
5178	>	Year = 2003}
5179
5180		@book{Leach2001,
5181		Address = {Harlow, England},
#	Line 4855 \| Line 5183
5183		Edition = {2nd},
5184		Publisher = {Pearson Educated Limited},
5185		Title = {Molecular Modeling: Principles and Applications},
5186	<	Year = {2001}}
5186	>	Year = 2001}
5187
5188		@article{Leimkuhler1999,
5189		Abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
#	Line 4875 \| Line 5203
5203		Issn = {1364-503X},
5204		Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
5205		Month = {Apr 15},
5206	<	Number = {1754},
5206	>	Number = 1754,
5207		Pages = {1101-1133},
5208		Title = {Reversible adaptive regularization: perturbed Kepler motion and classical atomic trajectories},
5209		Uri = {<Go to ISI>://000080466800007},
5210	<	Volume = {357},
5211	<	Year = {1999}}
5210	>	Volume = 357,
5211	>	Year = 1999}
5212
5213		@book{Leimkuhler2004,
5214		Address = {Cambridge},
5215		Author = {B. Leimkuhler and S. Reich},
5216		Publisher = {Cambridge University Press},
5217		Title = {Simulating Hamiltonian Dynamics},
5218	<	Year = {2004}}
5218	>	Year = 2004}
5219
5220		@article{Levelut1981,
5221		Annote = {Ml751 Times Cited:96 Cited References Count:16},
5222		Author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard and G. Sigaud},
5223		Issn = {1050-2947},
5224		Journal = {Physical Review A},
5225	<	Number = {4},
5225	>	Number = 4,
5226		Pages = {2180-2186},
5227		Title = {Number of Sa Phases},
5228		Uri = {<Go to ISI>://A1981ML75100057},
5229	<	Volume = {24},
5230	<	Year = {1981}}
5229	>	Volume = 24,
5230	>	Year = 1981}
5231
5232		@article{Lieb1982,
5233		Annote = {Nu461 Times Cited:40 Cited References Count:28},
5234		Author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
5235		Issn = {0006-3002},
5236		Journal = {Biochimica Et Biophysica Acta},
5237	<	Number = {2},
5237	>	Number = 2,
5238		Pages = {388-398},
5239		Title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - Evidence from Raman-Scattering},
5240		Uri = {<Go to ISI>://A1982NU46100012},
5241	<	Volume = {688},
5242	<	Year = {1982}}
5241	>	Volume = 688,
5242	>	Year = 1982}
5243
5244		@article{Link1997,
5245		Abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
#	Line 4929 \| Line 5257
5257		Issn = {0036-8075},
5258		Journal = {Science},
5259		Month = {Dec 12},
5260	<	Number = {5345},
5260	>	Number = 5345,
5261		Pages = {1924-1927},
5262		Title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic phase of achiral molecules},
5263		Uri = {<Go to ISI>://A1997YL00200028},
5264	<	Volume = {278},
5265	<	Year = {1997}}
5264	>	Volume = 278,
5265	>	Year = 1997}
5266
5267		@article{Liwo2005,
5268		Annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
#	Line 4945 \| Line 5273
5273		Pages = {359-360},
5274		Title = {Ab initio simulations of protein folding pathways by molecular dynamics with the united-residue (UNRES) model of polypeptide chains},
5275		Uri = {<Go to ISI>://000234826102043},
5276	<	Volume = {272},
5277	<	Year = {2005}}
5276	>	Volume = 272,
5277	>	Year = 2005}
5278
5279		@article{Luty1994,
5280		Abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
#	Line 4961 \| Line 5289
5289		Author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
5290		Issn = {0892-7022},
5291		Journal = {Molecular Simulation},
5292	<	Number = {1},
5292	>	Number = 1,
5293		Pages = {11-20},
5294		Title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
5295		Uri = {<Go to ISI>://A1994QF46400002},
5296	<	Volume = {14},
5297	<	Year = {1994}}
5296	>	Volume = 14,
5297	>	Year = 1994}
5298
5299		@book{Marion1990,
5300		Address = {New York},
#	Line 4974 \| Line 5302
5302		Edition = {2rd},
5303		Publisher = {Academic Press},
5304		Title = {Classical Dynamics of Particles and Systems},
5305	<	Year = {1990}}
5305	>	Year = 1990}
5306
5307		@article{Marrink1994,
5308		Abstract = {To obtain insight in the process of water permeation through a lipid
#	Line 5006 \| Line 5334
5334		Issn = {0022-3654},
5335		Journal = {Journal of Physical Chemistry},
5336		Month = {Apr 14},
5337	<	Number = {15},
5337	>	Number = 15,
5338		Pages = {4155-4168},
5339		Title = {Simulation of Water Transport through a Lipid-Membrane},
5340		Uri = {<Go to ISI>://A1994NG21900040},
5341	<	Volume = {98},
5342	<	Year = {1994}}
5341	>	Volume = 98,
5342	>	Year = 1994}
5343
5344		@article{Marrink2004,
5345		Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
5346		Journal = {J. Phys. Chem. B},
5347		Pages = {750-760},
5348		Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
5349	<	Volume = {108},
5350	<	Year = {2004}}
5349	>	Volume = 108,
5350	>	Year = 2004}
5351
5352		@article{Marsden1998,
5353		Abstract = {This paper presents a geometric-variational approach to continuous
#	Line 5047 \| Line 5375
5375		Issn = {0010-3616},
5376		Journal = {Communications in Mathematical Physics},
5377		Month = {Dec},
5378	<	Number = {2},
5378	>	Number = 2,
5379		Pages = {351-395},
