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5	<	%% Created for Dan Gezelter at 2008-01-11 16:20:18 -0500
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6
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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	+	@article{SunX._jp0762020,
57	+	Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556},
58	+	Author = {Sun, X. and Gezelter, J.D.},
59	+	Date-Added = {2008-02-15 13:48:18 -0500},
60	+	Date-Modified = {2008-02-15 13:48:18 -0500},
61	+	Issn = {1520-6106},
62	+	Journal = {Journal of Physical Chemistry B},
63	+	Number = {7},
64	+	Pages = {1968-1975},
65	+	Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes},
66	+	Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020},
67	+	Volume = {112},
68	+	Year = {2008},
69	+	Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}}
70	+
71	+	@book{Schlick2002,
72	+	Address = {Secaucus, NJ, USA},
73	+	Author = {Tamar Schlick},
74	+	Date-Added = {2008-02-12 16:52:19 -0500},
75	+	Date-Modified = {2008-02-12 16:53:15 -0500},
76	+	Isbn = {038795404X},
77	+	Publisher = {Springer-Verlag New York, Inc.},
78	+	Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
79	+	Year = {2002}}
80	+
81	+	@misc{Chun:2000fj,
82	+	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.},
83	+	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},
84	+	Date-Added = {2008-01-22 10:38:33 -0500},
85	+	Date-Modified = {2008-01-22 10:38:49 -0500},
86	+	Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
87	+	Note = {Journal of Computational Chemistry},
88	+	Pages = {159-184},
89	+	Timescited = {0},
90	+	Title = {MBO(N)D: A multibody method for long-time molecular dynamics simulations},
91	+	Volume = {21},
92	+	Year = {2000}}
93	+
94	+	@article{Fogolari:1996lr,
95	+	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.},
96	+	Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.},
97	+	Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
98	+	Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
99	+	Da = {19960924},
100	+	Date-Added = {2008-01-22 10:19:04 -0500},
101	+	Date-Modified = {2008-01-22 10:19:09 -0500},
102	+	Dcom = {19960924},
103	+	Edat = {1996/03/01},
104	+	Issn = {0006-3495 (Print)},
105	+	Jid = {0370626},
106	+	Journal = {Biophys J},
107	+	Jt = {Biophysical journal},
108	+	Language = {eng},
109	+	Lr = {20071115},
110	+	Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; Models, Molecular; Molecular Structure; Peptides/chemistry; *Protein Conformation; Software; Thermodynamics},
111	+	Mhda = {1996/03/01 00:01},
112	+	Number = {3},
113	+	Own = {NLM},
114	+	Pages = {1183--1197},
115	+	Pl = {UNITED STATES},
116	+	Pmid = {8785277},
117	+	Pst = {ppublish},
118	+	Pt = {Journal Article},
119	+	Pubm = {Print},
120	+	Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)},
121	+	Sb = {IM},
122	+	So = {Biophys J. 1996 Mar;70(3):1183-97. },
123	+	Stat = {MEDLINE},
124	+	Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.},
125	+	Volume = {70},
126	+	Year = {1996}}
127	+
128	+	@inbook{Ramachandran1996,
129	+	Address = {Providence, Rhode Island},
130	+	Author = {GOMATHI RAMACHANDRAN AND TAMAR SCHLICK},
131	+	Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
132	+	Date-Added = {2008-01-22 10:03:42 -0500},
133	+	Date-Modified = {2008-01-22 10:06:57 -0500},
134	+	Editor = {P. M. Pardalos and D. Shalloway and G. Xue},
135	+	Pages = {215-231},
136	+	Publisher = {American Mathematical Society},
137	+	Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
138	+	Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
139	+	Volume = {23},
140	+	Year = {1996}}
141	+
142	+	@article{FIXMAN:1986lr,
143	+	Author = {FIXMAN, M},
144	+	Date-Added = {2008-01-22 09:59:29 -0500},
145	+	Date-Modified = {2008-01-22 09:59:35 -0500},
146	+	Journal = {Macromolecules},
147	+	Pages = {1204-1207},
148	+	Timescited = {0},
149	+	Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION},
150	+	Volume = {19},
151	+	Year = {1986}}
152	+
153	+	@article{Berendsen87,
154	+	Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
155	+	Date-Added = {2008-01-22 09:53:15 -0500},
156	+	Date-Modified = {2008-01-22 09:53:15 -0500},
157	+	Journal = jpc,
158	+	Pages = {6269-6271},
159	+	Title = {The Missing Term in Effective Pair Potentials},
160	+	Volume = 91,
161	+	Year = 1987}
162	+
163	+	@incollection{Berendsen81,
164	+	Address = {Dordrecht},
165	+	Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
166	+	Booktitle = {Intermolecular Forces},
167	+	Date-Added = {2008-01-22 09:52:49 -0500},
168	+	Date-Modified = {2008-01-22 09:52:49 -0500},
169	+	Editor = {B. Pullman},
170	+	Pages = {331-342},
171	+	Publisher = {Reidel},
172	+	Title = {Simple Point Charge Water},
173	+	Year = 1981}
174
175	+	@article{Stillinger74,
176	+	Author = {F.~H. Stillinger and A. Rahman},
177	+	Date-Added = {2008-01-22 09:51:43 -0500},
178	+	Date-Modified = {2008-01-22 09:51:43 -0500},
179	+	Journal = jcp,
180	+	Number = 4,
181	+	Pages = {1545-1557},
182	+	Title = {Improved simulation of liquid water by molecular dynamics},
183	+	Volume = 60,
184	+	Year = 1974}
185
186		@article{Torre:1983lr,
187	<	Author = {de la Torre, Jose Garcia and Rodes, Vicente},
187	>	Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
188		Date-Added = {2008-01-11 16:16:43 -0500},
189		Date-Modified = {2008-01-11 16:16:43 -0500},
190		Journal = {The Journal of Chemical Physics},
191		Journal1 = {The Journal of Chemical Physics},
192		Journal2 = {J. Chem. Phys.},
193		Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
194	<	Number = {5},
194	>	Number = 5,
195		Pages = {2454--2460},
196		Publisher = {AIP},
197		Title = {Effects from bead size and hydrodynamic interactions on the translational and rotational coefficients of macromolecular bead models},
198		Ty = {JOUR},
199		Url = {http://link.aip.org/link/?JCP/79/2454/1},
200	<	Volume = {79},
201	<	Year = {1983}}
200	>	Volume = 79,
201	>	Year = 1983,
202	>	Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}}
203
204		@article{PhysRev.119.53,
205		Author = {Favro, L. Dale},
#	Line 33 \| Line 208
208		Doi = {10.1103/PhysRev.119.53},
209		Journal = {Phys. Rev.},
210		Month = {Jul},
211	<	Number = {1},
212	<	Numpages = {9},
211	>	Number = 1,
212	>	Numpages = 9,
213		Pages = {53--62},
214		Publisher = {American Physical Society},
215		Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body},
216	<	Volume = {119},
217	<	Year = {1960}}
216	>	Volume = 119,
217	>	Year = 1960,
218	>	Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}}
219
220		@article{hess:209,
221		Author = {Berk Hess},
#	Line 48 \| Line 224
224		Doi = {10.1063/1.1421362},
225		Journal = {The Journal of Chemical Physics},
226		Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
227	<	Number = {1},
227	>	Number = 1,
228		Pages = {209-217},
229		Publisher = {AIP},
230		Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
231		Url = {http://link.aip.org/link/?JCP/116/209/1},
232	<	Volume = {116},
233	<	Year = {2002}}
232	>	Volume = 116,
233	>	Year = 2002,
234	>	Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
235	>	Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}}
236
237		@article{Garcia-de-la-Torre:1997qy,
238		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.},
239		Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es},
240	<	Au = {Garcia de la Torre, J and Carrasco, B and Harding, SE},
241	<	Author = {Garcia de la Torre, J and Carrasco, B and Harding, S E},
242	<	Da = {19970709},
240	>	Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE},
241	>	Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E},
242	>	Da = 19970709,
243		Date-Added = {2008-01-08 15:45:31 -0500},
244		Date-Modified = {2008-01-08 15:46:57 -0500},
245	<	Dcom = {19970709},
245	>	Dcom = 19970709,
246		Edat = {1997/01/01},
247		Issn = {0175-7571 (Print)},
248	<	Jid = {8409413},
248	>	Jid = 8409413,
249		Journal = {Eur Biophys J},
250		Jt = {European biophysics journal : EBJ},
251		Keywords = {Birefringence; Fluorescence Polarization; Humans; Immunoglobulin G/chemistry; Models, Structural; Protein Conformation; Proteins/chemistry; Scattering, Radiation; *Software; Ultracentrifugation/methods},
252		Language = {eng},
253	<	Lr = {20061115},
253	>	Lr = 20061115,
254		Mhda = {1997/01/01 00:01},
255		Number = {5-6},
256		Own = {NLM},
257		Pages = {361--372},
258		Pl = {GERMANY},
259	<	Pmid = {9213556},
259	>	Pmid = 9213556,
260		Pst = {ppublish},
261		Pt = {Journal Article; Research Support, Non-U.S. Gov't},
262		Pubm = {Print},
#	Line 87 \| Line 265
265		So = {Eur Biophys J. 1997;25(5-6):361-72.},
266		Stat = {MEDLINE},
267		Title = {SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.},
268	<	Volume = {25},
269	<	Year = {1997}}
268	>	Volume = 25,
269	>	Year = 1997}
270
271		@article{Ravichandran:1999fk,
272		Abstract = {Detailed molecular dynamics simulations of the rotational and the translational motions of Gay-Berne ellipsoids in a sea of Lennard-Jones spheres have been carried out. It is found that while the translational motion of an ellipsoid is isotropic at low density, it becomes increasingly anisotropic with density until the ratio of the parallel to the perpendicular diffusion coefficients becomes nearly equal to the value of the aspect ratio at high density. The latter is in agreement with the prediction of Navier-Stokes hydrodynamics with slip boundary condition. The product of the translational diffusion coefficient and the rotational correlation time also attains a hydrodynamic-like density independent behavior only at high density. The reorientational correlation function becomes nonexponential at high density and low temperature where it also develops a slow decay. The perpendicular component of the velocity time correlation function exhibits a clear double minimum, only at high density, which becomes more pronounced as the aspect ratio is increased. (C) 1999 American Institute of Physics. [S0021-9606(99)51440-2].},
