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9	>
10	>
11	>	@string{acp = {Adv. Chem. Phys.}}
12	>
13	>	@string{ccp5 = {CCP5 Information Quarterly}}
14	>
15	>	@string{cp = {Chem. Phys.}}
16	>
17	>	@string{cpl = {Chem. Phys. Lett.}}
18	>
19	>	@string{jacs = {J. Am. Chem. Soc.}}
20	>
21	>	@string{jcc = {J. Comp. Chem.}}
22	>
23	>	@string{jcop = {J. Comp. Phys.}}
24	>
25	>	@string{jcp = {J. Chem. Phys.}}
26	>
27	>	@string{jml = {J. Mol. Liq.}}
28	>
29	>	@string{jpc = {J. Phys. Chem.}}
30	>
31	>	@string{jpca = {J. Phys. Chem. A}}
32	>
33	>	@string{jpcb = {J. Phys. Chem. B}}
34	>
35	>	@string{mp = {Mol. Phys.}}
36	>
37	>	@string{pams = {Proc. Am. Math Soc.}}
38	>
39	>	@string{pccp = {Phys. Chem. Chem. Phys.}}
40	>
41	>	@string{pnas = {Proc. Natl. Acad. Sci. USA}}
42	>
43	>	@string{pr = {Phys. Rev.}}
44	>
45	>	@string{pra = {Phys. Rev. A}}
46	>
47	>	@string{prb = {Phys. Rev. B}}
48	>
49	>	@string{pre = {Phys. Rev. E}}
50	>
51	>	@string{prl = {Phys. Rev. Lett.}}
52	>
53	>	@string{rmp = {Rev. Mod. Phys.}}
54	>
55	>
56	>	@book{Schlick2002,
57	>	Address = {Secaucus, NJ, USA},
58	>	Author = {Tamar Schlick},
59	>	Date-Added = {2008-02-12 16:52:19 -0500},
60	>	Date-Modified = {2008-02-12 16:53:15 -0500},
61	>	Isbn = {038795404X},
62	>	Publisher = {Springer-Verlag New York, Inc.},
63	>	Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
64	>	Year = {2002}}
65	>
66	>	@misc{Chun:2000fj,
67	>	Abstract = {A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5- to 30-fold over atomistic simulations have been realized in various applications of the method. (C) 2000 John Wiley \& Sons, Inc.},
68	>	Author = {Chun, HM and Padilla, CE and Chin, DN and Watanabe, M and Karlov, VI and Alper, HE and Soosaar, K and Blair, KB and Becker, OM and Caves, LSD and Nagle, R and Haney, DN and Farmer, BL},
69	>	Date-Added = {2008-01-22 10:38:33 -0500},
70	>	Date-Modified = {2008-01-22 10:38:49 -0500},
71	>	Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
72	>	Note = {Journal of Computational Chemistry},
73	>	Pages = {159-184},
74	>	Timescited = {0},
75	>	Title = {MBO(N)D: A multibody method for long-time molecular dynamics simulations},
76	>	Volume = {21},
77	>	Year = {2000}}
78	>
79	>	@article{Fogolari:1996lr,
80	>	Abstract = {In an effort to reduce the number of degrees of freedom necessary to describe a polypeptide chain we analyze the statistical behavior of polypeptide chains when represented as C alpha chains, C alpha chains with C beta atoms attached, and C alpha chains with rotational ellipsoids as models of side chains. A statistical analysis on a restricted data set of 75 unrelated protein structures is performed. The comparison of the database distributions with those obtained by model calculation on very short polypeptide stretches allows the dissection of local versus nonlocal features of the distributions. The database distribution of the bend angles of polypeptide chains of pseudo bonded C alpha atoms spans a restricted range of values and shows a bimodal structure. On the other hand, the torsion angles of the C alpha chain may assume almost all possible values. The distribution is bimodal, but with a much broader probability distribution than for bend angles. The C alpha - C beta vectors may be taken as representative of the orientation of the lateral chain, as the direction of the bond is close to the direction of the vector joining C alpha to the ad hoc defined center of the "steric mass" of the side chain. Interestingly, both the bend angle defined by C alpha i-C alpha i+1-C beta i+1 and the torsional angle offset of the pseudo-dihedral C alpha i-C alpha i+1-C alpha i+2-C beta i+2 with respect to C alpha i-C alpha i+1-C alpha i+2-C alpha i+3 span a limited range of values. The latter results show that it is possible to give a more realistic representation of polypeptide chains without introducing additional degrees of freedom, i.e., by just adding to the C alpha chain a C beta with given side-chain properties. However, a more realistic description of side chains may be attained by modeling side chains as rotational ellipsoids that have roughly the same orientation and steric hindrance. To this end, we define the steric mass of an atom as proportional to its van der Waals volume and we calculate the side-chain inertia ellipsoid assuming that the steric mass of each atom is uniformly distributed within its van der Waals volume. Finally, we define the rotational ellipsoid representing the side chain as the uniform density ellipsoid possessing the same rotationally averaged inertia tensor of the side chain. The statistics of ellipsoid parameters support the possibility of representing a side chain via an ellipsoid, independently of the local conformation. To make this description useful for molecular modeling we describe ellipsoid-ellipsoid interactions via a Lennard-Jones potential that preserves the repulsive core of the interacting ellipsoids and takes into account their mutual orientation. Tests are performed for two different forms of the interaction potential on a set of high-resolution protein structures. Results are encouraging, in view of the drastic simplifications that were introduced.},
81	>	Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.},
82	>	Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
83	>	Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
84	>	Da = {19960924},
85	>	Date-Added = {2008-01-22 10:19:04 -0500},
86	>	Date-Modified = {2008-01-22 10:19:09 -0500},
87	>	Dcom = {19960924},
88	>	Edat = {1996/03/01},
89	>	Issn = {0006-3495 (Print)},
90	>	Jid = {0370626},
91	>	Journal = {Biophys J},
92	>	Jt = {Biophysical journal},
93	>	Language = {eng},
94	>	Lr = {20071115},
95	>	Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; *Models, Molecular; Molecular Structure; Peptides/*chemistry; *Protein Conformation; Software; Thermodynamics},
96	>	Mhda = {1996/03/01 00:01},
97	>	Number = {3},
98	>	Own = {NLM},
99	>	Pages = {1183--1197},
100	>	Pl = {UNITED STATES},
101	>	Pmid = {8785277},
102	>	Pst = {ppublish},
103	>	Pt = {Journal Article},
104	>	Pubm = {Print},
105	>	Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)},
106	>	Sb = {IM},
107	>	So = {Biophys J. 1996 Mar;70(3):1183-97. },
108	>	Stat = {MEDLINE},
109	>	Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.},
110	>	Volume = {70},
111	>	Year = {1996}}
112	>
113	>	@inbook{Ramachandran1996,
114	>	Address = {Providence, Rhode Island},
115	>	Author = {GOMATHI RAMACHANDRAN AND TAMAR SCHLICK},
116	>	Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
117	>	Date-Added = {2008-01-22 10:03:42 -0500},
118	>	Date-Modified = {2008-01-22 10:06:57 -0500},
119	>	Editor = {P. M. Pardalos and D. Shalloway and G. Xue},
120	>	Pages = {215-231},
121	>	Publisher = {American Mathematical Society},
122	>	Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
123	>	Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
124	>	Volume = {23},
125	>	Year = {1996}}
126	>
127	>	@article{FIXMAN:1986lr,
128	>	Author = {FIXMAN, M},
129	>	Date-Added = {2008-01-22 09:59:29 -0500},
130	>	Date-Modified = {2008-01-22 09:59:35 -0500},
131	>	Journal = {Macromolecules},
132	>	Pages = {1204-1207},
133	>	Timescited = {0},
134	>	Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION},
135	>	Volume = {19},
136	>	Year = {1986}}
137	>
138	>	@article{Berendsen87,
139	>	Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
140	>	Date-Added = {2008-01-22 09:53:15 -0500},
141	>	Date-Modified = {2008-01-22 09:53:15 -0500},
142	>	Journal = jpc,
143	>	Pages = {6269-6271},
144	>	Title = {The Missing Term in Effective Pair Potentials},
145	>	Volume = 91,
146	>	Year = 1987}
147	>
148	>	@incollection{Berendsen81,
149	>	Address = {Dordrecht},
150	>	Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
151	>	Booktitle = {Intermolecular Forces},
152	>	Date-Added = {2008-01-22 09:52:49 -0500},
153	>	Date-Modified = {2008-01-22 09:52:49 -0500},
154	>	Editor = {B. Pullman},
155	>	Pages = {331-342},
156	>	Publisher = {Reidel},
157	>	Title = {Simple Point Charge Water},
158	>	Year = 1981}
159	>
160	>	@article{Stillinger74,
161	>	Author = {F.~H. Stillinger and A. Rahman},
162	>	Date-Added = {2008-01-22 09:51:43 -0500},
163	>	Date-Modified = {2008-01-22 09:51:43 -0500},
164	>	Journal = jcp,
165	>	Number = 4,
166	>	Pages = {1545-1557},
167	>	Title = {Improved simulation of liquid water by molecular dynamics},
168	>	Volume = 60,
169	>	Year = 1974}
170	>
171	>	@article{Torre:1983lr,
172	>	Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
173	>	Date-Added = {2008-01-11 16:16:43 -0500},
174	>	Date-Modified = {2008-01-11 16:16:43 -0500},
175	>	Journal = {The Journal of Chemical Physics},
176	>	Journal1 = {The Journal of Chemical Physics},
177	>	Journal2 = {J. Chem. Phys.},
178	>	Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
179	>	Number = 5,
180	>	Pages = {2454--2460},
181	>	Publisher = {AIP},
182	>	Title = {Effects from bead size and hydrodynamic interactions on the translational and rotational coefficients of macromolecular bead models},
183	>	Ty = {JOUR},
184	>	Url = {http://link.aip.org/link/?JCP/79/2454/1},
185	>	Volume = 79,
186	>	Year = 1983,
187	>	Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}}
188	>
189	>	@article{PhysRev.119.53,
190	>	Author = {Favro, L. Dale},
191	>	Date-Added = {2008-01-09 16:57:02 -0500},
192	>	Date-Modified = {2008-01-09 16:57:02 -0500},
193	>	Doi = {10.1103/PhysRev.119.53},
194	>	Journal = {Phys. Rev.},
195	>	Month = {Jul},
196	>	Number = 1,
197	>	Numpages = 9,
198	>	Pages = {53--62},
199	>	Publisher = {American Physical Society},
200	>	Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body},
201	>	Volume = 119,
202	>	Year = 1960,
203	>	Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}}
204	>
205	>	@article{hess:209,
206	>	Author = {Berk Hess},
207	>	Date-Added = {2008-01-08 16:41:06 -0500},
208	>	Date-Modified = {2008-01-08 16:41:06 -0500},
209	>	Doi = {10.1063/1.1421362},
210	>	Journal = {The Journal of Chemical Physics},
211	>	Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
212	>	Number = 1,
213	>	Pages = {209-217},
214	>	Publisher = {AIP},
215	>	Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
216	>	Url = {http://link.aip.org/link/?JCP/116/209/1},
217	>	Volume = 116,
218	>	Year = 2002,
219	>	Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
220	>	Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}}
221	>
222	>	@article{Garcia-de-la-Torre:1997qy,
223	>	Abstract = {Single-valued hydrodynamic coefficients of a rigid particle can be calculated from existing theories and computer programs for either bead models or ellipsoids. Starting from these coefficients, we review the procedures for the calculation of complex solution properties depending on rotational diffusion, such as the decays of electric birefringence and fluorescence anisotropy. We also describe the calculation of the scattering from factor of bead models. The hydrodynamic coefficients and solution properties can be combined to give universal, shape-dependent functions, which were initially intended for ellipsoidal particles, and are extended here for the most general case. We have implemented all three developments in a new computer program. SOLPRO, for calculation of SOLution PROperties, which can be linked to existing software for bead models or ellipsoids.},
224	>	Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es},
225	>	Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE},
226	>	Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E},
227	>	Da = 19970709,
228	>	Date-Added = {2008-01-08 15:45:31 -0500},
229	>	Date-Modified = {2008-01-08 15:46:57 -0500},
230	>	Dcom = 19970709,
231	>	Edat = {1997/01/01},
232	>	Issn = {0175-7571 (Print)},
233	>	Jid = 8409413,
234	>	Journal = {Eur Biophys J},
235	>	Jt = {European biophysics journal : EBJ},
236	>	Keywords = {Birefringence; Fluorescence Polarization; Humans; Immunoglobulin G/chemistry; Models, Structural; *Protein Conformation; Proteins/*chemistry; Scattering, Radiation; *Software; Ultracentrifugation/methods},
237	>	Language = {eng},
238	>	Lr = 20061115,
239	>	Mhda = {1997/01/01 00:01},
240	>	Number = {5-6},
241	>	Own = {NLM},
242	>	Pages = {361--372},
243	>	Pl = {GERMANY},
244	>	Pmid = 9213556,
245	>	Pst = {ppublish},
246	>	Pt = {Journal Article; Research Support, Non-U.S. Gov't},
247	>	Pubm = {Print},
248	>	Rn = {0 (Immunoglobulin G); 0 (Proteins)},
249	>	Sb = {IM},
250	>	So = {Eur Biophys J. 1997;25(5-6):361-72.},
251	>	Stat = {MEDLINE},
252	>	Title = {SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.},
253	>	Volume = 25,
254	>	Year = 1997}
255	>
256	>	@article{Ravichandran:1999fk,
257	>	Abstract = {Detailed molecular dynamics simulations of the rotational and the translational motions of Gay-Berne ellipsoids in a sea of Lennard-Jones spheres have been carried out. It is found that while the translational motion of an ellipsoid is isotropic at low density, it becomes increasingly anisotropic with density until the ratio of the parallel to the perpendicular diffusion coefficients becomes nearly equal to the value of the aspect ratio at high density. The latter is in agreement with the prediction of Navier-Stokes hydrodynamics with slip boundary condition. The product of the translational diffusion coefficient and the rotational correlation time also attains a hydrodynamic-like density independent behavior only at high density. The reorientational correlation function becomes nonexponential at high density and low temperature where it also develops a slow decay. The perpendicular component of the velocity time correlation function exhibits a clear double minimum, only at high density, which becomes more pronounced as the aspect ratio is increased. (C) 1999 American Institute of Physics. [S0021-9606(99)51440-2].},
258	>	Author = {Ravichandran, S and Bagchi, B},
259	>	Date-Added = {2008-01-08 15:24:48 -0500},
260	>	Date-Modified = {2008-01-08 15:25:41 -0500},
261	>	Journal = {Journal of Chemical Physics},
262	>	Pages = {7505-7511},
263	>	Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
264	>	Volume = 111,
265	>	Year = 1999}
266	>
267	>	@article{TANG:1993lr,
268	>	Abstract = {Translational friction coefficients of hard prolate ellipsoids (having aspect ratios of 1-10) have been calculated by solving the linearized Navier-Stokes equations of hydrodynamics, using the method of Faxen's theorem. When the stick boundary condition was used, the present results reproduce the famous work of Lamb. The new information derived from this study arises from the analysis of the friction under the influence of the slip hydrodynamic boundary condition. It was found that the slip friction perpendicular to the long axis of the prolate ellipsoid increases monotonically with aspect ratio, whereas the parallel component of the friction decreases monotonically to an apparent limiting value. The ratio f(perpendicular to)/f(parallel to) of friction coefficients perpendicular and parallel to the long axis of the particle, calculated using slip hydrodynamics, scales roughly as the aspect ratio of the ellipsoid, in accord with the findings from an Enskog (uncorrelated binary collision) kinetic theory of hard ellipsoids and from the estimate derived from molecular dynamics. In contrast, f(perpendicular to)/f(parallel to) derived by means of stick hydrodynamics shows a weak dependence on the aspect ratio and disagrees with kinetic theory and molecular dynamics findings.},
269	>	Author = {TANG, SA and EVANS, GT},
270	>	Date-Added = {2008-01-08 15:23:42 -0500},
271	>	Date-Modified = {2008-01-08 15:24:09 -0500},
272	>	Journal = {Molecular Physics},
273	>	Pages = {1443-1457},
274	>	Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
275	>	Volume = 80,
276	>	Year = 1993}
277	>
278	>	@article{Schmidt:2003kx,
279	>	Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a spherical solute in a dense fluid of spherical solvent particles. The size and mass of the solute particle are related in such a way that we can naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that as long as the solute radius is interpreted as an effective hydrodynamic radius, the Stokes-Einstein law with slip boundary conditions is satisfied as the Brownian limit is approached (specifically, when the solute is roughly 100 times more massive than the solvent particles). In contrast, the Stokes-Einstein law is not satisfied for a tagged particle of the neat solvent. We also find that in the Brownian limit the amplitude of the long-time tail of the solute's velocity autocorrelation function is in good agreement with theoretical hydrodynamic predictions. When the solvent density is substantially lower than the triple density, the Stokes-Einstein law is no longer satisfied, and the amplitude of the long-time tail is not in good agreement with theoretical predictions, signaling the breakdown of hydrodynamics. (C) 2003 American Institute of Physics.},
280	>	Author = {Schmidt, JR and Skinner, JL},
281	>	Date-Added = {2008-01-08 15:12:53 -0500},
282	>	Date-Modified = {2008-01-08 15:13:21 -0500},
283	>	Doi = {DOI 10.1063/1.1610442},
284	>	Journal = {Journal of Chemical Physics},
285	>	Pages = {8062-8068},
286	>	Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
287	>	Volume = 119,
288	>	Year = 2003,
289	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}
290	>
291	>	@article{Schmidt:2004fj,
292	>	Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a variety of solutes in a dense fluid of spherical solvent particles. We explore the effects of surface roughness of the solute on the resulting hydrodynamic boundary condition as we naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that when the solute and solvent interact through a purely repulsive isotropic potential, in the Brownian limit the Stokes-Einstein law is satisfied with slip boundary conditions. However, when surface roughness is introduced through an anisotropic solute-solvent interaction potential, we find that the Stokes-Einstein law is satisfied with stick boundary conditions. In addition, when the attractive strength of a short-range isotropic solute-solvent potential is increased, the solute becomes dressed with solvent particles, making it effectively rough, and so stick boundary conditions are again recovered.},
293	>	Author = {Schmidt, JR and Skinner, JL},
294	>	Date-Added = {2008-01-08 15:12:53 -0500},
295	>	Date-Modified = {2008-01-08 15:13:20 -0500},
296	>	Doi = {DOI 10.1021/jp037185r},
297	>	Journal = {Journal of Physical Chemistry B},
298	>	Pages = {6767-6771},
299	>	Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
300	>	Volume = 108,
301	>	Year = 2004,
302	>	Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}}
303	>
304	>	@article{Klein01,
305	>	Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
306	>	Date-Added = {2008-01-08 14:58:56 -0500},
307	>	Date-Modified = {2008-01-08 14:58:56 -0500},
308	>	Journal = {J. Phys. Chem. B},
309	>	Pages = {4464-4470},
310	>	Title = {A Coarse Grain Model for Phospholipid Simulations},
311	>	Volume = 105,
312	>	Year = 2001}
313	>
314	>	@article{Berardi98,
315	>	Author = {R. Berardi and C. Fava and C. Zannoni},
316	>	Date-Added = {2008-01-08 14:58:56 -0500},
317	>	Date-Modified = {2008-01-08 14:58:56 -0500},
318	>	Journal = cpl,
319	>	Pages = {8-14},
320	>	Title = {A Gay-Berne potential for dissimilar biaxial particles},
321	>	Volume = 297,
322	>	Year = 1998}
323	>
324	>	@article{Hura00,
325	>	Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
326	>	Date-Added = {2008-01-08 14:58:56 -0500},
327	>	Date-Modified = {2008-01-08 14:58:56 -0500},
328	>	Journal = {J. Chem. Phys.},
329	>	Pages = {9140-9148},
330	>	Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
331	>	Volume = 113,
332	>	Year = 2000}
333	>
334	>	@article{Peker93,
335	>	Author = {A. Peker and W.~L. Johnson},
336	>	Date-Added = {2008-01-08 14:58:56 -0500},
337	>	Date-Modified = {2008-01-08 14:58:56 -0500},
338	>	Journal = {Appl. Phys. Lett.},
339	>	Pages = {2342-2344},
340	>	Title = {A highly processable metallic-glass - $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
341	>	Volume = 63,
342	>	Year = 1993}
343	>
344	>	@article{Raphael2000,
345	>	Author = {Robert M. Raphael and Aleksander S. Popel and William E. Brownell},
346	>	Date-Added = {2008-01-08 14:58:56 -0500},
347	>	Date-Modified = {2008-01-08 14:58:56 -0500},
348	>	Journal = bj,
349	>	Pages = {2844-2862},
350	>	Title = {A Membrane Bending Model of Outer Hair Cell Electromotility},
351	>	Volume = 78,
352	>	Year = 2000}
353	>
354	>	@article{Heimburg00,
355	>	Author = {Thomas Heimburg},
356	>	Date-Added = {2008-01-08 14:58:56 -0500},
357	>	Date-Modified = {2008-01-08 14:58:56 -0500},
358	>	Journal = bj,
359	>	Pages = {1154-1165},
360	>	Title = {A Model for the Lipid Pretransition: Coupling of Ripple Formation with the Chain-Melting Transition},
361	>	Volume = 78,
362	>	Year = 2000}
363	>
364	>	@article{Tieleman98,
365	>	Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
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589	>	Journal = pccp,
590	>	Pages = {2114-2121},
591	>	Title = {An NMR line shape and relaxation analysis of heavy water powder spectra of the $L_\alpha$, $L_{\beta'}$ and $P_{\beta'}$ phases in the DPPC/water system},
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609	>	Date-Modified = {2008-01-08 14:58:57 -0500},
610	>	Edition = {6th},
611	>	Publisher = {Saunders College Publishing},
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617	>	Date-Added = {2008-01-08 14:58:56 -0500},
618	>	Date-Modified = {2008-01-08 14:58:57 -0500},
619	>	Journal = pre,
620	>	Number = 030902,
621	>	Pages = {1-4},
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650	>	Date-Added = {2008-01-08 14:58:56 -0500},
651	>	Date-Modified = {2008-01-08 14:58:57 -0500},
652	>	Editor = {J.~P. Hansen and D. Levesque and J. Zinn-Justin},
653	>	Pages = {287-503},
654	>	Publisher = {North-Holland},
655	>	Title = {Aspects of Structural Glass Transitions},
656	>	Volume = {I},
657	>	Year = 1989}
658	>
659	>	@article{Lewis91,
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662	>	Date-Modified = {2008-01-08 14:58:57 -0500},
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668	>
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672	>	Date-Modified = {2008-01-08 14:58:57 -0500},
673	>	Journal = prb,
674	>	Pages = 241406,
675	>	Title = {Bending strain-driven modification of surface resconstructions: Au(111)},
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682	>	Date-Modified = {2008-01-08 14:58:57 -0500},
683	>	Journal = {Physics Today},
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687	>	Year = 1996}
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692	>	Date-Modified = {2008-01-08 14:58:57 -0500},
693	>	Journal = {J. Phys. Chem.},
694	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
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696	>	Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
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754	>	Journal = {Annals of Mathematics},
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762	>	Date-Added = {2008-01-08 14:58:56 -0500},
763	>	Date-Modified = {2008-01-08 14:58:57 -0500},
764	>	Journal = pre,
765	>	Number = 5,
766	>	Pages = {5668-5677},
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770	>
771	>	@article{NorbertKucerka06012006,
772	>	Abstract = {X-ray data are presented for the benchmark dipalmitoylphosphatidylcholine lipid bilayer in the most biologically relevant state in which the bilayers are fully hydrated and in the fluid (liquid-crystalline) phase. Form factors F(qz) are obtained from a combination of two sample preparations, oriented stacks of bilayers for qz extending to 0.85 A-1 and unilamellar vesicles for smaller qz. Modeling obtains the electron density profile and values for the area per molecule, for the locations of the component groups, and for the different types of thicknesses of the bilayer, such as the hydrocarbon thickness and the steric thickness.