5380		Title = {Multisymplectic geometry, variational integrators, and nonlinear PDEs},
5381		Uri = {<Go to ISI>://000077902200006},
5382	<	Volume = {199},
5383	<	Year = {1998}}
5382	>	Volume = 199,
5383	>	Year = 1998}
5384
5385		@article{Matthey2004,
5386		Abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
#	Line 5077 \| Line 5405
5405		Issn = {0098-3500},
5406		Journal = {Acm Transactions on Mathematical Software},
5407		Month = {Sep},
5408	<	Number = {3},
5408	>	Number = 3,
5409		Pages = {237-265},
5410		Title = {ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics},
5411		Uri = {<Go to ISI>://000224325600001},
5412	<	Volume = {30},
5413	<	Year = {2004}}
5412	>	Volume = 30,
5413	>	Year = 2004}
5414
5415		@article{McLachlan1993,
5416		Author = {R.~I McLachlan},
5417		Journal = {prl},
5418		Pages = {3043-3046},
5419		Title = {Explicit Lie-Poisson integration and the Euler equations},
5420	<	Volume = {71},
5421	<	Year = {1993}}
5420	>	Volume = 71,
5421	>	Year = 1993}
5422
5423		@article{McLachlan1998,
5424		Abstract = {We give a survey and some new examples of generating functions for
#	Line 5108 \| Line 5436
5436		Pages = {298-309},
5437		Title = {Generating functions for dynamical systems with symmetries, integrals, and differential invariants},
5438		Uri = {<Go to ISI>://000071558900021},
5439	<	Volume = {112},
5440	<	Year = {1998}}
5439	>	Volume = 112,
5440	>	Year = 1998}
5441
5442		@article{McLachlan1998a,
5443		Abstract = {We consider properties of flows, the relationships between them, and
#	Line 5126 \| Line 5454
5454		Issn = {0036-1429},
5455		Journal = {Siam Journal on Numerical Analysis},
5456		Month = {Apr},
5457	<	Number = {2},
5457	>	Number = 2,
5458		Pages = {586-599},
5459		Title = {Numerical integrators that preserve symmetries and reversing symmetries},
5460		Uri = {<Go to ISI>://000072580500010},
5461	<	Volume = {35},
5462	<	Year = {1998}}
5461	>	Volume = 35,
5462	>	Year = 1998}
5463
5464		@article{McLachlan2005,
5465		Abstract = {In this paper we revisit the Moser-Veselov description of the free
#	Line 5152 \| Line 5480
5480		Issn = {1615-3375},
5481		Journal = {Foundations of Computational Mathematics},
5482		Month = {Feb},
5483	<	Number = {1},
5483	>	Number = 1,
5484		Pages = {87-123},
5485		Title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
5486		Uri = {<Go to ISI>://000228011900003},
5487	<	Volume = {5},
5488	<	Year = {2005}}
5487	>	Volume = 5,
5488	>	Year = 2005}
5489
5490		@article{Meineke2005,
5491		Abstract = {OOPSE is a new molecular dynamics simulation program that is capable
#	Line 5173 \| Line 5501
5501		Annote = {891CF Times Cited:1 Cited References Count:56},
5502		Author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and J. D. Gezelter},
5503		Issn = {0192-8651},
5504	<	Journal = {Journal of Computational Chemistry},
5504	>	Journal = jcc,
5505		Month = {Feb},
5506	<	Number = {3},
5506	>	Number = 3,
5507		Pages = {252-271},
5508		Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
5509		Uri = {<Go to ISI>://000226558200006},
5510	<	Volume = {26},
5511	<	Year = {2005}}
5510	>	Volume = 26,
5511	>	Year = 2005}
5512
5513		@article{Melchionna1993,
5514		Abstract = {In this paper we write down equations of motion (following the approach
#	Line 5192 \| Line 5520
5520		Annote = {Kq355 Times Cited:172 Cited References Count:17},
5521		Author = {S. Melchionna and G. Ciccotti and B. L. Holian},
5522		Issn = {0026-8976},
5523	<	Journal = {Molecular Physics},
5523	>	Journal = mp,
5524		Month = {Feb 20},
5525	<	Number = {3},
5525	>	Number = 3,
5526		Pages = {533-544},
5527		Title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
5528		Uri = {<Go to ISI>://A1993KQ35500002},
5529	<	Volume = {78},
5530	<	Year = {1993}}
5529	>	Volume = 78,
5530	>	Year = 1993}
5531
5532		@article{Memmer2002,
5533		Abstract = {The phase behaviour of achiral banana-shaped molecules was studied
#	Line 5232 \| Line 5560
5560		Issn = {0267-8292},
5561		Journal = {Liquid Crystals},
5562		Month = {Apr},
5563	<	Number = {4},
5563	>	Number = 4,
5564		Pages = {483-496},
5565		Title = {Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study},
5566		Uri = {<Go to ISI>://000174410500001},
5567	<	Volume = {29},
5568	<	Year = {2002}}
5567	>	Volume = 29,
5568	>	Year = 2002}
5569
5570		@article{Metropolis1949,
5571		Author = {N. Metropolis and S. Ulam},
5572		Journal = {J. Am. Stat. Ass.},
5573		Pages = {335-341},
5574		Title = {The $\mbox{Monte Carlo}$ Method},
5575	<	Volume = {44},
5576	<	Year = {1949}}
5575	>	Volume = 44,
5576	>	Year = 1949}
5577
5578		@article{Mielke2004,
5579		Abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
#	Line 5276 \| Line 5604
5604		Annote = {861ZF Times Cited:3 Cited References Count:34},
5605		Author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen and C. J. Benham},
5606		Issn = {0021-9606},
5607	<	Journal = {Journal of Chemical Physics},
5607	>	Journal = jcp,
5608		Month = {Oct 22},