#	Line 98 \| Line 276
276		Journal = {Journal of Chemical Physics},
277		Pages = {7505-7511},
278		Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
279	<	Volume = {111},
280	<	Year = {1999}}
279	>	Volume = 111,
280	>	Year = 1999}
281
282		@article{TANG:1993lr,
283		Abstract = {Translational friction coefficients of hard prolate ellipsoids (having aspect ratios of 1-10) have been calculated by solving the linearized Navier-Stokes equations of hydrodynamics, using the method of Faxen's theorem. When the stick boundary condition was used, the present results reproduce the famous work of Lamb. The new information derived from this study arises from the analysis of the friction under the influence of the slip hydrodynamic boundary condition. It was found that the slip friction perpendicular to the long axis of the prolate ellipsoid increases monotonically with aspect ratio, whereas the parallel component of the friction decreases monotonically to an apparent limiting value. The ratio f(perpendicular to)/f(parallel to) of friction coefficients perpendicular and parallel to the long axis of the particle, calculated using slip hydrodynamics, scales roughly as the aspect ratio of the ellipsoid, in accord with the findings from an Enskog (uncorrelated binary collision) kinetic theory of hard ellipsoids and from the estimate derived from molecular dynamics. In contrast, f(perpendicular to)/f(parallel to) derived by means of stick hydrodynamics shows a weak dependence on the aspect ratio and disagrees with kinetic theory and molecular dynamics findings.},
#	Line 109 \| Line 287
287		Journal = {Molecular Physics},
288		Pages = {1443-1457},
289		Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
290	<	Volume = {80},
291	<	Year = {1993}}
290	>	Volume = 80,
291	>	Year = 1993}
292
293		@article{Schmidt:2003kx,
294		Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a spherical solute in a dense fluid of spherical solvent particles. The size and mass of the solute particle are related in such a way that we can naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that as long as the solute radius is interpreted as an effective hydrodynamic radius, the Stokes-Einstein law with slip boundary conditions is satisfied as the Brownian limit is approached (specifically, when the solute is roughly 100 times more massive than the solvent particles). In contrast, the Stokes-Einstein law is not satisfied for a tagged particle of the neat solvent. We also find that in the Brownian limit the amplitude of the long-time tail of the solute's velocity autocorrelation function is in good agreement with theoretical hydrodynamic predictions. When the solvent density is substantially lower than the triple density, the Stokes-Einstein law is no longer satisfied, and the amplitude of the long-time tail is not in good agreement with theoretical predictions, signaling the breakdown of hydrodynamics. (C) 2003 American Institute of Physics.},
#	Line 121 \| Line 299
299		Journal = {Journal of Chemical Physics},
300		Pages = {8062-8068},
301		Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
302	<	Volume = {119},
303	<	Year = {2003}}
302	>	Volume = 119,
303	>	Year = 2003,
304	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}
305
306		@article{Schmidt:2004fj,
307		Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a variety of solutes in a dense fluid of spherical solvent particles. We explore the effects of surface roughness of the solute on the resulting hydrodynamic boundary condition as we naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that when the solute and solvent interact through a purely repulsive isotropic potential, in the Brownian limit the Stokes-Einstein law is satisfied with slip boundary conditions. However, when surface roughness is introduced through an anisotropic solute-solvent interaction potential, we find that the Stokes-Einstein law is satisfied with stick boundary conditions. In addition, when the attractive strength of a short-range isotropic solute-solvent potential is increased, the solute becomes dressed with solvent particles, making it effectively rough, and so stick boundary conditions are again recovered.},
#	Line 133 \| Line 312
312		Journal = {Journal of Physical Chemistry B},
313		Pages = {6767-6771},
314		Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
315	<	Volume = {108},
316	<	Year = {2004}}
315	>	Volume = 108,
316	>	Year = 2004,
317	>	Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}}
318
319		@article{Klein01,
320		Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
#	Line 274 \| Line 454
454		Date-Modified = {2008-01-08 14:58:56 -0500},
455		Journal = {J. Chem. Phys.},
456		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf},
457	<	Number = {19},
457	>	Number = 19,
458		Pages = {8577-8593},
459		Title = {A smooth particle mesh Ewald method},
460	<	Volume = {103},
461	<	Year = {1995}}
460	>	Volume = 103,
461	>	Year = 1995}
462
463		@article{Ricci94,
464		Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
#	Line 328 \| Line 508
508		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf},
509		Pages = {7320-7327},
510		Title = {Acceleration of Convergence for Lattice Sums},
511	<	Volume = {93},
512	<	Year = {1989}}
511	>	Volume = 93,
512	>	Year = 1989}
513
514		@article{Petersen95,
515		Author = {H.~G. Petersen},
#	Line 338 \| Line 518
518		Journal = {J. Chem. Phys.},
519		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
520		Month = {September},
521	<	Number = {9},
521	>	Number = 9,
522		Pages = {3668-3679},
523		Title = {Accuracy and efficiency of the particle mesh Ewald method},
524	<	Volume = {103},
525	<	Year = {1995}}
524	>	Volume = 103,
525	>	Year = 1995}
526
527		@article{Duncan06,
528		Author = {Peter D. Duncan and Philip J. Camp},
#	Line 428 \| Line 608
608		Year = 2003}
609
610		@article{Cascales98,
611	<	Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
611	>	Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and {Garc\'{i}a de la Torre}, Jose},
612		Date-Added = {2008-01-08 14:58:56 -0500},
613		Date-Modified = {2008-01-08 14:58:57 -0500},
614		Journal = {J. Phys. Chem. B},
#	Line 475 \| Line 655
655		Journal = {Phil. Mag. A},
656		Pages = {1057-1066},
657		Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
658	<	Volume = {75},
659	<	Year = {1997}}
658	>	Volume = 75,
659	>	Year = 1997}
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710		Pages = {1322-1331},
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2657		Date-Modified = {2008-01-08 14:59:01 -0500},
2658		Journal = {Proc. R. Soc. London Ser. A},
2659		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
2660	<	Number = {1752},
2660	>	Number = 1752,
2661		Pages = {27-56},
2662		Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
2663	<	Volume = {373},
2664	<	Year = {1980}}
2663	>	Volume = 373,
2664	>	Year = 1980}
2665
2666		@article{Ercolessi88,
2667		Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
#	Line 2584 \| Line 2774
2774		Doi = {10.1529/biophysj.104.056606},
2775		Eprint = {http://www.biophysj.org/cgi/reprint/88/4/2626.pdf},
2776		Journal = {Biophys. J.},
2777	<	Number = {4},
2777	>	Number = 4,
2778		Pages = {2626-2637},
2779		Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}},
2780		Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2781	<	Volume = {88},
2782	<	Year = {2005}}
2781	>	Volume = 88,
2782	>	Year = 2005,
2783	>	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2784	>	Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606}}
2785
2786		@article{Lenz07,
2787		Author = {Olaf Lenz and Friederike Schmid},
#	Line 2699 \| Line 2891
2891		Date-Added = {2008-01-08 14:58:56 -0500},
2892		Date-Modified = {2008-01-08 14:59:02 -0500},
2893		Journal = {Mol. Phys.},
2894	<	Number = {2},
2894	>	Number = 2,
2895		Pages = {387-400},
2896		Title = {The computer simulation of polar liquids},
2897	<	Volume = {38},
2898	<	Year = {1979}}
2897	>	Volume = 38,
2898	>	Year = 1979}
2899
2900		@article{Pense92,
2901		Author = {A. W. Pense},
#	Line 2743 \| Line 2935
2935		Journal = {Surf. Sci.},
2936		Pages = {433-440},
2937		Title = {The electrostatic potential in the surface region of an ionic crystal},
2938	<	Volume = {49},
2939	<	Year = {1975}}
2938	>	Volume = 49,
2939	>	Year = 1975}
2940
2941		@article{Daw93,
2942		Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes},
#	Line 2792 \| Line 2984
2984		Date-Modified = {2008-01-08 14:59:02 -0500},
2985		Journal = {J. Chem. Phys.},
2986		Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
2987	<	Number = {9},
2987	>	Number = 9,
2988		Pages = {4576-4584},
2989		Title = {The role of long ranged forces in determining the structure and properties of liquid water},
2990	<	Volume = {79},
2991	<	Year = {1983}}
2990	>	Volume = 79,
2991	>	Year = 1983}
2992
2993		@article{Brannigan04b,