773	>	},
774	>	Author = {Kucerka, Norbert and Tristram-Nagle, Stephanie and Nagle, John F.},
775	>	Date-Added = {2008-01-08 14:58:56 -0500},
776	>	Date-Modified = {2008-01-08 14:58:57 -0500},
777	>	Doi = {10.1529/biophysj.106.086017},
778	>	Eprint = {http://www.biophysj.org/cgi/reprint/90/11/L83.pdf},
779	>	Journal = {Biophys. J.},
780	>	Number = 11,
781	>	Pages = {L83-85},
782	>	Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}},
783	>	Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
784	>	Volume = 90,
785	>	Year = 2006,
786	>	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
787	>	Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017}}
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792	>	Date-Modified = {2008-01-08 14:58:57 -0500},
793	>	Journal = {Langmuir},
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813	>	Journal = jcp,
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1280	>	Year = 2002,
1281	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1282	>
1283	>	@article{Barenco95,
1284	>	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},
1285	>	Date-Added = {2008-01-08 14:58:56 -0500},
1286	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1287	>	Journal = {Phys. Rev. A},
1288	>	Pages = {3457-3467},
1289	>	Title = {elementary gates for quantum computation},
1290	>	Volume = 52,
1291	>	Year = 1995}
1292	>
1293	>	@article{Perram96,
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1295	>	Date-Added = {2008-01-08 14:58:56 -0500},
1296	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1297	>	Journal = pre,
1298	>	Pages = {6565-6572},
1299	>	Title = {Ellipsoid contact potential: Theory and relation to overlap potentials},
1300	>	Volume = 54,
1301	>	Year = 1996}
1302	>
1303	>	@article{Daw84,
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1305	>	Date-Added = {2008-01-08 14:58:56 -0500},
1306	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1307	>	Journal = prb,
1308	>	Number = 12,
1309	>	Pages = {6443-6453},
1310	>	Title = {Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals},
1311	>	Volume = 29,
1312	>	Year = 1984}
1313	>
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1316	>	Date-Added = {2008-01-08 14:58:56 -0500},
1317	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1318	>	Journal = prb,
1319	>	Number = 12,
1320	>	Pages = 7983,
1321	>	Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1322	>	Volume = 33,
1323	>	Year = 1986}
1324	>
1325	>	@article{Zahn02,
1326	>	Author = {D. Zahn and B. Schilling and S.~M. Kast},
1327	>	Date-Added = {2008-01-08 14:58:56 -0500},
1328	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1329	>	Journal = {J. Phys. Chem. B},
1330	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
1331	>	Number = 41,
1332	>	Pages = {10725-10732},
1333	>	Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
1334	>	Volume = 106,
1335	>	Year = 2002}
1336	>
1337	>	@article{Metropolis53,
1338	>	Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
1339	>	Date-Added = {2008-01-08 14:58:56 -0500},
1340	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1341	>	Journal = {J. Chem. Phys.},
1342	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Metropolis_MCCalculations_53.pdf},
1343	>	Pages = {1087-1092},
1344	>	Title = {Equation of State Calculations by Fast Computing Machines},
1345	>	Volume = 21,
1346	>	Year = 1953}
1347	>
1348	>	@article{Parry76,
1349	>	Author = {D.~E. Parry},
1350	>	Date-Added = {2008-01-08 14:58:56 -0500},
1351	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1352	>	Journal = {Surf. Sci.},
1353	>	Pages = 195,
1354	>	Title = {Errata: The electrostatic potential in the surface region of an ionic crystal},
1355	>	Volume = 54,
1356	>	Year = 1976}
1357	>
1358	>	@article{Steane96,
1359	>	Author = {A.~M. Steane},
1360	>	Date-Added = {2008-01-08 14:58:56 -0500},
1361	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1362	>	Journal = prl,
1363	>	Pages = {793-797},
1364	>	Title = {Error correcting codes in quantum theory},
1365	>	Volume = 77,
1366	>	Year = 1996}
1367	>
1368	>	@article{Todorova2004,
1369	>	Author = {L. Todorova and T. Angelov and Y. Marinov and A.~G. Petrov},
1370	>	Date-Added = {2008-01-08 14:58:56 -0500},
1371	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1372	>	Journal = {J. Mat. Sci. Mat. Elect.},
1373	>	Pages = {817-818},
1374	>	Title = {Evidence of flexoelectricity in polymer-dispersed liquid crystals},
1375	>	Volume = 14,
1376	>	Year = 2004}
1377	>
1378	>	@article{Hunenberger99a,
1379	>	Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
1380	>	Date-Added = {2008-01-08 14:58:56 -0500},
1381	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1382	>	Journal = {J. Chem. Phys.},
1383	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
1384	>	Number = 4,
1385	>	Pages = {1856-1872},
1386	>	Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study},
1387	>	Volume = 110,
1388	>	Year = 1999}
1389	>
1390	>	@article{Rhee89,
1391	>	Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
1392	>	Date-Added = {2008-01-08 14:58:56 -0500},
1393	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1394	>	Journal = {Phys. Rev. B},
1395	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
1396	>	Number = 1,
1397	>	Pages = {36-42},
1398	>	Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions},
1399	>	Volume = 40,
1400	>	Year = 1989}
1401	>
1402	>	@article{Yeh99,
1403	>	Author = {I.-C. Yeh and M.~L. Berkowitz},
1404	>	Date-Added = {2008-01-08 14:58:56 -0500},
1405	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1406	>	Journal = {J. Chem. Phys.},
1407	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
1408	>	Number = 7,
1409	>	Pages = {3155-3162},
1410	>	Title = {Ewald summation for systems with slab geometry},
1411	>	Volume = 111,
1412	>	Year = 1999}
1413	>
1414	>	@article{Brodka04,
1415	>	Author = {A. Br\'{o}dka},
1416	>	Date-Added = {2008-01-08 14:58:56 -0500},
1417	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1418	>	Doi = {10.1016/j.cplett.2004.10.086},
1419	>	Journal = {Chem. Phys. Lett.},
1420	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf},
1421	>	Pages = {62-67},
1422	>	Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
1423	>	Volume = 400,
1424	>	Year = 2004,
1425	>	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086}}
1426	>
1427	>	@article{Chuang98,
1428	>	Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
1429	>	Date-Added = {2008-01-08 14:58:56 -0500},
1430	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1431	>	Journal = prl,
1432	>	Pages = {3408-3411},
1433	>	Title = {Experimental Implementation of Fast Quantum Searching},
1434	>	Volume = 80,
1435	>	Year = 1998}
1436	>
1437	>	@article{Banerjee02,
1438	>	Author = {Srilekha Banerjee},
1439	>	Date-Added = {2008-01-08 14:58:56 -0500},
1440	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1441	>	Journal = {Physica A},
1442	>	Pages = {89-100},
1443	>	Title = {Exploring the Ripple Phase of Biomembranes},
1444	>	Volume = 308,
1445	>	Year = 2002}
1446	>
1447	>	@article{Bannerjee02,
1448	>	Author = {S. Bannerjee},
1449	>	Date-Added = {2008-01-08 14:58:56 -0500},
1450	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1451	>	Journal = {Physica A},
1452	>	Pages = {89-100},
1453	>	Title = {Exploring the ripple phase of biomembranes},
1454	>	Volume = 308,
1455	>	Year = 2002}
1456	>
1457	>	@article{Cleaver96,
1458	>	Author = {Douglas J. Cleaver and Christopher M. Care and Michael P. Allen and Maureen P. Neal},
1459	>	Date-Added = {2008-01-08 14:58:56 -0500},
1460	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1461	>	Journal = pre,
1462	>	Number = 1,
1463	>	Pages = {559-567},
1464	>	Title = {Extension and generalization of the Gay-Berne potential},
1465	>	Volume = 54,
1466	>	Year = 1996}
1467	>
1468	>	@article{Plimpton95,
1469	>	Author = {S. Plimpton},
1470	>	Date-Added = {2008-01-08 14:58:56 -0500},
1471	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1472	>	Journal = {J. Comp. Phys.},
1473	>	Pages = {1-19},
1474	>	Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
1475	>	Volume = 117,
1476	>	Year = 1995}
1477	>
1478	>	@article{Ayton97,
1479	>	Author = {G. Ayton and M. J. P. Gingras and G. N. Patey},
1480	>	Date-Added = {2008-01-08 14:58:56 -0500},
1481	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1482	>	Journal = pre,
1483	>	Number = 1,
1484	>	Pages = {562-570},
1485	>	Title = {Ferroelectric and dipolar glass phases of noncrystalline systems},
1486	>	Volume = 56,
1487	>	Year = 1997}
1488	>
1489	>	@article{Benninger:2005qy,
1490	>	Abstract = {The plasma membrane of cells is an ordered environment, giving rise to anisotropic orientation and restricted motion of molecules and proteins residing in the membrane. At the same time as being an organized matrix of defined structure, the cell membrane is heterogeneous and dynamic. Here we present a method where we use fluorescence imaging of linear dichroism to measure the orientation of molecules relative to the cell membrane. By detecting linear dichroism as well as fluorescence anisotropy, the orientation parameters are separated from dynamic properties such as rotational diffusion and homo energy transfer (energy migration). The sensitivity of the technique is enhanced by using two-photon excitation for higher photo-selection compared to single photon excitation. We show here that we can accurately image lipid organization in whole cell membranes and in delicate structures such as membrane nanotubes connecting two cells. The speed of our wide-field imaging system makes it possible to image changes in orientation and anisotropy occurring on a subsecond timescale. This is demonstrated by time-lapse studies showing that cholesterol depletion rapidly disrupts the orientation of a fluorophore located within the hydrophobic region of the cell membrane but not of a surface bound probe. This is consistent with cholesterol having an important role in stabilizing and ordering the lipid tails within the plasma membrane. },
1491	>	Annote = {10.1529/biophysj.104.050096},
1492	>	Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.},
1493	>	Date-Added = {2008-01-08 14:58:56 -0500},
1494	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1495	>	Journal = {Biophysical Journal},
1496	>	Journal1 = {Biophys. J.},
1497	>	Number = 1,
1498	>	Pages = {609--622},
1499	>	Title = {Fluorescence Imaging of Two-Photon Linear Dichroism: Cholesterol Depletion Disrupts Molecular Orientation in Cell Membranes},
1500	>	Ty = {JOUR},
1501	>	Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
1502	>	Volume = 88,
1503	>	Year = 2005,
1504	>	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609}}
1505	>
1506	>	@inbook{Blumen86,
1507	>	Address = {Amsterdam},
1508	>	Author = {A. Blumen and J. Klafter and G. Zumofen},
1509	>	Chapter = {Reactions in Disordered Media Modelled by Fractals},
1510	>	Date-Added = {2008-01-08 14:58:56 -0500},
1511	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1512	>	Editor = {Luciano Peitronero and E. Tosatti},
1513	>	Pages = 399,
1514	>	Publisher = {North-Holland},
1515	>	Series = {International Symposium on Fractals in Physics},
1516	>	Title = {Fractals in Physics},
1517	>	Year = 1986}
1518	>
1519	>	@article{Marland1979,
1520	>	Author = {L.~G. Marland and D.~D. Betts},
1521	>	Date-Added = {2008-01-08 14:58:56 -0500},
1522	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1523	>	Journal = prl,
1524	>	Number = 21,
1525	>	Pages = {1618-1621},
1526	>	Title = {Frustration Effect in Quantum Spin Systems},
1527	>	Volume = 43,
1528	>	Year = 1979}
1529	>
1530	>	@article{Berne72,
1531	>	Author = {B.~J. Berne and P. Pechukas},
1532	>	Date-Added = {2008-01-08 14:58:56 -0500},
1533	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1534	>	Journal = jcp,
1535	>	Pages = {4213-4216},
1536	>	Title = {Gaussian Model Potentials for Molecular Interactions},
1537	>	Volume = 56,
1538	>	Year = 1972}
1539	>
1540	>	@article{Golubkov06,
1541	>	Author = {Pavel A. Golubkov and Rengyu Ren},
1542	>	Date-Added = {2008-01-08 14:58:56 -0500},
1543	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1544	>	Journal = jcp,
1545	>	Pages = 064103,
1546	>	Title = {Generalized coarse-grained model based on point multipole and Gay-Berne potentials},
1547	>	Volume = 125,
1548	>	Year = 2006}
1549	>
1550	>	@article{Harden2006,
1551	>	Author = {J. Harden and B. Mbanga and N. Eber and K. Fodor-Csorba and S. Sprunt and J. T. Gleeson and A. Jakli},
1552	>	Date-Added = {2008-01-08 14:58:56 -0500},
1553	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1554	>	Eid = 157802,
1555	>	Journal = {Physical Review Letters},
1556	>	Number = 15,
1557	>	Numpages = 4,
1558	>	Pages = 157802,
1559	>	Publisher = {APS},
1560	>	Title = {Giant Flexoelectricity of Bent-Core Nematic Liquid Crystals},
1561	>	Volume = 97,
1562	>	Year = 2006}
1563	>
1564	>	@article{Dzugutov92,
1565	>	Author = {M. Dzugutov},
1566	>	Date-Added = {2008-01-08 14:58:56 -0500},
1567	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1568	>	Journal = pra,
1569	>	Pages = {R2984-R2987},
1570	>	Title = {Glass formation in a simple monatomic liquid with icosahedral inherent local order},
1571	>	Volume = 46,
1572	>	Year = 1992}
1573	>
1574	>	@article{Calderbank96,
1575	>	Author = {A.~R. Calderbank and P.~W. Shor},
1576	>	Date-Added = {2008-01-08 14:58:56 -0500},
1577	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1578	>	Journal = {Phys. Rev. A},
1579	>	Pages = {1098-1105},
1580	>	Title = {Good quantum error-correcting codes exist},
1581	>	Volume = 54,
1582	>	Year = 1996}
1583	>
1584	>	@article{Carraro1993,
1585	>	Author = {Carlo Carraro and David R. Nelson},
1586	>	Date-Added = {2008-01-08 14:58:56 -0500},
1587	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1588	>	Journal = pre,
1589	>	Number = 4,
1590	>	Pages = {3082-3090},
1591	>	Title = {Grain-boundary buckling and spin-glass models of disorder in membranes},
1592	>	Volume = 48,
1593	>	Year = 1993}
1594	>
1595	>	@article{Stillinger82,
1596	>	Author = {F.~H. Stillinger and T.~A. Weber},
1597	>	Date-Added = {2008-01-08 14:58:56 -0500},
1598	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1599	>	Journal = pra,
1600	>	Number = 2,
1601	>	Pages = {978-989},
1602	>	Title = {Hidden structure in liquids},
1603	>	Volume = 25,
1604	>	Year = 1982}
1605	>
1606	>	@article{Little96,
1607	>	Author = {H.~J. Little},
1608	>	Date-Added = {2008-01-08 14:58:56 -0500},
1609	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1610	>	Journal = {Pharmacology \& Therapeutics},
1611	>	Pages = {37-58},
1612	>	Title = {How has molecular pharmacology contributed to our understanding of the mechanism(s) of general anesthesia?},
1613	>	Volume = 69,
1614	>	Year = 1996}
1615	>
1616	>	@article{Roberts94,
1617	>	Author = {J.~E. Roberts and J. Schnitker},
1618	>	Date-Added = {2008-01-08 14:58:56 -0500},
1619	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1620	>	Journal = {J. Chem. Phys.},
1621	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
1622	>	Number = 6,
1623	>	Pages = {5024-5031},
1624	>	Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
1625	>	Volume = 101,
1626	>	Year = 1994}
1627	>
1628	>	@article{Stillinger85,
1629	>	Author = {F.~H. Stillinger and T.~A. Weber},
1630	>	Date-Added = {2008-01-08 14:58:56 -0500},
1631	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1632	>	Journal = jcp,
1633	>	Number = 9,
1634	>	Pages = {4767-4775},
1635	>	Title = {Inherent structure theory of liquids in the hard-sphere limit},
1636	>	Volume = 83,
1637	>	Year = 1985}
1638	>
1639	>	@article{Kast03,
1640	>	Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
1641	>	Date-Added = {2008-01-08 14:58:56 -0500},
1642	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1643	>	Journal = {Chem. Phys. Lett.},
1644	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
1645	>	Pages = {398-404},
1646	>	Title = {Integral equation theory for correcting truncation errors in molecular simulations},
1647	>	Volume = 367,
1648	>	Year = 2003}
1649	>
1650	>	@article{Ayton01,
1651	>	Author = {Gary Ayton and Scott G. Bardenhagen and Patrick McMurty and Deborah Sulsky and Gregory A. Voth},
1652	>	Date-Added = {2008-01-08 14:58:56 -0500},
1653	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1654	>	Journal = jcp,
1655	>	Number = 15,
1656	>	Pages = {6913-6924},
1657	>	Title = {Interfacing continuum and molecular dynamics: An application to lipid bilayers},
1658	>	Volume = 114,
1659	>	Year = 2001}
1660	>
1661	>	@inbook{Voter95b,
1662	>	Author = {A.~F. Voter},
1663	>	Chapter = 4,
1664	>	Date-Added = {2008-01-08 14:58:56 -0500},
1665	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1666	>	Editor = {J.~H. Westbrook and R.~L. Fleischer},
1667	>	Pages = 77,
1668	>	Publisher = {John Wiley and Sons Ltd},
1669	>	Title = {Intermetallic Compounds: Principles and Practice},
1670	>	Volume = 1,
1671	>	Year = 1995}
1672	>
1673	>	@article{Truhlar78,
1674	>	Author = {Donald G. Truhlar},
1675	>	Date-Added = {2008-01-08 14:58:56 -0500},
1676	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1677	>	Journal = {J. Chem. Ed.},
1678	>	Pages = 309,
1679	>	Title = {Interpretation of the Activation Energy},
1680	>	Volume = 55,
1681	>	Year = 1978}
1682	>
1683	>	@book{Chandler87,
1684	>	Author = {David Chandler},
1685	>	Date-Added = {2008-01-08 14:58:56 -0500},
1686	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1687	>	Publisher = {Oxford University Press},
1688	>	Title = {Introduction to Modern Statistical Mechanics},
1689	>	Year = 1987}
1690	>
1691	>	@article{Keshavamurthy94,
1692	>	Author = {S. Keshavamurthy and W.~H. Miller},
1693	>	Date-Added = {2008-01-08 14:58:56 -0500},
1694	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1695	>	Journal = cpl,
1696	>	Pages = 189,
1697	>	Title = {ivr},
1698	>	Volume = 218,
1699	>	Year = 1994}
1700	>
1701	>	@article{Luty95,
1702	>	Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
1703	>	Date-Added = {2008-01-08 14:58:56 -0500},
1704	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1705	>	Journal = {J. Chem. Phys.},
1706	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
1707	>	Number = 8,
1708	>	Pages = {3014-3021},
1709	>	Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
1710	>	Volume = 103,
1711	>	Year = 1995}
1712	>
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2644	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
2645	>	Number = 1752,
2646	>	Pages = {27-56},
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2665	>	Journal = jacs,
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2701	>
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2706	>	Date-Modified = {2008-01-08 14:59:02 -0500},
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2709	>	Title = {Statistical Mechanics with Applications to Physics and Chemistry},
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2711	>
2712	>	@book{Safran94,
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2716	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2717	>	Publisher = {Addison-Wesley},
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2719	>	Year = 1994}
2720	>
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2724	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2725	>	Journal = prl,
2726	>	Number = 7,
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2731	>
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2737	>	Number = 22,
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2752	>
2753	>	@article{NorbertKucerka04012005,
2754	>	Abstract = {Quantitative structures of the fully hydrated fluid phases of dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) were obtained at 30{degrees}C. Data for the relative form factors F(qz) for DMPC were obtained using a combination of four methods. 1), Volumetric data provided F(0). 2), Diffuse x-ray scattering from oriented stacks of bilayers provided relative form factors |F(qz)| for high qz, 0.22 < qz < 0.8 A-1. 3), X-ray scattering from extruded unilamellar vesicles with diameter 600 A provided |F(qz)| for low qz, 0.1 < qz < 0.3 A-1. 4), Previous measurements using a liquid crystallographic x-ray method provided |F(2{pi}h/D)| for h = 1 and 2 for a range of nearly fully hydrated D-spacings. The data from method 4 overlap and validate the new unilamellar vesicles data for DMPC, so method 4 is not required for DLPC or future studies. We used hybrid electron density models to obtain structural results from these form factors. Comparison of the model electron density profiles with that of gel phase DMPC provides areas per lipid A, 60.6 {+/-} 0.5 A2 for DMPC and 63.2 {+/-} 0.5 A2 for DLPC. Constraints on the model provided by volume measurements and component volumes obtained from simulations put the electron density profiles {rho}(z) and the corresponding form factors F(qz) on absolute scales. Various thicknesses, such as the hydrophobic thickness and the steric thickness, are obtained and compared to literature values.
2755	>	},
2756	>	Author = {Kucerka, Norbert and Liu, Yufeng and Chu, Nanjun and Petrache, Horia I. and Tristram-Nagle, Stephanie and Nagle, John F.},
2757	>	Date-Added = {2008-01-08 14:58:56 -0500},
2758	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2759	>	Doi = {10.1529/biophysj.104.056606},
2760	>	Eprint = {http://www.biophysj.org/cgi/reprint/88/4/2626.pdf},
2761	>	Journal = {Biophys. J.},
2762	>	Number = 4,
2763	>	Pages = {2626-2637},
2764	>	Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}},
2765	>	Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2766	>	Volume = 88,
2767	>	Year = 2005,
2768	>	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2769	>	Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606}}
2770	>
2771	>	@article{Lenz07,
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2773	>	Date-Added = {2008-01-08 14:58:56 -0500},
2774	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2775	>	Journal = prl,
2776	>	Number = 5,
2777	>	Pages = 058104,
2778	>	Title = {Structure of Symmetric and Asymmetric "Ripple" Phases in Lipid Bilayers},
2779	>	Volume = 98,
2780	>	Year = 2007}
2781	>
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2785	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2786	>	Journal = pnas,
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2795	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2796	>	Journal = pre,
2797	>	Number = 031710,
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2800	>	Volume = 68,
2801	>	Year = 2003}
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2811	>	Year = 1992}
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2838	>	Number = 1,
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2858	>	Journal = pre,
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2868	>	Journal = pre,
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2900	>	Number = 6,
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2910	>	Journal = {J. Phys.: Condens. Matter},
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2926	>	@article{Daw93,
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2930	>	Journal = {Mat. Sci. Rep.},
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2940	>	Journal = {Acc. Chem. Res.},
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2950	>	Journal = {Biochim. Biophys. Acta.},
2951	>	Pages = {95-109},
2952	>	Title = {The Rippled Structure in Bilayer Membranes of Phosphatidylcholine and Binary Mixture of Phosphatidylcholine and Cholesterol},
2953	>	Volume = 599,
2954	>	Year = 1980}
2955	>
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2957	>	Author = {S.~D. Bembenek and B.~B. Laird},
2958	>	Date-Added = {2008-01-08 14:58:56 -0500},
2959	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2960	>	Journal = jcp,
2961	>	Pages = 5199,
2962	>	Title = {The role of localization in glasses and supercooled liquids},
2963	>	Volume = 104,
2964	>	Year = 1996}
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2967	>	Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
2968	>	Date-Added = {2008-01-08 14:58:56 -0500},
2969	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2970	>	Journal = {J. Chem. Phys.},
2971	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
2972	>	Number = 9,
2973	>	Pages = {4576-4584},
2974	>	Title = {The role of long ranged forces in determining the structure and properties of liquid water},
2975	>	Volume = 79,
2976	>	Year = 1983}
2977	>
2978	>	@article{Brannigan04b,
2979	>	Author = {G. Brannigan and A.~C. Tamboli and F.~L.~H. Brown},
2980	>	Date-Added = {2008-01-08 14:58:56 -0500},
2981	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2982	>	Journal = jcp,
2983	>	Key = 121,
2984	>	Pages = {3259-3271},
2985	>	Title = {The role of molecular shape in bilayer elasticity and phase behavior},
2986	>	Volume = 7,
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2988	>
2989	>	@article{Buchner92,
2990	>	Author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt},
2991	>	Date-Added = {2008-01-08 14:58:56 -0500},
2992	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2993	>	Journal = jcp,
2994	>	Pages = {8522-8535},
2995	>	Title = {The short-time dynamics of molecular liquids. Instantaneous-normal-mode theory},
2996	>	Volume = 97,
2997	>	Year = 1992}
2998	>
2999	>	@article{Liu96a,
3000	>	Author = {Y. Liu and T. Ichiye},
3001	>	Date-Added = {2008-01-08 14:58:56 -0500},
3002	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3003	>	Journal = {Chem. Phys. Lett.},
3004	>	Pages = {334-340},
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3007	>	Year = 1996}
3008	>
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3010	>	Author = {C. Holm and J.-J. Weis},
3011	>	Date-Added = {2008-01-08 14:58:56 -0500},
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3021	>	Date-Added = {2008-01-08 14:58:56 -0500},
3022	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3023	>	Journal = {Physical Review},
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3055	>	Date-Modified = {2008-01-08 14:59:02 -0500},
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3064	>	Address = {London},
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3067	>	Date-Added = {2008-01-08 14:58:56 -0500},
3068	>	Date-Modified = {2008-01-08 14:59:02 -0500},
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3070	>	Publisher = {Academic Press},
3071	>	Title = {Theory of Simple Liquids},
3072	>	Year = 1986}
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3077	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3078	>	Journal = pnas,
3079	>	Pages = {6559-6561},
3080	>	Title = {Theory of the intermediate rippled phase of phospholipid bilayers},
3081	>	Volume = 81,
3082	>	Year = 1984}
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3085	>	Address = {Tucson},
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3088	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3089	>	Publisher = {Research Corp.},
3090	>	Title = {They're not Dumb. They're Different: Stalking the Second Tier},
3091	>	Year = 1990}
3092	>
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3094	>	Author = {R. Tao and J. M. Sun},
3095	>	Date-Added = {2008-01-08 14:58:56 -0500},
3096	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3097	>	Journal = prl,
3098	>	Number = 3,
3099	>	Pages = {398-401},
3100	>	Title = {Three-Dimensional Structure of Induced Electrorheological Solid},
3101	>	Volume = 67,
3102	>	Year = 1991}
3103	>
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3105	>	Author = {L. Blum and F. Vericat and D. Bratko},
3106	>	Date-Added = {2008-01-08 14:58:56 -0500},
3107	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3108	>	Journal = jcp,
3109	>	Number = 3,
3110	>	Pages = {1461-1462},
3111	>	Title = {Towards an analytical model of water: The octupolar model},
3112	>	Volume = 102,
3113	>	Year = 1995}
3114	>
3115	>	@article{Martin98,
3116	>	Author = {M. Martin and J.~I. Siepmann},
3117	>	Date-Added = {2008-01-08 14:58:56 -0500},
3118	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3119	>	Journal = jpcB,
3120	>	Pages = {2569-2577},
3121	>	Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes},
3122	>	Volume = 102,
3123	>	Year = 1998}
3124	>
3125	>	@article{Misbah98,
3126	>	Author = {C. Misbah and J. Duplat and B. Houchmandzadeh},
3127	>	Date-Added = {2008-01-08 14:58:56 -0500},
3128	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3129	>	Journal = prl,
3130	>	Number = 20,
3131	>	Pages = {4598-4601},
3132	>	Title = {Transition to Ripple Phases in Hydrated Amphiphiles},
3133	>	Volume = 80,
3134	>	Year = 1998}
3135	>
3136	>	@article{Alemany98,
3137	>	Author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego},
3138	>	Date-Added = {2008-01-08 14:58:56 -0500},
3139	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3140	>	Journal = jcp,
3141	>	Pages = {5175-5176},
3142	>	Title = {Transport coefficients of liquid transition metals: A computer simulation study using the embedded atom model},
3143	>	Volume = 109,
3144	>	Year = 1998}
3145	>
3146	>	@article{Born12,
3147	>	Author = {M. Born and Th. Von~Karman},
3148	>	Date-Added = {2008-01-08 14:58:56 -0500},
3149	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3150	>	Journal = {Physik Z.},
3151	>	Number = {297-309},
3152	>	Title = {Uber Schwingungen in Raumgittern},
3153	>	Volume = 13,
3154	>	Year = 1912}
3155	>
3156	>	@incollection{Angell85,
3157	>	Address = {Springfield, VA},
3158	>	Author = {C.~A. Angell},
3159	>	Booktitle = {Relaxations in Complex Systems},
3160	>	Date-Added = {2008-01-08 14:58:56 -0500},
3161	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3162	>	Editor = {K.~Ngai and G.~B. Wright},
3163	>	Pages = 1,
3164	>	Publisher = {National Technical Information Service, U.S. Department of Commerce},
3165	>	Title = {unknown},
3166	>	Year = 1985}
3167	>
3168	>	@article{Ribeiro98,
3169	>	Author = {M.~C.~C. Ribeiro and P.~A. Madden},
3170	>	Date-Added = {2008-01-08 14:58:56 -0500},
3171	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3172	>	Journal = jcp,
3173	>	Pages = {3256-3263},
3174	>	Title = {Unstable Modes in Ionic Melts},
3175	>	Volume = 108,
3176	>	Year = 1998}
3177	>
3178	>	@article{Mutz1991,
3179	>	Author = {Mutz, M. and Bensimon, D. and Brienne, M. J.},
3180	>	Date-Added = {2008-01-08 14:58:56 -0500},
3181	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3182	>	Doi = {10.1103/PhysRevLett.67.923},
3183	>	Journal = {Phys. Rev. Lett.},
3184	>	Month = {Aug},
3185	>	Number = 7,
3186	>	Numpages = 3,
3187	>	Pages = {923--926},
3188	>	Publisher = {American Physical Society},
3189	>	Title = {Wrinkling transition in partially polymerized vesicles},
3190	>	Volume = 67,
3191	>	Year = 1991,
3192	>	Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923}}
3193	>
3194	>	@article{Wendt78,
3195	>	Author = {H. Wendt and F.~F. Abraham},
3196	>	Date-Added = {2008-01-08 14:58:56 -0500},
3197	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3198	>	Journal = prl,
3199	>	Pages = 1244,
3200	>	Volume = 41,
3201	>	Year = 1978}
3202	>
3203	>	@unpublished{Truhlar00,
3204	>	Author = {D.~G. Truhlar and A. Kohen},
3205	>	Date-Added = {2008-01-08 14:58:56 -0500},
3206	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3207	>	Note = {private correspondence},
3208	>	Year = 2000}
3209	>
3210	>	@article{Dwyer1977,
3211	>	Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
3212	>	Date-Added = {2008-01-08 14:58:56 -0500},
3213	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3214	>	Journal = {Surf. Sci.},
3215	>	Pages = 617,
3216	>	Volume = 64,
3217	>	Year = 1977}
3218	>
3219	>	@article{Macritche78,
3220	>	Author = {F. MacRitche},
3221	>	Date-Added = {2008-01-08 14:58:56 -0500},
3222	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3223	>	Journal = {Adv. Protein Chem.},
3224	>	Pages = 283,
3225	>	Volume = 32,
3226	>	Year = 1978}
3227	>
3228	>	@article{Feder80,
3229	>	Author = {J. Feder},
3230	>	Date-Added = {2008-01-08 14:58:56 -0500},
3231	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3232	>	Journal = {J. Theor. Biol.},
3233	>	Pages = 237,
3234	>	Volume = 87,
3235	>	Year = 1980}
3236	>
3237	>	@article{Ramsden93,
3238	>	Author = {J.~J. Ramsden},
3239	>	Date-Added = {2008-01-08 14:58:56 -0500},
3240	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3241	>	Journal = prl,
3242	>	Pages = 295,
3243	>	Volume = 71,
3244	>	Year = 1993}
3245	>
3246	>	@article{Egelhoff89,
3247	>	Author = {W.~F. Egelhoff and I. Jacob},
3248	>	Date-Added = {2008-01-08 14:58:56 -0500},
3249	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3250	>	Journal = prl,
3251	>	Pages = 921,
3252	>	Volume = 62,
3253	>	Year = 1989}
3254
3255	<	@ARTICLE{Torre2003,
3256	<	author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez
3257	<	and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez},
3258	<	title = {Calculation of the solution properties of flexible macromolecules:
3259	<	methods and applications},
3260	<	journal = {European Biophysics Journal with Biophysics Letters},
3261	<	year = {2003},
3262	<	volume = {32},
3263	<	pages = {477-486},
3264	<	number = {5},
3265	<	month = {Aug},
3266	<	abstract = {While the prediction of hydrodynamic properties of rigid particles
3255	>	@article{Dobson1987,
3256	>	Author = {B.~W. Dobson},
3257	>	Date-Added = {2008-01-08 14:58:56 -0500},
3258	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3259	>	Journal = prb,
3260	>	Pages = 1068,
3261	>	Volume = 36,
3262	>	Year = 1987}
3263	>
3264	>	@article{Davis:1969uq,
3265	>	Abstract = { Exact solutions of the Stokes equations are derived for the case of two unequal spheres slowly rotating or translating perpendicular to their line of centers in a quiescent, unbounded viscous fluid, following Wakiya[16]. Numerical results are presented for the force and torque coefficients for size ratios from 1[middle dot]0 to 10[middle dot]0, and separations down to 0[middle dot]001 times the radius of the smaller.},
3266	>	Author = {Davis, M. H.},
3267	>	Date-Added = {2008-01-08 14:57:14 -0500},
3268	>	Date-Modified = {2008-01-08 14:57:14 -0500},
3269	>	Journal = {Chemical Engineering Science},
3270	>	Number = 12,
3271	>	Pages = {1769--1776},
3272	>	Title = {The slow translation and rotation of two unequal spheres in a viscous fluid},
3273	>	Ty = {JOUR},
3274	>	Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
3275	>	Volume = 24,
3276	>	Year = 1969,
3277	>	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}}
3278	>
3279	>	@article{Stimson:1926qy,
3280	>	Author = {Stimson, M and Jeffery, GB},
3281	>	Date-Added = {2008-01-08 14:51:23 -0500},
3282	>	Date-Modified = {2008-01-08 14:51:35 -0500},
3283	>	Journal = {Proceedings of the Royal Society of London Series A-Containing Papers of a Mathematical and Physical Character},
3284	>	Pages = {110-116},
3285	>	Title = {The motion of two spheres in a viscous fluid},
3286	>	Volume = 111,
3287	>	Year = 1926}
3288	>
3289	>	@article{Orlandi:2006fk,
3290	>	Abstract = {Liquid crystal phases formed by bent-shaped (or {\tt{}"{}}banana{\tt{}"{}}) molecules are currently of great interest. Here we investigate by Monte Carlo computer simulations the phases formed by rigid banana molecules modeled combining three Gay-Berne sites and containing either one central or two lateral and transversal dipoles. We show that changing the dipole position and orientation has a profound effect on the mesophase stability and molecular organization. In particular, we find a uniaxial nematic phase only for off-center dipolar models and tilted phases only for the one with terminal dipoles.},
3291	>	Address = {Dipartimento di Chimica Fisica e Inorganica, and INSTM, Universita di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.},
3292	>	Au = {Orlandi, S and Berardi, R and Steltzer, J and Zannoni, C},
3293	>	Author = {Orlandi, Silvia and Berardi, Roberto and Steltzer, Joachim and Zannoni, Claudio},
3294	>	Da = 20060407,
3295	>	Date-Added = {2008-01-08 14:47:56 -0500},
3296	>	Date-Modified = {2008-01-08 14:48:06 -0500},
3297	>	Dcom = 20070727,
3298	>	Doi = {10.1063/1.2176622},
3299	>	Edat = {2006/04/08 09:00},
3300	>	Issn = {0021-9606 (Print)},
3301	>	Jid = 0375360,
3302	>	Journal = {J Chem Phys},
3303	>	Jt = {The Journal of chemical physics},
3304	>	Language = {eng},
3305	>	Mhda = {2006/04/08 09:01},
3306	>	Number = 12,
3307	>	Own = {NLM},
3308	>	Pages = 124907,
3309	>	Pl = {United States},
3310	>	Pmid = 16599725,
3311	>	Pst = {ppublish},
3312	>	Pt = {Journal Article},
3313	>	Pubm = {Print},
3314	>	So = {J Chem Phys. 2006 Mar 28;124(12):124907.},
3315	>	Stat = {PubMed-not-MEDLINE},
3316	>	Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.},
3317	>	Volume = 124,
3318	>	Year = 2006,
3319	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}}
3320	>
3321	>	@article{sun:031602,
3322	>	Author = {Xiuquan Sun and J. Daniel Gezelter},
3323	>	Date-Added = {2008-01-08 14:42:33 -0500},
3324	>	Date-Modified = {2008-01-08 14:42:33 -0500},
3325	>	Doi = {10.1103/PhysRevE.75.031602},
3326	>	Eid = 031602,
3327	>	Journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)},
3328	>	Keywords = {lattice theory; membranes},
3329	>	Number = 3,
3330	>	Numpages = 7,
3331	>	Pages = 031602,
3332	>	Publisher = {APS},
3333	>	Title = {Spontaneous corrugation of dipolar membranes},
3334	>	Url = {http://link.aps.org/abstract/PRE/v75/e031602},
3335	>	Volume = 75,
3336	>	Year = 2007,
3337	>	Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602},
3338	>	Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}}
3339	>
3340	>	@article{Ortega:2007lr,
3341	>	Abstract = {The equivalent radius for any solution property is the radius of a spherical particle having the same value of solution property as that of the macromolecule under consideration. Equivalent radii for different properties present a dependence on size and shape that are more similar than the values of the properties themselves. Furthermore, the ratios of equivalent radii of two properties depend on the conformation (shape or flexibility), but not on the absolute sizes. We define equivalent radii and their ratios, and describe their evaluation for some common models of rigid and flexible macromolecules. Using radii and ratios, we have devised procedures to fit macromolecular models to experimental properties, allowing the determination of the model parameters. Using these quantities, we can construct target functions for an equilibrated, unbiased optimization. The procedures, which have been implemented in public-domain computer programs, are illustrated for rigid, globular proteins, and the rodlike tobacco mosaic virus, and for semiflexible, wormlike heparin molecules.},
3342	>	Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.},
3343	>	Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3344	>	Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3345	>	Da = 20070813,
3346	>	Date-Added = {2008-01-08 14:38:03 -0500},
3347	>	Date-Modified = {2008-01-08 14:38:49 -0500},
3348	>	Dcom = 20071017,
3349	>	Dep = 20070724,
3350	>	Doi = {10.1021/bm700473f},
3351	>	Edat = {2007/07/25 09:00},
3352	>	Issn = {1525-7797 (Print)},
3353	>	Jid = 100892849,
3354	>	Journal = {Biomacromolecules},
3355	>	Jt = {Biomacromolecules},
3356	>	Keywords = {Computer Simulation; Heparin/chemistry; Macromolecular Substances/*chemistry; *Models, Chemical; *Models, Molecular; Molecular Conformation; Particle Size; Protein Conformation; Proteins/chemistry; Software; Solutions},
3357	>	Language = {eng},
3358	>	Mhda = {2007/10/18 09:00},
3359	>	Number = 8,
3360	>	Own = {NLM},
3361	>	Pages = {2464--2475},
3362	>	Phst = {2007/07/24 {$[$}aheadofprint{$]$}},
3363	>	Pl = {United States},
3364	>	Pmid = 17645309,
3365	>	Pst = {ppublish},
3366	>	Pt = {Journal Article; Research Support, Non-U.S. Gov't},
3367	>	Pubm = {Print-Electronic},
3368	>	Rn = {0 (Macromolecular Substances); 0 (Proteins); 0 (Solutions); 9005-49-6 (Heparin)},
3369	>	Sb = {IM},
3370	>	So = {Biomacromolecules. 2007 Aug;8(8):2464-75. Epub 2007 Jul 24.},
3371	>	Stat = {MEDLINE},
3372	>	Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.},
3373	>	Volume = 8,
3374	>	Year = 2007,
3375	>	Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}}
3376	>
3377	>	@article{Torre2003,
3378	>	Abstract = {While the prediction of hydrodynamic properties of rigid particles
3379		is nowadays feasible using simple and efficient computer programs,
3380		the calculation of such properties and, in general, the dynamic
3381		behavior of flexible macromolecules has not reached a similar situation.
#	Line 34 | Line 3397 | Encoding: GBK
3397		such as bending, internal rotation, excluded volume effects, etc.