5609	<	Number = {16},
5609	>	Number = 16,
5610		Pages = {8104-8112},
5611		Title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study},
5612		Uri = {<Go to ISI>://000224456500064},
5613	<	Volume = {121},
5614	<	Year = {2004}}
5613	>	Volume = 121,
5614	>	Year = 2004}
5615
5616		@article{Naess2001,
5617		Abstract = {The three Eulerian angles constitute the classical choice of generalized
#	Line 5308 \| Line 5636
5636		Pages = {323-339},
5637		Title = {Brownian dynamics simulation of rigid bodies and segmented polymer chains. Use of Cartesian rotation vectors as the generalized coordinates describing angular orientations},
5638		Uri = {<Go to ISI>://000168774800005},
5639	<	Volume = {294},
5640	<	Year = {2001}}
5639	>	Volume = 294,
5640	>	Year = 2001}
5641
5642		@article{Niori1996,
5643		Abstract = {The synthesis of a banana-shaped molecule is reported and it is found
#	Line 5324 \| Line 5652
5652		Issn = {0959-9428},
5653		Journal = {Journal of Materials Chemistry},
5654		Month = {Jul},
5655	<	Number = {7},
5655	>	Number = 7,
5656		Pages = {1231-1233},
5657		Title = {Distinct ferroelectric smectic liquid crystals consisting of banana shaped achiral molecules},
5658		Uri = {<Go to ISI>://A1996UX85500025},
5659	<	Volume = {6},
5660	<	Year = {1996}}
5659	>	Volume = 6,
5660	>	Year = 1996}
5661
5662		@article{Noguchi2002,
5663		Abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
#	Line 5349 \| Line 5677
5677		Issn = {1063-651X},
5678		Journal = {Physical Review E},
5679		Month = {may},
5680	<	Number = {5},
5680	>	Number = 5,
5681		Pages = {-},
5682		Title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
5683		Uri = {<Go to ISI>://000176552300084},
5684	<	Volume = {65},
5685	<	Year = {2002}}
5684	>	Volume = 65,
5685	>	Year = 2002}
5686
5687		@article{Noguchi2001,
5688		Abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
#	Line 5371 \| Line 5699
5699		Annote = {491UW Times Cited:48 Cited References Count:25},
5700		Author = {H. Noguchi and M. Takasu},
5701		Issn = {0021-9606},
5702	<	Journal = {Journal of Chemical Physics},
5702	>	Journal = jcp,
5703		Month = {Nov 22},
5704	<	Number = {20},
5704	>	Number = 20,
5705		Pages = {9547-9551},
5706		Title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
5707		Uri = {<Go to ISI>://000172129300049},
5708	<	Volume = {115},
5709	<	Year = {2001}}
5708	>	Volume = 115,
5709	>	Year = 2001}
5710
5711		@book{Olver1986,
5712		Address = {New York},
5713		Author = {P.J. Olver},
5714		Publisher = {Springer},
5715		Title = {Applications of Lie groups to differential equatitons},
5716	<	Year = {1986}}
5716	>	Year = 1986}
5717
5718		@article{Omelyan1998,
5719		Abstract = {A revised version of the quaternion approach for numerical integration
#	Line 5404 \| Line 5732
5732		Issn = {0894-1866},
5733		Journal = {Computers in Physics},
5734		Month = {Jan-Feb},
5735	<	Number = {1},
5735	>	Number = 1,
5736		Pages = {97-103},
5737		Title = {On the numerical integration of motion for rigid polyatomics: The modified quaternion approach},
5738		Uri = {<Go to ISI>://000072024300025},
5739	<	Volume = {12},
5740	<	Year = {1998}}
5739	>	Volume = 12,
5740	>	Year = 1998}
5741
5742		@article{Omelyan1998a,
5743		Abstract = {An algorithm for numerical integration of the rigid-body equations
#	Line 5426 \| Line 5754
5754		Issn = {1063-651X},
5755		Journal = {Physical Review E},
5756		Month = {Jul},
5757	<	Number = {1},
5757	>	Number = 1,
5758		Pages = {1169-1172},
5759		Title = {Algorithm for numerical integration of the rigid-body equations of motion},
5760		Uri = {<Go to ISI>://000074893400151},
5761	<	Volume = {58},
5762	<	Year = {1998}}
5761	>	Volume = 58,
5762	>	Year = 1998}
5763
5764		@article{Owren1992,
5765		Abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
#	Line 5452 \| Line 5780
5780		Issn = {0196-5204},
5781		Journal = {Siam Journal on Scientific and Statistical Computing},
5782		Month = {Nov},
5783	<	Number = {6},
5783	>	Number = 6,
5784		Pages = {1488-1501},
5785		Title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
5786		Uri = {<Go to ISI>://A1992JU93600013},
5787	<	Volume = {13},
5788	<	Year = {1992}}
5787	>	Volume = 13,
5788	>	Year = 1992}
5789
5790		@article{Palacios1998,
5791		Abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
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5823		Issn = {0163-1829},
5824		Journal = {Physical Review B},
5825		Month = {Dec 1},
5826	<	Number = {22},
5826	>	Number = 22,
5827		Pages = {14937-14958},
5828		Title = {Langevin-dynamics study of the dynamical properties of small magnetic particles},
5829		Uri = {<Go to ISI>://000077460000052},
5830	<	Volume = {58},
5831	<	Year = {1998}}
5830	>	Volume = 58,
5831	>	Year = 1998}
5832
5833		@article{Parr1995,
5834		Abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
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5855		Issn = {0038-0644},