2994		Author = {G. Brannigan and A.~C. Tamboli and F.~L.~H. Brown},
#	Line 3005 \| Line 3197
3197		Doi = {10.1103/PhysRevLett.67.923},
3198		Journal = {Phys. Rev. Lett.},
3199		Month = {Aug},
3200	<	Number = {7},
3201	<	Numpages = {3},
3200	>	Number = 7,
3201	>	Numpages = 3,
3202		Pages = {923--926},
3203		Publisher = {American Physical Society},
3204		Title = {Wrinkling transition in partially polymerized vesicles},
3205	<	Volume = {67},
3206	<	Year = {1991}}
3205	>	Volume = 67,
3206	>	Year = 1991,
3207	>	Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923}}
3208
3209		@article{Wendt78,
3210		Author = {H. Wendt and F.~F. Abraham},
#	Line 3027 \| Line 3220
3220		Date-Added = {2008-01-08 14:58:56 -0500},
3221		Date-Modified = {2008-01-08 14:59:03 -0500},
3222		Note = {private correspondence},
3223	<	Year = {2000}}
3223	>	Year = 2000}
3224
3225		@article{Dwyer1977,
3226		Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
#	Line 3089 \| Line 3282
3282		Date-Added = {2008-01-08 14:57:14 -0500},
3283		Date-Modified = {2008-01-08 14:57:14 -0500},
3284		Journal = {Chemical Engineering Science},
3285	<	Number = {12},
3285	>	Number = 12,
3286		Pages = {1769--1776},
3287		Title = {The slow translation and rotation of two unequal spheres in a viscous fluid},
3288		Ty = {JOUR},
3289		Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
3290	<	Volume = {24},
3291	<	Year = {1969}}
3290	>	Volume = 24,
3291	>	Year = 1969,
3292	>	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}}
3293
3294		@article{Stimson:1926qy,
3295		Author = {Stimson, M and Jeffery, GB},
#	Line 3104 \| Line 3298
3298		Journal = {Proceedings of the Royal Society of London Series A-Containing Papers of a Mathematical and Physical Character},
3299		Pages = {110-116},
3300		Title = {The motion of two spheres in a viscous fluid},
3301	<	Volume = {111},
3302	<	Year = {1926}}
3301	>	Volume = 111,
3302	>	Year = 1926}
3303
3304		@article{Orlandi:2006fk,
3305		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.},
3306		Address = {Dipartimento di Chimica Fisica e Inorganica, and INSTM, Universita di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.},
3307		Au = {Orlandi, S and Berardi, R and Steltzer, J and Zannoni, C},
3308		Author = {Orlandi, Silvia and Berardi, Roberto and Steltzer, Joachim and Zannoni, Claudio},
3309	<	Da = {20060407},
3309	>	Da = 20060407,
3310		Date-Added = {2008-01-08 14:47:56 -0500},
3311		Date-Modified = {2008-01-08 14:48:06 -0500},
3312	<	Dcom = {20070727},
3312	>	Dcom = 20070727,
3313		Doi = {10.1063/1.2176622},
3314		Edat = {2006/04/08 09:00},
3315		Issn = {0021-9606 (Print)},
3316	<	Jid = {0375360},
3316	>	Jid = 0375360,
3317		Journal = {J Chem Phys},
3318		Jt = {The Journal of chemical physics},
3319		Language = {eng},
3320		Mhda = {2006/04/08 09:01},
3321	<	Number = {12},
3321	>	Number = 12,
3322		Own = {NLM},
3323	<	Pages = {124907},
3323	>	Pages = 124907,
3324		Pl = {United States},
3325	<	Pmid = {16599725},
3325	>	Pmid = 16599725,
3326		Pst = {ppublish},
3327		Pt = {Journal Article},
3328		Pubm = {Print},
3329		So = {J Chem Phys. 2006 Mar 28;124(12):124907.},
3330		Stat = {PubMed-not-MEDLINE},
3331		Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.},
3332	<	Volume = {124},
3333	<	Year = {2006}}
3332	>	Volume = 124,
3333	>	Year = 2006,
3334	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}}
3335
3336		@article{sun:031602,
3337		Author = {Xiuquan Sun and J. Daniel Gezelter},
3338		Date-Added = {2008-01-08 14:42:33 -0500},
3339		Date-Modified = {2008-01-08 14:42:33 -0500},
3340		Doi = {10.1103/PhysRevE.75.031602},
3341	<	Eid = {031602},
3341	>	Eid = 031602,
3342		Journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)},
3343		Keywords = {lattice theory; membranes},
3344	<	Number = {3},
3345	<	Numpages = {7},
3346	<	Pages = {031602},
3344	>	Number = 3,
3345	>	Numpages = 7,
3346	>	Pages = 031602,
3347		Publisher = {APS},
3348		Title = {Spontaneous corrugation of dipolar membranes},
3349		Url = {http://link.aps.org/abstract/PRE/v75/e031602},
3350	<	Volume = {75},
3351	<	Year = {2007}}
3350	>	Volume = 75,
3351	>	Year = 2007,
3352	>	Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602},
3353	>	Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}}
3354
3355		@article{Ortega:2007lr,
3356		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.},
3357		Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.},
3358	<	Au = {Ortega, A and Garcia de la Torre, J},
3359	<	Author = {Ortega, A and Garcia de la Torre, J},
3360	<	Da = {20070813},
3358	>	Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3359	>	Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3360	>	Da = 20070813,
3361		Date-Added = {2008-01-08 14:38:03 -0500},
3362		Date-Modified = {2008-01-08 14:38:49 -0500},
3363	<	Dcom = {20071017},
3364	<	Dep = {20070724},
3363	>	Dcom = 20071017,
3364	>	Dep = 20070724,
3365		Doi = {10.1021/bm700473f},
3366		Edat = {2007/07/25 09:00},
3367		Issn = {1525-7797 (Print)},
3368	<	Jid = {100892849},
3368	>	Jid = 100892849,
3369		Journal = {Biomacromolecules},
3370		Jt = {Biomacromolecules},
3371		Keywords = {Computer Simulation; Heparin/chemistry; Macromolecular Substances/chemistry; Models, Chemical; *Models, Molecular; Molecular Conformation; Particle Size; Protein Conformation; Proteins/chemistry; Software; Solutions},
3372		Language = {eng},
3373		Mhda = {2007/10/18 09:00},
3374	<	Number = {8},
3374	>	Number = 8,
3375		Own = {NLM},
3376		Pages = {2464--2475},
3377		Phst = {2007/07/24 {$[$}aheadofprint{$]$}},
3378		Pl = {United States},
3379	<	Pmid = {17645309},
3379	>	Pmid = 17645309,
3380		Pst = {ppublish},
3381		Pt = {Journal Article; Research Support, Non-U.S. Gov't},
3382		Pubm = {Print-Electronic},
#	Line 3188 \| Line 3385
3385		So = {Biomacromolecules. 2007 Aug;8(8):2464-75. Epub 2007 Jul 24.},
3386		Stat = {MEDLINE},
3387		Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.},
3388	<	Volume = {8},
3389	<	Year = {2007}}
3388	>	Volume = 8,
3389	>	Year = 2007,
3390	>	Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}}
3391
3392		@article{Torre2003,
3393		Abstract = {While the prediction of hydrodynamic properties of rigid particles
#	Line 3215 \| Line 3413
3413		We provide an example of the application of this methodology to
3414		the dynamics of a semiflexible, wormlike DNA.},
3415		Annote = {724XK Times Cited:6 Cited References Count:64},
3416	<	Author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez},
3416	>	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},
3417		Issn = {0175-7571},
3418		Journal = {European Biophysics Journal with Biophysics Letters},
3419		Month = {Aug},
3420	<	Number = {5},
3420	>	Number = 5,
3421		Pages = {477-486},
3422		Title = {Calculation of the solution properties of flexible macromolecules: methods and applications},
3423		Uri = {<Go to ISI>://000185513400011},
3424	<	Volume = {32},
3425	<	Year = {2003}}
3424	>	Volume = 32,
3425	>	Year = 2003}
3426
3427		@article{Alakent2005,
3428		Abstract = {Time series analysis tools are employed on the principal modes obtained
#	Line 3266 \| Line 3464
3464		Issn = {0021-9606},
3465		Journal = {Journal of Chemical Physics},
3466		Month = {Oct 8},
3467	<	Number = {14},
3467	>	Number = 14,
3468		Pages = {-},
3469		Title = {Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects},
3470		Uri = {<Go to ISI>://000232532000064},
3471	<	Volume = {123},
3472	<	Year = {2005}}
3471	>	Volume = 123,
3472	>	Year = 2005}
3473
3474		@book{Alexander1987,
3475		Address = {New York},
3476		Author = {C. Alexander},
3477		Publisher = {Oxford University Press},
3478		Title = {A Pattern Language: Towns, Buildings, Construction},
3479	<	Year = {1987}}
3479	>	Year = 1987}
3480
3481		@book{Allen1987,
3482		Address = {New York},
3483		Author = {M.~P. Allen and D.~J. Tildesley},
3484		Publisher = {Oxford University Press},
3485		Title = {Computer Simulations of Liquids},
3486	<	Year = {1987}}
3486	>	Year = 1987}
3487
3488		@article{Allison1991,
3489		Abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
#	Line 3307 \| Line 3505
3505		Issn = {0024-9297},
3506		Journal = {Macromolecules},
3507		Month = {Jan 21},
3508	<	Number = {2},
3508	>	Number = 2,
3509		Pages = {530-536},
3510		Title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application to Polarized Dynamic Light-Scattering},
3511		Uri = {<Go to ISI>://A1991EU81400029},
3512	<	Volume = {24},
3513	<	Year = {1991}}
3512	>	Volume = 24,
3513	>	Year = 1991}
3514
3515		@article{Andersen1983,
3516		Annote = {Rq238 Times Cited:559 Cited References Count:14},
3517		Author = {H. C. Andersen},
3518		Issn = {0021-9991},
3519		Journal = {Journal of Computational Physics},
3520	<	Number = {1},
3520	>	Number = 1,
3521		Pages = {24-34},
3522		Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
3523		Uri = {<Go to ISI>://A1983RQ23800002},
3524	<	Volume = {52},
3525	<	Year = {1983}}
3524	>	Volume = 52,
3525	>	Year = 1983}
3526
3527		@article{Auerbach2005,
3528		Abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
#	Line 3351 \| Line 3549
3549		Issn = {0027-8424},
3550		Journal = {Proceedings of the National Academy of Sciences of the United States of America},
3551		Month = {Feb 1},
3552	<	Number = {5},
3552	>	Number = 5,
3553		Pages = {1408-1412},
3554		Title = {Gating of acetylcholine receptor channels: Brownian motion across a broad transition state},
3555		Uri = {<Go to ISI>://000226877300030},
3556	<	Volume = {102},