3398		We provide an example of the application of this methodology to
3399		the dynamics of a semiflexible, wormlike DNA.},
3400	<	annote = {724XK Times Cited:6 Cited References Count:64},
3401	<	issn = {0175-7571},
3402	<	uri = {<Go to ISI>://000185513400011},
3403	<	}
3400	>	Annote = {724XK Times Cited:6 Cited References Count:64},
3401	>	Author = {{Garc\'{i}a de la Torre}, Jose and H. E. Sanchez and A. Ortega and J. G. Hernandez and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez},
3402	>	Issn = {0175-7571},
3403	>	Journal = {European Biophysics Journal with Biophysics Letters},
3404	>	Month = {Aug},
3405	>	Number = 5,
3406	>	Pages = {477-486},
3407	>	Title = {Calculation of the solution properties of flexible macromolecules: methods and applications},
3408	>	Uri = {<Go to ISI>://000185513400011},
3409	>	Volume = 32,
3410	>	Year = 2003}
3411
3412	<	@ARTICLE{Alakent2005,
3413	<	author = {B. Alakent and M. C. Camurdan and P. Doruker},
44	<	title = {Hierarchical structure of the energy landscape of proteins revisited
45	<	by time series analysis. II. Investigation of explicit solvent effects},
46	<	journal = {Journal of Chemical Physics},
47	<	year = {2005},
48	<	volume = {123},
49	<	pages = {-},
50	<	number = {14},
51	<	month = {Oct 8},
52	<	abstract = {Time series analysis tools are employed on the principal modes obtained
3412	>	@article{Alakent2005,
3413	>	Abstract = {Time series analysis tools are employed on the principal modes obtained
3414		from the C-alpha trajectories from two independent molecular-dynamics
3415		simulations of alpha-amylase inhibitor (tendamistat). Fluctuations
3416		inside an energy minimum (intraminimum motions), transitions between
#	Line 83 | Line 3444 | Encoding: GBK
3444		approximately 200 ps (about five times of that in vacuum) in the
3445		low-indexed modes, showing the lowering of energy barriers between
3446		the higher-level minima.},
3447	<	annote = {973OH Times Cited:1 Cited References Count:33},
3448	<	issn = {0021-9606},
3449	<	uri = {<Go to ISI>://000232532000064},
3450	<	}
3447	>	Annote = {973OH Times Cited:1 Cited References Count:33},
3448	>	Author = {B. Alakent and M. C. Camurdan and P. Doruker},
3449	>	Issn = {0021-9606},
3450	>	Journal = {Journal of Chemical Physics},
3451	>	Month = {Oct 8},
3452	>	Number = 14,
3453	>	Pages = {-},
3454	>	Title = {Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects},
3455	>	Uri = {<Go to ISI>://000232532000064},
3456	>	Volume = 123,
3457	>	Year = 2005}
3458
3459	<	@BOOK{Alexander1987,
3460	<	title = {A Pattern Language: Towns, Buildings, Construction},
3461	<	publisher = {Oxford University Press},
3462	<	year = {1987},
3463	<	author = {C. Alexander},
3464	<	address = {New York},
97	<	}
3459	>	@book{Alexander1987,
3460	>	Address = {New York},
3461	>	Author = {C. Alexander},
3462	>	Publisher = {Oxford University Press},
3463	>	Title = {A Pattern Language: Towns, Buildings, Construction},
3464	>	Year = 1987}
3465
3466	<	@BOOK{Allen1987,
3467	<	title = {Computer Simulations of Liquids},
3468	<	publisher = {Oxford University Press},
3469	<	year = {1987},
3470	<	author = {M.~P. Allen and D.~J. Tildesley},
3471	<	address = {New York},
105	<	}
3466	>	@book{Allen1987,
3467	>	Address = {New York},
3468	>	Author = {M.~P. Allen and D.~J. Tildesley},
3469	>	Publisher = {Oxford University Press},
3470	>	Title = {Computer Simulations of Liquids},
3471	>	Year = 1987}
3472
3473	<	@ARTICLE{Allison1991,
3474	<	author = {S. A. Allison},
109	<	title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application
110	<	to Polarized Dynamic Light-Scattering},
111	<	journal = {Macromolecules},
112	<	year = {1991},
113	<	volume = {24},
114	<	pages = {530-536},
115	<	number = {2},
116	<	month = {Jan 21},
117	<	abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
3473	>	@article{Allison1991,
3474	>	Abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
3475		of rigid macromolecules. It is applied to polarized dynamic light
3476		scattering from rodlike sturctures and from a model of a DNA fragment
3477		(762 base pairs). A number of rod cases are examined in which the
#	Line 128 | Line 3485 | Encoding: GBK
3485		of this fragment, it is shown directly that flexing contributes
3486		to the faster decay processes probed by light scattering and that
3487		the flexible model studies are in good agreement with experiment.},
3488	<	annote = {Eu814 Times Cited:8 Cited References Count:32},
3489	<	issn = {0024-9297},
3490	<	uri = {<Go to ISI>://A1991EU81400029},
3491	<	}
3488	>	Annote = {Eu814 Times Cited:8 Cited References Count:32},
3489	>	Author = {S. A. Allison},
3490	>	Issn = {0024-9297},
3491	>	Journal = {Macromolecules},
3492	>	Month = {Jan 21},
3493	>	Number = 2,
3494	>	Pages = {530-536},
3495	>	Title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application to Polarized Dynamic Light-Scattering},
3496	>	Uri = {<Go to ISI>://A1991EU81400029},
3497	>	Volume = 24,
3498	>	Year = 1991}
3499
3500	<	@ARTICLE{Andersen1983,
3501	<	author = {H. C. Andersen},
3502	<	title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics
3503	<	Calculations},
3504	<	journal = {Journal of Computational Physics},
3505	<	year = {1983},
3506	<	volume = {52},
3507	<	pages = {24-34},
3508	<	number = {1},
3509	<	annote = {Rq238 Times Cited:559 Cited References Count:14},
3510	<	issn = {0021-9991},
147	<	uri = {<Go to ISI>://A1983RQ23800002},
148	<	}
3500	>	@article{Andersen1983,
3501	>	Annote = {Rq238 Times Cited:559 Cited References Count:14},
3502	>	Author = {H. C. Andersen},
3503	>	Issn = {0021-9991},
3504	>	Journal = {Journal of Computational Physics},
3505	>	Number = 1,
3506	>	Pages = {24-34},
3507	>	Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
3508	>	Uri = {<Go to ISI>://A1983RQ23800002},
3509	>	Volume = 52,
3510	>	Year = 1983}
3511
3512	<	@ARTICLE{Auerbach2005,
3513	<	author = {A. Auerbach},
152	<	title = {Gating of acetylcholine receptor channels: Brownian motion across
153	<	a broad transition state},
154	<	journal = {Proceedings of the National Academy of Sciences of the United States
155	<	of America},
156	<	year = {2005},
157	<	volume = {102},
158	<	pages = {1408-1412},
159	<	number = {5},
160	<	month = {Feb 1},
161	<	abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
3512	>	@article{Auerbach2005,
3513	>	Abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
3514		stable #closed# and #open# conformations. In patch clamp recordings,
3515		diliganded AChR gating appears to be a simple, two-state reaction.
3516		However, mutagenesis studies indicate that during gating dozens
#	Line 177 | Line 3529 | Encoding: GBK
3529		coarse-grained AChR gating conformational change propagates through
3530		the protein with dynamics that are governed by the Brownian motion
3531		of individual gating blocks.},
3532	<	annote = {895QF Times Cited:9 Cited References Count:33},
3533	<	issn = {0027-8424},
3534	<	uri = {<Go to ISI>://000226877300030},
3535	<	}
3532	>	Annote = {895QF Times Cited:9 Cited References Count:33},
3533	>	Author = {A. Auerbach},
3534	>	Issn = {0027-8424},
3535	>	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
3536	>	Month = {Feb 1},
3537	>	Number = 5,
3538	>	Pages = {1408-1412},
3539	>	Title = {Gating of acetylcholine receptor channels: Brownian motion across a broad transition state},
3540	>	Uri = {<Go to ISI>://000226877300030},
3541	>	Volume = 102,
3542	>	Year = 2005}
3543
3544	<	@ARTICLE{Baber1995,
3545	<	author = {J. Baber and J. F. Ellena and D. S. Cafiso},
187	<	title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined
188	<	Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
189	<	journal = {Biochemistry},
190	<	year = {1995},
191	<	volume = {34},
192	<	pages = {6533-6539},
193	<	number = {19},
194	<	month = {May 16},
195	<	abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
3544	>	@article{Baber1995,
3545	>	Abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
3546		on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine
3547		membranes in the liquid crystalline phase was investigated using
3548		H-2 NMR. Upon the addition of the anesthetics, the first five methylene
#	Line 213 | Line 3563 | Encoding: GBK
3563		the NOE data indicate that anesthetics prefer the interfacial and
3564		hydrocarbon regions of the membrane and are not found in high concentrations
3565		in the phospholipid headgroup.},
3566	<	annote = {Qz716 Times Cited:38 Cited References Count:37},
3567	<	issn = {0006-2960},
3568	<	uri = {<Go to ISI>://A1995QZ71600035},
3569	<	}
3566	>	Annote = {Qz716 Times Cited:38 Cited References Count:37},
3567	>	Author = {J. Baber and J. F. Ellena and D. S. Cafiso},
3568	>	Issn = {0006-2960},
3569	>	Journal = {Biochemistry},
3570	>	Month = {May 16},
3571	>	Number = 19,
3572	>	Pages = {6533-6539},
3573	>	Title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
3574	>	Uri = {<Go to ISI>://A1995QZ71600035},
3575	>	Volume = 34,
3576	>	Year = 1995}
3577
3578	<	@ARTICLE{Banerjee2004,
3579	<	author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
223	<	title = {Solution of quantum Langevin equation: Approximations, theoretical
224	<	and numerical aspects},
225	<	journal = {Journal of Chemical Physics},
226	<	year = {2004},
227	<	volume = {120},
228	<	pages = {8960-8972},
229	<	number = {19},
230	<	month = {May 15},
231	<	abstract = {Based on a coherent state representation of noise operator and an
3578	>	@article{Banerjee2004,
3579	>	Abstract = {Based on a coherent state representation of noise operator and an
3580		ensemble averaging procedure using Wigner canonical thermal distribution
3581		for harmonic oscillators, a generalized quantum Langevin equation
3582		has been recently developed [Phys. Rev. E 65, 021109 (2002); 66,
#	Line 242 | Line 3590 | Encoding: GBK
3590		calculation of barrier crossing, in a cubic potential to demonstrate
3591		the quantum Kramers' turnover and the quantum Arrhenius plot. (C)
3592		2004 American Institute of Physics.},
3593	<	annote = {816YY Times Cited:8 Cited References Count:35},
3594	<	issn = {0021-9606},
3595	<	uri = {<Go to ISI>://000221146400009},
3596	<	}
3593	>	Annote = {816YY Times Cited:8 Cited References Count:35},
3594	>	Author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
3595	>	Issn = {0021-9606},
3596	>	Journal = {Journal of Chemical Physics},
3597	>	Month = {May 15},
3598	>	Number = 19,
3599	>	Pages = {8960-8972},
3600	>	Title = {Solution of quantum Langevin equation: Approximations, theoretical and numerical aspects},
3601	>	Uri = {<Go to ISI>://000221146400009},
3602	>	Volume = 120,
3603	>	Year = 2004}
3604
3605	<	@ARTICLE{Barojas1973,
3606	<	author = {J. Barojas and D. Levesque},
3607	<	title = {Simulation of Diatomic Homonuclear Liquids},
3608	<	journal = {Phys. Rev. A},
3609	<	year = {1973},
3610	<	volume = {7},
3611	<	pages = {1092-1105},
257	<	}
3605	>	@article{Barojas1973,
3606	>	Author = {J. Barojas and D. Levesque},
3607	>	Journal = {Phys. Rev. A},
3608	>	Pages = {1092-1105},
3609	>	Title = {Simulation of Diatomic Homonuclear Liquids},
3610	>	Volume = 7,
3611	>	Year = 1973}
3612
3613	<	@ARTICLE{Barth1998,
3614	<	author = {E. Barth and T. Schlick},
261	<	title = {Overcoming stability limitations in biomolecular dynamics. I. Combining
262	<	force splitting via extrapolation with Langevin dynamics in LN},
263	<	journal = {Journal of Chemical Physics},
264	<	year = {1998},
265	<	volume = {109},
266	<	pages = {1617-1632},
267	<	number = {5},
268	<	month = {Aug 1},
269	<	abstract = {We present an efficient new method termed LN for propagating biomolecular
3613	>	@article{Barth1998,
3614	>	Abstract = {We present an efficient new method termed LN for propagating biomolecular
3615		dynamics according to the Langevin equation that arose fortuitously
3616		upon analysis of the range of harmonic validity of our normal-mode
3617		scheme LIN. LN combines force linearization with force splitting
#	Line 292 | Line 3637 | Encoding: GBK
3637		of LN to biomolecular dynamics is well suited for configurational
3638		sampling, thermodynamic, and structural questions. (C) 1998 American
3639		Institute of Physics.},
3640	<	annote = {105HH Times Cited:29 Cited References Count:49},
3641	<	issn = {0021-9606},
3642	<	uri = {<Go to ISI>://000075066300006},
3643	<	}
3640	>	Annote = {105HH Times Cited:29 Cited References Count:49},
3641	>	Author = {E. Barth and T. Schlick},
3642	>	Issn = {0021-9606},
3643	>	Journal = {Journal of Chemical Physics},
3644	>	Month = {Aug 1},
3645	>	Number = 5,
3646	>	Pages = {1617-1632},
3647	>	Title = {Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN},
3648	>	Uri = {<Go to ISI>://000075066300006},
3649	>	Volume = 109,
3650	>	Year = 1998}
3651
3652	<	@ARTICLE{Batcho2001,
3653	<	author = {P. F. Batcho and T. Schlick},
302	<	title = {Special stability advantages of position-Verlet over velocity-Verlet
303	<	in multiple-time step integration},
304	<	journal = {Journal of Chemical Physics},
305	<	year = {2001},
306	<	volume = {115},
307	<	pages = {4019-4029},
308	<	number = {9},
309	<	month = {Sep 1},
310	<	abstract = {We present an analysis for a simple two-component harmonic oscillator
3652	>	@article{Batcho2001,
3653	>	Abstract = {We present an analysis for a simple two-component harmonic oscillator
3654		that compares the use of position-Verlet to velocity-Verlet for
3655		multiple-time step integration. The numerical stability analysis
3656		based on the impulse-Verlet splitting shows that position-Verlet
#	Line 318 | Line 3661 | Encoding: GBK
3661		to a biomolecule. a solvated protein, for both Newtonian and Langevin
3662		dynamics echo these trends over large outer time-step regimes. (C)
3663		2001 American Institute of Physics.},
3664	<	annote = {469KV Times Cited:6 Cited References Count:30},
3665	<	issn = {0021-9606},
3666	<	uri = {<Go to ISI>://000170813800005},
3667	<	}
3664	>	Annote = {469KV Times Cited:6 Cited References Count:30},
3665	>	Author = {P. F. Batcho and T. Schlick},
3666	>	Issn = {0021-9606},
3667	>	Journal = {Journal of Chemical Physics},
3668	>	Month = {Sep 1},
3669	>	Number = 9,
3670	>	Pages = {4019-4029},
3671	>	Title = {Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration},
3672	>	Uri = {<Go to ISI>://000170813800005},
3673	>	Volume = 115,
3674	>	Year = 2001}
3675
3676	<	@ARTICLE{Bates2005,
3677	<	author = {M. A. Bates and G. R. Luckhurst},
328	<	title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation
329	<	study},
330	<	journal = {Physical Review E},
331	<	year = {2005},
332	<	volume = {72},
333	<	pages = {-},
334	<	number = {5},
335	<	month = {Nov},
336	<	abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
3676	>	@article{Bates2005,
3677	>	Abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
3678		can exhibit the elusive biaxial nematic phase, we have developed
3679		a generic simulation model for such systems. This contains the features
3680		of the molecule that are essential to its liquid crystal behavior,
#	Line 351 | Line 3692 | Encoding: GBK
3692		determination of this. The simulation results show that, whereas
3693		some positions are extremely sensitive to the phase biaxiality,
3694		others are totally blind to this.},
3695	<	annote = {Part 1 988LQ Times Cited:0 Cited References Count:38},
3696	<	issn = {1539-3755},
3697	<	uri = {<Go to ISI>://000233603100030},
3698	<	}
3695	>	Annote = {Part 1 988LQ Times Cited:0 Cited References Count:38},
3696	>	Author = {M. A. Bates and G. R. Luckhurst},
3697	>	Issn = {1539-3755},
3698	>	Journal = {Physical Review E},
3699	>	Month = {Nov},
3700	>	Number = 5,
3701	>	Pages = {-},
3702	>	Title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation study},
3703	>	Uri = {<Go to ISI>://000233603100030},
3704	>	Volume = 72,
3705	>	Year = 2005}
3706
3707	<	@ARTICLE{Beard2003,
3708	<	author = {D. A. Beard and T. Schlick},
361	<	title = {Unbiased rotational moves for rigid-body dynamics},
362	<	journal = {Biophysical Journal},
363	<	year = {2003},
364	<	volume = {85},
365	<	pages = {2973-2976},
366	<	number = {5},
367	<	month = {Nov 1},
368	<	abstract = {We introduce an unbiased protocol for performing rotational moves
3707	>	@article{Beard2003,
3708	>	Abstract = {We introduce an unbiased protocol for performing rotational moves
3709		in rigid-body dynamics simulations. This approach - based on the
3710		analytic solution for the rotational equations of motion for an
3711		orthogonal coordinate system at constant angular velocity - removes
#	Line 374 | Line 3714 | Encoding: GBK
3714		applying the noncommuting rotational matrices in an arbitrary order.
3715		Our algorithm should thus replace standard approaches to rotate
3716		local coordinate frames in Langevin and Brownian dynamics simulations.},
3717	<	annote = {736UA Times Cited:0 Cited References Count:11},
3718	<	issn = {0006-3495},
3719	<	uri = {<Go to ISI>://000186190500018},
3720	<	}
3717	>	Annote = {736UA Times Cited:0 Cited References Count:11},
3718	>	Author = {D. A. Beard and T. Schlick},
3719	>	Issn = {0006-3495},
3720	>	Journal = {Biophysical Journal},
3721	>	Month = {Nov 1},
3722	>	Number = 5,
3723	>	Pages = {2973-2976},
3724	>	Title = {Unbiased rotational moves for rigid-body dynamics},
3725	>	Uri = {<Go to ISI>://000186190500018},
3726	>	Volume = 85,
3727	>	Year = 2003}
3728
3729	<	@ARTICLE{Beloborodov1998,
3730	<	author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev},
384	<	title = {Effect of coupling between rotational and translational Brownian
385	<	motions on NMR spin relaxation: Consideration using green function
386	<	of rigid body diffusion},
387	<	journal = {Journal of Magnetic Resonance},
388	<	year = {1998},
389	<	volume = {132},
390	<	pages = {328-329},
391	<	number = {2},
392	<	month = {Jun},
393	<	abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
3729	>	@article{Beloborodov1998,
3730	>	Abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
3731		Biopolymers 33, 409-436, 1993), it was analytically shown that coupling
3732		between translation and rotation diffusion degrees of freedom does
3733		not affect the correlation functions relevant to the NMR intramolecular
#	Line 399 | Line 3736 | Encoding: GBK
3736		647-654, 1962) can be regarded as exact in respect to the rotation-translation
3737		coupling for the spin system connected with a rigid body. (C) 1998
3738		Academic Press.},
3739	<	annote = {Zu605 Times Cited:2 Cited References Count:6},
3740	<	issn = {1090-7807},
3741	<	uri = {<Go to ISI>://000074214800017},
3742	<	}
3739	>	Annote = {Zu605 Times Cited:2 Cited References Count:6},
3740	>	Author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev},
3741	>	Issn = {1090-7807},
3742	>	Journal = {Journal of Magnetic Resonance},
3743	>	Month = {Jun},
3744	>	Number = 2,
3745	>	Pages = {328-329},
3746	>	Title = {Effect of coupling between rotational and translational Brownian motions on NMR spin relaxation: Consideration using green function of rigid body diffusion},
3747	>	Uri = {<Go to ISI>://000074214800017},
3748	>	Volume = 132,
3749	>	Year = 1998}
3750
3751	<	@ARTICLE{Berardi1996,
3752	<	author = {R. Berardi and S. Orlandi and C. Zannoni},
409	<	title = {Antiphase structures in polar smectic liquid crystals and their molecular
410	<	origin},
411	<	journal = {Chemical Physics Letters},
412	<	year = {1996},
413	<	volume = {261},
414	<	pages = {357-362},
415	<	number = {3},
416	<	month = {Oct 18},
417	<	abstract = {We demonstrate that the overall molecular dipole organization in a
3751	>	@article{Berardi1996,
3752	>	Abstract = {We demonstrate that the overall molecular dipole organization in a
3753		smectic liquid crystal formed of polar molecules can be strongly
3754		influenced by the position of the dipole in the molecule. We study
3755		by large scale Monte Carlo simulations systems of attractive-repulsive
#	Line 423 | Line 3758 | Encoding: GBK
3758		liquid crystals and modulated antiferroelectric bilayer stripe domains
3759		similar to the experimentally observed ''antiphase'' structures
3760		are obtained in the two cases.},
3761	<	annote = {Vn637 Times Cited:49 Cited References Count:26},
3762	<	issn = {0009-2614},
3763	<	uri = {<Go to ISI>://A1996VN63700023},
3764	<	}
3761	>	Annote = {Vn637 Times Cited:49 Cited References Count:26},
3762	>	Author = {R. Berardi and S. Orlandi and C. Zannoni},
3763	>	Issn = {0009-2614},
3764	>	Journal = {Chemical Physics Letters},
3765	>	Month = {Oct 18},
3766	>	Number = 3,
3767	>	Pages = {357-362},
3768	>	Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
3769	>	Uri = {<Go to ISI>://A1996VN63700023},
3770	>	Volume = 261,
3771	>	Year = 1996}
3772
3773	<	@ARTICLE{Berkov2005,
3774	<	author = {D. V. Berkov and N. L. Gorn},
433	<	title = {Magnetization precession due to a spin-polarized current in a thin
434	<	nanoelement: Numerical simulation study},
435	<	journal = {Physical Review B},
436	<	year = {2005},
437	<	volume = {72},
438	<	pages = {-},
439	<	number = {9},
440	<	month = {Sep},
441	<	abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
3773	>	@article{Berkov2005,
3774	>	Abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
3775		formalism) of magnetization oscillations driven by a spin-polarized
3776		current through a thin elliptical nanoelement is presented. We show
3777		that a sophisticated micromagnetic model, where a polycrystalline
#	Line 455 | Line 3788 | Encoding: GBK
3788		of reasonable parameter values, indicating that further model refinement
3789		is necessary for a complete understanding of the spin-driven magnetization
3790		precession even in this relatively simple experimental situation.},
3791	<	annote = {969IT Times Cited:2 Cited References Count:55},
3792	<	issn = {1098-0121},
3793	<	uri = {<Go to ISI>://000232228500058},
3794	<	}
3791	>	Annote = {969IT Times Cited:2 Cited References Count:55},
3792	>	Author = {D. V. Berkov and N. L. Gorn},
3793	>	Issn = {1098-0121},
3794	>	Journal = {Physical Review B},
3795	>	Month = {Sep},
3796	>	Number = 9,
3797	>	Pages = {-},
3798	>	Title = {Magnetization precession due to a spin-polarized current in a thin nanoelement: Numerical simulation study},
3799	>	Uri = {<Go to ISI>://000232228500058},
3800	>	Volume = 72,
3801	>	Year = 2005}
3802
3803	<	@ARTICLE{Berkov2005a,
3804	<	author = {D. V. Berkov and N. L. Gorn},
465	<	title = {Stochastic dynamic simulations of fast remagnetization processes:
466	<	recent advances and applications},
467	<	journal = {Journal of Magnetism and Magnetic Materials},
468	<	year = {2005},
469	<	volume = {290},
470	<	pages = {442-448},
471	<	month = {Apr},
472	<	abstract = {Numerical simulations of fast remagnetization processes using stochastic
3803	>	@article{Berkov2005a,
3804	>	Abstract = {Numerical simulations of fast remagnetization processes using stochastic
3805		dynamics are widely used to study various magnetic systems. In this
3806		paper, we first address several crucial methodological problems
3807		of such simulations: (i) the influence of finite-element discretization
#	Line 484 | Line 3816 | Encoding: GBK
3816		in pulsed fields and show some results for a remagnetization dynamics
3817		induced by a spin-polarized current. (c) 2004 Elsevier B.V. All
3818		rights reserved.},
3819	<	annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
3820	<	issn = {0304-8853},
3821	<	uri = {<Go to ISI>://000228837600109},
3822	<	}
3819	>	Annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
3820	>	Author = {D. V. Berkov and N. L. Gorn},
3821	>	Issn = {0304-8853},
3822	>	Journal = {Journal of Magnetism and Magnetic Materials},
3823	>	Month = {Apr},
3824	>	Pages = {442-448},
3825	>	Title = {Stochastic dynamic simulations of fast remagnetization processes: recent advances and applications},
3826	>	Uri = {<Go to ISI>://000228837600109},
3827	>	Volume = 290,
3828	>	Year = 2005}
3829
3830	<	@ARTICLE{Berkov2002,
3831	<	author = {D. V. Berkov and N. L. Gorn and P. Gornert},
494	<	title = {Magnetization dynamics in nanoparticle systems: Numerical simulation
495	<	using Langevin dynamics},
496	<	journal = {Physica Status Solidi a-Applied Research},
497	<	year = {2002},
498	<	volume = {189},
499	<	pages = {409-421},
500	<	number = {2},
501	<	month = {Feb 16},
502	<	abstract = {We report on recent progress achieved by the development of numerical
3830	>	@article{Berkov2002,
3831	>	Abstract = {We report on recent progress achieved by the development of numerical
3832		methods based on the stochastic (Langevin) dynamics applied to systems
3833		of interacting magnetic nanoparticles. The method enables direct
3834		simulations of the trajectories of magnetic moments taking into
#	Line 513 | Line 3842 | Encoding: GBK
3842		For the second system the complex ac susceptibility chi(omega, T)
3843		for various particle concentrations and particle anisotropies were
3844		computed and compared with numerous experimental results.},
3845	<	annote = {526TF Times Cited:4 Cited References Count:37},
3846	<	issn = {0031-8965},
3847	<	uri = {<Go to ISI>://000174145200026},
3848	<	}
3845	>	Annote = {526TF Times Cited:4 Cited References Count:37},
3846	>	Author = {D. V. Berkov and N. L. Gorn and P. Gornert},
3847	>	Issn = {0031-8965},
3848	>	Journal = {Physica Status Solidi a-Applied Research},
3849	>	Month = {Feb 16},
3850	>	Number = 2,
3851	>	Pages = {409-421},
3852	>	Title = {Magnetization dynamics in nanoparticle systems: Numerical simulation using Langevin dynamics},
3853	>	Uri = {<Go to ISI>://000174145200026},
3854	>	Volume = 189,
3855	>	Year = 2002}
3856
3857	<	@ARTICLE{Bernal1980,
3858	<	author = {J.M. Bernal and J. G. {de la Torre}},
3859	<	title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules
3860	<	with Arbitrary Shape},
3861	<	journal = {Biopolymers},
3862	<	year = {1980},
3863	<	volume = {19},
528	<	pages = {751-766},
529	<	}
3857	>	@article{Bernal1980,
3858	>	Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose},
3859	>	Journal = {Biopolymers},
3860	>	Pages = {751-766},
3861	>	Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape},
3862	>	Volume = 19,
3863	>	Year = 1980}
3864
3865	<	@ARTICLE{Brenner1967,
3866	<	author = {H. Brenner },
3867	<	title = {Coupling between the Translational and Rotational Brownian Motions
3868	<	of Rigid Particles of Arbitrary shape},
3869	<	journal = {J. Collid. Int. Sci.},
3870	<	year = {1967},
3871	<	volume = {23},
538	<	pages = {407-436},
539	<	}
3865	>	@article{Brenner1967,
3866	>	Author = {H. Brenner},
3867	>	Journal = {J. Collid. Int. Sci.},
3868	>	Pages = {407-436},
3869	>	Title = {Coupling between the Translational and Rotational Brownian Motions of Rigid Particles of Arbitrary shape},
3870	>	Volume = 23,
3871	>	Year = 1967}
3872
3873	<	@ARTICLE{Brooks1983,
3874	<	author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States
3875	<	and S. Swaminathan and M. Karplus},
3876	<	title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics
3877	<	Calculations},
3878	<	journal = {Journal of Computational Chemistry},
3879	<	year = {1983},
3880	<	volume = {4},
3881	<	pages = {187-217},
3882	<	number = {2},
3883	<	annote = {Qp423 Times Cited:6414 Cited References Count:96},
552	<	issn = {0192-8651},
553	<	uri = {<Go to ISI>://A1983QP42300010},
554	<	}
3873	>	@article{Brooks1983,
3874	>	Annote = {Qp423 Times Cited:6414 Cited References Count:96},
3875	>	Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus},
3876	>	Issn = {0192-8651},
3877	>	Journal = {Journal of Computational Chemistry},
3878	>	Number = 2,
3879	>	Pages = {187-217},
3880	>	Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
3881	>	Uri = {<Go to ISI>://A1983QP42300010},
3882	>	Volume = 4,
3883	>	Year = 1983}
3884
3885	<	@ARTICLE{Brunger1984,
3886	<	author = {A. Brunger and C. L. Brooks and M. Karplus},
3887	<	title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations
3888	<	of St2 Water},
3889	<	journal = {Chemical Physics Letters},
3890	<	year = {1984},
3891	<	volume = {105},
3892	<	pages = {495-500},
3893	<	number = {5},
3894	<	annote = {Sm173 Times Cited:143 Cited References Count:22},
3895	<	issn = {0009-2614},
567	<	uri = {<Go to ISI>://A1984SM17300007},
568	<	}
3885	>	@article{Brunger1984,
3886	>	Annote = {Sm173 Times Cited:143 Cited References Count:22},
3887	>	Author = {A. Brunger and C. L. Brooks and M. Karplus},
3888	>	Issn = {0009-2614},
3889	>	Journal = {Chemical Physics Letters},
3890	>	Number = 5,
3891	>	Pages = {495-500},
3892	>	Title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations of St2 Water},
3893	>	Uri = {<Go to ISI>://A1984SM17300007},
3894	>	Volume = 105,
3895	>	Year = 1984}
3896
3897	<	@ARTICLE{Budd1999,
3898	<	author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell},
572	<	title = {Self-similar numerical solutions of the porous-medium equation using
573	<	moving mesh methods},
574	<	journal = {Philosophical Transactions of the Royal Society of London Series
575	<	a-Mathematical Physical and Engineering Sciences},
576	<	year = {1999},
577	<	volume = {357},
578	<	pages = {1047-1077},
579	<	number = {1754},
580	<	month = {Apr 15},
581	<	abstract = {This paper examines a synthesis of adaptive mesh methods with the
3897	>	@article{Budd1999,
3898	>	Abstract = {This paper examines a synthesis of adaptive mesh methods with the
3899		use of symmetry to study a partial differential equation. In particular,
3900		it considers methods which admit discrete self-similar solutions,
3901		examining the convergence of these to the true self-similar solution
3902		as well as their stability. Special attention is given to the nonlinear
3903		diffusion equation describing flow in a porous medium.},
3904	<	annote = {199EE Times Cited:4 Cited References Count:14},
3905	<	issn = {1364-503X},
3906	<	uri = {<Go to ISI>://000080466800005},
3907	<	}
3904	>	Annote = {199EE Times Cited:4 Cited References Count:14},
3905	>	Author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell},
3906	>	Issn = {1364-503X},
3907	>	Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
3908	>	Month = {Apr 15},
3909	>	Number = 1754,
3910	>	Pages = {1047-1077},
3911	>	Title = {Self-similar numerical solutions of the porous-medium equation using moving mesh methods},
3912	>	Uri = {<Go to ISI>://000080466800005},
3913	>	Volume = 357,
3914	>	Year = 1999}
3915
3916	<	@ARTICLE{Camp1999,
3917	<	author = {P. J. Camp and M. P. Allen and A. J. Masters},
594	<	title = {Theory and computer simulation of bent-core molecules},
595	<	journal = {Journal of Chemical Physics},
596	<	year = {1999},
597	<	volume = {111},
598	<	pages = {9871-9881},
599	<	number = {21},
600	<	month = {Dec 1},
601	<	abstract = {Fluids of hard bent-core molecules have been studied using theory
3916	>	@article{Camp1999,
3917	>	Abstract = {Fluids of hard bent-core molecules have been studied using theory
3918		and computer simulation. The molecules are composed of two hard
3919		spherocylinders, with length-to-breadth ratio L/D, joined by their
3920		ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20
#	Line 628 | Line 3944 | Encoding: GBK
3944		bond angle-a feature that is also reflected in the lack of variation
3945		with angle of the calculated second and third virial coefficients.
3946		(C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].},
3947	<	annote = {255TC Times Cited:24 Cited References Count:38},
3948	<	issn = {0021-9606},
3949	<	uri = {<Go to ISI>://000083685400056},
3950	<	}
3947	>	Annote = {255TC Times Cited:24 Cited References Count:38},
3948	>	Author = {P. J. Camp and M. P. Allen and A. J. Masters},
3949	>	Issn = {0021-9606},
3950	>	Journal = {Journal of Chemical Physics},
3951	>	Month = {Dec 1},
3952	>	Number = 21,
3953	>	Pages = {9871-9881},
3954	>	Title = {Theory and computer simulation of bent-core molecules},
3955	>	Uri = {<Go to ISI>://000083685400056},
3956	>	Volume = 111,
3957	>	Year = 1999}
3958
3959	<	@ARTICLE{Care2005,
3960	<	author = {C. M. Care and D. J. Cleaver},
638	<	title = {Computer simulation of liquid crystals},
639	<	journal = {Reports on Progress in Physics},
640	<	year = {2005},
641	<	volume = {68},
642	<	pages = {2665-2700},
643	<	number = {11},
644	<	month = {Nov},
645	<	abstract = {A review is presented of molecular and mesoscopic computer simulations
3959	>	@article{Care2005,
3960	>	Abstract = {A review is presented of molecular and mesoscopic computer simulations
3961		of liquid crystalline systems. Molecular simulation approaches applied
3962		to such systems are described, and the key findings for bulk phase
3963		behaviour are reported. Following this, recently developed lattice
3964		Boltzmann approaches to the mesoscale modelling of nemato-dynanics
3965		are reviewed. This paper concludes with a discussion of possible
3966		areas for future development in this field.},
3967	<	annote = {989TU Times Cited:2 Cited References Count:258},
3968	<	issn = {0034-4885},
3969	<	uri = {<Go to ISI>://000233697600004},
3970	<	}
3967	>	Annote = {989TU Times Cited:2 Cited References Count:258},
3968	>	Author = {C. M. Care and D. J. Cleaver},
3969	>	Issn = {0034-4885},
3970	>	Journal = {Reports on Progress in Physics},
3971	>	Month = {Nov},
3972	>	Number = 11,
3973	>	Pages = {2665-2700},
3974	>	Title = {Computer simulation of liquid crystals},
3975	>	Uri = {<Go to ISI>://000233697600004},
3976	>	Volume = 68,
3977	>	Year = 2005}
3978
3979	<	@ARTICLE{Carrasco1999,
3980	<	author = {B. Carrasco and J. G. {de la Torre}},
659	<	title = {Hydrodynamic properties of rigid particles: Comparison of different
660	<	modeling and computational procedures},
661	<	journal = {Biophysical Journal},
662	<	year = {1999},
663	<	volume = {76},
664	<	pages = {3044-3057},
665	<	number = {6},
666	<	month = {Jun},
667	<	abstract = {The hydrodynamic properties of rigid particles are calculated from
3979	>	@article{Carrasco1999,
3980	>	Abstract = {The hydrodynamic properties of rigid particles are calculated from
3981		models composed of spherical elements (beads) using theories developed
3982		by Kirkwood, Bloomfield, and their coworkers. Bead models have usually
3983		been built in such a way that the beads fill the volume occupied
#	Line 682 | Line 3995 | Encoding: GBK
3995		comparison of the performance of the various strategies by applying
3996		them to some test cases, for which the properties are known a priori.