5856		Journal = {Software-Practice \& Experience},
5857		Month = {Jul},
5858	<	Number = {7},
5858	>	Number = 7,
5859		Pages = {789-810},
5860		Title = {Antlr - a Predicated-Ll(K) Parser Generator},
5861		Uri = {<Go to ISI>://A1995RK10400004},
5862	<	Volume = {25},
5863	<	Year = {1995}}
5862	>	Volume = 25,
5863	>	Year = 1995}
5864
5865		@article{Pastor1988,
5866		Annote = {T1302 Times Cited:61 Cited References Count:26},
5867		Author = {R. W. Pastor and B. R. Brooks and A. Szabo},
5868		Issn = {0026-8976},
5869	<	Journal = {Molecular Physics},
5869	>	Journal = mp,
5870		Month = {Dec 20},
5871	<	Number = {6},
5871	>	Number = 6,
5872		Pages = {1409-1419},
5873		Title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
5874		Uri = {<Go to ISI>://A1988T130200011},
5875	<	Volume = {65},
5876	<	Year = {1988}}
5875	>	Volume = 65,
5876	>	Year = 1988}
5877
5878		@article{Pelzl1999,
5879		Annote = {220RC Times Cited:313 Cited References Count:49},
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5881		Issn = {0935-9648},
5882		Journal = {Advanced Materials},
5883		Month = {Jul 5},
5884	<	Number = {9},
5884	>	Number = 9,
5885		Pages = {707-724},
5886		Title = {Banana-shaped compounds - A new field of liquid crystals},
5887		Uri = {<Go to ISI>://000081680400007},
5888	<	Volume = {11},
5889	<	Year = {1999}}
5888	>	Volume = 11,
5889	>	Year = 1999}
5890
5891		@article{Perram1985,
5892		Annote = {Akb93 Times Cited:71 Cited References Count:12},
5893		Author = {J. W. Perram and M. S. Wertheim},
5894		Issn = {0021-9991},
5895	<	Journal = {Journal of Computational Physics},
5896	<	Number = {3},
5895	>	Journal = jcop,
5896	>	Number = 3,
5897		Pages = {409-416},
5898		Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function},
5899		Uri = {<Go to ISI>://A1985AKB9300008},
5900	<	Volume = {58},
5901	<	Year = {1985}}
5900	>	Volume = 58,
5901	>	Year = 1985}
5902
5903		@article{Rotne1969,
5904		Author = {F. Perrin},
5905		Journal = {J. Chem. Phys.},
5906		Pages = {4831-4837},
5907		Title = {Variational treatment of hydrodynamic interaction in polymers},
5908	<	Volume = {50},
5909	<	Year = {1969}}
5908	>	Volume = 50,
5909	>	Year = 1969}
5910
5911		@article{Perrin1936,
5912		Author = {F. Perrin},
5913		Journal = {J. Phys. Radium},
5914		Pages = {1-11},
5915		Title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation des fluorescences. Translation et diffusion de moleculese ellipsoidales},
5916	<	Volume = {7},
5917	<	Year = {1936}}
5916	>	Volume = 7,
5917	>	Year = 1936}
5918
5919		@article{Perrin1934,
5920		Author = {F. Perrin},
5921		Journal = {J. Phys. Radium},
5922		Pages = {497-511},
5923		Title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour des molecules ellipsoidales},
5924	<	Volume = {5},
5925	<	Year = {1934}}
5924	>	Volume = 5,
5925	>	Year = 1934}
5926
5927		@article{Petrache2000,
5928		Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
5929	<	Journal = {Biophysical Journal},
5929	>	Journal = bj,
5930		Pages = {3172-3192},
5931		Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
5932	<	Volume = {79},
5933	<	Year = {2000}}
5932	>	Volume = 79,
5933	>	Year = 2000}
5934
5935		@article{Petrache1998,
5936		Abstract = {X-ray diffraction data taken at high instrumental resolution were
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5955		Issn = {0009-3084},
5956		Journal = {Chemistry and Physics of Lipids},
5957		Month = {Sep},
5958	<	Number = {1},
5958	>	Number = 1,
5959		Pages = {83-94},
5960		Title = {Fluid phase structure of EPC and DMPC bilayers},
5961		Uri = {<Go to ISI>://000076497600007},
5962	<	Volume = {95},
5963	<	Year = {1998}}
5962	>	Volume = 95,
5963	>	Year = 1998}
5964
5965		@article{Powles1973,
5966		Author = {J.~G. Powles},
5967		Journal = {Advan. Phys.},
5968		Pages = {1-56},
5969		Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
5970	<	Volume = {22},
5971	<	Year = {1973}}
5970	>	Volume = 22,
5971	>	Year = 1973}
5972
5973		@article{Recio2004,
5974		Abstract = {Protein recognition is one of the most challenging and intriguing
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5997		Annote = {763GQ Times Cited:21 Cited References Count:59},
5998		Author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
5999		Issn = {0022-2836},
6000	<	Journal = {Journal of Molecular Biology},
6000	>	Journal = jmb,
6001		Month = {Jan 16},
6002	<	Number = {3},
6002	>	Number = 3,
6003		Pages = {843-865},
6004		Title = {Identification of protein-protein interaction sites from docking energy landscapes},
6005		Uri = {<Go to ISI>://000188066900016},
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6007	<	Year = {2004}}
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6007	>	Year = 2004}
6008
6009		@article{Reddy2006,
6010		Abstract = {An overview on the recent developments in the field of liquid crystalline
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6022		Author = {R. A. Reddy and C. Tschierske},