3557	<	Year = {2005}}
3556	>	Volume = 102,
3557	>	Year = 2005}
3558
3559		@article{Baber1995,
3560		Abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
#	Line 3385 \| Line 3583
3583		Issn = {0006-2960},
3584		Journal = {Biochemistry},
3585		Month = {May 16},
3586	<	Number = {19},
3586	>	Number = 19,
3587		Pages = {6533-6539},
3588		Title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
3589		Uri = {<Go to ISI>://A1995QZ71600035},
3590	<	Volume = {34},
3591	<	Year = {1995}}
3590	>	Volume = 34,
3591	>	Year = 1995}
3592
3593		@article{Banerjee2004,
3594		Abstract = {Based on a coherent state representation of noise operator and an
#	Line 3412 \| Line 3610
3610		Issn = {0021-9606},
3611		Journal = {Journal of Chemical Physics},
3612		Month = {May 15},
3613	<	Number = {19},
3613	>	Number = 19,
3614		Pages = {8960-8972},
3615		Title = {Solution of quantum Langevin equation: Approximations, theoretical and numerical aspects},
3616		Uri = {<Go to ISI>://000221146400009},
3617	<	Volume = {120},
3618	<	Year = {2004}}
3617	>	Volume = 120,
3618	>	Year = 2004}
3619
3620		@article{Barojas1973,
3621		Author = {J. Barojas and D. Levesque},
3622		Journal = {Phys. Rev. A},
3623		Pages = {1092-1105},
3624		Title = {Simulation of Diatomic Homonuclear Liquids},
3625	<	Volume = {7},
3626	<	Year = {1973}}
3625	>	Volume = 7,
3626	>	Year = 1973}
3627
3628		@article{Barth1998,
3629		Abstract = {We present an efficient new method termed LN for propagating biomolecular
#	Line 3459 \| Line 3657
3657		Issn = {0021-9606},
3658		Journal = {Journal of Chemical Physics},
3659		Month = {Aug 1},
3660	<	Number = {5},
3660	>	Number = 5,
3661		Pages = {1617-1632},
3662		Title = {Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN},
3663		Uri = {<Go to ISI>://000075066300006},
3664	<	Volume = {109},
3665	<	Year = {1998}}
3664	>	Volume = 109,
3665	>	Year = 1998}
3666
3667		@article{Batcho2001,
3668		Abstract = {We present an analysis for a simple two-component harmonic oscillator
#	Line 3483 \| Line 3681
3681		Issn = {0021-9606},
3682		Journal = {Journal of Chemical Physics},
3683		Month = {Sep 1},
3684	<	Number = {9},
3684	>	Number = 9,
3685		Pages = {4019-4029},
3686		Title = {Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration},
3687		Uri = {<Go to ISI>://000170813800005},
3688	<	Volume = {115},
3689	<	Year = {2001}}
3688	>	Volume = 115,
3689	>	Year = 2001}
3690
3691		@article{Bates2005,
3692		Abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
#	Line 3514 \| Line 3712
3712		Issn = {1539-3755},
3713		Journal = {Physical Review E},
3714		Month = {Nov},
3715	<	Number = {5},
3715	>	Number = 5,
3716		Pages = {-},
3717		Title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation study},
3718		Uri = {<Go to ISI>://000233603100030},
3719	<	Volume = {72},
3720	<	Year = {2005}}
3719	>	Volume = 72,
3720	>	Year = 2005}
3721
3722		@article{Beard2003,
3723		Abstract = {We introduce an unbiased protocol for performing rotational moves
#	Line 3536 \| Line 3734
3734		Issn = {0006-3495},
3735		Journal = {Biophysical Journal},
3736		Month = {Nov 1},
3737	<	Number = {5},
3737	>	Number = 5,
3738		Pages = {2973-2976},
3739		Title = {Unbiased rotational moves for rigid-body dynamics},
3740		Uri = {<Go to ISI>://000186190500018},
3741	<	Volume = {85},
3742	<	Year = {2003}}
3741	>	Volume = 85,
3742	>	Year = 2003}
3743
3744		@article{Beloborodov1998,
3745		Abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
#	Line 3558 \| Line 3756
3756		Issn = {1090-7807},
3757		Journal = {Journal of Magnetic Resonance},
3758		Month = {Jun},
3759	<	Number = {2},
3759	>	Number = 2,
3760		Pages = {328-329},
3761		Title = {Effect of coupling between rotational and translational Brownian motions on NMR spin relaxation: Consideration using green function of rigid body diffusion},
3762		Uri = {<Go to ISI>://000074214800017},
3763	<	Volume = {132},
3764	<	Year = {1998}}
3763	>	Volume = 132,
3764	>	Year = 1998}
3765
3766		@article{Berardi1996,
3767		Abstract = {We demonstrate that the overall molecular dipole organization in a
#	Line 3580 \| Line 3778
3778		Issn = {0009-2614},
3779		Journal = {Chemical Physics Letters},
3780		Month = {Oct 18},
3781	<	Number = {3},
3781	>	Number = 3,
3782		Pages = {357-362},
3783		Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
3784		Uri = {<Go to ISI>://A1996VN63700023},
3785	<	Volume = {261},
3786	<	Year = {1996}}
3785	>	Volume = 261,
3786	>	Year = 1996}
3787
3788		@article{Berkov2005,
3789		Abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
#	Line 3610 \| Line 3808
3808		Issn = {1098-0121},
3809		Journal = {Physical Review B},
3810		Month = {Sep},
3811	<	Number = {9},
3811	>	Number = 9,
3812		Pages = {-},
3813		Title = {Magnetization precession due to a spin-polarized current in a thin nanoelement: Numerical simulation study},
3814		Uri = {<Go to ISI>://000232228500058},
3815	<	Volume = {72},
3816	<	Year = {2005}}
3815	>	Volume = 72,
3816	>	Year = 2005}
3817
3818		@article{Berkov2005a,
3819		Abstract = {Numerical simulations of fast remagnetization processes using stochastic
#	Line 3641 \| Line 3839
3839		Pages = {442-448},
3840		Title = {Stochastic dynamic simulations of fast remagnetization processes: recent advances and applications},
3841		Uri = {<Go to ISI>://000228837600109},
3842	<	Volume = {290},
3843	<	Year = {2005}}
3842	>	Volume = 290,
3843	>	Year = 2005}
3844
3845		@article{Berkov2002,
3846		Abstract = {We report on recent progress achieved by the development of numerical
#	Line 3664 \| Line 3862
3862		Issn = {0031-8965},
3863		Journal = {Physica Status Solidi a-Applied Research},
3864		Month = {Feb 16},
3865	<	Number = {2},
3865	>	Number = 2,
3866		Pages = {409-421},
3867		Title = {Magnetization dynamics in nanoparticle systems: Numerical simulation using Langevin dynamics},
3868		Uri = {<Go to ISI>://000174145200026},
3869	<	Volume = {189},
3870	<	Year = {2002}}
3869	>	Volume = 189,
3870	>	Year = 2002}
3871
3872		@article{Bernal1980,
3873	<	Author = {J.M. Bernal and J. G. {de la Torre}},
3873	>	Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose},
3874		Journal = {Biopolymers},
3875		Pages = {751-766},
3876		Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape},
3877	<	Volume = {19},
3878	<	Year = {1980}}
3877	>	Volume = 19,
3878	>	Year = 1980}
3879
3880		@article{Brenner1967,
3881		Author = {H. Brenner},
3882		Journal = {J. Collid. Int. Sci.},
3883		Pages = {407-436},
3884		Title = {Coupling between the Translational and Rotational Brownian Motions of Rigid Particles of Arbitrary shape},
3885	<	Volume = {23},
3886	<	Year = {1967}}
3885	>	Volume = 23,
3886	>	Year = 1967}
3887
3888		@article{Brooks1983,
3889		Annote = {Qp423 Times Cited:6414 Cited References Count:96},
3890		Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus},
3891		Issn = {0192-8651},
3892		Journal = {Journal of Computational Chemistry},
3893	<	Number = {2},
3893	>	Number = 2,
3894		Pages = {187-217},
3895		Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
3896		Uri = {<Go to ISI>://A1983QP42300010},
3897	<	Volume = {4},
3898	<	Year = {1983}}
3897	>	Volume = 4,
3898	>	Year = 1983}
3899
3900		@article{Brunger1984,
3901		Annote = {Sm173 Times Cited:143 Cited References Count:22},
3902		Author = {A. Brunger and C. L. Brooks and M. Karplus},
3903		Issn = {0009-2614},
3904		Journal = {Chemical Physics Letters},
3905	<	Number = {5},
3905	>	Number = 5,
3906		Pages = {495-500},
3907		Title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations of St2 Water},
3908		Uri = {<Go to ISI>://A1984SM17300007},
3909	<	Volume = {105},
3910	<	Year = {1984}}
3909	>	Volume = 105,
3910	>	Year = 1984}
3911
3912		@article{Budd1999,
3913		Abstract = {This paper examines a synthesis of adaptive mesh methods with the
#	Line 3723 \| Line 3921
3921		Issn = {1364-503X},
3922		Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
3923		Month = {Apr 15},
3924	<	Number = {1754},
3924	>	Number = 1754,
3925		Pages = {1047-1077},
3926		Title = {Self-similar numerical solutions of the porous-medium equation using moving mesh methods},
3927		Uri = {<Go to ISI>://000080466800005},
3928	<	Volume = {357},
3929	<	Year = {1999}}
3928	>	Volume = 357,
3929	>	Year = 1999}
3930
3931		@article{Camp1999,
3932		Abstract = {Fluids of hard bent-core molecules have been studied using theory
#	Line 3766 \| Line 3964
3964		Issn = {0021-9606},
3965		Journal = {Journal of Chemical Physics},
3966		Month = {Dec 1},
3967	<	Number = {21},
3967	>	Number = 21,
3968		Pages = {9871-9881},
3969		Title = {Theory and computer simulation of bent-core molecules},
3970		Uri = {<Go to ISI>://000083685400056},
3971	<	Volume = {111},
3972	<	Year = {1999}}
3971	>	Volume = 111,
3972	>	Year = 1999}
3973
3974		@article{Care2005,
3975		Abstract = {A review is presented of molecular and mesoscopic computer simulations
#	Line 3786 \| Line 3984
3984		Issn = {0034-4885},
3985		Journal = {Reports on Progress in Physics},
3986		Month = {Nov},
3987	<	Number = {11},
3987	>	Number = 11,
3988		Pages = {2665-2700},
3989		Title = {Computer simulation of liquid crystals},
3990		Uri = {<Go to ISI>://000233697600004},
3991	<	Volume = {68},
3992	<	Year = {2005}}
3991	>	Volume = 68,
3992	>	Year = 2005}
3993
3994		@article{Carrasco1999,
3995		Abstract = {The hydrodynamic properties of rigid particles are calculated from
#	Line 3813 \| Line 4011
4011		them to some test cases, for which the properties are known a priori.