3997		We provide guidelines and computational tools for bead modeling.},
3998	<	annote = {200TT Times Cited:46 Cited References Count:57},
3999	<	issn = {0006-3495},
4000	<	uri = {<Go to ISI>://000080556700016},
4001	<	}
3998	>	Annote = {200TT Times Cited:46 Cited References Count:57},
3999	>	Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
4000	>	Issn = {0006-3495},
4001	>	Journal = {Biophysical Journal},
4002	>	Month = {Jun},
4003	>	Number = 6,
4004	>	Pages = {3044-3057},
4005	>	Title = {Hydrodynamic properties of rigid particles: Comparison of different modeling and computational procedures},
4006	>	Uri = {<Go to ISI>://000080556700016},
4007	>	Volume = 76,
4008	>	Year = 1999}
4009
4010	<	@ARTICLE{Chandra1999,
4011	<	author = {A. Chandra and T. Ichiye},
692	<	title = {Dynamical properties of the soft sticky dipole model of water: Molecular
693	<	dynamics simulations},
694	<	journal = {Journal of Chemical Physics},
695	<	year = {1999},
696	<	volume = {111},
697	<	pages = {2701-2709},
698	<	number = {6},
699	<	month = {Aug 8},
700	<	abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
4010	>	@article{Chandra1999,
4011	>	Abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
4012		are calculated by means of molecular dynamics simulations. Since
4013		this is not a simple point model, the forces and torques arising
4014		from the SSD potential are derived here. Simulations are carried
#	Line 715 | Line 4026 | Encoding: GBK
4026		dynamics simulations of the SSD model are found to run much faster
4027		than TIP3P, SPC/E, and other multisite models. (C) 1999 American
4028		Institute of Physics. [S0021-9606(99)51430-X].},
4029	<	annote = {221EN Times Cited:14 Cited References Count:66},
4030	<	issn = {0021-9606},
4031	<	uri = {<Go to ISI>://000081711200038},
4032	<	}
4029	>	Annote = {221EN Times Cited:14 Cited References Count:66},
4030	>	Author = {A. Chandra and T. Ichiye},
4031	>	Issn = {0021-9606},
4032	>	Journal = {Journal of Chemical Physics},
4033	>	Month = {Aug 8},
4034	>	Number = 6,
4035	>	Pages = {2701-2709},
4036	>	Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations},
4037	>	Uri = {<Go to ISI>://000081711200038},
4038	>	Volume = 111,
4039	>	Year = 1999}
4040
4041	<	@ARTICLE{Channell1990,
4042	<	author = {P. J. Channell and C. Scovel},
4043	<	title = {Symplectic Integration of Hamiltonian-Systems},
4044	<	journal = {Nonlinearity},
4045	<	year = {1990},
4046	<	volume = {3},
4047	<	pages = {231-259},
4048	<	number = {2},
4049	<	month = {may},
4050	<	annote = {Dk631 Times Cited:152 Cited References Count:34},
4051	<	issn = {0951-7715},
4052	<	uri = {<Go to ISI>://A1990DK63100001},
735	<	}
4041	>	@article{Channell1990,
4042	>	Annote = {Dk631 Times Cited:152 Cited References Count:34},
4043	>	Author = {P. J. Channell and C. Scovel},
4044	>	Issn = {0951-7715},
4045	>	Journal = {Nonlinearity},
4046	>	Month = {may},
4047	>	Number = 2,
4048	>	Pages = {231-259},
4049	>	Title = {Symplectic Integration of Hamiltonian-Systems},
4050	>	Uri = {<Go to ISI>://A1990DK63100001},
4051	>	Volume = 3,
4052	>	Year = 1990}
4053
4054	<	@ARTICLE{Chen2003,
4055	<	author = {B. Chen and F. Solis},
739	<	title = {Explicit mixed finite order Runge-Kutta methods},
740	<	journal = {Applied Numerical Mathematics},
741	<	year = {2003},
742	<	volume = {44},
743	<	pages = {21-30},
744	<	number = {1-2},
745	<	month = {Jan},
746	<	abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
4054	>	@article{Chen2003,
4055	>	Abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
4056		equations and introduce a family of mixed methods from combinations
4057		of explicit Runge-Kutta methods. These methods have better stability
4058		behavior than traditional Runge-Kutta methods and generally extend
#	Line 752 | Line 4061 | Encoding: GBK
4061		or spurious. Emphasis is put on examples coming from mathematical
4062		models in ecology. (C) 2002 IMACS. Published by Elsevier Science
4063		B.V. All rights reserved.},
4064	<	annote = {633ZD Times Cited:0 Cited References Count:9},
4065	<	issn = {0168-9274},
4066	<	uri = {<Go to ISI>://000180314200002},
4067	<	}
4064	>	Annote = {633ZD Times Cited:0 Cited References Count:9},
4065	>	Author = {B. Chen and F. Solis},
4066	>	Issn = {0168-9274},
4067	>	Journal = {Applied Numerical Mathematics},
4068	>	Month = {Jan},
4069	>	Number = {1-2},
4070	>	Pages = {21-30},
4071	>	Title = {Explicit mixed finite order Runge-Kutta methods},
4072	>	Uri = {<Go to ISI>://000180314200002},
4073	>	Volume = 44,
4074	>	Year = 2003}
4075
4076	<	@ARTICLE{Cheung2004,
4077	<	author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
762	<	title = {Calculation of flexoelectric coefficients for a nematic liquid crystal
763	<	by atomistic simulation},
764	<	journal = {Journal of Chemical Physics},
765	<	year = {2004},
766	<	volume = {121},
767	<	pages = {9131-9139},
768	<	number = {18},
769	<	month = {Nov 8},
770	<	abstract = {Equilibrium molecular dynamics calculations have been performed for
4076	>	@article{Cheung2004,
4077	>	Abstract = {Equilibrium molecular dynamics calculations have been performed for
4078		the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile
4079		(PCH5) using a fully atomistic model. Simulation data have been
4080		obtained for a series of temperatures in the nematic phase. The
#	Line 779 | Line 4086 | Encoding: GBK
4086		different intermolecular interactions. Values of e(s) and e(b) calculated
4087		from simulation are consistent with those found from experiment.
4088		(C) 2004 American Institute of Physics.},
4089	<	annote = {866UM Times Cited:4 Cited References Count:61},
4090	<	issn = {0021-9606},
4091	<	uri = {<Go to ISI>://000224798900053},
4092	<	}
4089	>	Annote = {866UM Times Cited:4 Cited References Count:61},
4090	>	Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
4091	>	Issn = {0021-9606},
4092	>	Journal = {Journal of Chemical Physics},
4093	>	Month = {Nov 8},
4094	>	Number = 18,
4095	>	Pages = {9131-9139},
4096	>	Title = {Calculation of flexoelectric coefficients for a nematic liquid crystal by atomistic simulation},
4097	>	Uri = {<Go to ISI>://000224798900053},
4098	>	Volume = 121,
4099	>	Year = 2004}
4100
4101	<	@ARTICLE{Cheung2002,
4102	<	author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
789	<	title = {Calculation of the rotational viscosity of a nematic liquid crystal},
790	<	journal = {Chemical Physics Letters},
791	<	year = {2002},
792	<	volume = {356},
793	<	pages = {140-146},
794	<	number = {1-2},
795	<	month = {Apr 15},
796	<	abstract = {Equilibrium molecular dynamics calculations have been performed for
4101	>	@article{Cheung2002,
4102	>	Abstract = {Equilibrium molecular dynamics calculations have been performed for
4103		the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile
4104		(PCH5) using a fully atomistic model. Simulation data has been obtained
4105		for a series of temperatures in the nematic phase. The rotational
#	Line 803 | Line 4109 | Encoding: GBK
4109		on the rotational diffusion co-efficient. We find good agreement
4110		between the first two methods and experimental values. (C) 2002
4111		Published by Elsevier Science B.V.},
4112	<	annote = {547KF Times Cited:8 Cited References Count:31},
4113	<	issn = {0009-2614},
4114	<	uri = {<Go to ISI>://000175331000020},
4115	<	}
4112	>	Annote = {547KF Times Cited:8 Cited References Count:31},
4113	>	Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
4114	>	Issn = {0009-2614},
4115	>	Journal = {Chemical Physics Letters},
4116	>	Month = {Apr 15},
4117	>	Number = {1-2},
4118	>	Pages = {140-146},
4119	>	Title = {Calculation of the rotational viscosity of a nematic liquid crystal},
4120	>	Uri = {<Go to ISI>://000175331000020},
4121	>	Volume = 356,
4122	>	Year = 2002}
4123
4124	<	@ARTICLE{Chin2004,
4125	<	author = {S. A. Chin},
813	<	title = {Dynamical multiple-time stepping methods for overcoming resonance
814	<	instabilities},
815	<	journal = {Journal of Chemical Physics},
816	<	year = {2004},
817	<	volume = {120},
818	<	pages = {8-13},
819	<	number = {1},
820	<	month = {Jan 1},
821	<	abstract = {Current molecular dynamics simulations of biomolecules using multiple
4124	>	@article{Chin2004,
4125	>	Abstract = {Current molecular dynamics simulations of biomolecules using multiple
4126		time steps to update the slowly changing force are hampered by instabilities
4127		beginning at time steps near the half period of the fastest vibrating
4128		mode. These #resonance# instabilities have became a critical barrier
#	Line 833 | Line 4137 | Encoding: GBK
4137		changing force, one must also update the position with a modified
4138		mass. Thus multiple-time stepping must be done dynamically. (C)
4139		2004 American Institute of Physics.},
4140	<	annote = {757TK Times Cited:1 Cited References Count:22},
4141	<	issn = {0021-9606},
4142	<	uri = {<Go to ISI>://000187577400003},
4143	<	}
4140	>	Annote = {757TK Times Cited:1 Cited References Count:22},
4141	>	Author = {S. A. Chin},
4142	>	Issn = {0021-9606},
4143	>	Journal = {Journal of Chemical Physics},
4144	>	Month = {Jan 1},
4145	>	Number = 1,
4146	>	Pages = {8-13},
4147	>	Title = {Dynamical multiple-time stepping methods for overcoming resonance instabilities},
4148	>	Uri = {<Go to ISI>://000187577400003},
4149	>	Volume = 120,
4150	>	Year = 2004}
4151
4152	<	@ARTICLE{Cook2000,
4153	<	author = {M. J. Cook and M. R. Wilson},
843	<	title = {Simulation studies of dipole correlation in the isotropic liquid
844	<	phase},
845	<	journal = {Liquid Crystals},
846	<	year = {2000},
847	<	volume = {27},
848	<	pages = {1573-1583},
849	<	number = {12},
850	<	month = {Dec},
851	<	abstract = {The Kirkwood correlation factor g(1) determines the preference for
4152	>	@article{Cook2000,
4153	>	Abstract = {The Kirkwood correlation factor g(1) determines the preference for
4154		local parallel or antiparallel dipole association in the isotropic
4155		phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood
4156		factors greater than 1 have an enhanced effective dipole moment
#	Line 864 | Line 4166 | Encoding: GBK
4166		experimental dielectric measurements. Analysis of the molecular
4167		dynamics trajectories allows an assessment of why these molecules
4168		behave differently.},
4169	<	annote = {376BF Times Cited:10 Cited References Count:16},
4170	<	issn = {0267-8292},
4171	<	uri = {<Go to ISI>://000165437800002},
4172	<	}
4169	>	Annote = {376BF Times Cited:10 Cited References Count:16},
4170	>	Author = {M. J. Cook and M. R. Wilson},
4171	>	Issn = {0267-8292},
4172	>	Journal = {Liquid Crystals},
4173	>	Month = {Dec},
4174	>	Number = 12,
4175	>	Pages = {1573-1583},
4176	>	Title = {Simulation studies of dipole correlation in the isotropic liquid phase},
4177	>	Uri = {<Go to ISI>://000165437800002},
4178	>	Volume = 27,
4179	>	Year = 2000}
4180
4181	<	@ARTICLE{Cui2003,
4182	<	author = {B. X. Cui and M. Y. Shen and K. F. Freed},
874	<	title = {Folding and misfolding of the papillomavirus E6 interacting peptide
875	<	E6ap},
876	<	journal = {Proceedings of the National Academy of Sciences of the United States
877	<	of America},
878	<	year = {2003},
879	<	volume = {100},
880	<	pages = {7087-7092},
881	<	number = {12},
882	<	month = {Jun 10},
883	<	abstract = {All-atom Langevin dynamics simulations have been performed to study
4181	>	@article{Cui2003,
4182	>	Abstract = {All-atom Langevin dynamics simulations have been performed to study
4183		the folding pathways of the 18-residue binding domain fragment E6ap
4184		of the human papillomavirus E6 interacting peptide. Six independent
4185		folding trajectories, with a total duration of nearly 2 mus, all
#	Line 897 | Line 4196 | Encoding: GBK
4196		reveals a significant barrier between the basins separating the
4197		native and misfolded states. We also discuss the various underlying
4198		forces that drive the peptide into its native state.},
4199	<	annote = {689LC Times Cited:3 Cited References Count:48},
4200	<	issn = {0027-8424},
4201	<	uri = {<Go to ISI>://000183493500037},
4202	<	}
4199	>	Annote = {689LC Times Cited:3 Cited References Count:48},
4200	>	Author = {B. X. Cui and M. Y. Shen and K. F. Freed},
4201	>	Issn = {0027-8424},
4202	>	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
4203	>	Month = {Jun 10},
4204	>	Number = 12,
4205	>	Pages = {7087-7092},
4206	>	Title = {Folding and misfolding of the papillomavirus E6 interacting peptide E6ap},
4207	>	Uri = {<Go to ISI>://000183493500037},
4208	>	Volume = 100,
4209	>	Year = 2003}
4210
4211	<	@ARTICLE{Denisov2003,
4212	<	author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou},
907	<	title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
908	<	journal = {Physical Review B},
909	<	year = {2003},
910	<	volume = {67},
911	<	pages = {-},
912	<	number = {1},
913	<	month = {Jan 1},
914	<	abstract = {We study the slow phase of thermally activated magnetic relaxation
4211	>	@article{Denisov2003,
4212	>	Abstract = {We study the slow phase of thermally activated magnetic relaxation
4213		in finite two-dimensional ensembles of dipolar interacting ferromagnetic
4214		nanoparticles whose easy axes of magnetization are perpendicular
4215		to the distribution plane. We develop a method to numerically simulate
#	Line 921 | Line 4219 | Encoding: GBK
4219		Within this framework, we analyze in detail the role that the correlations
4220		of the nanoparticle magnetic moments and the finite size of the
4221		nanoparticle ensemble play in magnetic relaxation.},
4222	<	annote = {642XH Times Cited:11 Cited References Count:31},
4223	<	issn = {1098-0121},
4224	<	uri = {<Go to ISI>://000180830400056},
4225	<	}
4222	>	Annote = {642XH Times Cited:11 Cited References Count:31},
4223	>	Author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou},
4224	>	Issn = {1098-0121},
4225	>	Journal = {Physical Review B},
4226	>	Month = {Jan 1},
4227	>	Number = 1,
4228	>	Pages = {-},
4229	>	Title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
4230	>	Uri = {<Go to ISI>://000180830400056},
4231	>	Volume = 67,
4232	>	Year = 2003}
4233
4234	<	@ARTICLE{Derreumaux1998,
4235	<	author = {P. Derreumaux and T. Schlick},
931	<	title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
932	<	journal = {Biophysical Journal},
933	<	year = {1998},
934	<	volume = {74},
935	<	pages = {72-81},
936	<	number = {1},
937	<	month = {Jan},
938	<	abstract = {To explore the origin of the large-scale motion of triosephosphate
4234	>	@article{Derreumaux1998,
4235	>	Abstract = {To explore the origin of the large-scale motion of triosephosphate
4236		isomerase's flexible loop (residues 166 to 176) at the active site,
4237		several simulation protocols are employed both for the free enzyme
4238		in vacuo and for the free enzyme with some solvent modeling: high-temperature
#	Line 959 | Line 4256 | Encoding: GBK
4256		is of rigid-body type and that the specific interaction between
4257		residues Ala(176) and Tyr(208) plays a crucial role in the loop
4258		opening/closing mechanism.},
4259	<	annote = {Zl046 Times Cited:30 Cited References Count:29},
4260	<	issn = {0006-3495},
4261	<	uri = {<Go to ISI>://000073393400009},
4262	<	}
4259	>	Annote = {Zl046 Times Cited:30 Cited References Count:29},
4260	>	Author = {P. Derreumaux and T. Schlick},
4261	>	Issn = {0006-3495},
4262	>	Journal = {Biophysical Journal},
4263	>	Month = {Jan},
4264	>	Number = 1,
4265	>	Pages = {72-81},
4266	>	Title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
4267	>	Uri = {<Go to ISI>://000073393400009},
4268	>	Volume = 74,
4269	>	Year = 1998}
4270
4271	<	@ARTICLE{Dullweber1997,
4272	<	author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
969	<	title = {Symplectic splitting methods for rigid body molecular dynamics},
970	<	journal = {Journal of Chemical Physics},
971	<	year = {1997},
972	<	volume = {107},
973	<	pages = {5840-5851},
974	<	number = {15},
975	<	month = {Oct 15},
976	<	abstract = {Rigid body molecular models possess symplectic structure and time-reversal
4271	>	@article{Dullweber1997,
4272	>	Abstract = {Rigid body molecular models possess symplectic structure and time-reversal
4273		symmetry. Standard numerical integration methods destroy both properties,
4274		introducing nonphysical dynamical behavior such as numerically induced
4275		dissipative states and drift in the energy during long term simulations.
#	Line 992 | Line 4288 | Encoding: GBK
4288		model of water. Our experiments show that the symplectic-reversible
4289		scheme is far superior to the more traditional quaternion method.
4290		(C) 1997 American Institute of Physics.},
4291	<	annote = {Ya587 Times Cited:35 Cited References Count:32},
4292	<	issn = {0021-9606},
4293	<	uri = {<Go to ISI>://A1997YA58700024},
4294	<	}
4291	>	Annote = {Ya587 Times Cited:35 Cited References Count:32},
4292	>	Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
4293	>	Issn = {0021-9606},
4294	>	Journal = {Journal of Chemical Physics},
4295	>	Month = {Oct 15},
4296	>	Number = 15,
4297	>	Pages = {5840-5851},
4298	>	Title = {Symplectic splitting methods for rigid body molecular dynamics},
4299	>	Uri = {<Go to ISI>://A1997YA58700024},
4300	>	Volume = 107,
4301	>	Year = 1997}
4302
4303	<	@BOOK{Gamma1994,
4304	<	title = {Design Patterns: Elements of Reusable Object-Oriented Software},
4305	<	publisher = {Perason Education},
4306	<	year = {1994},
4307	<	author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
4308	<	address = {London},
4309	<	chapter = {7},
1007	<	}
4303	>	@book{Gamma1994,
4304	>	Address = {London},
4305	>	Author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
4306	>	Chapter = 7,
4307	>	Publisher = {Perason Education},
4308	>	Title = {Design Patterns: Elements of Reusable Object-Oriented Software},
4309	>	Year = 1994}
4310
4311	<	@ARTICLE{Edwards2005,
4312	<	author = {S. A. Edwards and D. R. M. Williams},
1011	<	title = {Stretching a single diblock copolymer in a selective solvent: Langevin
1012	<	dynamics simulations},
1013	<	journal = {Macromolecules},
1014	<	year = {2005},
1015	<	volume = {38},
1016	<	pages = {10590-10595},
1017	<	number = {25},
1018	<	month = {Dec 13},
1019	<	abstract = {Using the Langevin dynamics technique, we have carried out simulations
4311	>	@article{Edwards2005,
4312	>	Abstract = {Using the Langevin dynamics technique, we have carried out simulations
4313		of a single-chain flexible diblock copolymer. The polymer consists
4314		of two blocks of equal length, one very poorly solvated and the
4315		other close to theta-conditions. We study what happens when such
#	Line 1026 | Line 4319 | Encoding: GBK
4319		not increase monotonically, in disagreement with earlier predictions,
4320		and that at high speeds there is a strong dependence on which end
4321		of the polymer is pulled, as well as a high level of hysteresis.},
4322	<	annote = {992EC Times Cited:0 Cited References Count:13},
4323	<	issn = {0024-9297},
4324	<	uri = {<Go to ISI>://000233866200035},
4325	<	}
4322	>	Annote = {992EC Times Cited:0 Cited References Count:13},
4323	>	Author = {S. A. Edwards and D. R. M. Williams},
4324	>	Issn = {0024-9297},
4325	>	Journal = {Macromolecules},
4326	>	Month = {Dec 13},
4327	>	Number = 25,
4328	>	Pages = {10590-10595},
4329	>	Title = {Stretching a single diblock copolymer in a selective solvent: Langevin dynamics simulations},
4330	>	Uri = {<Go to ISI>://000233866200035},
4331	>	Volume = 38,
4332	>	Year = 2005}
4333
4334	<	@ARTICLE{Egberts1988,
4335	<	author = {E. Egberts and H. J. C. Berendsen},
4336	<	title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic
4337	<	Detail},
4338	<	journal = {Journal of Chemical Physics},
4339	<	year = {1988},
4340	<	volume = {89},
4341	<	pages = {3718-3732},
4342	<	number = {6},
4343	<	month = {Sep 15},
4344	<	annote = {Q0188 Times Cited:219 Cited References Count:43},
4345	<	issn = {0021-9606},
1046	<	uri = {<Go to ISI>://A1988Q018800036},
1047	<	}
4334	>	@article{Egberts1988,
4335	>	Annote = {Q0188 Times Cited:219 Cited References Count:43},
4336	>	Author = {E. Egberts and H. J. C. Berendsen},
4337	>	Issn = {0021-9606},
4338	>	Journal = {Journal of Chemical Physics},
4339	>	Month = {Sep 15},
4340	>	Number = 6,
4341	>	Pages = {3718-3732},
4342	>	Title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic Detail},
4343	>	Uri = {<Go to ISI>://A1988Q018800036},
4344	>	Volume = 89,
4345	>	Year = 1988}
4346
4347	<	@ARTICLE{Ermak1978,
4348	<	author = {D. L. Ermak and J. A. Mccammon},
4349	<	title = {Brownian Dynamics with Hydrodynamic Interactions},
4350	<	journal = {Journal of Chemical Physics},
4351	<	year = {1978},
4352	<	volume = {69},
4353	<	pages = {1352-1360},
4354	<	number = {4},
4355	<	annote = {Fp216 Times Cited:785 Cited References Count:42},
4356	<	issn = {0021-9606},
4357	<	uri = {<Go to ISI>://A1978FP21600004},
1060	<	}
4347	>	@article{Ermak1978,
4348	>	Annote = {Fp216 Times Cited:785 Cited References Count:42},
4349	>	Author = {D. L. Ermak and J. A. Mccammon},
4350	>	Issn = {0021-9606},
4351	>	Journal = {Journal of Chemical Physics},
4352	>	Number = 4,
4353	>	Pages = {1352-1360},
4354	>	Title = {Brownian Dynamics with Hydrodynamic Interactions},
4355	>	Uri = {<Go to ISI>://A1978FP21600004},
4356	>	Volume = 69,
4357	>	Year = 1978}
4358
4359	<	@ARTICLE{Evans1977,
4360	<	author = {D. J. Evans},
4361	<	title = {Representation of Orientation Space},
4362	<	journal = {Molecular Physics},
4363	<	year = {1977},
4364	<	volume = {34},
4365	<	pages = {317-325},
4366	<	number = {2},
4367	<	annote = {Ds757 Times Cited:271 Cited References Count:18},
4368	<	issn = {0026-8976},
4369	<	uri = {<Go to ISI>://A1977DS75700002},
1073	<	}
4359	>	@article{Evans1977,
4360	>	Annote = {Ds757 Times Cited:271 Cited References Count:18},
4361	>	Author = {D. J. Evans},
4362	>	Issn = {0026-8976},
4363	>	Journal = {Molecular Physics},
4364	>	Number = 2,
4365	>	Pages = {317-325},
4366	>	Title = {Representation of Orientation Space},
4367	>	Uri = {<Go to ISI>://A1977DS75700002},
4368	>	Volume = 34,
4369	>	Year = 1977}
4370
4371	<	@ARTICLE{Fennell2004,
4372	<	author = {C. J. Fennell and J. D. Gezelter},
1077	<	title = {On the structural and transport properties of the soft sticky dipole
1078	<	and related single-point water models},
1079	<	journal = {Journal of Chemical Physics},
1080	<	year = {2004},
1081	<	volume = {120},
1082	<	pages = {9175-9184},
1083	<	number = {19},
1084	<	month = {May 15},
1085	<	abstract = {The density maximum and temperature dependence of the self-diffusion
4371	>	@article{Fennell2004,
4372	>	Abstract = {The density maximum and temperature dependence of the self-diffusion
4373		constant were investigated for the soft sticky dipole (SSD) water
4374		model and two related reparametrizations of this single-point model.
4375		A combination of microcanonical and isobaric-isothermal molecular
#	Line 1105 | Line 4392 | Encoding: GBK
4392		ice structure is presented which appears to be the most stable ice
4393		structure for the entire SSD family. (C) 2004 American Institute
4394		of Physics.},
4395	<	annote = {816YY Times Cited:5 Cited References Count:39},
4396	<	issn = {0021-9606},
4397	<	uri = {<Go to ISI>://000221146400032},
4398	<	}
4395	>	Annote = {816YY Times Cited:5 Cited References Count:39},
4396	>	Author = {C. J. Fennell and J. D. Gezelter},
4397	>	Issn = {0021-9606},
4398	>	Journal = {Journal of Chemical Physics},
4399	>	Month = {May 15},
4400	>	Number = 19,
4401	>	Pages = {9175-9184},
4402	>	Title = {On the structural and transport properties of the soft sticky dipole and related single-point water models},
4403	>	Uri = {<Go to ISI>://000221146400032},
4404	>	Volume = 120,
4405	>	Year = 2004}
4406
4407	<	@ARTICLE{Fernandes2002,
4408	<	author = {M. X. Fernandes and J. G. {de la Torre}},
1115	<	title = {Brownian dynamics simulation of rigid particles of arbitrary shape
1116	<	in external fields},
1117	<	journal = {Biophysical Journal},
1118	<	year = {2002},
1119	<	volume = {83},
1120	<	pages = {3039-3048},
1121	<	number = {6},
1122	<	month = {Dec},
1123	<	abstract = {We have developed a Brownian dynamics simulation algorithm to generate
4407	>	@article{Fernandes2002,
4408	>	Abstract = {We have developed a Brownian dynamics simulation algorithm to generate
4409		Brownian trajectories of an isolated, rigid particle of arbitrary
4410		shape in the presence of electric fields or any other external agents.
4411		Starting from the generalized diffusion tensor, which can be calculated
#	Line 1131 | Line 4416 | Encoding: GBK
4416		method, which serve as tests of its performance, and also illustrate
4417		its applicability. Examples include free diffusion, transport in
4418		an electric field, and diffusion in a restricting environment.},
4419	<	annote = {633AD Times Cited:2 Cited References Count:43},
4420	<	issn = {0006-3495},
4421	<	uri = {<Go to ISI>://000180256300012},
4422	<	}
4419	>	Annote = {633AD Times Cited:2 Cited References Count:43},
4420	>	Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4421	>	Issn = {0006-3495},
4422	>	Journal = {Biophysical Journal},
4423	>	Month = {Dec},
4424	>	Number = 6,
4425	>	Pages = {3039-3048},
4426	>	Title = {Brownian dynamics simulation of rigid particles of arbitrary shape in external fields},
4427	>	Uri = {<Go to ISI>://000180256300012},
4428	>	Volume = 83,
4429	>	Year = 2002}
4430
4431	<	@BOOK{Frenkel1996,
4432	<	title = {Understanding Molecular Simulation : From Algorithms to Applications},
4433	<	publisher = {Academic Press},
4434	<	year = {1996},
4435	<	author = {D. Frenkel and B. Smit},
4436	<	address = {New York},
1145	<	}
4431	>	@book{Frenkel1996,
4432	>	Address = {New York},
4433	>	Author = {D. Frenkel and B. Smit},
4434	>	Publisher = {Academic Press},
4435	>	Title = {Understanding Molecular Simulation : From Algorithms to Applications},
4436	>	Year = 1996}
4437
4438	<	@ARTICLE{Gay1981,
4439	<	author = {J. G. Gay and B. J. Berne},
4440	<	title = {Modification of the Overlap Potential to Mimic a Linear Site-Site
4441	<	Potential},
4442	<	journal = {Journal of Chemical Physics},
4443	<	year = {1981},
4444	<	volume = {74},
4445	<	pages = {3316-3319},
4446	<	number = {6},
4447	<	annote = {Lj347 Times Cited:482 Cited References Count:13},
4448	<	issn = {0021-9606},
1158	<	uri = {<Go to ISI>://A1981LJ34700029},
1159	<	}
4438	>	@article{Gay1981,
4439	>	Annote = {Lj347 Times Cited:482 Cited References Count:13},
4440	>	Author = {J. G. Gay and B. J. Berne},
4441	>	Issn = {0021-9606},
4442	>	Journal = {Journal of Chemical Physics},
4443	>	Number = 6,
4444	>	Pages = {3316-3319},
4445	>	Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
4446	>	Uri = {<Go to ISI>://A1981LJ34700029},
4447	>	Volume = 74,
4448	>	Year = 1981}
4449
4450	<	@ARTICLE{Gelin1999,
4451	<	author = {M. F. Gelin},
1163	<	title = {Inertial effects in the Brownian dynamics with rigid constraints},
1164	<	journal = {Macromolecular Theory and Simulations},
1165	<	year = {1999},
1166	<	volume = {8},
1167	<	pages = {529-543},
1168	<	number = {6},
1169	<	month = {Nov},
1170	<	abstract = {To investigate the influence of inertial effects on the dynamics of
4450	>	@article{Gelin1999,
4451	>	Abstract = {To investigate the influence of inertial effects on the dynamics of
4452		an assembly of beads subjected to rigid constraints and placed in
4453		a buffer medium, a convenient method to introduce suitable generalized
4454		coordinates is presented. Without any restriction on the nature
#	Line 1185 | Line 4466 | Encoding: GBK
4466		behavior, which is irreproducible within the standard diffusion
4467		equation. Several methods are considered for the approximate solution
4468		of the DEM, and their application to three dimensional DEMs is discussed.},
4469	<	annote = {257MM Times Cited:2 Cited References Count:82},
4470	<	issn = {1022-1344},
4471	<	uri = {<Go to ISI>://000083785700002},
4472	<	}
4469	>	Annote = {257MM Times Cited:2 Cited References Count:82},
4470	>	Author = {M. F. Gelin},
4471	>	Issn = {1022-1344},
4472	>	Journal = {Macromolecular Theory and Simulations},
4473	>	Month = {Nov},
4474	>	Number = 6,
4475	>	Pages = {529-543},
4476	>	Title = {Inertial effects in the Brownian dynamics with rigid constraints},
4477	>	Uri = {<Go to ISI>://000083785700002},
4478	>	Volume = 8,
4479	>	Year = 1999}
4480
4481	<	@ARTICLE{Goetz1998,
4482	<	author = {R. Goetz and R. Lipowsky},
4483	<	title = {Computer simulations of bilayer membranes: Self-assembly and interfacial
4484	<	tension},
4485	<	journal = {Journal of Chemical Physics},
4486	<	year = {1998},
4487	<	volume = {108},
4488	<	pages = {7397},
1201	<	number = {17},
1202	<	}
4481	>	@article{Goetz1998,
4482	>	Author = {R. Goetz and R. Lipowsky},
4483	>	Journal = {Journal of Chemical Physics},
4484	>	Number = 17,
4485	>	Pages = 7397,
4486	>	Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
4487	>	Volume = 108,
4488	>	Year = 1998}
4489
4490	<	@BOOK{Goldstein2001,
4491	<	title = {Classical Mechanics},
4492	<	publisher = {Addison Wesley},
4493	<	year = {2001},
4494	<	author = {H. Goldstein and C. Poole and J. Safko},
4495	<	address = {San Francisco},
4496	<	edition = {3rd},
1211	<	}
4490	>	@book{Goldstein2001,
4491	>	Address = {San Francisco},
4492	>	Author = {H. Goldstein and C. Poole and J. Safko},
4493	>	Edition = {3rd},
4494	>	Publisher = {Addison Wesley},
4495	>	Title = {Classical Mechanics},
4496	>	Year = 2001}
4497
4498	<	@ARTICLE{Gray2003,
4499	<	author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and
1215	<	B. Kuhlman and C. A. Rohl and D. Baker},
1216	<	title = {Protein-protein docking with simultaneous optimization of rigid-body
1217	<	displacement and side-chain conformations},
1218	<	journal = {Journal of Molecular Biology},
1219	<	year = {2003},
1220	<	volume = {331},
1221	<	pages = {281-299},
1222	<	number = {1},
1223	<	month = {Aug 1},
1224	<	abstract = {Protein-protein docking algorithms provide a means to elucidate structural
4498	>	@article{Gray2003,
4499	>	Abstract = {Protein-protein docking algorithms provide a means to elucidate structural
4500		details for presently unknown complexes. Here, we present and evaluate
4501		a new method to predict protein-protein complexes from the coordinates
4502		of the unbound monomer components. The method employs a low-resolution,
#	Line 1245 | Line 4520 | Encoding: GBK
4520		but they also highlight the challenges that must be met to achieve
4521		consistent and accurate prediction of protein-protein interactions.