6023		Issn = {0959-9428},
6024		Journal = {Journal of Materials Chemistry},
6025	<	Number = {10},
6025	>	Number = 10,
6026		Pages = {907-961},
6027		Title = {Bent-core liquid crystals: polar order, superstructural chirality and spontaneous desymmetrisation in soft matter systems},
6028		Uri = {<Go to ISI>://000235990500001},
6029	<	Volume = {16},
6030	<	Year = {2006}}
6029	>	Volume = 16,
6030	>	Year = 2006}
6031
6032		@article{Reich1999,
6033		Abstract = {Backward error analysis has become an important tool for understanding
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6057		Issn = {0036-1429},
6058		Journal = {Siam Journal on Numerical Analysis},
6059		Month = {Sep 8},
6060	<	Number = {5},
6060	>	Number = 5,
6061		Pages = {1549-1570},
6062		Title = {Backward error analysis for numerical integrators},
6063		Uri = {<Go to ISI>://000082650600010},
6064	<	Volume = {36},
6065	<	Year = {1999}}
6064	>	Volume = 36,
6065	>	Year = 1999}
6066
6067		@article{Ros2005,
6068		Abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
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6077		Author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
6078		Issn = {0959-9428},
6079		Journal = {Journal of Materials Chemistry},
6080	<	Number = {48},
6080	>	Number = 48,
6081		Pages = {5093-5098},
6082		Title = {Banana-shaped liquid crystals: a new field to explore},
6083		Uri = {<Go to ISI>://000233775500001},
6084	<	Volume = {15},
6085	<	Year = {2005}}
6084	>	Volume = 15,
6085	>	Year = 2005}
6086
6087		@article{Roux1991,
6088		Abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
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6110		Issn = {0022-3654},
6111		Journal = {Journal of Physical Chemistry},
6112		Month = {Jun 13},
6113	<	Number = {12},
6113	>	Number = 12,
6114		Pages = {4856-4868},
6115		Title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
6116		Uri = {<Go to ISI>://A1991FR75600049},
6117	<	Volume = {95},
6118	<	Year = {1991}}
6117	>	Volume = 95,
6118	>	Year = 1991}
6119
6120		@article{Roy2005,
6121		Abstract = {A vast majority of compounds with bent core or banana shaped molecules
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6134		Issn = {1292-8941},
6135		Journal = {European Physical Journal E},
6136		Month = {Nov},
6137	<	Number = {3},
6137	>	Number = 3,
6138		Pages = {253-258},
6139		Title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases in banana shaped molecules},
6140		Uri = {<Go to ISI>://000233363300002},
6141	<	Volume = {18},
6142	<	Year = {2005}}
6141	>	Volume = 18,
6142	>	Year = 2005}
6143
6144		@article{Ryckaert1977,
6145		Annote = {Cz253 Times Cited:3680 Cited References Count:7},
6146		Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
6147		Issn = {0021-9991},
6148	<	Journal = {Journal of Computational Physics},
6149	<	Number = {3},
6148	>	Journal = jcop,
6149	>	Number = 3,
6150		Pages = {327-341},
6151		Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes},
6152		Uri = {<Go to ISI>://A1977CZ25300007},
6153	<	Volume = {23},
6154	<	Year = {1977}}
6153	>	Volume = 23,
6154	>	Year = 1977}
6155
6156		@article{Sagui1999,
6157		Abstract = {Current computer simulations of biomolecules typically make use of
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6176		Pages = {155-179},
6177		Title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic effects},
6178		Uri = {<Go to ISI>://000081271400008},
6179	<	Volume = {28},
6180	<	Year = {1999}}
6179	>	Volume = 28,
6180	>	Year = 1999}
6181
6182		@article{Sandu1999,
6183		Abstract = {Numerical resonance artifacts have become recognized recently as a
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6220		Annote = {194FM Times Cited:14 Cited References Count:32},
6221		Author = {A. Sandu and T. Schlick},
6222		Issn = {0021-9991},
6223	<	Journal = {Journal of Computational Physics},
6223	>	Journal = jcop,
6224		Month = {May 1},
6225	<	Number = {1},
6225	>	Number = 1,
6226		Pages = {74-113},
6227		Title = {Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics},
6228		Uri = {<Go to ISI>://000080181500004},
6229	<	Volume = {151},
6230	<	Year = {1999}}
6229	>	Volume = 151,
6230	>	Year = 1999}
6231
6232		@article{Sasaki2004,
6233		Abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
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6241		Author = {Y. Sasaki and R. Shukla and B. D. Smith},
6242		Issn = {1477-0520},
6243		Journal = {Organic \& Biomolecular Chemistry},
6244	<	Number = {2},
6244	>	Number = 2,
6245		Pages = {214-219},
6246		Title = {Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases},
6247		Uri = {<Go to ISI>://000187843800012},
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6249	<	Year = {2004}}
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6249	>	Year = 2004}
6250
6251		@article{Satoh1996,
6252		Abstract = {The effects of dipole-dipole interaction on mesophase formation are