4012		We provide guidelines and computational tools for bead modeling.},
4013		Annote = {200TT Times Cited:46 Cited References Count:57},
4014	<	Author = {B. Carrasco and J. G. {de la Torre}},
4014	>	Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
4015		Issn = {0006-3495},
4016		Journal = {Biophysical Journal},
4017		Month = {Jun},
4018	<	Number = {6},
4018	>	Number = 6,
4019		Pages = {3044-3057},
4020		Title = {Hydrodynamic properties of rigid particles: Comparison of different modeling and computational procedures},
4021		Uri = {<Go to ISI>://000080556700016},
4022	<	Volume = {76},
4023	<	Year = {1999}}
4022	>	Volume = 76,
4023	>	Year = 1999}
4024
4025		@article{Chandra1999,
4026		Abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
#	Line 3848 \| Line 4046
4046		Issn = {0021-9606},
4047		Journal = {Journal of Chemical Physics},
4048		Month = {Aug 8},
4049	<	Number = {6},
4049	>	Number = 6,
4050		Pages = {2701-2709},
4051		Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations},
4052		Uri = {<Go to ISI>://000081711200038},
4053	<	Volume = {111},
4054	<	Year = {1999}}
4053	>	Volume = 111,
4054	>	Year = 1999}
4055
4056		@article{Channell1990,
4057		Annote = {Dk631 Times Cited:152 Cited References Count:34},
#	Line 3861 \| Line 4059
4059		Issn = {0951-7715},
4060		Journal = {Nonlinearity},
4061		Month = {may},
4062	<	Number = {2},
4062	>	Number = 2,
4063		Pages = {231-259},
4064		Title = {Symplectic Integration of Hamiltonian-Systems},
4065		Uri = {<Go to ISI>://A1990DK63100001},
4066	<	Volume = {3},
4067	<	Year = {1990}}
4066	>	Volume = 3,
4067	>	Year = 1990}
4068
4069		@article{Chen2003,
4070		Abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
#	Line 3887 \| Line 4085
4085		Pages = {21-30},
4086		Title = {Explicit mixed finite order Runge-Kutta methods},
4087		Uri = {<Go to ISI>://000180314200002},
4088	<	Volume = {44},
4089	<	Year = {2003}}
4088	>	Volume = 44,
4089	>	Year = 2003}
4090
4091		@article{Cheung2004,
4092		Abstract = {Equilibrium molecular dynamics calculations have been performed for
#	Line 3908 \| Line 4106
4106		Issn = {0021-9606},
4107		Journal = {Journal of Chemical Physics},
4108		Month = {Nov 8},
4109	<	Number = {18},
4109	>	Number = 18,
4110		Pages = {9131-9139},
4111		Title = {Calculation of flexoelectric coefficients for a nematic liquid crystal by atomistic simulation},
4112		Uri = {<Go to ISI>://000224798900053},
4113	<	Volume = {121},
4114	<	Year = {2004}}
4113	>	Volume = 121,
4114	>	Year = 2004}
4115
4116		@article{Cheung2002,
4117		Abstract = {Equilibrium molecular dynamics calculations have been performed for
#	Line 3935 \| Line 4133
4133		Pages = {140-146},
4134		Title = {Calculation of the rotational viscosity of a nematic liquid crystal},
4135		Uri = {<Go to ISI>://000175331000020},
4136	<	Volume = {356},
4137	<	Year = {2002}}
4136	>	Volume = 356,
4137	>	Year = 2002}
4138
4139		@article{Chin2004,
4140		Abstract = {Current molecular dynamics simulations of biomolecules using multiple
#	Line 3959 \| Line 4157
4157		Issn = {0021-9606},
4158		Journal = {Journal of Chemical Physics},
4159		Month = {Jan 1},
4160	<	Number = {1},
4160	>	Number = 1,
4161		Pages = {8-13},
4162		Title = {Dynamical multiple-time stepping methods for overcoming resonance instabilities},
4163		Uri = {<Go to ISI>://000187577400003},
4164	<	Volume = {120},
4165	<	Year = {2004}}
4164	>	Volume = 120,
4165	>	Year = 2004}
4166
4167		@article{Cook2000,
4168		Abstract = {The Kirkwood correlation factor g(1) determines the preference for
#	Line 3988 \| Line 4186
4186		Issn = {0267-8292},
4187		Journal = {Liquid Crystals},
4188		Month = {Dec},
4189	<	Number = {12},
4189	>	Number = 12,
4190		Pages = {1573-1583},
4191		Title = {Simulation studies of dipole correlation in the isotropic liquid phase},
4192		Uri = {<Go to ISI>://000165437800002},
4193	<	Volume = {27},
4194	<	Year = {2000}}
4193	>	Volume = 27,
4194	>	Year = 2000}
4195
4196		@article{Cui2003,
4197		Abstract = {All-atom Langevin dynamics simulations have been performed to study
#	Line 4018 \| Line 4216
4216		Issn = {0027-8424},
4217		Journal = {Proceedings of the National Academy of Sciences of the United States of America},
4218		Month = {Jun 10},
4219	<	Number = {12},
4219	>	Number = 12,
4220		Pages = {7087-7092},
4221		Title = {Folding and misfolding of the papillomavirus E6 interacting peptide E6ap},
4222		Uri = {<Go to ISI>://000183493500037},
4223	<	Volume = {100},
4224	<	Year = {2003}}
4223	>	Volume = 100,
4224	>	Year = 2003}
4225
4226		@article{Denisov2003,
4227		Abstract = {We study the slow phase of thermally activated magnetic relaxation
#	Line 4041 \| Line 4239
4239		Issn = {1098-0121},
4240		Journal = {Physical Review B},
4241		Month = {Jan 1},
4242	<	Number = {1},
4242	>	Number = 1,
4243		Pages = {-},
4244		Title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
4245		Uri = {<Go to ISI>://000180830400056},
4246	<	Volume = {67},
4247	<	Year = {2003}}
4246	>	Volume = 67,
4247	>	Year = 2003}
4248
4249		@article{Derreumaux1998,
4250		Abstract = {To explore the origin of the large-scale motion of triosephosphate
#	Line 4078 \| Line 4276
4276		Issn = {0006-3495},
4277		Journal = {Biophysical Journal},
4278		Month = {Jan},
4279	<	Number = {1},
4279	>	Number = 1,
4280		Pages = {72-81},
4281		Title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
4282		Uri = {<Go to ISI>://000073393400009},
4283	<	Volume = {74},
4284	<	Year = {1998}}
4283	>	Volume = 74,
4284	>	Year = 1998}
4285
4286		@article{Dullweber1997,
4287		Abstract = {Rigid body molecular models possess symplectic structure and time-reversal
#	Line 4110 \| Line 4308
4308		Issn = {0021-9606},
4309		Journal = {Journal of Chemical Physics},
4310		Month = {Oct 15},
4311	<	Number = {15},
4311	>	Number = 15,
4312		Pages = {5840-5851},
4313		Title = {Symplectic splitting methods for rigid body molecular dynamics},
4314		Uri = {<Go to ISI>://A1997YA58700024},
4315	<	Volume = {107},
4316	<	Year = {1997}}
4315	>	Volume = 107,
4316	>	Year = 1997}
4317
4318		@book{Gamma1994,
4319		Address = {London},
4320		Author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
4321	<	Chapter = {7},
4321	>	Chapter = 7,
4322		Publisher = {Perason Education},
4323		Title = {Design Patterns: Elements of Reusable Object-Oriented Software},
4324	<	Year = {1994}}
4324	>	Year = 1994}
4325
4326		@article{Edwards2005,
4327		Abstract = {Using the Langevin dynamics technique, we have carried out simulations
#	Line 4141 \| Line 4339
4339		Issn = {0024-9297},
4340		Journal = {Macromolecules},
4341		Month = {Dec 13},
4342	<	Number = {25},
4342	>	Number = 25,
4343		Pages = {10590-10595},
4344		Title = {Stretching a single diblock copolymer in a selective solvent: Langevin dynamics simulations},
4345		Uri = {<Go to ISI>://000233866200035},
4346	<	Volume = {38},
4347	<	Year = {2005}}
4346	>	Volume = 38,
4347	>	Year = 2005}
4348
4349		@article{Egberts1988,
4350		Annote = {Q0188 Times Cited:219 Cited References Count:43},
#	Line 4154 \| Line 4352
4352		Issn = {0021-9606},
4353		Journal = {Journal of Chemical Physics},
4354		Month = {Sep 15},
4355	<	Number = {6},
4355	>	Number = 6,
4356		Pages = {3718-3732},
4357		Title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic Detail},
4358		Uri = {<Go to ISI>://A1988Q018800036},
4359	<	Volume = {89},
4360	<	Year = {1988}}
4359	>	Volume = 89,
4360	>	Year = 1988}
4361
4362		@article{Ermak1978,
4363		Annote = {Fp216 Times Cited:785 Cited References Count:42},
4364		Author = {D. L. Ermak and J. A. Mccammon},
4365		Issn = {0021-9606},
4366		Journal = {Journal of Chemical Physics},
4367	<	Number = {4},
4367	>	Number = 4,
4368		Pages = {1352-1360},
4369		Title = {Brownian Dynamics with Hydrodynamic Interactions},
4370		Uri = {<Go to ISI>://A1978FP21600004},
4371	<	Volume = {69},
4372	<	Year = {1978}}
4371	>	Volume = 69,
4372	>	Year = 1978}
4373
4374		@article{Evans1977,
4375		Annote = {Ds757 Times Cited:271 Cited References Count:18},
4376		Author = {D. J. Evans},
4377		Issn = {0026-8976},
4378		Journal = {Molecular Physics},
4379	<	Number = {2},
4379	>	Number = 2,
4380		Pages = {317-325},
4381		Title = {Representation of Orientation Space},
4382		Uri = {<Go to ISI>://A1977DS75700002},
4383	<	Volume = {34},
4384	<	Year = {1977}}
4383	>	Volume = 34,
4384	>	Year = 1977}
4385
4386		@article{Fennell2004,
4387		Abstract = {The density maximum and temperature dependence of the self-diffusion
#	Line 4214 \| Line 4412
4412		Issn = {0021-9606},
4413		Journal = {Journal of Chemical Physics},
4414		Month = {May 15},
4415	<	Number = {19},
4415	>	Number = 19,
4416		Pages = {9175-9184},
4417		Title = {On the structural and transport properties of the soft sticky dipole and related single-point water models},
4418		Uri = {<Go to ISI>://000221146400032},
4419	<	Volume = {120},
4420	<	Year = {2004}}
4419	>	Volume = 120,
4420	>	Year = 2004}
4421
4422		@article{Fernandes2002,
4423		Abstract = {We have developed a Brownian dynamics simulation algorithm to generate
#	Line 4234 \| Line 4432
4432		its applicability. Examples include free diffusion, transport in
4433		an electric field, and diffusion in a restricting environment.},
4434		Annote = {633AD Times Cited:2 Cited References Count:43},
4435	<	Author = {M. X. Fernandes and J. G. {de la Torre}},
4435	>	Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4436		Issn = {0006-3495},
4437		Journal = {Biophysical Journal},
4438		Month = {Dec},
4439	<	Number = {6},
4439	>	Number = 6,
4440		Pages = {3039-3048},
4441		Title = {Brownian dynamics simulation of rigid particles of arbitrary shape in external fields},
4442		Uri = {<Go to ISI>://000180256300012},
4443	<	Volume = {83},
4444	<	Year = {2002}}
4443	>	Volume = 83,
4444	>	Year = 2002}
4445
4446		@book{Frenkel1996,