4522		(C) 2003 Elsevier Ltd. All rights reserved.},
4523	<	annote = {704QL Times Cited:48 Cited References Count:60},
4524	<	issn = {0022-2836},
4525	<	uri = {<Go to ISI>://000184351300022},
4526	<	}
4523	>	Annote = {704QL Times Cited:48 Cited References Count:60},
4524	>	Author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and B. Kuhlman and C. A. Rohl and D. Baker},
4525	>	Issn = {0022-2836},
4526	>	Journal = {Journal of Molecular Biology},
4527	>	Month = {Aug 1},
4528	>	Number = 1,
4529	>	Pages = {281-299},
4530	>	Title = {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations},
4531	>	Uri = {<Go to ISI>://000184351300022},
4532	>	Volume = 331,
4533	>	Year = 2003}
4534
4535	<	@ARTICLE{Greengard1994,
4536	<	author = {L. Greengard},
1255	<	title = {Fast Algorithms for Classical Physics},
1256	<	journal = {Science},
1257	<	year = {1994},
1258	<	volume = {265},
1259	<	pages = {909-914},
1260	<	number = {5174},
1261	<	month = {Aug 12},
1262	<	abstract = {Some of the recently developed fast summation methods that have arisen
4535	>	@article{Greengard1994,
4536	>	Abstract = {Some of the recently developed fast summation methods that have arisen
4537		in scientific computing are described. These methods require an
4538		amount of work proportional to N or N log N to evaluate all pairwise
4539		interactions in an ensemble of N particles. Traditional methods,
#	Line 1268 | Line 4542 | Encoding: GBK
4542		computer resources. In combination with supercomputers, it is possible
4543		to address questions that were previously out of reach. Problems
4544		from diffusion, gravitation, and wave propagation are considered.},
4545	<	annote = {Pb499 Times Cited:99 Cited References Count:44},
4546	<	issn = {0036-8075},
4547	<	uri = {<Go to ISI>://A1994PB49900031},
4548	<	}
4545	>	Annote = {Pb499 Times Cited:99 Cited References Count:44},
4546	>	Author = {L. Greengard},
4547	>	Issn = {0036-8075},
4548	>	Journal = {Science},
4549	>	Month = {Aug 12},
4550	>	Number = 5174,
4551	>	Pages = {909-914},
4552	>	Title = {Fast Algorithms for Classical Physics},
4553	>	Uri = {<Go to ISI>://A1994PB49900031},
4554	>	Volume = 265,
4555	>	Year = 1994}
4556
4557	<	@ARTICLE{Greengard1987,
4558	<	author = {L. Greengard and V. Rokhlin},
4559	<	title = {A Fast Algorithm for Particle Simulations},
4560	<	journal = {Journal of Computational Physics},
4561	<	year = {1987},
4562	<	volume = {73},
4563	<	pages = {325-348},
4564	<	number = {2},
4565	<	month = {Dec},
4566	<	annote = {L0498 Times Cited:899 Cited References Count:7},
4567	<	issn = {0021-9991},
4568	<	uri = {<Go to ISI>://A1987L049800006},
1288	<	}
4557	>	@article{Greengard1987,
4558	>	Annote = {L0498 Times Cited:899 Cited References Count:7},
4559	>	Author = {L. Greengard and V. Rokhlin},
4560	>	Issn = {0021-9991},
4561	>	Journal = {Journal of Computational Physics},
4562	>	Month = {Dec},
4563	>	Number = 2,
4564	>	Pages = {325-348},
4565	>	Title = {A Fast Algorithm for Particle Simulations},
4566	>	Uri = {<Go to ISI>://A1987L049800006},
4567	>	Volume = 73,
4568	>	Year = 1987}
4569
4570	<	@ARTICLE{Hairer1997,
4571	<	author = {E. Hairer and C. Lubich},
1292	<	title = {The life-span of backward error analysis for numerical integrators},
1293	<	journal = {Numerische Mathematik},
1294	<	year = {1997},
1295	<	volume = {76},
1296	<	pages = {441-462},
1297	<	number = {4},
1298	<	month = {Jun},
1299	<	abstract = {Backward error analysis is a useful tool for the study of numerical
4570	>	@article{Hairer1997,
4571	>	Abstract = {Backward error analysis is a useful tool for the study of numerical
4572		approximations to ordinary differential equations. The numerical
4573		solution is formally interpreted as the exact solution of a perturbed
4574		differential equation, given as a formal and usually divergent series
#	Line 1309 | Line 4581 | Encoding: GBK
4581		near hyperbolic equilibrium points, to asymptotically stable periodic
4582		orbits and Hopf bifurcation, and to energy conservation and approximation
4583		of invariant tori in Hamiltonian systems.},
4584	<	annote = {Xj488 Times Cited:50 Cited References Count:19},
4585	<	issn = {0029-599X},
4586	<	uri = {<Go to ISI>://A1997XJ48800002},
4587	<	}
4584	>	Annote = {Xj488 Times Cited:50 Cited References Count:19},
4585	>	Author = {E. Hairer and C. Lubich},
4586	>	Issn = {0029-599X},
4587	>	Journal = {Numerische Mathematik},
4588	>	Month = {Jun},
4589	>	Number = 4,
4590	>	Pages = {441-462},
4591	>	Title = {The life-span of backward error analysis for numerical integrators},
4592	>	Uri = {<Go to ISI>://A1997XJ48800002},
4593	>	Volume = 76,
4594	>	Year = 1997}
4595
4596	<	@ARTICLE{Hao1993,
4597	<	author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga},
1319	<	title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic
1320	<	Trypsin-Inhibitor Studied by Computer-Simulations},
1321	<	journal = {Biochemistry},
1322	<	year = {1993},
1323	<	volume = {32},
1324	<	pages = {9614-9631},
1325	<	number = {37},
1326	<	month = {Sep 21},
1327	<	abstract = {A new procedure for studying the folding and unfolding of proteins,
4596	>	@article{Hao1993,
4597	>	Abstract = {A new procedure for studying the folding and unfolding of proteins,
4598		with an application to bovine pancreatic trypsin inhibitor (BPTI),
4599		is reported. The unfolding and refolding of the native structure
4600		of the protein are characterized by the dimensions of the protein,
#	Line 1358 | Line 4628 | Encoding: GBK
4628		progressive formation of partially folded structural units, followed
4629		by collapse to the compact native structure. The general applicability
4630		of the procedure is also discussed.},
4631	<	annote = {Ly294 Times Cited:27 Cited References Count:57},
4632	<	issn = {0006-2960},
4633	<	uri = {<Go to ISI>://A1993LY29400014},
4634	<	}
4631	>	Annote = {Ly294 Times Cited:27 Cited References Count:57},
4632	>	Author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga},
4633	>	Issn = {0006-2960},
4634	>	Journal = {Biochemistry},
4635	>	Month = {Sep 21},
4636	>	Number = 37,
4637	>	Pages = {9614-9631},
4638	>	Title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic Trypsin-Inhibitor Studied by Computer-Simulations},
4639	>	Uri = {<Go to ISI>://A1993LY29400014},
4640	>	Volume = 32,
4641	>	Year = 1993}
4642
4643	<	@ARTICLE{Hinsen2000,
4644	<	author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel
1368	<	and G. R. Kneller},
1369	<	title = {Harmonicity in slow protein dynamics},
1370	<	journal = {Chemical Physics},
1371	<	year = {2000},
1372	<	volume = {261},
1373	<	pages = {25-37},
1374	<	number = {1-2},
1375	<	month = {Nov 1},
1376	<	abstract = {The slow dynamics of proteins around its native folded state is usually
4643	>	@article{Hinsen2000,
4644	>	Abstract = {The slow dynamics of proteins around its native folded state is usually
4645		described by diffusion in a strongly anharmonic potential. In this
4646		paper, we try to understand the form and origin of the anharmonicities,
4647		with the principal aim of gaining a better understanding of the
#	Line 1400 | Line 4668 | Encoding: GBK
4668		MD simulations, which are best suited for detailed studies on smaller
4669		systems or for shorter time scales. (C) 2000 Elsevier Science B.V.
4670		All rights reserved.},
4671	<	annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31},
4672	<	issn = {0301-0104},
4673	<	uri = {<Go to ISI>://000090121700003},
4674	<	}
4671	>	Annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31},
4672	>	Author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel and G. R. Kneller},
4673	>	Issn = {0301-0104},
4674	>	Journal = {Chemical Physics},
4675	>	Month = {Nov 1},
4676	>	Number = {1-2},
4677	>	Pages = {25-37},
4678	>	Title = {Harmonicity in slow protein dynamics},
4679	>	Uri = {<Go to ISI>://000090121700003},
4680	>	Volume = 261,
4681	>	Year = 2000}
4682
4683	<	@ARTICLE{Ho1992,
4684	<	author = {C. Ho and C. D. Stubbs},
1410	<	title = {Hydration at the Membrane Protein-Lipid Interface},
1411	<	journal = {Biophysical Journal},
1412	<	year = {1992},
1413	<	volume = {63},
1414	<	pages = {897-902},
1415	<	number = {4},
1416	<	month = {Oct},
1417	<	abstract = {Evidence has been found for the existence water at the protein-lipid
4683	>	@article{Ho1992,
4684	>	Abstract = {Evidence has been found for the existence water at the protein-lipid
4685		hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome
4686		C, using two related fluorescence spectroscopic approaches. The
4687		first approach exploited the fact that the presence of water in
#	Line 1441 | Line 4708 | Encoding: GBK
4708		hydration at the protein-lipid interface could affect conformation,
4709		thereby offering a new route by which membrane protein functioning
4710		may be modified.},
4711	<	annote = {Ju251 Times Cited:55 Cited References Count:44},
4712	<	issn = {0006-3495},
4713	<	uri = {<Go to ISI>://A1992JU25100002},
4714	<	}
4711	>	Annote = {Ju251 Times Cited:55 Cited References Count:44},
4712	>	Author = {C. Ho and C. D. Stubbs},
4713	>	Issn = {0006-3495},
4714	>	Journal = {Biophysical Journal},
4715	>	Month = {Oct},
4716	>	Number = 4,
4717	>	Pages = {897-902},
4718	>	Title = {Hydration at the Membrane Protein-Lipid Interface},
4719	>	Uri = {<Go to ISI>://A1992JU25100002},
4720	>	Volume = 63,
4721	>	Year = 1992}
4722
4723	<	@BOOK{Hockney1981,
4724	<	title = {Computer Simulation Using Particles},
4725	<	publisher = {McGraw-Hill},
4726	<	year = {1981},
4727	<	author = {R.W. Hockney and J.W. Eastwood},
4728	<	address = {New York},
1455	<	}
4723	>	@book{Hockney1981,
4724	>	Address = {New York},
4725	>	Author = {R.W. Hockney and J.W. Eastwood},
4726	>	Publisher = {McGraw-Hill},
4727	>	Title = {Computer Simulation Using Particles},
4728	>	Year = 1981}
4729
4730	<	@ARTICLE{Hoover1985,
4731	<	author = {W. G. Hoover},
4732	<	title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
4733	<	journal = {Physical Review A},
4734	<	year = {1985},
4735	<	volume = {31},
4736	<	pages = {1695-1697},
4737	<	number = {3},
4738	<	annote = {Acr30 Times Cited:1809 Cited References Count:11},
4739	<	issn = {1050-2947},
4740	<	uri = {<Go to ISI>://A1985ACR3000056},
1468	<	}
4730	>	@article{Hoover1985,
4731	>	Annote = {Acr30 Times Cited:1809 Cited References Count:11},
4732	>	Author = {W. G. Hoover},
4733	>	Issn = {1050-2947},
4734	>	Journal = {Physical Review A},
4735	>	Number = 3,
4736	>	Pages = {1695-1697},
4737	>	Title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
4738	>	Uri = {<Go to ISI>://A1985ACR3000056},
4739	>	Volume = 31,
4740	>	Year = 1985}
4741
4742	<	@ARTICLE{Huh2004,
4743	<	author = {Y. Huh and N. M. Cann},
1472	<	title = {Discrimination in isotropic, nematic, and smectic phases of chiral
1473	<	calamitic molecules: A computer simulation study},
1474	<	journal = {Journal of Chemical Physics},
1475	<	year = {2004},
1476	<	volume = {121},
1477	<	pages = {10299-10308},
1478	<	number = {20},
1479	<	month = {Nov 22},
1480	<	abstract = {Racemic fluids of chiral calamitic molecules are investigated with
4742	>	@article{Huh2004,
4743	>	Abstract = {Racemic fluids of chiral calamitic molecules are investigated with
4744		molecular dynamics simulations. In particular, the phase behavior
4745		as a function of density is examined for eight racemates. The relationship
4746		between chiral discrimination and orientational order in the phase
#	Line 1487 | Line 4750 | Encoding: GBK
4750		Among ordered phases, discrimination is largest for smectic phases
4751		with a significant preference for heterochiral contact within the
4752		layers. (C) 2004 American Institute of Physics.},
4753	<	annote = {870FJ Times Cited:0 Cited References Count:63},
4754	<	issn = {0021-9606},
4755	<	uri = {<Go to ISI>://000225042700059},
4756	<	}
4753	>	Annote = {870FJ Times Cited:0 Cited References Count:63},
4754	>	Author = {Y. Huh and N. M. Cann},
4755	>	Issn = {0021-9606},
4756	>	Journal = {Journal of Chemical Physics},
4757	>	Month = {Nov 22},
4758	>	Number = 20,
4759	>	Pages = {10299-10308},
4760	>	Title = {Discrimination in isotropic, nematic, and smectic phases of chiral calamitic molecules: A computer simulation study},
4761	>	Uri = {<Go to ISI>://000225042700059},
4762	>	Volume = 121,
4763	>	Year = 2004}
4764
4765	<	@ARTICLE{Humphrey1996,
4766	<	author = {W. Humphrey and A. Dalke and K. Schulten},
1497	<	title = {VMD: Visual molecular dynamics},
1498	<	journal = {Journal of Molecular Graphics},
1499	<	year = {1996},
1500	<	volume = {14},
1501	<	pages = {33-\&},
1502	<	number = {1},
1503	<	month = {Feb},
1504	<	abstract = {VMD is a molecular graphics program designed for the display and analysis
4765	>	@article{Humphrey1996,
4766	>	Abstract = {VMD is a molecular graphics program designed for the display and analysis
4767		of molecular assemblies, in particular biopolymers such as proteins
4768		and nucleic acids. VMD can simultaneously display any number of
4769		structures using a wide variety of rendering styles and coloring
#	Line 1527 | Line 4789 | Encoding: GBK
4789		using an object-oriented design; the program, including source code
4790		and extensive documentation, is freely available via anonymous ftp
4791		and through the World Wide Web.},
4792	<	annote = {Uh515 Times Cited:1418 Cited References Count:19},
4793	<	issn = {0263-7855},
4794	<	uri = {<Go to ISI>://A1996UH51500005},
4795	<	}
4792	>	Annote = {Uh515 Times Cited:1418 Cited References Count:19},
4793	>	Author = {W. Humphrey and A. Dalke and K. Schulten},
4794	>	Issn = {0263-7855},
4795	>	Journal = {Journal of Molecular Graphics},
4796	>	Month = {Feb},
4797	>	Number = 1,
4798	>	Pages = {33-\&},
4799	>	Title = {VMD: Visual molecular dynamics},
4800	>	Uri = {<Go to ISI>://A1996UH51500005},
4801	>	Volume = 14,
4802	>	Year = 1996}
4803
4804	<	@ARTICLE{Izaguirre2001,
4805	<	author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
1537	<	title = {Langevin stabilization of molecular dynamics},
1538	<	journal = {Journal of Chemical Physics},
1539	<	year = {2001},
1540	<	volume = {114},
1541	<	pages = {2090-2098},
1542	<	number = {5},
1543	<	month = {Feb 1},
1544	<	abstract = {In this paper we show the possibility of using very mild stochastic
4804	>	@article{Izaguirre2001,
4805	>	Abstract = {In this paper we show the possibility of using very mild stochastic
4806		damping to stabilize long time step integrators for Newtonian molecular
4807		dynamics. More specifically, stable and accurate integrations are
4808		obtained for damping coefficients that are only a few percent of
#	Line 1568 | Line 4829 | Encoding: GBK
4829		of diffusion coefficients for flexible water and ER/ERE shows that
4830		when mild damping of up to 0.2 ps-1 is used the dynamics are not
4831		significantly distorted. (C) 2001 American Institute of Physics.},
4832	<	annote = {397CQ Times Cited:14 Cited References Count:36},
4833	<	issn = {0021-9606},
4834	<	uri = {<Go to ISI>://000166676100020},
4835	<	}
4832	>	Annote = {397CQ Times Cited:14 Cited References Count:36},
4833	>	Author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
4834	>	Issn = {0021-9606},
4835	>	Journal = {Journal of Chemical Physics},
4836	>	Month = {Feb 1},
4837	>	Number = 5,
4838	>	Pages = {2090-2098},
4839	>	Title = {Langevin stabilization of molecular dynamics},
4840	>	Uri = {<Go to ISI>://000166676100020},
4841	>	Volume = 114,
4842	>	Year = 2001}
4843
4844	<	@ARTICLE{Torre1977,
4845	<	author = {Jose Garcia De La Torre, V.A. Bloomfield},
4846	<	title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
4847	<	journal = {Biopolymers},
4848	<	year = {1977},
4849	<	volume = {16},
4850	<	pages = {1747-1763},
1583	<	}
4844	>	@article{Torre1977,
4845	>	Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield},
4846	>	Journal = {Biopolymers},
4847	>	Pages = {1747-1763},
4848	>	Title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
4849	>	Volume = 16,
4850	>	Year = 1977}
4851
4852	<	@ARTICLE{Kale1999,
4853	<	author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy
1587	<	and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan
1588	<	and K. Schulten},
1589	<	title = {NAMD2: Greater scalability for parallel molecular dynamics},
1590	<	journal = {Journal of Computational Physics},
1591	<	year = {1999},
1592	<	volume = {151},
1593	<	pages = {283-312},
1594	<	number = {1},
1595	<	month = {May 1},
1596	<	abstract = {Molecular dynamics programs simulate the behavior of biomolecular
4852	>	@article{Kale1999,
4853	>	Abstract = {Molecular dynamics programs simulate the behavior of biomolecular
4854		systems, leading to understanding of their functions. However, the
4855		computational complexity of such simulations is enormous. Parallel
4856		machines provide the potential to meet this computational challenge.
#	Line 1615 | Line 4872 | Encoding: GBK
4872		and has yielded speedups in excess of 180 on 220 processors. This
4873		paper also describes the performance obtained on some benchmark
4874		applications. (C) 1999 Academic Press.},
4875	<	annote = {194FM Times Cited:373 Cited References Count:51},
4876	<	issn = {0021-9991},
4877	<	uri = {<Go to ISI>://000080181500013},
4878	<	}
4875	>	Annote = {194FM Times Cited:373 Cited References Count:51},
4876	>	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},
4877	>	Issn = {0021-9991},
4878	>	Journal = {Journal of Computational Physics},
4879	>	Month = {May 1},
4880	>	Number = 1,
4881	>	Pages = {283-312},
4882	>	Title = {NAMD2: Greater scalability for parallel molecular dynamics},
4883	>	Uri = {<Go to ISI>://000080181500013},
4884	>	Volume = 151,
4885	>	Year = 1999}
4886
4887	<	@ARTICLE{Kane2000,
4888	<	author = {C. Kane and J. E. Marsden and M. Ortiz and M. West},
1625	<	title = {Variational integrators and the Newmark algorithm for conservative
1626	<	and dissipative mechanical systems},
1627	<	journal = {International Journal for Numerical Methods in Engineering},
1628	<	year = {2000},
1629	<	volume = {49},
1630	<	pages = {1295-1325},
1631	<	number = {10},
1632	<	month = {Dec 10},
1633	<	abstract = {The purpose of this work is twofold. First, we demonstrate analytically
4887	>	@article{Kane2000,
4888	>	Abstract = {The purpose of this work is twofold. First, we demonstrate analytically
4889		that the classical Newmark family as well as related integration
4890		algorithms are variational in the sense of the Veselov formulation
4891		of discrete mechanics. Such variational algorithms are well known
#	Line 1646 | Line 4901 | Encoding: GBK
4901		in terms of obtaining the correct amounts by which the energy changes
4902		over the integration run. Copyright (C) 2000 John Wiley & Sons,
4903		Ltd.},
4904	<	annote = {373CJ Times Cited:30 Cited References Count:41},
4905	<	issn = {0029-5981},
4906	<	uri = {<Go to ISI>://000165270600004},
4907	<	}
4904	>	Annote = {373CJ Times Cited:30 Cited References Count:41},
4905	>	Author = {C. Kane and J. E. Marsden and M. Ortiz and M. West},
4906	>	Issn = {0029-5981},
4907	>	Journal = {International Journal for Numerical Methods in Engineering},
4908	>	Month = {Dec 10},
4909	>	Number = 10,
4910	>	Pages = {1295-1325},
4911	>	Title = {Variational integrators and the Newmark algorithm for conservative and dissipative mechanical systems},
4912	>	Uri = {<Go to ISI>://000165270600004},
4913	>	Volume = 49,
4914	>	Year = 2000}
4915
4916	<	@ARTICLE{Klimov1997,
4917	<	author = {D. K. Klimov and D. Thirumalai},
1656	<	title = {Viscosity dependence of the folding rates of proteins},
1657	<	journal = {Physical Review Letters},
1658	<	year = {1997},
1659	<	volume = {79},
1660	<	pages = {317-320},
1661	<	number = {2},
1662	<	month = {Jul 14},
1663	<	abstract = {The viscosity (eta) dependence of the folding rates for four sequences
4916	>	@article{Klimov1997,
4917	>	Abstract = {The viscosity (eta) dependence of the folding rates for four sequences
4918		(the native state of three sequences is a beta sheet, while the
4919		fourth forms an alpha helix) is calculated for off-lattice models
4920		of proteins. Assuming that the dynamics is given by the Langevin
#	Line 1671 | Line 4925 | Encoding: GBK
4925		the simulation results to real proteins we estimate that for optimized
4926		sequences the time scale for forming a four turn alpha-helix topology
4927		is about 500 ns, whereas for beta sheet it is about 10 mu s.},
4928	<	annote = {Xk293 Times Cited:77 Cited References Count:17},
4929	<	issn = {0031-9007},
4930	<	uri = {<Go to ISI>://A1997XK29300035},
4931	<	}
4928	>	Annote = {Xk293 Times Cited:77 Cited References Count:17},
4929	>	Author = {D. K. Klimov and D. Thirumalai},
4930	>	Issn = {0031-9007},
4931	>	Journal = {Physical Review Letters},
4932	>	Month = {Jul 14},
4933	>	Number = 2,
4934	>	Pages = {317-320},
4935	>	Title = {Viscosity dependence of the folding rates of proteins},
4936	>	Uri = {<Go to ISI>://A1997XK29300035},
4937	>	Volume = 79,
4938	>	Year = 1997}
4939
4940	<	@ARTICLE{Kol1997,
4941	<	author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
1681	<	title = {A symplectic method for rigid-body molecular simulation},
1682	<	journal = {Journal of Chemical Physics},
1683	<	year = {1997},
1684	<	volume = {107},
1685	<	pages = {2580-2588},
1686	<	number = {7},
1687	<	month = {Aug 15},
1688	<	abstract = {Rigid-body molecular dynamics simulations typically are performed
4940	>	@article{Kol1997,
4941	>	Abstract = {Rigid-body molecular dynamics simulations typically are performed
4942		in a quaternion representation. The nonseparable form of the Hamiltonian
4943		in quaternions prevents the use of a standard leapfrog (Verlet)
4944		integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation
#	Line 1705 | Line 4958 | Encoding: GBK
4958		tolerance can be achieved by using a larger time step, The superiority
4959		of RSHAKE increases with system size. (C) 1997 American Institute
4960		of Physics.},
4961	<	annote = {Xq332 Times Cited:11 Cited References Count:18},
4962	<	issn = {0021-9606},
4963	<	uri = {<Go to ISI>://A1997XQ33200046},
4964	<	}
4961	>	Annote = {Xq332 Times Cited:11 Cited References Count:18},
4962	>	Author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
4963	>	Issn = {0021-9606},
4964	>	Journal = {Journal of Chemical Physics},
4965	>	Month = {Aug 15},
4966	>	Number = 7,
4967	>	Pages = {2580-2588},
4968	>	Title = {A symplectic method for rigid-body molecular simulation},
4969	>	Uri = {<Go to ISI>://A1997XQ33200046},
4970	>	Volume = 107,
4971	>	Year = 1997}
4972
4973	<	@ARTICLE{Lansac2001,
4974	<	author = {Y. Lansac and M. A. Glaser and N. A. Clark},
1715	<	title = {Microscopic structure and dynamics of a partial bilayer smectic liquid
1716	<	crystal},
1717	<	journal = {Physical Review E},
1718	<	year = {2001},
1719	<	volume = {6405},
1720	<	pages = {-},
1721	<	number = {5},
1722	<	month = {Nov},
1723	<	abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
4973	>	@article{Lansac2001,
4974	>	Abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
4975		class of mesogens. Many of the peculiar properties of nCB's (e.g.,
4976		the occurence of the partial bilayer smectic-A(d) phase) are thought
4977		to be a manifestation of short-range antiparallel association of
#	Line 1741 | Line 4992 | Encoding: GBK
4992		antiparallel association of molecules arising from dipole-dipole
4993		interactions plays a dominant role in determining the molecular-scale
4994		structure of 8CB.},
4995	<	annote = {Part 1 496QF Times Cited:10 Cited References Count:60},
4996	<	issn = {1063-651X},
4997	<	uri = {<Go to ISI>://000172406900063},
4998	<	}
4995	>	Annote = {Part 1 496QF Times Cited:10 Cited References Count:60},
4996	>	Author = {Y. Lansac and M. A. Glaser and N. A. Clark},
4997	>	Issn = {1063-651X},
4998	>	Journal = {Physical Review E},
4999	>	Month = {Nov},
5000	>	Number = 5,
5001	>	Pages = {-},
5002	>	Title = {Microscopic structure and dynamics of a partial bilayer smectic liquid crystal},
5003	>	Uri = {<Go to ISI>://000172406900063},
5004	>	Volume = 6405,
5005	>	Year = 2001}
5006
5007	<	@ARTICLE{Lansac2003,
5008	<	author = {Y. Lansac and P. K. Maiti and N. A. Clark and M. A. Glaser},
1751	<	title = {Phase behavior of bent-core molecules},
1752	<	journal = {Physical Review E},
1753	<	year = {2003},
1754	<	volume = {67},
1755	<	pages = {-},
1756	<	number = {1},
1757	<	month = {Jan},
1758	<	abstract = {Recently, a new class of smectic liquid crystal phases characterized
5007	>	@article{Lansac2003,
5008	>	Abstract = {Recently, a new class of smectic liquid crystal phases characterized
5009		by the spontaneous formation of macroscopic chiral domains from
5010		achiral bent-core molecules has been discovered. We have carried
5011		out Monte Carlo simulations of a minimal hard spherocylinder dimer
#	Line 1770 | Line 5020 | Encoding: GBK
5020		Free energy calculations indicate that the antipolar smectic A (SmAP(A))
5021		phase is more stable than the polar smectic A phase (SmAP(F)). No
5022		chiral smectic or biaxial nematic phases were found.},
5023	<	annote = {Part 1 646CM Times Cited:15 Cited References Count:38},
5024	<	issn = {1063-651X},
5025	<	uri = {<Go to ISI>://000181017300042},
5026	<	}
5023	>	Annote = {Part 1 646CM Times Cited:15 Cited References Count:38},
5024	>	Author = {Y. Lansac and P. K. Maiti and N. A. Clark and M. A. Glaser},
5025	>	Issn = {1063-651X},
5026	>	Journal = {Physical Review E},
5027	>	Month = {Jan},
5028	>	Number = 1,
5029	>	Pages = {-},
5030	>	Title = {Phase behavior of bent-core molecules},
5031	>	Uri = {<Go to ISI>://000181017300042},
5032	>	Volume = 67,
5033	>	Year = 2003}
5034
5035	<	@BOOK{Leach2001,
5036	<	title = {Molecular Modeling: Principles and Applications},
5037	<	publisher = {Pearson Educated Limited},
5038	<	year = {2001},
5039	<	author = {A. Leach},
5040	<	address = {Harlow, England},
5041	<	edition = {2nd},
1785	<	}
5035	>	@book{Leach2001,
5036	>	Address = {Harlow, England},
5037	>	Author = {A. Leach},
5038	>	Edition = {2nd},
5039	>	Publisher = {Pearson Educated Limited},
5040	>	Title = {Molecular Modeling: Principles and Applications},
5041	>	Year = 2001}
5042
5043	<	@ARTICLE{Leimkuhler1999,
5044	<	author = {B. Leimkuhler},
1789	<	title = {Reversible adaptive regularization: perturbed Kepler motion and classical
1790	<	atomic trajectories},
1791	<	journal = {Philosophical Transactions of the Royal Society of London Series
1792	<	a-Mathematical Physical and Engineering Sciences},
1793	<	year = {1999},
1794	<	volume = {357},
1795	<	pages = {1101-1133},
1796	<	number = {1754},
1797	<	month = {Apr 15},
1798	<	abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
5043	>	@article{Leimkuhler1999,
5044	>	Abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
5045		regularization and modified Sundman transformations are applied
5046		to simulate general perturbed Kepler motion and to compute classical
5047		trajectories of atomic systems (e.g. Rydberg atoms). The new family
#	Line 1807 | Line 5053 | Encoding: GBK
5053		of atomic dynamics. The components of an algorithm for trajectory
5054		calculations are described. Numerical experiments illustrate the
5055		effectiveness of the reversible approach.},
5056	<	annote = {199EE Times Cited:11 Cited References Count:48},
5057	<	issn = {1364-503X},
5058	<	uri = {<Go to ISI>://000080466800007},
5059	<	}
5056	>	Annote = {199EE Times Cited:11 Cited References Count:48},
5057	>	Author = {B. Leimkuhler},
5058	>	Issn = {1364-503X},
5059	>	Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
5060	>	Month = {Apr 15},
5061	>	Number = 1754,
5062	>	Pages = {1101-1133},
5063	>	Title = {Reversible adaptive regularization: perturbed Kepler motion and classical atomic trajectories},
5064	>	Uri = {<Go to ISI>://000080466800007},
5065	>	Volume = 357,
5066	>	Year = 1999}
5067	>
5068	>	@book{Leimkuhler2004,
5069	>	Address = {Cambridge},
5070	>	Author = {B. Leimkuhler and S. Reich},
5071	>	Publisher = {Cambridge University Press},
5072	>	Title = {Simulating Hamiltonian Dynamics},
5073	>	Year = 2004}
5074
5075	<	@BOOK{Leimkuhler2004,
5076	<	title = {Simulating Hamiltonian Dynamics},
5077	<	publisher = {Cambridge University Press},
5078	<	year = {2004},
5079	<	author = {B. Leimkuhler and S. Reich},
5080	<	address = {Cambridge},
5081	<	}
5075	>	@article{Levelut1981,
5076	>	Annote = {Ml751 Times Cited:96 Cited References Count:16},
5077	>	Author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard and G. Sigaud},
5078	>	Issn = {1050-2947},
5079	>	Journal = {Physical Review A},
5080	>	Number = 4,
5081	>	Pages = {2180-2186},
5082	>	Title = {Number of Sa Phases},
5083	>	Uri = {<Go to ISI>://A1981ML75100057},
5084	>	Volume = 24,
5085	>	Year = 1981}
5086
5087	<	@ARTICLE{Levelut1981,
5088	<	author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard
5089	<	and G. Sigaud},
5090	<	title = {Number of Sa Phases},
5091	<	journal = {Physical Review A},
5092	<	year = {1981},
5093	<	volume = {24},
5094	<	pages = {2180-2186},
5095	<	number = {4},
5096	<	annote = {Ml751 Times Cited:96 Cited References Count:16},
5097	<	issn = {1050-2947},
1834	<	uri = {<Go to ISI>://A1981ML75100057},
1835	<	}
5087	>	@article{Lieb1982,
5088	>	Annote = {Nu461 Times Cited:40 Cited References Count:28},
5089	>	Author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
5090	>	Issn = {0006-3002},
5091	>	Journal = {Biochimica Et Biophysica Acta},
5092	>	Number = 2,
5093	>	Pages = {388-398},
5094	>	Title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - Evidence from Raman-Scattering},
5095	>	Uri = {<Go to ISI>://A1982NU46100012},
5096	>	Volume = 688,
5097	>	Year = 1982}
5098
5099	<	@ARTICLE{Lieb1982,
5100	<	author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
1839	<	title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers -
1840	<	Evidence from Raman-Scattering},
1841	<	journal = {Biochimica Et Biophysica Acta},
1842	<	year = {1982},
1843	<	volume = {688},
1844	<	pages = {388-398},
1845	<	number = {2},
1846	<	annote = {Nu461 Times Cited:40 Cited References Count:28},
1847	<	issn = {0006-3002},
1848	<	uri = {<Go to ISI>://A1982NU46100012},
1849	<	}
1850	<
1851	<	@ARTICLE{Link1997,
1852	<	author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A.