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6265		Pages = {99-104},
6266		Title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect of terminal dipole moment on mesophase formation},
6267		Uri = {<Go to ISI>://A1996UQ97500017},
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6269	<	Year = {1996}}
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6269	>	Year = 1996}
6270
6271		@article{Schaps1999,
6272		Annote = {163EC Times Cited:0 Cited References Count:0},
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6274		Issn = {1044-789X},
6275		Journal = {Dr Dobbs Journal},
6276		Month = {Mar},
6277	<	Number = {3},
6277	>	Number = 3,
6278		Pages = {84-+},
6279		Title = {Compiler construction with ANTLR and Java - Tools for building tools},
6280		Uri = {<Go to ISI>://000078389200023},
6281	<	Volume = {24},
6282	<	Year = {1999}}
6281	>	Volume = 24,
6282	>	Year = 1999}
6283
6284		@article{Shen2002,
6285		Abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
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6304		Annote = {540MH Times Cited:36 Cited References Count:45},
6305		Author = {M. Y. Shen and K. F. Freed},
6306		Issn = {0006-3495},
6307	<	Journal = {Biophysical Journal},
6307	>	Journal = bj,
6308		Month = {Apr},
6309	<	Number = {4},
6309	>	Number = 4,
6310		Pages = {1791-1808},
6311		Title = {Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models},
6312		Uri = {<Go to ISI>://000174932400010},
6313	<	Volume = {82},
6314	<	Year = {2002}}
6313	>	Volume = 82,
6314	>	Year = 2002}
6315
6316		@article{Shillcock2005,
6317		Annote = {901QJ Times Cited:9 Cited References Count:23},
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6319		Issn = {1476-1122},
6320		Journal = {Nature Materials},
6321		Month = {Mar},
6322	<	Number = {3},
6322	>	Number = 3,
6323		Pages = {225-228},
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6325		Uri = {<Go to ISI>://000227296700019},
6326	<	Volume = {4},
6327	<	Year = {2005}}
6326	>	Volume = 4,
6327	>	Year = 2005}
6328
6329		@article{Shimada1993,
6330		Abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
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6347		Annote = {Lh164 Times Cited:27 Cited References Count:47},
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6349		Issn = {0192-8651},
6350	<	Journal = {Journal of Computational Chemistry},
6350	>	Journal = jcc,
6351		Month = {Jul},
6352	<	Number = {7},
6352	>	Number = 7,
6353		Pages = {867-878},
6354		Title = {Efficient Calculations of Coulombic Interactions in Biomolecular Simulations with Periodic Boundary-Conditions},
6355		Uri = {<Go to ISI>://A1993LH16400011},
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6357	<	Year = {1993}}
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6357	>	Year = 1993}
6358
6359		@article{Skeel2002,
6360		Abstract = {The best simple method for Newtonian molecular dynamics is indisputably
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6370		Annote = {633RX Times Cited:8 Cited References Count:22},
6371		Author = {R. D. Skeel and J. A. Izaguirre},
6372		Issn = {0026-8976},
6373	<	Journal = {Molecular Physics},
6373	>	Journal = mp,
6374		Month = {Dec 20},
6375	<	Number = {24},
6375	>	Number = 24,
6376		Pages = {3885-3891},
6377		Title = {An impulse integrator for Langevin dynamics},
6378		Uri = {<Go to ISI>://000180297200014},
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6380	<	Year = {2002}}
6379	>	Volume = 100,
6380	>	Year = 2002}
6381
6382		@article{Skeel1997,
6383		Abstract = {The following integration methods for special second-order ordinary
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6398		Issn = {1064-8275},
6399		Journal = {Siam Journal on Scientific Computing},
6400		Month = {Jan},
6401	<	Number = {1},
6401	>	Number = 1,
6402		Pages = {203-222},
6403		Title = {A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications},
6404		Uri = {<Go to ISI>://A1997WE98100012},
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6406	<	Year = {1997}}
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6407
6408		@article{Tao2005,
6409		Abstract = {Recently a microscopic theory for the dynamics of suspensions of long
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6429		Annote = {943DN Times Cited:3 Cited References Count:26},
6430		Author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont and W. J. Briels},
6431		Issn = {0021-9606},
6432	<	Journal = {Journal of Chemical Physics},
6432	>	Journal = jcp,
6433		Month = {Jun 22},
6434	<	Number = {24},
6434	>	Number = 24,
6435		Pages = {-},
6436		Title = {Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods},
6437		Uri = {<Go to ISI>://000230332400077},
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6439	<	Year = {2005}}
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6441		@book{Tolman1979,
6442		Address = {New York},
6443		Author = {R.~C. Tolman},
6444	<	Chapter = {2},