4447		Address = {New York},
4448		Author = {D. Frenkel and B. Smit},
4449		Publisher = {Academic Press},
4450		Title = {Understanding Molecular Simulation : From Algorithms to Applications},
4451	<	Year = {1996}}
4451	>	Year = 1996}
4452
4453		@article{Gay1981,
4454		Annote = {Lj347 Times Cited:482 Cited References Count:13},
4455		Author = {J. G. Gay and B. J. Berne},
4456		Issn = {0021-9606},
4457		Journal = {Journal of Chemical Physics},
4458	<	Number = {6},
4458	>	Number = 6,
4459		Pages = {3316-3319},
4460		Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
4461		Uri = {<Go to ISI>://A1981LJ34700029},
4462	<	Volume = {74},
4463	<	Year = {1981}}
4462	>	Volume = 74,
4463	>	Year = 1981}
4464
4465		@article{Gelin1999,
4466		Abstract = {To investigate the influence of inertial effects on the dynamics of
#	Line 4288 \| Line 4486
4486		Issn = {1022-1344},
4487		Journal = {Macromolecular Theory and Simulations},
4488		Month = {Nov},
4489	<	Number = {6},
4489	>	Number = 6,
4490		Pages = {529-543},
4491		Title = {Inertial effects in the Brownian dynamics with rigid constraints},
4492		Uri = {<Go to ISI>://000083785700002},
4493	<	Volume = {8},
4494	<	Year = {1999}}
4493	>	Volume = 8,
4494	>	Year = 1999}
4495
4496		@article{Goetz1998,
4497		Author = {R. Goetz and R. Lipowsky},
4498		Journal = {Journal of Chemical Physics},
4499	<	Number = {17},
4500	<	Pages = {7397},
4499	>	Number = 17,
4500	>	Pages = 7397,
4501		Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
4502	<	Volume = {108},
4503	<	Year = {1998}}
4502	>	Volume = 108,
4503	>	Year = 1998}
4504
4505		@book{Goldstein2001,
4506		Address = {San Francisco},
#	Line 4310 \| Line 4508
4508		Edition = {3rd},
4509		Publisher = {Addison Wesley},
4510		Title = {Classical Mechanics},
4511	<	Year = {2001}}
4511	>	Year = 2001}
4512
4513		@article{Gray2003,
4514		Abstract = {Protein-protein docking algorithms provide a means to elucidate structural
#	Line 4342 \| Line 4540
4540		Issn = {0022-2836},
4541		Journal = {Journal of Molecular Biology},
4542		Month = {Aug 1},
4543	<	Number = {1},
4543	>	Number = 1,
4544		Pages = {281-299},
4545		Title = {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations},
4546		Uri = {<Go to ISI>://000184351300022},
4547	<	Volume = {331},
4548	<	Year = {2003}}
4547	>	Volume = 331,
4548	>	Year = 2003}
4549
4550		@article{Greengard1994,
4551		Abstract = {Some of the recently developed fast summation methods that have arisen
#	Line 4364 \| Line 4562
4562		Issn = {0036-8075},
4563		Journal = {Science},
4564		Month = {Aug 12},
4565	<	Number = {5174},
4565	>	Number = 5174,
4566		Pages = {909-914},
4567		Title = {Fast Algorithms for Classical Physics},
4568		Uri = {<Go to ISI>://A1994PB49900031},
4569	<	Volume = {265},
4570	<	Year = {1994}}
4569	>	Volume = 265,
4570	>	Year = 1994}
4571
4572		@article{Greengard1987,
4573		Annote = {L0498 Times Cited:899 Cited References Count:7},
#	Line 4377 \| Line 4575
4575		Issn = {0021-9991},
4576		Journal = {Journal of Computational Physics},
4577		Month = {Dec},
4578	<	Number = {2},
4578	>	Number = 2,
4579		Pages = {325-348},
4580		Title = {A Fast Algorithm for Particle Simulations},
4581		Uri = {<Go to ISI>://A1987L049800006},
4582	<	Volume = {73},
4583	<	Year = {1987}}
4582	>	Volume = 73,
4583	>	Year = 1987}
4584
4585		@article{Hairer1997,
4586		Abstract = {Backward error analysis is a useful tool for the study of numerical
#	Line 4403 \| Line 4601
4601		Issn = {0029-599X},
4602		Journal = {Numerische Mathematik},
4603		Month = {Jun},
4604	<	Number = {4},
4604	>	Number = 4,
4605		Pages = {441-462},
4606		Title = {The life-span of backward error analysis for numerical integrators},
4607		Uri = {<Go to ISI>://A1997XJ48800002},
4608	<	Volume = {76},
4609	<	Year = {1997}}
4608	>	Volume = 76,
4609	>	Year = 1997}
4610
4611		@article{Hao1993,
4612		Abstract = {A new procedure for studying the folding and unfolding of proteins,
#	Line 4450 \| Line 4648
4648		Issn = {0006-2960},
4649		Journal = {Biochemistry},
4650		Month = {Sep 21},
4651	<	Number = {37},
4651	>	Number = 37,
4652		Pages = {9614-9631},
4653		Title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic Trypsin-Inhibitor Studied by Computer-Simulations},
4654		Uri = {<Go to ISI>://A1993LY29400014},
4655	<	Volume = {32},
4656	<	Year = {1993}}
4655	>	Volume = 32,
4656	>	Year = 1993}
4657
4658		@article{Hinsen2000,
4659		Abstract = {The slow dynamics of proteins around its native folded state is usually
#	Line 4494 \| Line 4692
4692		Pages = {25-37},
4693		Title = {Harmonicity in slow protein dynamics},
4694		Uri = {<Go to ISI>://000090121700003},
4695	<	Volume = {261},
4696	<	Year = {2000}}
4695	>	Volume = 261,
4696	>	Year = 2000}
4697
4698		@article{Ho1992,
4699		Abstract = {Evidence has been found for the existence water at the protein-lipid
#	Line 4530 \| Line 4728
4728		Issn = {0006-3495},
4729		Journal = {Biophysical Journal},
4730		Month = {Oct},
4731	<	Number = {4},
4731	>	Number = 4,
4732		Pages = {897-902},
4733		Title = {Hydration at the Membrane Protein-Lipid Interface},
4734		Uri = {<Go to ISI>://A1992JU25100002},
4735	<	Volume = {63},
4736	<	Year = {1992}}
4735	>	Volume = 63,
4736	>	Year = 1992}
4737
4738		@book{Hockney1981,
4739		Address = {New York},
4740		Author = {R.W. Hockney and J.W. Eastwood},
4741		Publisher = {McGraw-Hill},
4742		Title = {Computer Simulation Using Particles},
4743	<	Year = {1981}}
4743	>	Year = 1981}
4744
4745		@article{Hoover1985,
4746		Annote = {Acr30 Times Cited:1809 Cited References Count:11},
4747		Author = {W. G. Hoover},
4748		Issn = {1050-2947},
4749		Journal = {Physical Review A},
4750	<	Number = {3},
4750	>	Number = 3,
4751		Pages = {1695-1697},
4752		Title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
4753		Uri = {<Go to ISI>://A1985ACR3000056},
4754	<	Volume = {31},
4755	<	Year = {1985}}
4754	>	Volume = 31,
4755	>	Year = 1985}
4756
4757		@article{Huh2004,
4758		Abstract = {Racemic fluids of chiral calamitic molecules are investigated with
#	Line 4572 \| Line 4770
4770		Issn = {0021-9606},
4771		Journal = {Journal of Chemical Physics},
4772		Month = {Nov 22},
4773	<	Number = {20},
4773	>	Number = 20,
4774		Pages = {10299-10308},
4775		Title = {Discrimination in isotropic, nematic, and smectic phases of chiral calamitic molecules: A computer simulation study},
4776		Uri = {<Go to ISI>://000225042700059},
4777	<	Volume = {121},
4778	<	Year = {2004}}
4777	>	Volume = 121,
4778	>	Year = 2004}
4779
4780		@article{Humphrey1996,
4781		Abstract = {VMD is a molecular graphics program designed for the display and analysis
#	Line 4611 \| Line 4809
4809		Issn = {0263-7855},
4810		Journal = {Journal of Molecular Graphics},
4811		Month = {Feb},
4812	<	Number = {1},
4812	>	Number = 1,
4813		Pages = {33-\&},
4814		Title = {VMD: Visual molecular dynamics},
4815		Uri = {<Go to ISI>://A1996UH51500005},
4816	<	Volume = {14},
4817	<	Year = {1996}}
4816	>	Volume = 14,
4817	>	Year = 1996}
4818
4819		@article{Izaguirre2001,
4820		Abstract = {In this paper we show the possibility of using very mild stochastic
#	Line 4651 \| Line 4849
4849		Issn = {0021-9606},
4850		Journal = {Journal of Chemical Physics},
4851		Month = {Feb 1},
4852	<	Number = {5},
4852	>	Number = 5,
4853		Pages = {2090-2098},
4854		Title = {Langevin stabilization of molecular dynamics},
4855		Uri = {<Go to ISI>://000166676100020},
4856	<	Volume = {114},
4857	<	Year = {2001}}
4856	>	Volume = 114,
4857	>	Year = 2001}
4858
4859		@article{Torre1977,
4860	<	Author = {Jose Garcia De La Torre, V.A. Bloomfield},
4860	>	Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield},
4861		Journal = {Biopolymers},
4862		Pages = {1747-1763},
4863		Title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
4864	<	Volume = {16},
4865	<	Year = {1977}}
4864	>	Volume = 16,
4865	>	Year = 1977}
4866
4867		@article{Kale1999,
4868		Abstract = {Molecular dynamics programs simulate the behavior of biomolecular
#	Line 4694 \| Line 4892
4892		Issn = {0021-9991},
4893		Journal = {Journal of Computational Physics},
4894		Month = {May 1},
4895	<	Number = {1},
4895	>	Number = 1,
4896		Pages = {283-312},
4897		Title = {NAMD2: Greater scalability for parallel molecular dynamics},
4898		Uri = {<Go to ISI>://000080181500013},
4899	<	Volume = {151},
4900	<	Year = {1999}}
4899	>	Volume = 151,
4900	>	Year = 1999}
4901
4902		@article{Kane2000,
4903		Abstract = {The purpose of this work is twofold. First, we demonstrate analytically
#	Line 4723 \| Line 4921
4921		Issn = {0029-5981},
4922		Journal = {International Journal for Numerical Methods in Engineering},
4923		Month = {Dec 10},
4924	<	Number = {10},
4924	>	Number = 10,
4925		Pages = {1295-1325},
4926		Title = {Variational integrators and the Newmark algorithm for conservative and dissipative mechanical systems},
4927		Uri = {<Go to ISI>://000165270600004},
4928	<	Volume = {49},
4929	<	Year = {2000}}
4928	>	Volume = 49,
4929	>	Year = 2000}
4930
4931		@article{Klimov1997,
4932		Abstract = {The viscosity (eta) dependence of the folding rates for four sequences
#	Line 4747 \| Line 4945
4945		Issn = {0031-9007},
4946		Journal = {Physical Review Letters},
4947		Month = {Jul 14},
4948	<	Number = {2},
4948	>	Number = 2,
4949		Pages = {317-320},
4950		Title = {Viscosity dependence of the folding rates of proteins},
4951		Uri = {<Go to ISI>://A1997XK29300035},
4952	<	Volume = {79},
4953	<	Year = {1997}}
4952	>	Volume = 79,
4953	>	Year = 1997}
4954
4955		@article{Kol1997,
4956		Abstract = {Rigid-body molecular dynamics simulations typically are performed
#	Line 4780 \| Line 4978
4978		Issn = {0021-9606},
4979		Journal = {Journal of Chemical Physics},
4980		Month = {Aug 15},
4981	<	Number = {7},
4981	>	Number = 7,
4982		Pages = {2580-2588},