1853	<	Clark and E. Korblova and D. M. Walba},
1854	<	title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic
1855	<	phase of achiral molecules},
1856	<	journal = {Science},
1857	<	year = {1997},
1858	<	volume = {278},
1859	<	pages = {1924-1927},
1860	<	number = {5345},
1861	<	month = {Dec 12},
1862	<	abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
5099	>	@article{Link1997,
5100	>	Abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
5101		cores was found to have fluid layers that exhibit two spontaneous
5102		symmetry-breaking instabilities: polar molecular orientational ordering
5103		about the layer normal and molecular tilt. These instabilities combine
#	Line 1869 | Line 5107 | Encoding: GBK
5107		from layer to layer, or antiferroelectric-chiral, which is of uniform
5108		layer handedness. Both states exhibit an electric field-induced
5109		transition from antiferroelectric to ferroelectric.},
5110	<	annote = {Yl002 Times Cited:407 Cited References Count:25},
5111	<	issn = {0036-8075},
5112	<	uri = {<Go to ISI>://A1997YL00200028},
5113	<	}
5110	>	Annote = {Yl002 Times Cited:407 Cited References Count:25},
5111	>	Author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A. Clark and E. Korblova and D. M. Walba},
5112	>	Issn = {0036-8075},
5113	>	Journal = {Science},
5114	>	Month = {Dec 12},
5115	>	Number = 5345,
5116	>	Pages = {1924-1927},
5117	>	Title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic phase of achiral molecules},
5118	>	Uri = {<Go to ISI>://A1997YL00200028},
5119	>	Volume = 278,
5120	>	Year = 1997}
5121
5122	<	@ARTICLE{Liwo2005,
5123	<	author = {A. Liwo and M. Khalili and H. A. Scheraga},
5124	<	title = {Ab initio simulations of protein folding pathways by molecular dynamics
5125	<	with the united-residue (UNRES) model of polypeptide chains},
5126	<	journal = {Febs Journal},
5127	<	year = {2005},
5128	<	volume = {272},
5129	<	pages = {359-360},
5130	<	month = {Jul},
5131	<	annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
5132	<	issn = {1742-464X},
1888	<	uri = {<Go to ISI>://000234826102043},
1889	<	}
5122	>	@article{Liwo2005,
5123	>	Annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
5124	>	Author = {A. Liwo and M. Khalili and H. A. Scheraga},
5125	>	Issn = {1742-464X},
5126	>	Journal = {Febs Journal},
5127	>	Month = {Jul},
5128	>	Pages = {359-360},
5129	>	Title = {Ab initio simulations of protein folding pathways by molecular dynamics with the united-residue (UNRES) model of polypeptide chains},
5130	>	Uri = {<Go to ISI>://000234826102043},
5131	>	Volume = 272,
5132	>	Year = 2005}
5133
5134	<	@ARTICLE{Luty1994,
5135	<	author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
1893	<	title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods
1894	<	for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
1895	<	journal = {Molecular Simulation},
1896	<	year = {1994},
1897	<	volume = {14},
1898	<	pages = {11-20},
1899	<	number = {1},
1900	<	abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
5134	>	@article{Luty1994,
5135	>	Abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
5136		for calculating electrostatic interactions in periodic molecular
5137		systems. A brief comparison of the theories shows that the methods
5138		are very similar differing mainly in the technique which is used
#	Line 1905 | Line 5140 | Encoding: GBK
5140		utilizes the highly efficient numerical Fast Fourier Transform (FFT)
5141		method it requires significantly less computational effort than
5142		the Ewald method and scale's almost linearly with system size.},
5143	<	annote = {Qf464 Times Cited:50 Cited References Count:20},
5144	<	issn = {0892-7022},
5145	<	uri = {<Go to ISI>://A1994QF46400002},
5146	<	}
5143	>	Annote = {Qf464 Times Cited:50 Cited References Count:20},
5144	>	Author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
5145	>	Issn = {0892-7022},
5146	>	Journal = {Molecular Simulation},
5147	>	Number = 1,
5148	>	Pages = {11-20},
5149	>	Title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
5150	>	Uri = {<Go to ISI>://A1994QF46400002},
5151	>	Volume = 14,
5152	>	Year = 1994}
5153
5154	<	@BOOK{Marion1990,
5155	<	title = {Classical Dynamics of Particles and Systems},
5156	<	publisher = {Academic Press},
5157	<	year = {1990},
5158	<	author = {J.~B. Marion},
5159	<	address = {New York},
5160	<	edition = {2rd},
1920	<	}
5154	>	@book{Marion1990,
5155	>	Address = {New York},
5156	>	Author = {J.~B. Marion},
5157	>	Edition = {2rd},
5158	>	Publisher = {Academic Press},
5159	>	Title = {Classical Dynamics of Particles and Systems},
5160	>	Year = 1990}
5161
5162	<	@ARTICLE{Marrink1994,
5163	<	author = {S. J. Marrink and H. J. C. Berendsen},
1924	<	title = {Simulation of Water Transport through a Lipid-Membrane},
1925	<	journal = {Journal of Physical Chemistry},
1926	<	year = {1994},
1927	<	volume = {98},
1928	<	pages = {4155-4168},
1929	<	number = {15},
1930	<	month = {Apr 14},
1931	<	abstract = {To obtain insight in the process of water permeation through a lipid
5162	>	@article{Marrink1994,
5163	>	Abstract = {To obtain insight in the process of water permeation through a lipid
5164		membrane, we performed molecular dynamics simulations on a phospholipid
5165		(DPPC)/water system with atomic detail. Since the actual process
5166		of permeation is too slow to be studied directly, we deduced the
#	Line 1952 | Line 5184 | Encoding: GBK
5184		the inhomogeneity of the membrane into account, we define a new
5185		''four-region'' model which seems to be more realistic than the
5186		''two-phase'' solubility-diffusion model.},
5187	<	annote = {Ng219 Times Cited:187 Cited References Count:25},
5188	<	issn = {0022-3654},
5189	<	uri = {<Go to ISI>://A1994NG21900040},
5190	<	}
5187	>	Annote = {Ng219 Times Cited:187 Cited References Count:25},
5188	>	Author = {S. J. Marrink and H. J. C. Berendsen},
5189	>	Issn = {0022-3654},
5190	>	Journal = {Journal of Physical Chemistry},
5191	>	Month = {Apr 14},
5192	>	Number = 15,
5193	>	Pages = {4155-4168},
5194	>	Title = {Simulation of Water Transport through a Lipid-Membrane},
5195	>	Uri = {<Go to ISI>://A1994NG21900040},
5196	>	Volume = 98,
5197	>	Year = 1994}
5198
5199	<	@ARTICLE{Marrink2004,
5200	<	author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
5201	<	title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
5202	<	journal = {J. Phys. Chem. B},
5203	<	year = {2004},
5204	<	volume = {108},
5205	<	pages = {750-760},
1967	<	}
5199	>	@article{Marrink2004,
5200	>	Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
5201	>	Journal = {J. Phys. Chem. B},
5202	>	Pages = {750-760},
5203	>	Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
5204	>	Volume = 108,
5205	>	Year = 2004}
5206
5207	<	@ARTICLE{Marsden1998,
5208	<	author = {J. E. Marsden and G. W. Patrick and S. Shkoller},
1971	<	title = {Multisymplectic geometry, variational integrators, and nonlinear
1972	<	PDEs},
1973	<	journal = {Communications in Mathematical Physics},
1974	<	year = {1998},
1975	<	volume = {199},
1976	<	pages = {351-395},
1977	<	number = {2},
1978	<	month = {Dec},
1979	<	abstract = {This paper presents a geometric-variational approach to continuous
5207	>	@article{Marsden1998,
5208	>	Abstract = {This paper presents a geometric-variational approach to continuous
5209		and discrete mechanics and field theories. Using multisymplectic
5210		geometry, we show that the existence of the fundamental geometric
5211		structures as well as their preservation along solutions can be
#	Line 1996 | Line 5225 | Encoding: GBK
5225		All of the aspects of our method are demonstrated with a nonlinear
5226		sine-Gordon equation, including computational results and a comparison
5227		with other discretization schemes.},
5228	<	annote = {154RH Times Cited:88 Cited References Count:36},
5229	<	issn = {0010-3616},
5230	<	uri = {<Go to ISI>://000077902200006},
5231	<	}
5228	>	Annote = {154RH Times Cited:88 Cited References Count:36},
5229	>	Author = {J. E. Marsden and G. W. Patrick and S. Shkoller},
5230	>	Issn = {0010-3616},
5231	>	Journal = {Communications in Mathematical Physics},
5232	>	Month = {Dec},
5233	>	Number = 2,
5234	>	Pages = {351-395},
5235	>	Title = {Multisymplectic geometry, variational integrators, and nonlinear PDEs},
5236	>	Uri = {<Go to ISI>://000077902200006},
5237	>	Volume = 199,
5238	>	Year = 1998}
5239
5240	<	@ARTICLE{Matthey2004,
5241	<	author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and
2006	<	M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre},
2007	<	title = {ProtoMol, an object-oriented framework for prototyping novel algorithms
2008	<	for molecular dynamics},
2009	<	journal = {Acm Transactions on Mathematical Software},
2010	<	year = {2004},
2011	<	volume = {30},
2012	<	pages = {237-265},
2013	<	number = {3},
2014	<	month = {Sep},
2015	<	abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
5240	>	@article{Matthey2004,
5241	>	Abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
5242		of novel algorithms for molecular dynamics and related applications.
5243		Its flexibility is achieved primarily through the use of inheritance
5244		and design patterns (object-oriented programming): Performance is
#	Line 2029 | Line 5255 | Encoding: GBK
5255		of processors. Binaries and source codes for Windows, Linux, Solaris,
5256		IRIX, HP-UX, and AIX platforms are available under open source license
5257		at http://protomol.sourceforge.net.},
5258	<	annote = {860EP Times Cited:2 Cited References Count:52},
5259	<	issn = {0098-3500},
5260	<	uri = {<Go to ISI>://000224325600001},
5261	<	}
5262	<
5263	<	@ARTICLE{McLachlan1993,
5264	<	author = {R.~I McLachlan},
5265	<	title = {Explicit Lie-Poisson integration and the Euler equations},
5266	<	journal = {prl},
5267	<	year = {1993},
5268	<	volume = {71},
2043	<	pages = {3043-3046},
2044	<	}
5258	>	Annote = {860EP Times Cited:2 Cited References Count:52},
5259	>	Author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre},
5260	>	Issn = {0098-3500},
5261	>	Journal = {Acm Transactions on Mathematical Software},
5262	>	Month = {Sep},
5263	>	Number = 3,
5264	>	Pages = {237-265},
5265	>	Title = {ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics},
5266	>	Uri = {<Go to ISI>://000224325600001},
5267	>	Volume = 30,
5268	>	Year = 2004}
5269
5270	<	@ARTICLE{McLachlan1998,
5271	<	author = {R. I. McLachlan and G. R. W. Quispel},
5272	<	title = {Generating functions for dynamical systems with symmetries, integrals,
5273	<	and differential invariants},
5274	<	journal = {Physica D},
5275	<	year = {1998},
5276	<	volume = {112},
5277	<	pages = {298-309},
5278	<	number = {1-2},
5279	<	month = {Jan 15},
2056	<	abstract = {We give a survey and some new examples of generating functions for
5270	>	@article{McLachlan1993,
5271	>	Author = {R.~I McLachlan},
5272	>	Journal = {prl},
5273	>	Pages = {3043-3046},
5274	>	Title = {Explicit Lie-Poisson integration and the Euler equations},
5275	>	Volume = 71,
5276	>	Year = 1993}
5277	>
5278	>	@article{McLachlan1998,
5279	>	Abstract = {We give a survey and some new examples of generating functions for
5280		systems with symplectic structure, systems with a first integral,
5281		systems that preserve volume, and systems with symmetries and/or
5282		time-reversing symmetries. Both ODEs and maps are treated, and we
5283		discuss how generating functions may be used in the structure-preserving
5284		numerical integration of ODEs with the above properties.},
5285	<	annote = {Yt049 Times Cited:7 Cited References Count:26},
5286	<	issn = {0167-2789},
5287	<	uri = {<Go to ISI>://000071558900021},
5288	<	}
5285	>	Annote = {Yt049 Times Cited:7 Cited References Count:26},
5286	>	Author = {R. I. McLachlan and G. R. W. Quispel},
5287	>	Issn = {0167-2789},
5288	>	Journal = {Physica D},
5289	>	Month = {Jan 15},
5290	>	Number = {1-2},
5291	>	Pages = {298-309},
5292	>	Title = {Generating functions for dynamical systems with symmetries, integrals, and differential invariants},
5293	>	Uri = {<Go to ISI>://000071558900021},
5294	>	Volume = 112,
5295	>	Year = 1998}
5296
5297	<	@ARTICLE{McLachlan1998a,
5298	<	author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner},
2069	<	title = {Numerical integrators that preserve symmetries and reversing symmetries},
2070	<	journal = {Siam Journal on Numerical Analysis},
2071	<	year = {1998},
2072	<	volume = {35},
2073	<	pages = {586-599},
2074	<	number = {2},
2075	<	month = {Apr},
2076	<	abstract = {We consider properties of flows, the relationships between them, and
5297	>	@article{McLachlan1998a,
5298	>	Abstract = {We consider properties of flows, the relationships between them, and
5299		whether numerical integrators can be made to preserve these properties.
5300		This is done in the context of automorphisms and antiautomorphisms
5301		of a certain group generated by maps associated to vector fields.
#	Line 2082 | Line 5304 | Encoding: GBK
5304		to a group of coordinate transformations. The main application is
5305		to explore the relationship between spatial symmetries, reversing
5306		symmetries, and time symmetry of flows and numerical integrators.},
5307	<	annote = {Zc449 Times Cited:14 Cited References Count:33},
5308	<	issn = {0036-1429},
5309	<	uri = {<Go to ISI>://000072580500010},
5310	<	}
5307	>	Annote = {Zc449 Times Cited:14 Cited References Count:33},
5308	>	Author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner},
5309	>	Issn = {0036-1429},
5310	>	Journal = {Siam Journal on Numerical Analysis},
5311	>	Month = {Apr},
5312	>	Number = 2,
5313	>	Pages = {586-599},
5314	>	Title = {Numerical integrators that preserve symmetries and reversing symmetries},
5315	>	Uri = {<Go to ISI>://000072580500010},
5316	>	Volume = 35,
5317	>	Year = 1998}
5318
5319	<	@ARTICLE{McLachlan2005,
5320	<	author = {R. I. McLachlan and A. Zanna},
2092	<	title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
2093	<	journal = {Foundations of Computational Mathematics},
2094	<	year = {2005},
2095	<	volume = {5},
2096	<	pages = {87-123},
2097	<	number = {1},
2098	<	month = {Feb},
2099	<	abstract = {In this paper we revisit the Moser-Veselov description of the free
5319	>	@article{McLachlan2005,
5320	>	Abstract = {In this paper we revisit the Moser-Veselov description of the free
5321		rigid body in body coordinates, which, in the 3 x 3 case, can be
5322		implemented as an explicit, second-order, integrable approximation
5323		of the continuous solution. By backward error analysis, we study
#	Line 2109 | Line 5330 | Encoding: GBK
5330		algorithm. Numerical integration with these preprocessed initial
5331		data is several orders of magnitude more accurate than the original
5332		DMV and RATTLE approach.},
5333	<	annote = {911NS Times Cited:0 Cited References Count:14},
5334	<	issn = {1615-3375},
5335	<	uri = {<Go to ISI>://000228011900003},
5336	<	}
5333	>	Annote = {911NS Times Cited:0 Cited References Count:14},
5334	>	Author = {R. I. McLachlan and A. Zanna},
5335	>	Issn = {1615-3375},
5336	>	Journal = {Foundations of Computational Mathematics},
5337	>	Month = {Feb},
5338	>	Number = 1,
5339	>	Pages = {87-123},
5340	>	Title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
5341	>	Uri = {<Go to ISI>://000228011900003},
5342	>	Volume = 5,
5343	>	Year = 2005}
5344
5345	<	@ARTICLE{Meineke2005,
5346	<	author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and
2119	<	J. D. Gezelter},
2120	<	title = {OOPSE: An object-oriented parallel simulation engine for molecular
2121	<	dynamics},
2122	<	journal = {Journal of Computational Chemistry},
2123	<	year = {2005},
2124	<	volume = {26},
2125	<	pages = {252-271},
2126	<	number = {3},
2127	<	month = {Feb},
2128	<	abstract = {OOPSE is a new molecular dynamics simulation program that is capable
5345	>	@article{Meineke2005,
5346	>	Abstract = {OOPSE is a new molecular dynamics simulation program that is capable
5347		of efficiently integrating equations of motion for atom types with
5348		orientational degrees of freedom (e.g. #sticky# atoms and point
5349		dipoles). Transition metals can also be simulated using the embedded
#	Line 2135 | Line 5353 | Encoding: GBK
5353		number of advanced integrators are included, and the basic integrator
5354		for orientational dynamics provides substantial improvements over
5355		older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.},
5356	<	annote = {891CF Times Cited:1 Cited References Count:56},
5357	<	issn = {0192-8651},
5358	<	uri = {<Go to ISI>://000226558200006},
5359	<	}
5356	>	Annote = {891CF Times Cited:1 Cited References Count:56},
5357	>	Author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and J. D. Gezelter},
5358	>	Issn = {0192-8651},
5359	>	Journal = {Journal of Computational Chemistry},
5360	>	Month = {Feb},
5361	>	Number = 3,
5362	>	Pages = {252-271},
5363	>	Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
5364	>	Uri = {<Go to ISI>://000226558200006},
5365	>	Volume = 26,
5366	>	Year = 2005}
5367
5368	<	@ARTICLE{Melchionna1993,
5369	<	author = {S. Melchionna and G. Ciccotti and B. L. Holian},
2145	<	title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
2146	<	journal = {Molecular Physics},
2147	<	year = {1993},
2148	<	volume = {78},
2149	<	pages = {533-544},
2150	<	number = {3},
2151	<	month = {Feb 20},
2152	<	abstract = {In this paper we write down equations of motion (following the approach
5368	>	@article{Melchionna1993,
5369	>	Abstract = {In this paper we write down equations of motion (following the approach
5370		pioneered by Hoover) for an exact isothermal-isobaric molecular
5371		dynamics simulation, and we extend them to multiple thermostating
5372		rates, to a shape-varying cell and to molecular systems, coherently
5373		with the previous 'extended system method'. An integration scheme
5374		is proposed together with a numerical illustration of the method.},
5375	<	annote = {Kq355 Times Cited:172 Cited References Count:17},
5376	<	issn = {0026-8976},
5377	<	uri = {<Go to ISI>://A1993KQ35500002},
5378	<	}
5375	>	Annote = {Kq355 Times Cited:172 Cited References Count:17},
5376	>	Author = {S. Melchionna and G. Ciccotti and B. L. Holian},
5377	>	Issn = {0026-8976},
5378	>	Journal = {Molecular Physics},
5379	>	Month = {Feb 20},
5380	>	Number = 3,
5381	>	Pages = {533-544},
5382	>	Title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
5383	>	Uri = {<Go to ISI>://A1993KQ35500002},
5384	>	Volume = 78,
5385	>	Year = 1993}
5386
5387	<	@ARTICLE{Memmer2002,
5388	<	author = {R. Memmer},
2165	<	title = {Liquid crystal phases of achiral banana-shaped molecules: a computer
2166	<	simulation study},
2167	<	journal = {Liquid Crystals},
2168	<	year = {2002},
2169	<	volume = {29},
2170	<	pages = {483-496},
2171	<	number = {4},
2172	<	month = {Apr},
2173	<	abstract = {The phase behaviour of achiral banana-shaped molecules was studied
5387	>	@article{Memmer2002,
5388	>	Abstract = {The phase behaviour of achiral banana-shaped molecules was studied
5389		by computer simulation. The banana-shaped molecules were described
5390		by model intermolecular interactions based on the Gay-Berne potential.
5391		The characteristic molecular structure was considered by joining
#	Line 2195 | Line 5410 | Encoding: GBK
5410		phases have been characterized by visual representations of selected
5411		configurations, scalar and pseudoscalar correlation functions, and
5412		order parameters.},
5413	<	annote = {531HT Times Cited:12 Cited References Count:37},
5414	<	issn = {0267-8292},
5415	<	uri = {<Go to ISI>://000174410500001},
5416	<	}
5413	>	Annote = {531HT Times Cited:12 Cited References Count:37},
5414	>	Author = {R. Memmer},
5415	>	Issn = {0267-8292},
5416	>	Journal = {Liquid Crystals},
5417	>	Month = {Apr},
5418	>	Number = 4,
5419	>	Pages = {483-496},
5420	>	Title = {Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study},
5421	>	Uri = {<Go to ISI>://000174410500001},
5422	>	Volume = 29,
5423	>	Year = 2002}
5424
5425	<	@ARTICLE{Metropolis1949,
5426	<	author = {N. Metropolis and S. Ulam},
5427	<	title = {The $\mbox{Monte Carlo}$ Method},
5428	<	journal = {J. Am. Stat. Ass.},
5429	<	year = {1949},
5430	<	volume = {44},
5431	<	pages = {335-341},
2210	<	}
5425	>	@article{Metropolis1949,
5426	>	Author = {N. Metropolis and S. Ulam},
5427	>	Journal = {J. Am. Stat. Ass.},
5428	>	Pages = {335-341},
5429	>	Title = {The $\mbox{Monte Carlo}$ Method},
5430	>	Volume = 44,
5431	>	Year = 1949}
5432
5433	<	@ARTICLE{Mielke2004,
5434	<	author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen
2214	<	and C. J. Benham},
2215	<	title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian
2216	<	dynamics study},
2217	<	journal = {Journal of Chemical Physics},
2218	<	year = {2004},
2219	<	volume = {121},
2220	<	pages = {8104-8112},
2221	<	number = {16},
2222	<	month = {Oct 22},
2223	<	abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
5433	>	@article{Mielke2004,
5434	>	Abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
5435		DNA can potentially induce long-range structural deformations integral
5436		to mechanisms of biological significance in both prokaryotes and
5437		eukaryotes. In this paper, we introduce a dynamic computer model
#	Line 2245 | Line 5456 | Encoding: GBK
5456		agree well with predictions from theory, and the generated stress
5457		is ample for driving secondary structural transitions in physiological
5458		DNA. (C) 2004 American Institute of Physics.},
5459	<	annote = {861ZF Times Cited:3 Cited References Count:34},
5460	<	issn = {0021-9606},
5461	<	uri = {<Go to ISI>://000224456500064},
5462	<	}
5459	>	Annote = {861ZF Times Cited:3 Cited References Count:34},
5460	>	Author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen and C. J. Benham},
5461	>	Issn = {0021-9606},
5462	>	Journal = {Journal of Chemical Physics},
5463	>	Month = {Oct 22},
5464	>	Number = 16,
5465	>	Pages = {8104-8112},
5466	>	Title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study},
5467	>	Uri = {<Go to ISI>://000224456500064},
5468	>	Volume = 121,
5469	>	Year = 2004}
5470
5471	<	@ARTICLE{Naess2001,
5472	<	author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter},
2255	<	title = {Brownian dynamics simulation of rigid bodies and segmented polymer
2256	<	chains. Use of Cartesian rotation vectors as the generalized coordinates
2257	<	describing angular orientations},
2258	<	journal = {Physica A},
2259	<	year = {2001},
2260	<	volume = {294},
2261	<	pages = {323-339},
2262	<	number = {3-4},
2263	<	month = {May 15},
2264	<	abstract = {The three Eulerian angles constitute the classical choice of generalized
5471	>	@article{Naess2001,
5472	>	Abstract = {The three Eulerian angles constitute the classical choice of generalized
5473		coordinates used to describe the three degrees of rotational freedom
5474		of a rigid body, but it has long been known that this choice yields
5475		singular equations of motion. The latter is also true when Eulerian
#	Line 2274 | Line 5482 | Encoding: GBK
5482		The suitability of Cartesian rotation vectors in Brownian dynamics
5483		simulations of segmented polymer chains with spring-like or ball-socket
5484		joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.},
5485	<	annote = {433TA Times Cited:7 Cited References Count:19},
5486	<	issn = {0378-4371},
5487	<	uri = {<Go to ISI>://000168774800005},
5488	<	}
5485	>	Annote = {433TA Times Cited:7 Cited References Count:19},
5486	>	Author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter},
5487	>	Issn = {0378-4371},
5488	>	Journal = {Physica A},
5489	>	Month = {May 15},
5490	>	Number = {3-4},
5491	>	Pages = {323-339},
5492	>	Title = {Brownian dynamics simulation of rigid bodies and segmented polymer chains. Use of Cartesian rotation vectors as the generalized coordinates describing angular orientations},
5493	>	Uri = {<Go to ISI>://000168774800005},
5494	>	Volume = 294,
5495	>	Year = 2001}
5496
5497	<	@ARTICLE{Niori1996,
5498	<	author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe},
2284	<	title = {Distinct ferroelectric smectic liquid crystals consisting of banana
2285	<	shaped achiral molecules},
2286	<	journal = {Journal of Materials Chemistry},
2287	<	year = {1996},
2288	<	volume = {6},
2289	<	pages = {1231-1233},
2290	<	number = {7},
2291	<	month = {Jul},
2292	<	abstract = {The synthesis of a banana-shaped molecule is reported and it is found
5497	>	@article{Niori1996,
5498	>	Abstract = {The synthesis of a banana-shaped molecule is reported and it is found
5499		that the smectic phase which it forms is biaxial with the molecules
5500		packed in the best,direction into a layer. Because of this characteristic
5501		packing, spontaneous polarization appears parallel to the layer
5502		and switches on reversal of an applied electric field. This is the
5503		first obvious example of ferroelectricity in an achiral smectic
5504		phase and is ascribed to the C-2v symmetry of the molecular packing.},
5505	<	annote = {Ux855 Times Cited:447 Cited References Count:18},
5506	<	issn = {0959-9428},
5507	<	uri = {<Go to ISI>://A1996UX85500025},
5508	<	}
5505	>	Annote = {Ux855 Times Cited:447 Cited References Count:18},
5506	>	Author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe},
5507	>	Issn = {0959-9428},
5508	>	Journal = {Journal of Materials Chemistry},
5509	>	Month = {Jul},
5510	>	Number = 7,
5511	>	Pages = {1231-1233},
5512	>	Title = {Distinct ferroelectric smectic liquid crystals consisting of banana shaped achiral molecules},
5513	>	Uri = {<Go to ISI>://A1996UX85500025},
5514	>	Volume = 6,
5515	>	Year = 1996}
5516
5517	<	@ARTICLE{Noguchi2002,
5518	<	author = {H. Noguchi and M. Takasu},
2306	<	title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
2307	<	journal = {Physical Review E},
2308	<	year = {2002},
2309	<	volume = {65},
2310	<	pages = {-},
2311	<	number = {5},
2312	<	month = {may},
2313	<	abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
5517	>	@article{Noguchi2002,
5518	>	Abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
5519		forces using a Brownian dynamics simulation. Two nanoparticles,
5520		which interact repulsively with amphiphilic molecules, are put inside
5521		a vesicle. The position of one nanoparticle is fixed, and the other
#	Line 2322 | Line 5527 | Encoding: GBK
5527		after this the cylindrical region shrinks. The trapping force similar
5528		to 100 pN is needed to induce the formation of the cylindrical structure
5529		and fission.},
5530	<	annote = {Part 1 568PX Times Cited:5 Cited References Count:39},
5531	<	issn = {1063-651X},
5532	<	uri = {<Go to ISI>://000176552300084},
5533	<	}
5530	>	Annote = {Part 1 568PX Times Cited:5 Cited References Count:39},
5531	>	Author = {H. Noguchi and M. Takasu},
5532	>	Issn = {1063-651X},
5533	>	Journal = {Physical Review E},
5534	>	Month = {may},
5535	>	Number = 5,
5536	>	Pages = {-},
5537	>	Title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
5538	>	Uri = {<Go to ISI>://000176552300084},
5539	>	Volume = 65,
5540	>	Year = 2002}
5541
5542	<	@ARTICLE{Noguchi2001,
5543	<	author = {H. Noguchi and M. Takasu},
2332	<	title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
2333	<	journal = {Journal of Chemical Physics},
2334	<	year = {2001},
2335	<	volume = {115},
2336	<	pages = {9547-9551},
2337	<	number = {20},
2338	<	month = {Nov 22},
2339	<	abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
5542	>	@article{Noguchi2001,
5543	>	Abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
5544		simulation. Amphiphilic molecules spontaneously form vesicles with
5545		a bilayer structure. Two vesicles come into contact and form a stalk
5546		intermediate, in which a necklike structure only connects the outer
#	Line 2347 | Line 5551 | Encoding: GBK
5551		that the pore-opening process at low temperature agrees with the
5552		modified stalk model: a pore is induced by contact between the inner
5553		monolayers inside the stalk. (C) 2001 American Institute of Physics.},
5554	<	annote = {491UW Times Cited:48 Cited References Count:25},
5555	<	issn = {0021-9606},
5556	<	uri = {<Go to ISI>://000172129300049},
5557	<	}
5554	>	Annote = {491UW Times Cited:48 Cited References Count:25},
5555	>	Author = {H. Noguchi and M. Takasu},
5556	>	Issn = {0021-9606},
5557	>	Journal = {Journal of Chemical Physics},
5558	>	Month = {Nov 22},
5559	>	Number = 20,
5560	>	Pages = {9547-9551},
5561	>	Title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
5562	>	Uri = {<Go to ISI>://000172129300049},
5563	>	Volume = 115,
5564	>	Year = 2001}
5565
5566	<	@BOOK{Olver1986,
5567	<	title = {Applications of Lie groups to differential equatitons},
5568	<	publisher = {Springer},
5569	<	year = {1986},
5570	<	author = {P.J. Olver},
5571	<	address = {New York},
2361	<	}
5566	>	@book{Olver1986,
5567	>	Address = {New York},
5568	>	Author = {P.J. Olver},
5569	>	Publisher = {Springer},
5570	>	Title = {Applications of Lie groups to differential equatitons},
5571	>	Year = 1986}
5572
5573	<	@ARTICLE{Omelyan1998,
5574	<	author = {I. P. Omelyan},
2365	<	title = {On the numerical integration of motion for rigid polyatomics: The
2366	<	modified quaternion approach},
2367	<	journal = {Computers in Physics},
2368	<	year = {1998},
2369	<	volume = {12},
2370	<	pages = {97-103},
2371	<	number = {1},
2372	<	month = {Jan-Feb},
2373	<	abstract = {A revised version of the quaternion approach for numerical integration
5573	>	@article{Omelyan1998,
5574	>	Abstract = {A revised version of the quaternion approach for numerical integration
5575		of the equations of motion for rigid polyatomic molecules is proposed.
5576		The modified approach is based on a formulation of the quaternion
5577		dynamics with constraints. This allows one to resolve the rigidity
#	Line 2381 | Line 5582 | Encoding: GBK
5582		stability with respect to the usual quaternion rescaling scheme
5583		and it is roughly as good as the cumbersome atomic-constraint technique.