6444	>	Chapter = 2,
6445		Pages = {19-22},
6446		Publisher = {Dover Publications, Inc.},
6447		Title = {The Principles of Statistical Mechanics},
6448	<	Year = {1979}}
6448	>	Year = 1979}
6449
6450		@article{Tu1995,
6451		Abstract = {We report a constant pressure and temperature molecular dynamics simulation
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6470		Annote = {Tv018 Times Cited:108 Cited References Count:34},
6471		Author = {K. Tu and D. J. Tobias and M. L. Klein},
6472		Issn = {0006-3495},
6473	<	Journal = {Biophysical Journal},
6473	>	Journal = bj,
6474		Month = {Dec},
6475	<	Number = {6},
6475	>	Number = 6,
6476		Pages = {2558-2562},
6477		Title = {Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer},
6478		Uri = {<Go to ISI>://A1995TV01800037},
6479	<	Volume = {69},
6480	<	Year = {1995}}
6479	>	Volume = 69,
6480	>	Year = 1995}
6481
6482		@article{Tuckerman1992,
6483		Abstract = {The Trotter factorization of the Liouville propagator is used to generate
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6495		Annote = {Je891 Times Cited:680 Cited References Count:19},
6496		Author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
6497		Issn = {0021-9606},
6498	<	Journal = {Journal of Chemical Physics},
6498	>	Journal = jcp,
6499		Month = {Aug 1},
6500	<	Number = {3},
6500	>	Number = 3,
6501		Pages = {1990-2001},
6502		Title = {Reversible Multiple Time Scale Molecular-Dynamics},
6503		Uri = {<Go to ISI>://A1992JE89100044},
6504	<	Volume = {97},
6505	<	Year = {1992}}
6504	>	Volume = 97,
6505	>	Year = 1992}
6506
6507		@book{Varadarajan1974,
6508		Address = {New York},
6509		Author = {V.S. Varadarajan},
6510		Publisher = {Prentice-Hall},
6511		Title = {Lie groups, Lie algebras, and their representations},
6512	<	Year = {1974}}
6512	>	Year = 1974}
6513
6514		@article{Vincent1995,
6515		Abstract = {We have implemented a portable parallel version of the macromolecular
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6529		Annote = {Ta403 Times Cited:16 Cited References Count:23},
6530		Author = {J. J. Vincent and K. M. Merz},
6531		Issn = {0192-8651},
6532	<	Journal = {Journal of Computational Chemistry},
6532	>	Journal = jcc,
6533		Month = {Nov},
6534	<	Number = {11},
6534	>	Number = 11,
6535		Pages = {1420-1427},
6536		Title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing Interface Standard},
6537		Uri = {<Go to ISI>://A1995TA40300009},
6538	<	Volume = {16},
6539	<	Year = {1995}}
6538	>	Volume = 16,
6539	>	Year = 1995}
6540
6541		@article{Wegener1979,
6542		Author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
6543		Journal = {Proc. Natl. Acad. Sci.},
6544	<	Number = {12},
6544	>	Number = 12,
6545		Pages = {6356-6360},
6546		Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
6547	<	Volume = {76},
6548	<	Year = {1979}}
6547	>	Volume = 76,
6548	>	Year = 1979}
6549
6550		@article{Wilson2006,
6551		Author = {G.~V. Wilson},
6552		Journal = {American Scientist},
6553		Title = {Where's the Real Bottleneck in Scientific Computing?},
6554	<	Volume = {94},
6555	<	Year = {2006}}
6554	>	Volume = 94,
6555	>	Year = 2006}
6556
6557		@article{Withers2003,
6558		Abstract = {The effects of longitudinal quadrupole moments on the formation of
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6585		Annote = {738EF Times Cited:3 Cited References Count:43},
6586		Author = {I. M. Withers},
6587		Issn = {0021-9606},
6588	<	Journal = {Journal of Chemical Physics},
6588	>	Journal = jcp,
6589		Month = {Nov 15},
6590	<	Number = {19},
6590	>	Number = 19,
6591		Pages = {10209-10223},
6592		Title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne fluid},
6593		Uri = {<Go to ISI>://000186273200027},
6594	<	Volume = {119},
6595	<	Year = {2003}}
6594	>	Volume = 119,
6595	>	Year = 2003}
6596
6597		@article{Wolf1999,
6598		Abstract = {Based on a recent result showing that the net Coulomb potential in
#	Line 6291 \| Line 6619
6619		Annote = {189PD Times Cited:70 Cited References Count:34},
6620		Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
6621		Issn = {0021-9606},
6622	<	Journal = {Journal of Chemical Physics},
6622	>	Journal = jcp,
6623		Month = {May 1},
6624	<	Number = {17},
6624	>	Number = 17,
6625		Pages = {8254-8282},
6626		Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r(-1) summation},
6627		Uri = {<Go to ISI>://000079913000008},
6628	<	Volume = {110},
6629	<	Year = {1999}}
6628	>	Volume = 110,
6629	>	Year = 1999}
6630
6631		@article{Yoshida1990,
6632		Annote = {Ej798 Times Cited:492 Cited References Count:9},
#	Line 6310 \| Line 6638
6638		Pages = {262-268},
6639		Title = {Construction of Higher-Order Symplectic Integrators},
6640		Uri = {<Go to ISI>://A1990EJ79800009},
6641	<	Volume = {150},
6642	<	Year = {1990}}
6641	>	Volume = 150,
6642	>	Year = 1990}
6643
6644		@article{Blum1972,
6645		Author = {L. Blum and A.~J. Torruella},
6646	<	Journal = {Journal of Chemical Physics},