4983		Title = {A symplectic method for rigid-body molecular simulation},
4984		Uri = {<Go to ISI>://A1997XQ33200046},
4985	<	Volume = {107},
4986	<	Year = {1997}}
4985	>	Volume = 107,
4986	>	Year = 1997}
4987
4988		@article{Lansac2001,
4989		Abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
#	Line 4814 \| Line 5012
5012		Issn = {1063-651X},
5013		Journal = {Physical Review E},
5014		Month = {Nov},
5015	<	Number = {5},
5015	>	Number = 5,
5016		Pages = {-},
5017		Title = {Microscopic structure and dynamics of a partial bilayer smectic liquid crystal},
5018		Uri = {<Go to ISI>://000172406900063},
5019	<	Volume = {6405},
5020	<	Year = {2001}}
5019	>	Volume = 6405,
5020	>	Year = 2001}
5021
5022		@article{Lansac2003,
5023		Abstract = {Recently, a new class of smectic liquid crystal phases characterized
#	Line 4842 \| Line 5040
5040		Issn = {1063-651X},
5041		Journal = {Physical Review E},
5042		Month = {Jan},
5043	<	Number = {1},
5043	>	Number = 1,
5044		Pages = {-},
5045		Title = {Phase behavior of bent-core molecules},
5046		Uri = {<Go to ISI>://000181017300042},
5047	<	Volume = {67},
5048	<	Year = {2003}}
5047	>	Volume = 67,
5048	>	Year = 2003}
5049
5050		@book{Leach2001,
5051		Address = {Harlow, England},
#	Line 4855 \| Line 5053
5053		Edition = {2nd},
5054		Publisher = {Pearson Educated Limited},
5055		Title = {Molecular Modeling: Principles and Applications},
5056	<	Year = {2001}}
5056	>	Year = 2001}
5057
5058		@article{Leimkuhler1999,
5059		Abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
#	Line 4875 \| Line 5073
5073		Issn = {1364-503X},
5074		Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
5075		Month = {Apr 15},
5076	<	Number = {1754},
5076	>	Number = 1754,
5077		Pages = {1101-1133},
5078		Title = {Reversible adaptive regularization: perturbed Kepler motion and classical atomic trajectories},
5079		Uri = {<Go to ISI>://000080466800007},
5080	<	Volume = {357},
5081	<	Year = {1999}}
5080	>	Volume = 357,
5081	>	Year = 1999}
5082
5083		@book{Leimkuhler2004,
5084		Address = {Cambridge},
5085		Author = {B. Leimkuhler and S. Reich},
5086		Publisher = {Cambridge University Press},
5087		Title = {Simulating Hamiltonian Dynamics},
5088	<	Year = {2004}}
5088	>	Year = 2004}
5089
5090		@article{Levelut1981,
5091		Annote = {Ml751 Times Cited:96 Cited References Count:16},
5092		Author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard and G. Sigaud},
5093		Issn = {1050-2947},
5094		Journal = {Physical Review A},
5095	<	Number = {4},
5095	>	Number = 4,
5096		Pages = {2180-2186},
5097		Title = {Number of Sa Phases},
5098		Uri = {<Go to ISI>://A1981ML75100057},
5099	<	Volume = {24},
5100	<	Year = {1981}}
5099	>	Volume = 24,
5100	>	Year = 1981}
5101
5102		@article{Lieb1982,
5103		Annote = {Nu461 Times Cited:40 Cited References Count:28},
5104		Author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
5105		Issn = {0006-3002},
5106		Journal = {Biochimica Et Biophysica Acta},
5107	<	Number = {2},
5107	>	Number = 2,
5108		Pages = {388-398},
5109		Title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - Evidence from Raman-Scattering},
5110		Uri = {<Go to ISI>://A1982NU46100012},
5111	<	Volume = {688},
5112	<	Year = {1982}}
5111	>	Volume = 688,
5112	>	Year = 1982}
5113
5114		@article{Link1997,
5115		Abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
#	Line 4929 \| Line 5127
5127		Issn = {0036-8075},
5128		Journal = {Science},
5129		Month = {Dec 12},
5130	<	Number = {5345},
5130	>	Number = 5345,
5131		Pages = {1924-1927},
5132		Title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic phase of achiral molecules},
5133		Uri = {<Go to ISI>://A1997YL00200028},
5134	<	Volume = {278},
5135	<	Year = {1997}}
5134	>	Volume = 278,
5135	>	Year = 1997}
5136
5137		@article{Liwo2005,
5138		Annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
#	Line 4945 \| Line 5143
5143		Pages = {359-360},
5144		Title = {Ab initio simulations of protein folding pathways by molecular dynamics with the united-residue (UNRES) model of polypeptide chains},
5145		Uri = {<Go to ISI>://000234826102043},
5146	<	Volume = {272},
5147	<	Year = {2005}}
5146	>	Volume = 272,
5147	>	Year = 2005}
5148
5149		@article{Luty1994,
5150		Abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
#	Line 4961 \| Line 5159
5159		Author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
5160		Issn = {0892-7022},
5161		Journal = {Molecular Simulation},
5162	<	Number = {1},
5162	>	Number = 1,
5163		Pages = {11-20},
5164		Title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
5165		Uri = {<Go to ISI>://A1994QF46400002},
5166	<	Volume = {14},
5167	<	Year = {1994}}
5166	>	Volume = 14,
5167	>	Year = 1994}
5168
5169		@book{Marion1990,
5170		Address = {New York},
#	Line 4974 \| Line 5172
5172		Edition = {2rd},
5173		Publisher = {Academic Press},
5174		Title = {Classical Dynamics of Particles and Systems},
5175	<	Year = {1990}}
5175	>	Year = 1990}
5176
5177		@article{Marrink1994,
5178		Abstract = {To obtain insight in the process of water permeation through a lipid
#	Line 5006 \| Line 5204
5204		Issn = {0022-3654},
5205		Journal = {Journal of Physical Chemistry},
5206		Month = {Apr 14},
5207	<	Number = {15},
5207	>	Number = 15,
5208		Pages = {4155-4168},
5209		Title = {Simulation of Water Transport through a Lipid-Membrane},
5210		Uri = {<Go to ISI>://A1994NG21900040},
5211	<	Volume = {98},
5212	<	Year = {1994}}
5211	>	Volume = 98,
5212	>	Year = 1994}
5213
5214		@article{Marrink2004,
5215		Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
5216		Journal = {J. Phys. Chem. B},
5217		Pages = {750-760},
5218		Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
5219	<	Volume = {108},
5220	<	Year = {2004}}
5219	>	Volume = 108,
5220	>	Year = 2004}
5221
5222		@article{Marsden1998,
5223		Abstract = {This paper presents a geometric-variational approach to continuous
#	Line 5047 \| Line 5245
5245		Issn = {0010-3616},
5246		Journal = {Communications in Mathematical Physics},
5247		Month = {Dec},
5248	<	Number = {2},
5248	>	Number = 2,
5249		Pages = {351-395},
5250		Title = {Multisymplectic geometry, variational integrators, and nonlinear PDEs},
5251		Uri = {<Go to ISI>://000077902200006},
5252	<	Volume = {199},
5253	<	Year = {1998}}
5252	>	Volume = 199,
5253	>	Year = 1998}
5254
5255		@article{Matthey2004,
5256		Abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
#	Line 5077 \| Line 5275
5275		Issn = {0098-3500},
5276		Journal = {Acm Transactions on Mathematical Software},
5277		Month = {Sep},
5278	<	Number = {3},
5278	>	Number = 3,
5279		Pages = {237-265},
5280		Title = {ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics},
5281		Uri = {<Go to ISI>://000224325600001},
5282	<	Volume = {30},
5283	<	Year = {2004}}
5282	>	Volume = 30,
5283	>	Year = 2004}
5284
5285		@article{McLachlan1993,
5286		Author = {R.~I McLachlan},
5287		Journal = {prl},
5288		Pages = {3043-3046},
5289		Title = {Explicit Lie-Poisson integration and the Euler equations},
5290	<	Volume = {71},
5291	<	Year = {1993}}
5290	>	Volume = 71,
5291	>	Year = 1993}
5292
5293		@article{McLachlan1998,
5294		Abstract = {We give a survey and some new examples of generating functions for
#	Line 5108 \| Line 5306
5306		Pages = {298-309},
5307		Title = {Generating functions for dynamical systems with symmetries, integrals, and differential invariants},
5308		Uri = {<Go to ISI>://000071558900021},
5309	<	Volume = {112},
5310	<	Year = {1998}}
5309	>	Volume = 112,
5310	>	Year = 1998}
5311
5312		@article{McLachlan1998a,
5313		Abstract = {We consider properties of flows, the relationships between them, and
#	Line 5126 \| Line 5324
5324		Issn = {0036-1429},
5325		Journal = {Siam Journal on Numerical Analysis},
5326		Month = {Apr},
5327	<	Number = {2},
5327	>	Number = 2,
5328		Pages = {586-599},
5329		Title = {Numerical integrators that preserve symmetries and reversing symmetries},
5330		Uri = {<Go to ISI>://000072580500010},
5331	<	Volume = {35},
5332	<	Year = {1998}}
5331	>	Volume = 35,
5332	>	Year = 1998}
5333
5334		@article{McLachlan2005,
5335		Abstract = {In this paper we revisit the Moser-Veselov description of the free
#	Line 5152 \| Line 5350
5350		Issn = {1615-3375},
5351		Journal = {Foundations of Computational Mathematics},
5352		Month = {Feb},
5353	<	Number = {1},
5353	>	Number = 1,
5354		Pages = {87-123},
5355		Title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
5356		Uri = {<Go to ISI>://000228011900003},
5357	<	Volume = {5},
5358	<	Year = {2005}}
5357	>	Volume = 5,
5358	>	Year = 2005}
5359
5360		@article{Meineke2005,
5361		Abstract = {OOPSE is a new molecular dynamics simulation program that is capable
#	Line 5175 \| Line 5373
5373		Issn = {0192-8651},
5374		Journal = {Journal of Computational Chemistry},
5375		Month = {Feb},
5376	<	Number = {3},
5376	>	Number = 3,
5377		Pages = {252-271},
5378		Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
5379		Uri = {<Go to ISI>://000226558200006},
5380	<	Volume = {26},
5381	<	Year = {2005}}
5380	>	Volume = 26,
5381	>	Year = 2005}
5382
5383		@article{Melchionna1993,
5384		Abstract = {In this paper we write down equations of motion (following the approach
#	Line 5194 \| Line 5392
5392		Issn = {0026-8976},
5393		Journal = {Molecular Physics},
5394		Month = {Feb 20},
5395	<	Number = {3},
5395	>	Number = 3,
5396		Pages = {533-544},
5397		Title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
5398		Uri = {<Go to ISI>://A1993KQ35500002},
5399	<	Volume = {78},
5400	<	Year = {1993}}
5399	>	Volume = 78,
5400	>	Year = 1993}
5401
5402		@article{Memmer2002,
5403		Abstract = {The phase behaviour of achiral banana-shaped molecules was studied
#	Line 5232 \| Line 5430
5430		Issn = {0267-8292},
5431		Journal = {Liquid Crystals},
5432		Month = {Apr},
5433	<	Number = {4},
5433	>	Number = 4,