5584		(C) 1998 American Institute of Physics.},
5585	<	annote = {Yx279 Times Cited:12 Cited References Count:28},
5586	<	issn = {0894-1866},
5587	<	uri = {<Go to ISI>://000072024300025},
5588	<	}
5585	>	Annote = {Yx279 Times Cited:12 Cited References Count:28},
5586	>	Author = {I. P. Omelyan},
5587	>	Issn = {0894-1866},
5588	>	Journal = {Computers in Physics},
5589	>	Month = {Jan-Feb},
5590	>	Number = 1,
5591	>	Pages = {97-103},
5592	>	Title = {On the numerical integration of motion for rigid polyatomics: The modified quaternion approach},
5593	>	Uri = {<Go to ISI>://000072024300025},
5594	>	Volume = 12,
5595	>	Year = 1998}
5596
5597	<	@ARTICLE{Omelyan1998a,
5598	<	author = {I. P. Omelyan},
2391	<	title = {Algorithm for numerical integration of the rigid-body equations of
2392	<	motion},
2393	<	journal = {Physical Review E},
2394	<	year = {1998},
2395	<	volume = {58},
2396	<	pages = {1169-1172},
2397	<	number = {1},
2398	<	month = {Jul},
2399	<	abstract = {An algorithm for numerical integration of the rigid-body equations
5597	>	@article{Omelyan1998a,
5598	>	Abstract = {An algorithm for numerical integration of the rigid-body equations
5599		of motion is proposed. The algorithm uses the leapfrog scheme and
5600		the quantities involved are angular velocities and orientational
5601		variables that can be expressed in terms of either principal axes
#	Line 2405 | Line 5604 | Encoding: GBK
5604		despite an approximate character of the produced trajectories. It
5605		is shown that the method presented appears to be the most efficient
5606		among all such algorithms known.},
5607	<	annote = {101XL Times Cited:8 Cited References Count:22},
5608	<	issn = {1063-651X},
5609	<	uri = {<Go to ISI>://000074893400151},
5610	<	}
5607	>	Annote = {101XL Times Cited:8 Cited References Count:22},
5608	>	Author = {I. P. Omelyan},
5609	>	Issn = {1063-651X},
5610	>	Journal = {Physical Review E},
5611	>	Month = {Jul},
5612	>	Number = 1,
5613	>	Pages = {1169-1172},
5614	>	Title = {Algorithm for numerical integration of the rigid-body equations of motion},
5615	>	Uri = {<Go to ISI>://000074893400151},
5616	>	Volume = 58,
5617	>	Year = 1998}
5618
5619	<	@ARTICLE{Orlandi2006,
5620	<	author = {S. Orlandi and R. Berardi and J. Steltzer and C. Zannoni},
2415	<	title = {A Monte Carlo study of the mesophases formed by polar bent-shaped
2416	<	molecules},
2417	<	journal = {Journal of Chemical Physics},
2418	<	year = {2006},
2419	<	volume = {124},
2420	<	pages = {-},
2421	<	number = {12},
2422	<	month = {Mar 28},
2423	<	abstract = {Liquid crystal phases formed by bent-shaped (or #banana#) molecules
2424	<	are currently of great interest. Here we investigate by Monte Carlo
2425	<	computer simulations the phases formed by rigid banana molecules
2426	<	modeled combining three Gay-Berne sites and containing either one
2427	<	central or two lateral and transversal dipoles. We show that changing
2428	<	the dipole position and orientation has a profound effect on the
2429	<	mesophase stability and molecular organization. In particular, we
2430	<	find a uniaxial nematic phase only for off-center dipolar models
2431	<	and tilted phases only for the one with terminal dipoles. (c) 2006
2432	<	American Institute of Physics.},
2433	<	annote = {028CP Times Cited:0 Cited References Count:42},
2434	<	issn = {0021-9606},
2435	<	uri = {<Go to ISI>://000236464000072},
2436	<	}
2437	<
2438	<	@ARTICLE{Owren1992,
2439	<	author = {B. Owren and M. Zennaro},
2440	<	title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
2441	<	journal = {Siam Journal on Scientific and Statistical Computing},
2442	<	year = {1992},
2443	<	volume = {13},
2444	<	pages = {1488-1501},
2445	<	number = {6},
2446	<	month = {Nov},
2447	<	abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
5619	>	@article{Owren1992,
5620	>	Abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
5621		stages are considered. These methods are continuously differentiable
5622		if and only if one of the stages is the FSAL evaluation. A characterization
5623		of a subclass of these methods is developed for orders 3, 4, and
#	Line 2457 | Line 5630 | Encoding: GBK
5630		implementation of the Dormand-Prince 5(4) pair with interpolant,
5631		showing a significant advantage in the new method for the chosen
5632		problems.},
5633	<	annote = {Ju936 Times Cited:25 Cited References Count:20},
5634	<	issn = {0196-5204},
5635	<	uri = {<Go to ISI>://A1992JU93600013},
5636	<	}
5633	>	Annote = {Ju936 Times Cited:25 Cited References Count:20},
5634	>	Author = {B. Owren and M. Zennaro},
5635	>	Issn = {0196-5204},
5636	>	Journal = {Siam Journal on Scientific and Statistical Computing},
5637	>	Month = {Nov},
5638	>	Number = 6,
5639	>	Pages = {1488-1501},
5640	>	Title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
5641	>	Uri = {<Go to ISI>://A1992JU93600013},
5642	>	Volume = 13,
5643	>	Year = 1992}
5644
5645	<	@ARTICLE{Palacios1998,
5646	<	author = {J. L. Garcia-Palacios and F. J. Lazaro},
2467	<	title = {Langevin-dynamics study of the dynamical properties of small magnetic
2468	<	particles},
2469	<	journal = {Physical Review B},
2470	<	year = {1998},
2471	<	volume = {58},
2472	<	pages = {14937-14958},
2473	<	number = {22},
2474	<	month = {Dec 1},
2475	<	abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
5645	>	@article{Palacios1998,
5646	>	Abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
5647		magnetic moment is numerically solved (properly observing the customary
5648		interpretation of it as a Stratonovich stochastic differential equation),
5649		in order to study the dynamics of magnetic nanoparticles. The corresponding
#	Line 2502 | Line 5673 | Encoding: GBK
5673		frequencies of the magnetic moment in the anisotropy field to the
5674		dynamic response at intermediate-to-high temperatures. [S0163-1829
5675		(98)00446-9].},
5676	<	annote = {146XW Times Cited:66 Cited References Count:45},
5677	<	issn = {0163-1829},
5678	<	uri = {<Go to ISI>://000077460000052},
5679	<	}
5676	>	Annote = {146XW Times Cited:66 Cited References Count:45},
5677	>	Author = {J. L. Garcia-Palacios and F. J. Lazaro},
5678	>	Issn = {0163-1829},
5679	>	Journal = {Physical Review B},
5680	>	Month = {Dec 1},
5681	>	Number = 22,
5682	>	Pages = {14937-14958},
5683	>	Title = {Langevin-dynamics study of the dynamical properties of small magnetic particles},
5684	>	Uri = {<Go to ISI>://000077460000052},
5685	>	Volume = 58,
5686	>	Year = 1998}
5687
5688	<	@ARTICLE{Parr1995,
5689	<	author = {T. J. Parr and R. W. Quong},
2512	<	title = {Antlr - a Predicated-Ll(K) Parser Generator},
2513	<	journal = {Software-Practice \& Experience},
2514	<	year = {1995},
2515	<	volume = {25},
2516	<	pages = {789-810},
2517	<	number = {7},
2518	<	month = {Jul},
2519	<	abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
5688	>	@article{Parr1995,
5689	>	Abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
5690		often choose to write recursive-descent parsers by hand to obtain
5691		increased flexibility, better error handling, and ease of debugging.
5692		We introduce ANTLR, a public-domain parser generator that combines
#	Line 2535 | Line 5705 | Encoding: GBK
5705		the PC, Macintosh, and a variety of UNIX platforms; a commercial
5706		C++ front-end has been developed as a result of one of our industrial
5707		collaborations.},
5708	<	annote = {Rk104 Times Cited:19 Cited References Count:10},
5709	<	issn = {0038-0644},
5710	<	uri = {<Go to ISI>://A1995RK10400004},
5711	<	}
5708	>	Annote = {Rk104 Times Cited:19 Cited References Count:10},
5709	>	Author = {T. J. Parr and R. W. Quong},
5710	>	Issn = {0038-0644},
5711	>	Journal = {Software-Practice \& Experience},
5712	>	Month = {Jul},
5713	>	Number = 7,
5714	>	Pages = {789-810},
5715	>	Title = {Antlr - a Predicated-Ll(K) Parser Generator},
5716	>	Uri = {<Go to ISI>://A1995RK10400004},
5717	>	Volume = 25,
5718	>	Year = 1995}
5719
5720	<	@ARTICLE{Pastor1988,
5721	<	author = {R. W. Pastor and B. R. Brooks and A. Szabo},
5722	<	title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
5723	<	journal = {Molecular Physics},
5724	<	year = {1988},
5725	<	volume = {65},
5726	<	pages = {1409-1419},
5727	<	number = {6},
5728	<	month = {Dec 20},
5729	<	annote = {T1302 Times Cited:61 Cited References Count:26},
5730	<	issn = {0026-8976},
5731	<	uri = {<Go to ISI>://A1988T130200011},
2555	<	}
5720	>	@article{Pastor1988,
5721	>	Annote = {T1302 Times Cited:61 Cited References Count:26},
5722	>	Author = {R. W. Pastor and B. R. Brooks and A. Szabo},
5723	>	Issn = {0026-8976},
5724	>	Journal = {Molecular Physics},
5725	>	Month = {Dec 20},
5726	>	Number = 6,
5727	>	Pages = {1409-1419},
5728	>	Title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
5729	>	Uri = {<Go to ISI>://A1988T130200011},
5730	>	Volume = 65,
5731	>	Year = 1988}
5732
5733	<	@ARTICLE{Pelzl1999,
5734	<	author = {G. Pelzl and S. Diele and W. Weissflog},
5735	<	title = {Banana-shaped compounds - A new field of liquid crystals},
5736	<	journal = {Advanced Materials},
5737	<	year = {1999},
5738	<	volume = {11},
5739	<	pages = {707-724},
5740	<	number = {9},
5741	<	month = {Jul 5},
5742	<	annote = {220RC Times Cited:313 Cited References Count:49},
5743	<	issn = {0935-9648},
5744	<	uri = {<Go to ISI>://000081680400007},
2569	<	}
5733	>	@article{Pelzl1999,
5734	>	Annote = {220RC Times Cited:313 Cited References Count:49},
5735	>	Author = {G. Pelzl and S. Diele and W. Weissflog},
5736	>	Issn = {0935-9648},
5737	>	Journal = {Advanced Materials},
5738	>	Month = {Jul 5},
5739	>	Number = 9,
5740	>	Pages = {707-724},
5741	>	Title = {Banana-shaped compounds - A new field of liquid crystals},
5742	>	Uri = {<Go to ISI>://000081680400007},
5743	>	Volume = 11,
5744	>	Year = 1999}
5745
5746	<	@ARTICLE{Perram1985,
5747	<	author = {J. W. Perram and M. S. Wertheim},
5748	<	title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and
5749	<	the Contact Function},
5750	<	journal = {Journal of Computational Physics},
5751	<	year = {1985},
5752	<	volume = {58},
5753	<	pages = {409-416},
5754	<	number = {3},
5755	<	annote = {Akb93 Times Cited:71 Cited References Count:12},
5756	<	issn = {0021-9991},
2582	<	uri = {<Go to ISI>://A1985AKB9300008},
2583	<	}
5746	>	@article{Perram1985,
5747	>	Annote = {Akb93 Times Cited:71 Cited References Count:12},
5748	>	Author = {J. W. Perram and M. S. Wertheim},
5749	>	Issn = {0021-9991},
5750	>	Journal = {Journal of Computational Physics},
5751	>	Number = 3,
5752	>	Pages = {409-416},
5753	>	Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function},
5754	>	Uri = {<Go to ISI>://A1985AKB9300008},
5755	>	Volume = 58,
5756	>	Year = 1985}
5757
5758	<	@ARTICLE{Rotne1969,
5759	<	author = {F. Perrin},
5760	<	title = {Variational treatment of hydrodynamic interaction in polymers},
5761	<	journal = {J. Chem. Phys.},
5762	<	year = {1969},
5763	<	volume = {50},
5764	<	pages = {4831¨C4837},
2592	<	}
5758	>	@article{Rotne1969,
5759	>	Author = {F. Perrin},
5760	>	Journal = {J. Chem. Phys.},
5761	>	Pages = {4831-4837},
5762	>	Title = {Variational treatment of hydrodynamic interaction in polymers},
5763	>	Volume = 50,
5764	>	Year = 1969}
5765
5766	<	@ARTICLE{Perrin1936,
5767	<	author = {F. Perrin},
5768	<	title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation
5769	<	des fluorescences. Translation et diffusion de moleculese ellipsoidales},
5770	<	journal = {J. Phys. Radium},
5771	<	year = {1936},
5772	<	volume = {7},
2601	<	pages = {1-11},
2602	<	}
5766	>	@article{Perrin1936,
5767	>	Author = {F. Perrin},
5768	>	Journal = {J. Phys. Radium},
5769	>	Pages = {1-11},
5770	>	Title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation des fluorescences. Translation et diffusion de moleculese ellipsoidales},
5771	>	Volume = 7,
5772	>	Year = 1936}
5773
5774	<	@ARTICLE{Perrin1934,
5775	<	author = {F. Perrin},
5776	<	title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour
5777	<	des molecules ellipsoidales},
5778	<	journal = {J. Phys. Radium},
5779	<	year = {1934},
5780	<	volume = {5},
2611	<	pages = {497-511},
2612	<	}
5774	>	@article{Perrin1934,
5775	>	Author = {F. Perrin},
5776	>	Journal = {J. Phys. Radium},
5777	>	Pages = {497-511},
5778	>	Title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour des molecules ellipsoidales},
5779	>	Volume = 5,
5780	>	Year = 1934}
5781
5782	<	@ARTICLE{Petrache2000,
5783	<	author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
5784	<	title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines
5785	<	Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
5786	<	journal = {Biophysical Journal},
5787	<	year = {2000},
5788	<	volume = {79},
2621	<	pages = {3172-3192},
2622	<	}
5782	>	@article{Petrache2000,
5783	>	Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
5784	>	Journal = {Biophysical Journal},
5785	>	Pages = {3172-3192},
5786	>	Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
5787	>	Volume = 79,
5788	>	Year = 2000}
5789
5790	<	@ARTICLE{Petrache1998,
5791	<	author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle},
2626	<	title = {Fluid phase structure of EPC and DMPC bilayers},
2627	<	journal = {Chemistry and Physics of Lipids},
2628	<	year = {1998},
2629	<	volume = {95},
2630	<	pages = {83-94},
2631	<	number = {1},
2632	<	month = {Sep},
2633	<	abstract = {X-ray diffraction data taken at high instrumental resolution were
5790	>	@article{Petrache1998,
5791	>	Abstract = {X-ray diffraction data taken at high instrumental resolution were
5792		obtained for EPC and DMPC under various osmotic pressures, primarily
5793		at T = 30 degrees C. The headgroup thickness D-HH was obtained from
5794		relative electron density profiles. By using volumetric results
#	Line 2647 | Line 5805 | Encoding: GBK
5805		increased water spacing reported by Simon et al. (1995) Biophys.
5806		J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights
5807		reserved.},
5808	<	annote = {130AT Times Cited:98 Cited References Count:39},
5809	<	issn = {0009-3084},
5810	<	uri = {<Go to ISI>://000076497600007},
5811	<	}
5808	>	Annote = {130AT Times Cited:98 Cited References Count:39},
5809	>	Author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle},
5810	>	Issn = {0009-3084},
5811	>	Journal = {Chemistry and Physics of Lipids},
5812	>	Month = {Sep},
5813	>	Number = 1,
5814	>	Pages = {83-94},
5815	>	Title = {Fluid phase structure of EPC and DMPC bilayers},
5816	>	Uri = {<Go to ISI>://000076497600007},
5817	>	Volume = 95,
5818	>	Year = 1998}
5819
5820	<	@ARTICLE{Powles1973,
5821	<	author = {J.~G. Powles},
5822	<	title = {A general ellipsoid can not always serve as a modle for the rotational
5823	<	diffusion properties of arbitrary shaped rigid molecules},
5824	<	journal = {Advan. Phys.},
5825	<	year = {1973},
5826	<	volume = {22},
2662	<	pages = {1-56},
2663	<	}
5820	>	@article{Powles1973,
5821	>	Author = {J.~G. Powles},
5822	>	Journal = {Advan. Phys.},
5823	>	Pages = {1-56},
5824	>	Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
5825	>	Volume = 22,
5826	>	Year = 1973}
5827
5828	<	@ARTICLE{Recio2004,
5829	<	author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
2667	<	title = {Identification of protein-protein interaction sites from docking
2668	<	energy landscapes},
2669	<	journal = {Journal of Molecular Biology},
2670	<	year = {2004},
2671	<	volume = {335},
2672	<	pages = {843-865},
2673	<	number = {3},
2674	<	month = {Jan 16},
2675	<	abstract = {Protein recognition is one of the most challenging and intriguing
5828	>	@article{Recio2004,
5829	>	Abstract = {Protein recognition is one of the most challenging and intriguing
5830		problems in structural biology. Despite all the available structural,
5831		sequence and biophysical information about protein-protein complexes,
5832		the physico-chemical patterns, if any, that make a protein surface
#	Line 2695 | Line 5849 | Encoding: GBK
5849		of proteins, provide geometrical details of a possible interaction,
5850		and help to annotate protein surfaces in structural proteomics.
5851		(C) 2003 Elsevier Ltd. All rights reserved.},
5852	<	annote = {763GQ Times Cited:21 Cited References Count:59},
5853	<	issn = {0022-2836},
5854	<	uri = {<Go to ISI>://000188066900016},
5855	<	}
5852	>	Annote = {763GQ Times Cited:21 Cited References Count:59},
5853	>	Author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
5854	>	Issn = {0022-2836},
5855	>	Journal = {Journal of Molecular Biology},
5856	>	Month = {Jan 16},
5857	>	Number = 3,
5858	>	Pages = {843-865},
5859	>	Title = {Identification of protein-protein interaction sites from docking energy landscapes},
5860	>	Uri = {<Go to ISI>://000188066900016},
5861	>	Volume = 335,
5862	>	Year = 2004}
5863
5864	<	@ARTICLE{Reddy2006,
5865	<	author = {R. A. Reddy and C. Tschierske},
2705	<	title = {Bent-core liquid crystals: polar order, superstructural chirality
2706	<	and spontaneous desymmetrisation in soft matter systems},
2707	<	journal = {Journal of Materials Chemistry},
2708	<	year = {2006},
2709	<	volume = {16},
2710	<	pages = {907-961},
2711	<	number = {10},
2712	<	abstract = {An overview on the recent developments in the field of liquid crystalline
5864	>	@article{Reddy2006,
5865	>	Abstract = {An overview on the recent developments in the field of liquid crystalline
5866		bent-core molecules (so-called banana liquid crystals) is given.
5867		After some basic issues, dealing with general aspects of the systematisation
5868		of the mesophases, development of polar order and chirality in this
#	Line 2720 | Line 5873 | Encoding: GBK
5873		polar order in smectic and columnar phases, amplification and switching
5874		of chirality and the spontaneous formation of superstructural and
5875		supramolecular chirality.},
5876	<	annote = {021NS Times Cited:2 Cited References Count:316},
5877	<	issn = {0959-9428},
5878	<	uri = {<Go to ISI>://000235990500001},
5879	<	}
5876	>	Annote = {021NS Times Cited:2 Cited References Count:316},
5877	>	Author = {R. A. Reddy and C. Tschierske},
5878	>	Issn = {0959-9428},
5879	>	Journal = {Journal of Materials Chemistry},
5880	>	Number = 10,
5881	>	Pages = {907-961},
5882	>	Title = {Bent-core liquid crystals: polar order, superstructural chirality and spontaneous desymmetrisation in soft matter systems},
5883	>	Uri = {<Go to ISI>://000235990500001},
5884	>	Volume = 16,
5885	>	Year = 2006}
5886
5887	<	@ARTICLE{Reich1999,
5888	<	author = {S. Reich},
2730	<	title = {Backward error analysis for numerical integrators},
2731	<	journal = {Siam Journal on Numerical Analysis},
2732	<	year = {1999},
2733	<	volume = {36},
2734	<	pages = {1549-1570},
2735	<	number = {5},
2736	<	month = {Sep 8},
2737	<	abstract = {Backward error analysis has become an important tool for understanding
5887	>	@article{Reich1999,
5888	>	Abstract = {Backward error analysis has become an important tool for understanding
5889		the long time behavior of numerical integration methods. This is
5890		true in particular for the integration of Hamiltonian systems where
5891		backward error analysis can be used to show that a symplectic method
#	Line 2756 | Line 5907 | Encoding: GBK
5907		an application we discuss the long time integration of chaotic Hamiltonian
5908		systems and the approximation of time averages along numerically
5909		computed trajectories.},
5910	<	annote = {237HV Times Cited:43 Cited References Count:41},
5911	<	issn = {0036-1429},
5912	<	uri = {<Go to ISI>://000082650600010},
5913	<	}
5910	>	Annote = {237HV Times Cited:43 Cited References Count:41},
5911	>	Author = {S. Reich},
5912	>	Issn = {0036-1429},
5913	>	Journal = {Siam Journal on Numerical Analysis},
5914	>	Month = {Sep 8},
5915	>	Number = 5,
5916	>	Pages = {1549-1570},
5917	>	Title = {Backward error analysis for numerical integrators},
5918	>	Uri = {<Go to ISI>://000082650600010},
5919	>	Volume = 36,
5920	>	Year = 1999}
5921
5922	<	@ARTICLE{Ros2005,
5923	<	author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
2766	<	title = {Banana-shaped liquid crystals: a new field to explore},
2767	<	journal = {Journal of Materials Chemistry},
2768	<	year = {2005},
2769	<	volume = {15},
2770	<	pages = {5093-5098},
2771	<	number = {48},
2772	<	abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
5922	>	@article{Ros2005,
5923	>	Abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
5924		mesogenic materials represent a bewitching and stimulating field
5925		of research that is interesting both academically and in terms of
5926		applications. Numerous topics are open to investigation in this
#	Line 2777 | Line 5928 | Encoding: GBK
5928		these materials offer. The principal concepts in this area are reviewed
5929		along with recent results. In addition, new directions to stimulate
5930		further research activities are highlighted.},
5931	<	annote = {990XA Times Cited:3 Cited References Count:72},
5932	<	issn = {0959-9428},
5933	<	uri = {<Go to ISI>://000233775500001},
5934	<	}
5931	>	Annote = {990XA Times Cited:3 Cited References Count:72},
5932	>	Author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
5933	>	Issn = {0959-9428},
5934	>	Journal = {Journal of Materials Chemistry},
5935	>	Number = 48,
5936	>	Pages = {5093-5098},
5937	>	Title = {Banana-shaped liquid crystals: a new field to explore},
5938	>	Uri = {<Go to ISI>://000233775500001},
5939	>	Volume = 15,
5940	>	Year = 2005}
5941
5942	<	@ARTICLE{Roux1991,
5943	<	author = {B. Roux and M. Karplus},
2787	<	title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
2788	<	journal = {Journal of Physical Chemistry},
2789	<	year = {1991},
2790	<	volume = {95},
2791	<	pages = {4856-4868},
2792	<	number = {12},
2793	<	month = {Jun 13},
2794	<	abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
5942	>	@article{Roux1991,
5943	>	Abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
5944		poly-(L,D)-alanine beta-helix, a model for the interior of the gramicidin
5945		channel. Because of the different dynamical regimes for the three
5946		species (high barrier for Na+, low barrier for K+, almost free diffusion
#	Line 2811 | Line 5960 | Encoding: GBK
5960		and their dynamics is overdamped and noninertial. Thus, the selectivity
5961		sequence of ions in the beta-helix is not influenced strongly by
5962		their masses.},
5963	<	annote = {Fr756 Times Cited:97 Cited References Count:65},
5964	<	issn = {0022-3654},
5965	<	uri = {<Go to ISI>://A1991FR75600049},
5966	<	}
5963	>	Annote = {Fr756 Times Cited:97 Cited References Count:65},
5964	>	Author = {B. Roux and M. Karplus},
5965	>	Issn = {0022-3654},
5966	>	Journal = {Journal of Physical Chemistry},
5967	>	Month = {Jun 13},
5968	>	Number = 12,
5969	>	Pages = {4856-4868},
5970	>	Title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
5971	>	Uri = {<Go to ISI>://A1991FR75600049},
5972	>	Volume = 95,
5973	>	Year = 1991}
5974
5975	<	@ARTICLE{Roy2005,
5976	<	author = {A. Roy and N. V. Madhusudana},
2821	<	title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases
2822	<	in banana shaped molecules},
2823	<	journal = {European Physical Journal E},
2824	<	year = {2005},
2825	<	volume = {18},
2826	<	pages = {253-258},
2827	<	number = {3},
2828	<	month = {Nov},
2829	<	abstract = {A vast majority of compounds with bent core or banana shaped molecules
5975	>	@article{Roy2005,
5976	>	Abstract = {A vast majority of compounds with bent core or banana shaped molecules
5977		exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased
5978		in a homologous series. The B-6 phase has an intercalated fluid
5979		lamellar structure with a layer spacing of half the molecular length.
#	Line 2837 | Line 5984 | Encoding: GBK
5984		a frustrated packing model to describe this phase sequence qualitatively.
5985		The model has some analogy with that of the frustrated smectics
5986		exhibited by highly polar rod like molecules.},
5987	<	annote = {985FW Times Cited:0 Cited References Count:30},
5988	<	issn = {1292-8941},
5989	<	uri = {<Go to ISI>://000233363300002},
5990	<	}
5987	>	Annote = {985FW Times Cited:0 Cited References Count:30},
5988	>	Author = {A. Roy and N. V. Madhusudana},
5989	>	Issn = {1292-8941},
5990	>	Journal = {European Physical Journal E},
5991	>	Month = {Nov},
5992	>	Number = 3,
5993	>	Pages = {253-258},
5994	>	Title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases in banana shaped molecules},
5995	>	Uri = {<Go to ISI>://000233363300002},
5996	>	Volume = 18,
5997	>	Year = 2005}
5998
5999	<	@ARTICLE{Ryckaert1977,
6000	<	author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
6001	<	title = {Numerical-Integration of Cartesian Equations of Motion of a System
6002	<	with Constraints - Molecular-Dynamics of N-Alkanes},
6003	<	journal = {Journal of Computational Physics},
6004	<	year = {1977},
6005	<	volume = {23},
6006	<	pages = {327-341},
6007	<	number = {3},
6008	<	annote = {Cz253 Times Cited:3680 Cited References Count:7},
6009	<	issn = {0021-9991},
2856	<	uri = {<Go to ISI>://A1977CZ25300007},
2857	<	}
5999	>	@article{Ryckaert1977,
6000	>	Annote = {Cz253 Times Cited:3680 Cited References Count:7},
6001	>	Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
6002	>	Issn = {0021-9991},
6003	>	Journal = {Journal of Computational Physics},
6004	>	Number = 3,
6005	>	Pages = {327-341},
6006	>	Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes},
6007	>	Uri = {<Go to ISI>://A1977CZ25300007},
6008	>	Volume = 23,
6009	>	Year = 1977}
6010
6011	<	@ARTICLE{Sagui1999,
6012	<	author = {C. Sagui and T. A. Darden},
2861	<	title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic
2862	<	effects},
2863	<	journal = {Annual Review of Biophysics and Biomolecular Structure},
2864	<	year = {1999},
2865	<	volume = {28},
2866	<	pages = {155-179},
2867	<	abstract = {Current computer simulations of biomolecules typically make use of
6011	>	@article{Sagui1999,
6012	>	Abstract = {Current computer simulations of biomolecules typically make use of
6013		classical molecular dynamics methods, as a very large number (tens
6014		to hundreds of thousands) of atoms are involved over timescales
6015		of many nanoseconds. The methodology for treating short-range bonded
#	Line 2879 | Line 6024 | Encoding: GBK
6024		methods. We also review recent efforts to understand the role of
6025		boundary conditions in systems with long-range interactions, and
6026		conclude with a short perspective on future trends.},
6027	<	annote = {213KJ Times Cited:126 Cited References Count:73},
6028	<	issn = {1056-8700},
6029	<	uri = {<Go to ISI>://000081271400008},
6030	<	}
6027	>	Annote = {213KJ Times Cited:126 Cited References Count:73},
6028	>	Author = {C. Sagui and T. A. Darden},
6029	>	Issn = {1056-8700},
6030	>	Journal = {Annual Review of Biophysics and Biomolecular Structure},
6031	>	Pages = {155-179},
6032	>	Title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic effects},
6033	>	Uri = {<Go to ISI>://000081271400008},
6034	>	Volume = 28,
6035	>	Year = 1999}
6036
6037	<	@ARTICLE{Sandu1999,
6038	<	author = {A. Sandu and T. Schlick},
2889	<	title = {Masking resonance artifacts in force-splitting methods for biomolecular
2890	<	simulations by extrapolative Langevin dynamics},
2891	<	journal = {Journal of Computational Physics},
2892	<	year = {1999},
2893	<	volume = {151},
2894	<	pages = {74-113},
2895	<	number = {1},
2896	<	month = {May 1},
2897	<	abstract = {Numerical resonance artifacts have become recognized recently as a
6037	>	@article{Sandu1999,
6038	>	Abstract = {Numerical resonance artifacts have become recognized recently as a
6039		limiting factor to increasing the timestep in multiple-timestep
6040		(MTS) biomolecular dynamics simulations. At certain timesteps correlated
6041		to internal motions (e.g., 5 fs, around half the period of the fastest
#	Line 2931 | Line 6072 | Encoding: GBK
6072		spectral density functions also show how the Newtonian modes can
6073		be approximated by using a small gamma in the range Of 5-20 ps(-1).
6074		(C) 1999 Academic Press.},
6075	<	annote = {194FM Times Cited:14 Cited References Count:32},
6076	<	issn = {0021-9991},
6077	<	uri = {<Go to ISI>://000080181500004},
6078	<	}
6075	>	Annote = {194FM Times Cited:14 Cited References Count:32},
6076	>	Author = {A. Sandu and T. Schlick},
6077	>	Issn = {0021-9991},
6078	>	Journal = {Journal of Computational Physics},
6079	>	Month = {May 1},
6080	>	Number = 1,
6081	>	Pages = {74-113},
6082	>	Title = {Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics},
6083	>	Uri = {<Go to ISI>://000080181500004},
6084	>	Volume = 151,
6085	>	Year = 1999}
6086
6087	<	@ARTICLE{Sasaki2004,
6088	<	author = {Y. Sasaki and R. Shukla and B. D. Smith},
2941	<	title = {Facilitated phosphatidylserine flip-flop across vesicle and cell
2942	<	membranes using urea-derived synthetic translocases},
2943	<	journal = {Organic \& Biomolecular Chemistry},
2944	<	year = {2004},
2945	<	volume = {2},
2946	<	pages = {214-219},
2947	<	number = {2},
2948	<	abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
6087	>	@article{Sasaki2004,
6088	>	Abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
6089		groups are shown to facilitate the translocation of fluorescent
6090		phospholipid probes and endogenous phosphatidylserine across vesicle
6091		and erythrocyte cell membranes. The synthetic translocases appear
6092		to operate by binding to the phospholipid head groups and forming
6093		lipophilic supramolecular complexes which diffuse through the non-polar
6094		interior of the bilayer membrane.},
6095	<	annote = {760PX Times Cited:8 Cited References Count:25},
6096	<	issn = {1477-0520},
6097	<	uri = {<Go to ISI>://000187843800012},
6098	<	}
6095	>	Annote = {760PX Times Cited:8 Cited References Count:25},
6096	>	Author = {Y. Sasaki and R. Shukla and B. D. Smith},
6097	>	Issn = {1477-0520},
6098	>	Journal = {Organic \& Biomolecular Chemistry},
6099	>	Number = 2,
6100	>	Pages = {214-219},
6101	>	Title = {Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases},
6102	>	Uri = {<Go to ISI>://000187843800012},
6103	>	Volume = 2,
6104	>	Year = 2004}
6105
6106	<	@ARTICLE{Satoh1996,
6107	<	author = {K. Satoh and S. Mita and S. Kondo},
2962	<	title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect
2963	<	of terminal dipole moment on mesophase formation},
2964	<	journal = {Chemical Physics Letters},
2965	<	year = {1996},
2966	<	volume = {255},
2967	<	pages = {99-104},
2968	<	number = {1-3},
2969	<	month = {Jun 7},
2970	<	abstract = {The effects of dipole-dipole interaction on mesophase formation are
6106	>	@article{Satoh1996,
6107	>	Abstract = {The effects of dipole-dipole interaction on mesophase formation are
6108		investigated with a Monte Carlo simulation using the dipolar Gay-Berne
6109		potential. It is shown that the dipole moment at the end of a molecule
6110		causes a shift in the nematic-isotropic transition toward higher
6111		temperature and a spread of the temperature range of the nematic
6112		phase and that layer structures with various interdigitations are
6113		formed in the smectic phase.},
6114	<	annote = {Uq975 Times Cited:32 Cited References Count:33},
6115	<	issn = {0009-2614},
6116	<	uri = {<Go to ISI>://A1996UQ97500017},
6117	<	}
6114	>	Annote = {Uq975 Times Cited:32 Cited References Count:33},
6115	>	Author = {K. Satoh and S. Mita and S. Kondo},
6116	>	Issn = {0009-2614},
6117	>	Journal = {Chemical Physics Letters},
6118	>	Month = {Jun 7},
6119	>	Number = {1-3},
6120	>	Pages = {99-104},
6121	>	Title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect of terminal dipole moment on mesophase formation},
6122	>	Uri = {<Go to ISI>://A1996UQ97500017},
6123	>	Volume = 255,
6124	>	Year = 1996}
6125
6126	<	@ARTICLE{Schaps1999,
6127	<	author = {G. L. Schaps},
6128	<	title = {Compiler construction with ANTLR and Java - Tools for building tools},
6129	<	journal = {Dr Dobbs Journal},
6130	<	year = {1999},
6131	<	volume = {24},
6132	<	pages = {84-+},
6133	<	number = {3},
6134	<	month = {Mar},
6135	<	annote = {163EC Times Cited:0 Cited References Count:0},
6136	<	issn = {1044-789X},
6137	<	uri = {<Go to ISI>://000078389200023},
2994	<	}
6126	>	@article{Schaps1999,
6127	>	Annote = {163EC Times Cited:0 Cited References Count:0},
6128	>	Author = {G. L. Schaps},
6129	>	Issn = {1044-789X},
6130	>	Journal = {Dr Dobbs Journal},
6131	>	Month = {Mar},
6132	>	Number = 3,
6133	>	Pages = {84-+},
6134	>	Title = {Compiler construction with ANTLR and Java - Tools for building tools},
6135	>	Uri = {<Go to ISI>://000078389200023},
6136	>	Volume = 24,
6137	>	Year = 1999}
6138
6139	<	@ARTICLE{Shen2002,
6140	<	author = {M. Y. Shen and K. F. Freed},
2998	<	title = {Long time dynamics of met-enkephalin: Comparison of explicit and
2999	<	implicit solvent models},
3000	<	journal = {Biophysical Journal},
3001	<	year = {2002},
3002	<	volume = {82},
3003	<	pages = {1791-1808},
3004	<	number = {4},
3005	<	month = {Apr},
3006	<	abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
6139	>	@article{Shen2002,
6140	>	Abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
6141		structure and receptor docking mechanism are still not well understood.