6646	>	Journal = jcp,
6647		Number = 1,
6648		Pages = {303-309},
6649		Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
#	Line 6324 \| Line 6652
6652
6653		@article{Stone1978,
6654		Author = {A.~J. Stone},
6655	<	Journal = {Molecular Physics},
6655	>	Journal = mp,
6656		Number = 1,
6657		Pages = {241-256},
6658		Title = {The description of bimolecular potentials, forces and torques: the S and V function expansions},
#	Line 6333 \| Line 6661
6661
6662		@article{Berardi2003,
6663		Author = {R. Berardi, M. Cecchini and C. Zannoni},
6664	<	Journal = {Journal of Chemical Physics},
6664	>	Journal = jcp,
6665		Number = 18,
6666		Pages = {9933-9946},
6667		Title = {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
#	Line 6342 \| Line 6670
6670
6671		@article{Beard2000,
6672		Author = {D. A. Beard and T. Schlick},
6673	<	Journal = {Journal of Chemical Physics},
6673	>	Journal = jcp,
6674		Number = 17,
6675		Pages = {7313-7322},
6676		Title = {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
#	Line 6354 \| Line 6682
6682		Author = {M.W. Hirsch},
6683		Publisher = {Springer},
6684		Title = {Differential Topology},
6685	<	Year = {1997}}
6685	>	Year = 1997}
6686
6687		@book{Jost2002,
6688		Address = {Berlin},
6689		Author = {J. Jost},
6690		Publisher = {Springer-Verlag},
6691		Title = {Riemannian Geometry and Geometric Analysis},
6692	<	Year = {2002}}
6692	>	Year = 2002}
6693
6694		@book{McDuff1998,
6695		Address = {Oxford},
6696		Author = {D. McDuff and D. Salamon},
6697		Publisher = {Oxford Mathematical Monographs},
6698		Title = {Introduction to Symplectic Topology},
6699	<	Year = {1998}}
6699	>	Year = 1998}
6700
6701		@article{Matubayasi1999,
6702		Author = {N. Matubayasi and M. Nakahara},
6703	<	Journal = {Journal of Chemical Physics},
6703	>	Journal = jcp,
6704		Number = 7,
6705		Pages = {3291-3301},
6706		Title = {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
#	Line 6381 \| Line 6709
6709
6710		@article{Miller2002,
6711		Author = {T.F. Miller III, M. Eleftheriou},
6712	<	Journal = {Journal of Chemical Physics},
6712	>	Journal = jcp,
6713		Number = 20,
6714		Pages = {8649-8659},
6715		Title = {Symplectic quaternion scheme for biophysical molecular dynamics},
#	Line 6390 \| Line 6718
6718
6719		@article{McMillan1971,
6720		Author = {W.L. McMillan},
6721	<	Journal = {Journal of Chemical Physics},
6721	>	Journal = jcp,
6722		Number = 3,
6723		Pages = {1238-1246},
6724		Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},
#	Line 6432 \| Line 6760
6760		Title = {The Dynamics of Runge-Kutta Methods},
6761		Volume = 2,
6762		Year = 1992}
6763	+
6764	+	@article{HuseyinKaya07012005,
6765	+	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.
6766	+	},
6767	+	Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun},
6768	+	Doi = {10.1529/biophysj.104.057471},
6769	+	Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf},
6770	+	Journal = {Biophys. J.},
6771	+	Number = 1,
6772	+	Pages = {520-535},
6773	+	Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}},
6774	+	Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6775	+	Volume = 89,
6776	+	Year = 2005,
6777	+	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6778	+	Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}}
6779	+
6780	+	@article{JoseGarciadelaTorre02012000,
6781	+	Abstract = {The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (Carrasco and Garcia de la Torre, 1999, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overlapping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 proteins. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 A, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A computational shortcut makes the procedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer program.
6782	+	},
6783	+	Author = {{Garc\'{i}a de la Torre}, Jose and Huertas, Maria L. and Carrasco, Beatriz},
6784	+	Eprint = {http://www.biophysj.org/cgi/reprint/78/2/719.pdf},
6785	+	Journal = bj,
6786	+	Number = {2},
6787	+	Pages = {719-730},
6788	+	Title = {{Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure}},
6789	+	Url = {http://www.biophysj.org/cgi/content/abstract/78/2/719},
6790	+	Volume = {78},
6791	+	Year = {2000},
6792	+	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/78/2/719}}
6793	+
6794	+	@article{GarciadelaTorreJ2002,
6795	+	Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain},
6796	+	Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B.},
6797	+	Journal = {Biopolymers},
6798	+	Number = {3},
6799	+	Pages = {163-167},
6800	+	Title = {Hydrodynamic Properties of Rigid Macromolecules Composed of Ellipsoidal and Cylindrical Subunits},
6801	+	Volume = {63},
6802	+	Year = {2002}}

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Comparing trunk/langevin/langevin.bib (file contents):
Revision 3310 by gezelter, Fri Jan 11 22:08:57 2008 UTC vs.
Revision 3391 by gezelter, Wed Apr 30 16:16:25 2008 UTC