6142		The conformational dynamics of this neuron peptide in liquid water
6143		are studied here by using all-atom molecular dynamics (MID) and
#	Line 3022 | Line 6156 | Encoding: GBK
6156		The simulations provide insights into the conformational restrictions
6157		that are associated with the bioactivity of the opiate peptide dermorphin
6158		for the delta-receptor.},
6159	<	annote = {540MH Times Cited:36 Cited References Count:45},
6160	<	issn = {0006-3495},
6161	<	uri = {<Go to ISI>://000174932400010},
6162	<	}
6159	>	Annote = {540MH Times Cited:36 Cited References Count:45},
6160	>	Author = {M. Y. Shen and K. F. Freed},
6161	>	Issn = {0006-3495},
6162	>	Journal = {Biophysical Journal},
6163	>	Month = {Apr},
6164	>	Number = 4,
6165	>	Pages = {1791-1808},
6166	>	Title = {Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models},
6167	>	Uri = {<Go to ISI>://000174932400010},
6168	>	Volume = 82,
6169	>	Year = 2002}
6170
6171	<	@ARTICLE{Shillcock2005,
6172	<	author = {J. C. Shillcock and R. Lipowsky},
6173	<	title = {Tension-induced fusion of bilayer membranes and vesicles},
6174	<	journal = {Nature Materials},
6175	<	year = {2005},
6176	<	volume = {4},
6177	<	pages = {225-228},
6178	<	number = {3},
6179	<	month = {Mar},
6180	<	annote = {901QJ Times Cited:9 Cited References Count:23},
6181	<	issn = {1476-1122},
6182	<	uri = {<Go to ISI>://000227296700019},
3042	<	}
6171	>	@article{Shillcock2005,
6172	>	Annote = {901QJ Times Cited:9 Cited References Count:23},
6173	>	Author = {J. C. Shillcock and R. Lipowsky},
6174	>	Issn = {1476-1122},
6175	>	Journal = {Nature Materials},
6176	>	Month = {Mar},
6177	>	Number = 3,
6178	>	Pages = {225-228},
6179	>	Title = {Tension-induced fusion of bilayer membranes and vesicles},
6180	>	Uri = {<Go to ISI>://000227296700019},
6181	>	Volume = 4,
6182	>	Year = 2005}
6183
6184	<	@ARTICLE{Shimada1993,
6185	<	author = {J. Shimada and H. Kaneko and T. Takada},
3046	<	title = {Efficient Calculations of Coulombic Interactions in Biomolecular
3047	<	Simulations with Periodic Boundary-Conditions},
3048	<	journal = {Journal of Computational Chemistry},
3049	<	year = {1993},
3050	<	volume = {14},
3051	<	pages = {867-878},
3052	<	number = {7},
3053	<	month = {Jul},
3054	<	abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
6184	>	@article{Shimada1993,
6185	>	Abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
6186		simulations, two possibilities are considered. The first is the
6187		famous particle-particle and particle-mesh (PPPM) method developed
6188		by Hockney and Eastwood, and the second is a new one developed here
#	Line 3068 | Line 6199 | Encoding: GBK
6199		first method has the drawback that the accuracy in the total electrostatic
6200		energy is not high for configurations of charged particles randomly
6201		generated.},
6202	<	annote = {Lh164 Times Cited:27 Cited References Count:47},
6203	<	issn = {0192-8651},
6204	<	uri = {<Go to ISI>://A1993LH16400011},
6205	<	}
6202	>	Annote = {Lh164 Times Cited:27 Cited References Count:47},
6203	>	Author = {J. Shimada and H. Kaneko and T. Takada},
6204	>	Issn = {0192-8651},
6205	>	Journal = {Journal of Computational Chemistry},
6206	>	Month = {Jul},
6207	>	Number = 7,
6208	>	Pages = {867-878},
6209	>	Title = {Efficient Calculations of Coulombic Interactions in Biomolecular Simulations with Periodic Boundary-Conditions},
6210	>	Uri = {<Go to ISI>://A1993LH16400011},
6211	>	Volume = 14,
6212	>	Year = 1993}
6213
6214	<	@ARTICLE{Skeel2002,
6215	<	author = {R. D. Skeel and J. A. Izaguirre},
3078	<	title = {An impulse integrator for Langevin dynamics},
3079	<	journal = {Molecular Physics},
3080	<	year = {2002},
3081	<	volume = {100},
3082	<	pages = {3885-3891},
3083	<	number = {24},
3084	<	month = {Dec 20},
3085	<	abstract = {The best simple method for Newtonian molecular dynamics is indisputably
6214	>	@article{Skeel2002,
6215	>	Abstract = {The best simple method for Newtonian molecular dynamics is indisputably
6216		the leapfrog Stormer-Verlet method. The appropriate generalization
6217		to simple Langevin dynamics is unclear. An analysis is presented
6218		comparing an 'impulse method' (kick; fluctuate; kick), the 1982
#	Line 3092 | Line 6222 | Encoding: GBK
6222		considerations suggest that the impulse method is the best basic
6223		method for simple Langevin dynamics, with the van Gunsteren-Berendsen
6224		method a close contender.},
6225	<	annote = {633RX Times Cited:8 Cited References Count:22},
6226	<	issn = {0026-8976},
6227	<	uri = {<Go to ISI>://000180297200014},
6228	<	}
6225	>	Annote = {633RX Times Cited:8 Cited References Count:22},
6226	>	Author = {R. D. Skeel and J. A. Izaguirre},
6227	>	Issn = {0026-8976},
6228	>	Journal = {Molecular Physics},
6229	>	Month = {Dec 20},
6230	>	Number = 24,
6231	>	Pages = {3885-3891},
6232	>	Title = {An impulse integrator for Langevin dynamics},
6233	>	Uri = {<Go to ISI>://000180297200014},
6234	>	Volume = 100,
6235	>	Year = 2002}
6236
6237	<	@ARTICLE{Skeel1997,
6238	<	author = {R. D. Skeel and G. H. Zhang and T. Schlick},
3102	<	title = {A family of symplectic integrators: Stability, accuracy, and molecular
3103	<	dynamics applications},
3104	<	journal = {Siam Journal on Scientific Computing},
3105	<	year = {1997},
3106	<	volume = {18},
3107	<	pages = {203-222},
3108	<	number = {1},
3109	<	month = {Jan},
3110	<	abstract = {The following integration methods for special second-order ordinary
6237	>	@article{Skeel1997,
6238	>	Abstract = {The following integration methods for special second-order ordinary
6239		differential equations are studied: leapfrog, implicit midpoint,
6240		trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all
6241		are members, or equivalent to members, of a one-parameter family
#	Line 3120 | Line 6248 | Encoding: GBK
6248		leads to higher accuracy and better energy conservation. Hence,
6249		we suggest that the straightforward analysis of energy conservation
6250		is misleading.},
6251	<	annote = {We981 Times Cited:30 Cited References Count:35},
6252	<	issn = {1064-8275},
6253	<	uri = {<Go to ISI>://A1997WE98100012},
6254	<	}
6251	>	Annote = {We981 Times Cited:30 Cited References Count:35},
6252	>	Author = {R. D. Skeel and G. H. Zhang and T. Schlick},
6253	>	Issn = {1064-8275},
6254	>	Journal = {Siam Journal on Scientific Computing},
6255	>	Month = {Jan},
6256	>	Number = 1,
6257	>	Pages = {203-222},
6258	>	Title = {A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications},
6259	>	Uri = {<Go to ISI>://A1997WE98100012},
6260	>	Volume = 18,
6261	>	Year = 1997}
6262
6263	<	@ARTICLE{Tao2005,
6264	<	author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont
3130	<	and W. J. Briels},
3131	<	title = {Brownian dynamics simulations of the self- and collective rotational
3132	<	diffusion coefficients of rigid long thin rods},
3133	<	journal = {Journal of Chemical Physics},
3134	<	year = {2005},
3135	<	volume = {122},
3136	<	pages = {-},
3137	<	number = {24},
3138	<	month = {Jun 22},
3139	<	abstract = {Recently a microscopic theory for the dynamics of suspensions of long
6263	>	@article{Tao2005,
6264	>	Abstract = {Recently a microscopic theory for the dynamics of suspensions of long
6265		thin rigid rods was presented, confirming and expanding the well-known
6266		theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon,
6267		Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here
#	Line 3156 | Line 6281 | Encoding: GBK
6281		predicted by the theory, which is attributed to an oversimplification
6282		of dynamic correlations in the theory. (c) 2005 American Institute
6283		of Physics.},
6284	<	annote = {943DN Times Cited:3 Cited References Count:26},
6285	<	issn = {0021-9606},
6286	<	uri = {<Go to ISI>://000230332400077},
6287	<	}
6284	>	Annote = {943DN Times Cited:3 Cited References Count:26},
6285	>	Author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont and W. J. Briels},
6286	>	Issn = {0021-9606},
6287	>	Journal = {Journal of Chemical Physics},
6288	>	Month = {Jun 22},
6289	>	Number = 24,
6290	>	Pages = {-},
6291	>	Title = {Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods},
6292	>	Uri = {<Go to ISI>://000230332400077},
6293	>	Volume = 122,
6294	>	Year = 2005}
6295
6296	<	@BOOK{Tolman1979,
6297	<	title = {The Principles of Statistical Mechanics},
6298	<	publisher = {Dover Publications, Inc.},
6299	<	year = {1979},
6300	<	author = {R.~C. Tolman},
6301	<	address = {New York},
6302	<	chapter = {2},
6303	<	pages = {19-22},
3172	<	}
6296	>	@book{Tolman1979,
6297	>	Address = {New York},
6298	>	Author = {R.~C. Tolman},
6299	>	Chapter = 2,
6300	>	Pages = {19-22},
6301	>	Publisher = {Dover Publications, Inc.},
6302	>	Title = {The Principles of Statistical Mechanics},
6303	>	Year = 1979}
6304
6305	<	@ARTICLE{Tu1995,
6306	<	author = {K. Tu and D. J. Tobias and M. L. Klein},
3176	<	title = {Constant pressure and temperature molecular dynamics simulation of
3177	<	a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine
3178	<	bilayer},
3179	<	journal = {Biophysical Journal},
3180	<	year = {1995},
3181	<	volume = {69},
3182	<	pages = {2558-2562},
3183	<	number = {6},
3184	<	month = {Dec},
3185	<	abstract = {We report a constant pressure and temperature molecular dynamics simulation
6305	>	@article{Tu1995,
6306	>	Abstract = {We report a constant pressure and temperature molecular dynamics simulation
6307		of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine
6308		at 50 degrees C and 28 water molecules/lipid. We have shown that
6309		the bilayer is stable throughout the 1550-ps simulation and have
#	Line 3201 | Line 6322 | Encoding: GBK
6322		order parameters for the glycerol and choline groups, as well as
6323		the phosphorus chemical shift anisotropy, are in qualitative agreement
6324		with those extracted from NMR measurements.},
6325	<	annote = {Tv018 Times Cited:108 Cited References Count:34},
6326	<	issn = {0006-3495},
6327	<	uri = {<Go to ISI>://A1995TV01800037},
6328	<	}
6325	>	Annote = {Tv018 Times Cited:108 Cited References Count:34},
6326	>	Author = {K. Tu and D. J. Tobias and M. L. Klein},
6327	>	Issn = {0006-3495},
6328	>	Journal = {Biophysical Journal},
6329	>	Month = {Dec},
6330	>	Number = 6,
6331	>	Pages = {2558-2562},
6332	>	Title = {Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer},
6333	>	Uri = {<Go to ISI>://A1995TV01800037},
6334	>	Volume = 69,
6335	>	Year = 1995}
6336
6337	<	@ARTICLE{Tuckerman1992,
6338	<	author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
3211	<	title = {Reversible Multiple Time Scale Molecular-Dynamics},
3212	<	journal = {Journal of Chemical Physics},
3213	<	year = {1992},
3214	<	volume = {97},
3215	<	pages = {1990-2001},
3216	<	number = {3},
3217	<	month = {Aug 1},
3218	<	abstract = {The Trotter factorization of the Liouville propagator is used to generate
6337	>	@article{Tuckerman1992,
6338	>	Abstract = {The Trotter factorization of the Liouville propagator is used to generate
6339		new reversible molecular dynamics integrators. This strategy is
6340		applied to derive reversible reference system propagator algorithms
6341		(RESPA) that greatly accelerate simulations of systems with a separation
#	Line 3227 | Line 6347 | Encoding: GBK
6347		integrators. Finally, we show how these methods can be used to accelerate
6348		the integration of the equations of motion of systems with Nose
6349		thermostats.},
6350	<	annote = {Je891 Times Cited:680 Cited References Count:19},
6351	<	issn = {0021-9606},
6352	<	uri = {<Go to ISI>://A1992JE89100044},
6353	<	}
6350	>	Annote = {Je891 Times Cited:680 Cited References Count:19},
6351	>	Author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
6352	>	Issn = {0021-9606},
6353	>	Journal = {Journal of Chemical Physics},
6354	>	Month = {Aug 1},
6355	>	Number = 3,
6356	>	Pages = {1990-2001},
6357	>	Title = {Reversible Multiple Time Scale Molecular-Dynamics},
6358	>	Uri = {<Go to ISI>://A1992JE89100044},
6359	>	Volume = 97,
6360	>	Year = 1992}
6361
6362	<	@BOOK{Varadarajan1974,
6363	<	title = {Lie groups, Lie algebras, and their representations},
6364	<	publisher = {Prentice-Hall},
6365	<	year = {1974},
6366	<	author = {V.S. Varadarajan},
6367	<	address = {New York},
3241	<	}
6362	>	@book{Varadarajan1974,
6363	>	Address = {New York},
6364	>	Author = {V.S. Varadarajan},
6365	>	Publisher = {Prentice-Hall},
6366	>	Title = {Lie groups, Lie algebras, and their representations},
6367	>	Year = 1974}
6368
6369	<	@ARTICLE{Vincent1995,
6370	<	author = {J. J. Vincent and K. M. Merz},
3245	<	title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing
3246	<	Interface Standard},
3247	<	journal = {Journal of Computational Chemistry},
3248	<	year = {1995},
3249	<	volume = {16},
3250	<	pages = {1420-1427},
3251	<	number = {11},
3252	<	month = {Nov},
3253	<	abstract = {We have implemented a portable parallel version of the macromolecular
6369	>	@article{Vincent1995,
6370	>	Abstract = {We have implemented a portable parallel version of the macromolecular
6371		modeling package AMBER4. The message passing paradigm was used.
6372		All message passing constructs are compliant with the Message Passing
6373		Interface (MPI) standard. The molecular dynamics/minimization module
#	Line 3264 | Line 6381 | Encoding: GBK
6381		Performance results for a Lipid bilayer molecular dynamics simulation
6382		on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995
6383		by John Wiley & Sons, Inc.},
6384	<	annote = {Ta403 Times Cited:16 Cited References Count:23},
6385	<	issn = {0192-8651},
6386	<	uri = {<Go to ISI>://A1995TA40300009},
6387	<	}
6384	>	Annote = {Ta403 Times Cited:16 Cited References Count:23},
6385	>	Author = {J. J. Vincent and K. M. Merz},
6386	>	Issn = {0192-8651},
6387	>	Journal = {Journal of Computational Chemistry},
6388	>	Month = {Nov},
6389	>	Number = 11,
6390	>	Pages = {1420-1427},
6391	>	Title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing Interface Standard},
6392	>	Uri = {<Go to ISI>://A1995TA40300009},
6393	>	Volume = 16,
6394	>	Year = 1995}
6395
6396	<	@ARTICLE{Wegener1979,
6397	<	author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
6398	<	title = {A general ellipsoid can not always serve as a modle for the rotational
6399	<	diffusion properties of arbitrary shaped rigid molecules},
6400	<	journal = {Proc. Natl. Acad. Sci.},
6401	<	year = {1979},
6402	<	volume = {76},
6403	<	pages = {6356-6360},
3280	<	number = {12},
3281	<	}
6396	>	@article{Wegener1979,
6397	>	Author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
6398	>	Journal = {Proc. Natl. Acad. Sci.},
6399	>	Number = 12,
6400	>	Pages = {6356-6360},
6401	>	Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
6402	>	Volume = 76,
6403	>	Year = 1979}
6404
6405	<	@ARTICLE{Wilson2006,
6406	<	author = {G.~V. Wilson },
6407	<	title = {Where's the Real Bottleneck in Scientific Computing?},
6408	<	journal = {American Scientist},
6409	<	year = {2006},
6410	<	volume = {94},
3289	<	}
6405	>	@article{Wilson2006,
6406	>	Author = {G.~V. Wilson},
6407	>	Journal = {American Scientist},
6408	>	Title = {Where's the Real Bottleneck in Scientific Computing?},
6409	>	Volume = 94,
6410	>	Year = 2006}
6411
6412	<	@ARTICLE{Withers2003,
6413	<	author = {I. M. Withers},
3293	<	title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne
3294	<	fluid},
3295	<	journal = {Journal of Chemical Physics},
3296	<	year = {2003},
3297	<	volume = {119},
3298	<	pages = {10209-10223},
3299	<	number = {19},
3300	<	month = {Nov 15},
3301	<	abstract = {The effects of longitudinal quadrupole moments on the formation of
6412	>	@article{Withers2003,
6413	>	Abstract = {The effects of longitudinal quadrupole moments on the formation of
6414		liquid crystalline phases are studied by means of constant NPT Monte
6415		Carlo simulation methods. The popular Gay-Berne model mesogen is
6416		used as the reference fluid, which displays the phase sequences
#	Line 3325 | Line 6437 | Encoding: GBK
6437		This behavior is in much closer agreement with experimental findings
6438		than has been observed previously for nonpolar Gay-Berne and hard
6439		spherocylinder models. (C) 2003 American Institute of Physics.},
6440	<	annote = {738EF Times Cited:3 Cited References Count:43},
6441	<	issn = {0021-9606},
6442	<	uri = {<Go to ISI>://000186273200027},
6443	<	}
6440	>	Annote = {738EF Times Cited:3 Cited References Count:43},
6441	>	Author = {I. M. Withers},
6442	>	Issn = {0021-9606},
6443	>	Journal = {Journal of Chemical Physics},
6444	>	Month = {Nov 15},
6445	>	Number = 19,
6446	>	Pages = {10209-10223},
6447	>	Title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne fluid},
6448	>	Uri = {<Go to ISI>://000186273200027},
6449	>	Volume = 119,
6450	>	Year = 2003}
6451
6452	<	@ARTICLE{Wolf1999,
6453	<	author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
3335	<	title = {Exact method for the simulation of Coulombic systems by spherically
3336	<	truncated, pairwise r(-1) summation},
3337	<	journal = {Journal of Chemical Physics},
3338	<	year = {1999},
3339	<	volume = {110},
3340	<	pages = {8254-8282},
3341	<	number = {17},
3342	<	month = {May 1},
3343	<	abstract = {Based on a recent result showing that the net Coulomb potential in
6452	>	@article{Wolf1999,
6453	>	Abstract = {Based on a recent result showing that the net Coulomb potential in
6454		condensed ionic systems is rather short ranged, an exact and physically
6455		transparent method permitting the evaluation of the Coulomb potential
6456		by direct summation over the r(-1) Coulomb pair potential is presented.
#	Line 3361 | Line 6471 | Encoding: GBK
6471		simulations of crystals, liquids, and interfacial systems, such
6472		as free surfaces and grain boundaries. (C) 1999 American Institute
6473		of Physics. [S0021-9606(99)51517-1].},
6474	<	annote = {189PD Times Cited:70 Cited References Count:34},
6475	<	issn = {0021-9606},
6476	<	uri = {<Go to ISI>://000079913000008},
6477	<	}
6474	>	Annote = {189PD Times Cited:70 Cited References Count:34},
6475	>	Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
6476	>	Issn = {0021-9606},
6477	>	Journal = {Journal of Chemical Physics},
6478	>	Month = {May 1},
6479	>	Number = 17,
6480	>	Pages = {8254-8282},
6481	>	Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r(-1) summation},
6482	>	Uri = {<Go to ISI>://000079913000008},
6483	>	Volume = 110,
6484	>	Year = 1999}
6485
6486	<	@ARTICLE{Yoshida1990,
6487	<	author = {H. Yoshida},
6488	<	title = {Construction of Higher-Order Symplectic Integrators},
6489	<	journal = {Physics Letters A},
6490	<	year = {1990},
6491	<	volume = {150},
6492	<	pages = {262-268},
6493	<	number = {5-7},
6494	<	month = {Nov 12},
6495	<	annote = {Ej798 Times Cited:492 Cited References Count:9},
6496	<	issn = {0375-9601},
6497	<	uri = {<Go to ISI>://A1990EJ79800009},
3381	<	}
6486	>	@article{Yoshida1990,
6487	>	Annote = {Ej798 Times Cited:492 Cited References Count:9},
6488	>	Author = {H. Yoshida},
6489	>	Issn = {0375-9601},
6490	>	Journal = {Physics Letters A},
6491	>	Month = {Nov 12},
6492	>	Number = {5-7},
6493	>	Pages = {262-268},
6494	>	Title = {Construction of Higher-Order Symplectic Integrators},
6495	>	Uri = {<Go to ISI>://A1990EJ79800009},
6496	>	Volume = 150,
6497	>	Year = 1990}
6498
6499	<	@Article{Blum1972,
6500	<	author =   {L. Blum and A.~J. Torruella},
6501	<	title =    {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
6502	<	journal =  {Journal of Chemical Physics},
6503	<	year =     1972,
6504	<	volume =   56,
6505	<	number =   1,
6506	<	pages =    {303-309}
3391	<	}
6499	>	@article{Blum1972,
6500	>	Author = {L. Blum and A.~J. Torruella},
6501	>	Journal = {Journal of Chemical Physics},
6502	>	Number = 1,
6503	>	Pages = {303-309},
6504	>	Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
6505	>	Volume = 56,
6506	>	Year = 1972}
6507
6508	<	@Article{Stone1978,
6509	<	author =   {A.~J. Stone},
6510	<	title =    {The description of bimolecular potentials, forces and torques: the S and V function expansions},
6511	<	journal =  {Molecular Physics},
6512	<	year =     1978,
6513	<	volume =   36,
6514	<	number =   1,
6515	<	pages =    {241-256}
3401	<	}
6508	>	@article{Stone1978,
6509	>	Author = {A.~J. Stone},
6510	>	Journal = {Molecular Physics},
6511	>	Number = 1,
6512	>	Pages = {241-256},
6513	>	Title = {The description of bimolecular potentials, forces and torques: the S and V function expansions},
6514	>	Volume = 36,
6515	>	Year = 1978}
6516
6517	<	@Article{Berardi2003,
6518	<	author =   {R. Berardi, M. Cecchini and C. Zannoni},
6519	<	title =    {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
6520	<	journal =  {Journal of Chemical Physics},
6521	<	year =     2003,
6522	<	volume =   119,
6523	<	number =   18,
6524	<	pages =    {9933-9946}
3411	<	}
6517	>	@article{Berardi2003,
6518	>	Author = {R. Berardi, M. Cecchini and C. Zannoni},
6519	>	Journal = {Journal of Chemical Physics},
6520	>	Number = 18,
6521	>	Pages = {9933-9946},
6522	>	Title = {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
6523	>	Volume = 119,
6524	>	Year = 2003}
6525
6526	<	@Article{Beard2000,
6527	<	author =   {D. A. Beard and T. Schlick},
6528	<	title =    {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
6529	<	journal =  {Journal of Chemical Physics},
6530	<	year =     2000,
6531	<	volume =   112,
6532	<	number =   17,
6533	<	pages =    {7313-7322}
3421	<	}
6526	>	@article{Beard2000,
6527	>	Author = {D. A. Beard and T. Schlick},
6528	>	Journal = {Journal of Chemical Physics},
6529	>	Number = 17,
6530	>	Pages = {7313-7322},
6531	>	Title = {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
6532	>	Volume = 112,
6533	>	Year = 2000}
6534
6535	<	@BOOK{Hirsch1997,
6536	<	title = {Differential Topology},
6537	<	publisher = {Springer},
6538	<	year = {1997},
6539	<	author = {M.W. Hirsch},
6540	<	address = {New York}
3429	<	}
6535	>	@book{Hirsch1997,
6536	>	Address = {New York},
6537	>	Author = {M.W. Hirsch},
6538	>	Publisher = {Springer},
6539	>	Title = {Differential Topology},
6540	>	Year = 1997}
6541
6542	<	@BOOK{Jost2002,
6543	<	title = {Riemannian Geometry and Geometric Analysis},
6544	<	publisher = {Springer-Verlag},
6545	<	year = {2002},
6546	<	author = {J. Jost},
6547	<	address = {Berlin}
3437	<	}
6542	>	@book{Jost2002,
6543	>	Address = {Berlin},
6544	>	Author = {J. Jost},
6545	>	Publisher = {Springer-Verlag},
6546	>	Title = {Riemannian Geometry and Geometric Analysis},
6547	>	Year = 2002}
6548
6549	<	@BOOK{McDuff1998,
6550	<	title = {Introduction to Symplectic Topology },
6551	<	publisher = {Oxford Mathematical Monographs},
6552	<	year = {1998},
6553	<	author = {D. McDuff and D. Salamon},
6554	<	address = {Oxford}
3445	<	}
6549	>	@book{McDuff1998,
6550	>	Address = {Oxford},
6551	>	Author = {D. McDuff and D. Salamon},
6552	>	Publisher = {Oxford Mathematical Monographs},
6553	>	Title = {Introduction to Symplectic Topology},
6554	>	Year = 1998}
6555
6556	<	@Article{Matubayasi1999,
6557	<	author =   {N. Matubayasi and M. Nakahara},
6558	<	title =    {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
6559	<	journal =  {Journal of Chemical Physics},
6560	<	year =     1999,
6561	<	volume =   110,
6562	<	number =   7,
6563	<	pages =    {3291-3301}
3455	<	}
6556	>	@article{Matubayasi1999,
6557	>	Author = {N. Matubayasi and M. Nakahara},
6558	>	Journal = {Journal of Chemical Physics},
6559	>	Number = 7,
6560	>	Pages = {3291-3301},
6561	>	Title = {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
6562	>	Volume = 110,
6563	>	Year = 1999}
6564
6565	<	@Article{Miller2002,
6566	<	author =   {T.F. Miller III, M. Eleftheriou},
6567	<	title =    {Symplectic quaternion scheme for biophysical molecular dynamics},
6568	<	journal =  {Journal of Chemical Physics},
6569	<	year =     1999,
6570	<	volume =   116,
6571	<	number =   20,
6572	<	pages =    {8649-8659}
3465	<	}
6565	>	@article{Miller2002,
6566	>	Author = {T.F. Miller III, M. Eleftheriou},
6567	>	Journal = {Journal of Chemical Physics},
6568	>	Number = 20,
6569	>	Pages = {8649-8659},
6570	>	Title = {Symplectic quaternion scheme for biophysical molecular dynamics},
6571	>	Volume = 116,
6572	>	Year = 1999}
6573
6574	<	@Article{McMillan1971,
6575	<	author =   {W.L. McMillan},
6576	<	title =    {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},
6577	<	journal =  {Journal of Chemical Physics},
6578	<	year =     1971,
6579	<	volume =   4,
6580	<	number =   3,
6581	<	pages =    {1238¨C1246 }
3475	<	}
6574	>	@article{McMillan1971,
6575	>	Author = {W.L. McMillan},
6576	>	Journal = {Journal of Chemical Physics},
6577	>	Number = 3,
6578	>	Pages = {1238-1246},
6579	>	Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},
6580	>	Volume = 4,
6581	>	Year = 1971}
6582
6583	<	@Article{Gilmore1974,
6584	<	author =   {R. Gilmore},
6585	<	title =    {Baker-Campbell-Hausdorff Formulas},
6586	<	journal =  {Journal of Mathematical Physics},
6587	<	year =     1974,
6588	<	volume =   15,
6589	<	number =   12,
6590	<	pages =    {2090-2092}
3485	<	}
6583	>	@article{Gilmore1974,
6584	>	Author = {R. Gilmore},
6585	>	Journal = {Journal of Mathematical Physics},
6586	>	Number = 12,
6587	>	Pages = {2090-2092},
6588	>	Title = {Baker-Campbell-Hausdorff Formulas},
6589	>	Volume = 15,
6590	>	Year = 1974}
6591
6592	<	@Article{Strang1968,
6593	<	author =   {G. Strang},
6594	<	title =    {On the construction and comparision of difference schemes},
6595	<	journal =  {SIAM Journal on Numerical Analysis},
6596	<	year =     1968,
6597	<	volume =   5,
6598	<	number =   3,
6599	<	pages =    {506-517}
3495	<	}
6592	>	@article{Strang1968,
6593	>	Author = {G. Strang},
6594	>	Journal = {SIAM Journal on Numerical Analysis},
6595	>	Number = 3,
6596	>	Pages = {506-517},
6597	>	Title = {On the construction and comparision of difference schemes},
6598	>	Volume = 5,
6599	>	Year = 1968}
6600
6601	<	@Article{Trotter1959,
6602	<	author =   {H.F. Trotter},
6603	<	title =    {On the product of semi-groups of operators},
6604	<	journal =  {SIAM Journal on Numerical Analysis},
6605	<	year =     1959,
6606	<	volume =   10,
6607	<	number =   14,
6608	<	pages =    {545-551}
3505	<	}
6601	>	@article{Trotter1959,
6602	>	Author = {H.F. Trotter},
6603	>	Journal = {SIAM Journal on Numerical Analysis},
6604	>	Number = 14,
6605	>	Pages = {545-551},
6606	>	Title = {On the product of semi-groups of operators},
6607	>	Volume = 10,
6608	>	Year = 1959}
6609
6610	<	@Article{Cartwright1992,
6611	<	author =   {J.H.E. Cartwright and O. Piro},
6612	<	title =    {The Dynamics of Runge-Kutta Methods},
6613	<	journal =  {International Journal of Bifurcation and Chaos},
6614	<	year =     1992,
6615	<	volume =   2,
6616	<	number =   3,
6617	<	pages =    {427-449}
6618	<	}
6610	>	@article{Cartwright1992,
6611	>	Author = {J.H.E. Cartwright and O. Piro},
6612	>	Journal = {International Journal of Bifurcation and Chaos},
6613	>	Number = 3,
6614	>	Pages = {427-449},
6615	>	Title = {The Dynamics of Runge-Kutta Methods},
6616	>	Volume = 2,
6617	>	Year = 1992}
6618	>
6619	>	@article{HuseyinKaya07012005,
6620	>	Abstract = {It has been demonstrated that a "near-Levinthal" cooperative mechanism, whereby the common G[o] interaction scheme is augmented by an extra favorability for the native state as a whole, can lead to apparent two-state folding/unfolding kinetics over a broad range of native stabilities in lattice models of proteins. Here such a mechanism is shown to be generalizable to a simplified continuum (off-lattice) Langevin dynamics model with a C{alpha} protein chain representation, with the resulting chevron plots exhibiting an extended quasilinear regime reminiscent of that of apparent two-state real proteins. Similarly high degrees of cooperativity are possible in G[o]-like continuum models with rudimentary pairwise desolvation barriers as well. In these models, cooperativity increases with increasing desolvation barrier height, suggesting strongly that two-state-like folding/unfolding kinetics would be achievable when the pairwise desolvation barrier becomes sufficiently high. Besides cooperativity, another generic folding property of interest that has emerged from published experiments on several apparent two-state proteins is that their folding relaxation under constant native stability (isostability) conditions is essentially Arrhenius, entailing high intrinsic enthalpic folding barriers of [~]17-30 kcal/mol. Based on a new analysis of published data on barnase, here we propose that a similar property should also apply to a certain class of non-two-state proteins that fold with chevron rollovers. However, several continuum G[o]-like constructs considered here fail to predict any significant intrinsic enthalpic folding barrier under isostability conditions; thus the physical origin of such barriers in real proteins remains to be elucidated.
6621	>	},
6622	>	Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun},
6623	>	Doi = {10.1529/biophysj.104.057471},
6624	>	Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf},
6625	>	Journal = {Biophys. J.},
6626	>	Number = 1,
6627	>	Pages = {520-535},
6628	>	Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}},
6629	>	Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6630	>	Volume = 89,
6631	>	Year = 2005,
6632	>	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6633	>	Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}}

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