5434		Pages = {483-496},
5435		Title = {Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study},
5436		Uri = {<Go to ISI>://000174410500001},
5437	<	Volume = {29},
5438	<	Year = {2002}}
5437	>	Volume = 29,
5438	>	Year = 2002}
5439
5440		@article{Metropolis1949,
5441		Author = {N. Metropolis and S. Ulam},
5442		Journal = {J. Am. Stat. Ass.},
5443		Pages = {335-341},
5444		Title = {The $\mbox{Monte Carlo}$ Method},
5445	<	Volume = {44},
5446	<	Year = {1949}}
5445	>	Volume = 44,
5446	>	Year = 1949}
5447
5448		@article{Mielke2004,
5449		Abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
#	Line 5278 \| Line 5476
5476		Issn = {0021-9606},
5477		Journal = {Journal of Chemical Physics},
5478		Month = {Oct 22},
5479	<	Number = {16},
5479	>	Number = 16,
5480		Pages = {8104-8112},
5481		Title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study},
5482		Uri = {<Go to ISI>://000224456500064},
5483	<	Volume = {121},
5484	<	Year = {2004}}
5483	>	Volume = 121,
5484	>	Year = 2004}
5485
5486		@article{Naess2001,
5487		Abstract = {The three Eulerian angles constitute the classical choice of generalized
#	Line 5308 \| Line 5506
5506		Pages = {323-339},
5507		Title = {Brownian dynamics simulation of rigid bodies and segmented polymer chains. Use of Cartesian rotation vectors as the generalized coordinates describing angular orientations},
5508		Uri = {<Go to ISI>://000168774800005},
5509	<	Volume = {294},
5510	<	Year = {2001}}
5509	>	Volume = 294,
5510	>	Year = 2001}
5511
5512		@article{Niori1996,
5513		Abstract = {The synthesis of a banana-shaped molecule is reported and it is found
#	Line 5324 \| Line 5522
5522		Issn = {0959-9428},
5523		Journal = {Journal of Materials Chemistry},
5524		Month = {Jul},
5525	<	Number = {7},
5525	>	Number = 7,
5526		Pages = {1231-1233},
5527		Title = {Distinct ferroelectric smectic liquid crystals consisting of banana shaped achiral molecules},
5528		Uri = {<Go to ISI>://A1996UX85500025},
5529	<	Volume = {6},
5530	<	Year = {1996}}
5529	>	Volume = 6,
5530	>	Year = 1996}
5531
5532		@article{Noguchi2002,
5533		Abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
#	Line 5349 \| Line 5547
5547		Issn = {1063-651X},
5548		Journal = {Physical Review E},
5549		Month = {may},
5550	<	Number = {5},
5550	>	Number = 5,
5551		Pages = {-},
5552		Title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
5553		Uri = {<Go to ISI>://000176552300084},
5554	<	Volume = {65},
5555	<	Year = {2002}}
5554	>	Volume = 65,
5555	>	Year = 2002}
5556
5557		@article{Noguchi2001,
5558		Abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
#	Line 5373 \| Line 5571
5571		Issn = {0021-9606},
5572		Journal = {Journal of Chemical Physics},
5573		Month = {Nov 22},
5574	<	Number = {20},
5574	>	Number = 20,
5575		Pages = {9547-9551},
5576		Title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
5577		Uri = {<Go to ISI>://000172129300049},
5578	<	Volume = {115},
5579	<	Year = {2001}}
5578	>	Volume = 115,
5579	>	Year = 2001}
5580
5581		@book{Olver1986,
5582		Address = {New York},
5583		Author = {P.J. Olver},
5584		Publisher = {Springer},
5585		Title = {Applications of Lie groups to differential equatitons},
5586	<	Year = {1986}}
5586	>	Year = 1986}
5587
5588		@article{Omelyan1998,
5589		Abstract = {A revised version of the quaternion approach for numerical integration
#	Line 5404 \| Line 5602
5602		Issn = {0894-1866},
5603		Journal = {Computers in Physics},
5604		Month = {Jan-Feb},
5605	<	Number = {1},
5605	>	Number = 1,
5606		Pages = {97-103},
5607		Title = {On the numerical integration of motion for rigid polyatomics: The modified quaternion approach},
5608		Uri = {<Go to ISI>://000072024300025},
5609	<	Volume = {12},
5610	<	Year = {1998}}
5609	>	Volume = 12,
5610	>	Year = 1998}
5611
5612		@article{Omelyan1998a,
5613		Abstract = {An algorithm for numerical integration of the rigid-body equations
#	Line 5426 \| Line 5624
5624		Issn = {1063-651X},
5625		Journal = {Physical Review E},
5626		Month = {Jul},
5627	<	Number = {1},
5627	>	Number = 1,
5628		Pages = {1169-1172},
5629		Title = {Algorithm for numerical integration of the rigid-body equations of motion},
5630		Uri = {<Go to ISI>://000074893400151},
5631	<	Volume = {58},
5632	<	Year = {1998}}
5631	>	Volume = 58,
5632	>	Year = 1998}
5633
5634		@article{Owren1992,
5635		Abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
#	Line 5452 \| Line 5650
5650		Issn = {0196-5204},
5651		Journal = {Siam Journal on Scientific and Statistical Computing},
5652		Month = {Nov},
5653	<	Number = {6},
5653	>	Number = 6,
5654		Pages = {1488-1501},
5655		Title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
5656		Uri = {<Go to ISI>://A1992JU93600013},
5657	<	Volume = {13},
5658	<	Year = {1992}}
5657	>	Volume = 13,
5658	>	Year = 1992}
5659
5660		@article{Palacios1998,
5661		Abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
#	Line 5495 \| Line 5693
5693		Issn = {0163-1829},
5694		Journal = {Physical Review B},
5695		Month = {Dec 1},
5696	<	Number = {22},
5696	>	Number = 22,
5697		Pages = {14937-14958},
5698		Title = {Langevin-dynamics study of the dynamical properties of small magnetic particles},
5699		Uri = {<Go to ISI>://000077460000052},
5700	<	Volume = {58},
5701	<	Year = {1998}}
5700	>	Volume = 58,
5701	>	Year = 1998}
5702
5703		@article{Parr1995,
5704		Abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
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5725		Issn = {0038-0644},
5726		Journal = {Software-Practice \& Experience},
5727		Month = {Jul},
5728	<	Number = {7},
5728	>	Number = 7,
5729		Pages = {789-810},
5730		Title = {Antlr - a Predicated-Ll(K) Parser Generator},
5731		Uri = {<Go to ISI>://A1995RK10400004},
5732	<	Volume = {25},
5733	<	Year = {1995}}
5732	>	Volume = 25,
5733	>	Year = 1995}
5734
5735		@article{Pastor1988,
5736		Annote = {T1302 Times Cited:61 Cited References Count:26},
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5738		Issn = {0026-8976},
5739		Journal = {Molecular Physics},
5740		Month = {Dec 20},
5741	<	Number = {6},
5741	>	Number = 6,
5742		Pages = {1409-1419},
5743		Title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
5744		Uri = {<Go to ISI>://A1988T130200011},
5745	<	Volume = {65},
5746	<	Year = {1988}}
5745	>	Volume = 65,
5746	>	Year = 1988}
5747
5748		@article{Pelzl1999,
5749		Annote = {220RC Times Cited:313 Cited References Count:49},
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5751		Issn = {0935-9648},
5752		Journal = {Advanced Materials},
5753		Month = {Jul 5},
5754	<	Number = {9},
5754	>	Number = 9,
5755		Pages = {707-724},
5756		Title = {Banana-shaped compounds - A new field of liquid crystals},
5757		Uri = {<Go to ISI>://000081680400007},
5758	<	Volume = {11},
5759	<	Year = {1999}}
5758	>	Volume = 11,
5759	>	Year = 1999}
5760
5761		@article{Perram1985,
5762		Annote = {Akb93 Times Cited:71 Cited References Count:12},
5763		Author = {J. W. Perram and M. S. Wertheim},
5764		Issn = {0021-9991},
5765		Journal = {Journal of Computational Physics},
5766	<	Number = {3},
5766	>	Number = 3,
5767		Pages = {409-416},
5768		Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function},
5769		Uri = {<Go to ISI>://A1985AKB9300008},
5770	<	Volume = {58},
5771	<	Year = {1985}}
5770	>	Volume = 58,
5771	>	Year = 1985}
5772
5773		@article{Rotne1969,
5774		Author = {F. Perrin},
5775		Journal = {J. Chem. Phys.},
5776		Pages = {4831-4837},
5777		Title = {Variational treatment of hydrodynamic interaction in polymers},
5778	<	Volume = {50},
5779	<	Year = {1969}}
5778	>	Volume = 50,
5779	>	Year = 1969}
5780
5781		@article{Perrin1936,
5782		Author = {F. Perrin},
5783		Journal = {J. Phys. Radium},
5784		Pages = {1-11},
5785		Title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation des fluorescences. Translation et diffusion de moleculese ellipsoidales},
5786	<	Volume = {7},
5787	<	Year = {1936}}
5786	>	Volume = 7,
5787	>	Year = 1936}
5788
5789		@article{Perrin1934,
5790		Author = {F. Perrin},
5791		Journal = {J. Phys. Radium},
5792		Pages = {497-511},
5793		Title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour des molecules ellipsoidales},
5794	<	Volume = {5},
5795	<	Year = {1934}}
5794	>	Volume = 5,
5795	>	Year = 1934}
5796
5797		@article{Petrache2000,
5798		Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
5799		Journal = {Biophysical Journal},
5800		Pages = {3172-3192},
5801		Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
5802	<	Volume = {79},
5803	<	Year = {2000}}
5802	>	Volume = 79,
5803	>	Year = 2000}
5804
5805		@article{Petrache1998,
5806		Abstract = {X-ray diffraction data taken at high instrumental resolution were
#	Line 5627 \| Line 5825
5825		Issn = {0009-3084},
5826		Journal = {Chemistry and Physics of Lipids},
5827		Month = {Sep},
5828	<	Number = {1},
5828	>	Number = 1,
5829		Pages = {83-94},
5830		Title = {Fluid phase structure of EPC and DMPC bilayers},
5831		Uri = {<Go to ISI>://000076497600007},
5832	<	Volume = {95},
5833	<	Year = {1998}}
5832	>	Volume = 95,
5833	>	Year = 1998}
5834
5835		@article{Powles1973,
5836		Author = {J.~G. Powles},
5837		Journal = {Advan. Phys.},
5838		Pages = {1-56},
5839		Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
5840	<	Volume = {22},
5841	<	Year = {1973}}
5840	>	Volume = 22,
5841	>	Year = 1973}
5842
5843		@article{Recio2004,
5844		Abstract = {Protein recognition is one of the most challenging and intriguing
#	Line 5671 \| Line 5869
5869		Issn = {0022-2836},
5870		Journal = {Journal of Molecular Biology},
5871		Month = {Jan 16},
5872	<	Number = {3},
5872	>	Number = 3,
5873		Pages = {843-865},
5874		Title = {Identification of protein-protein interaction sites from docking energy landscapes},
5875		Uri = {<Go to ISI>://000188066900016},
5876	<	Volume = {335},
5877	<	Year = {2004}}
5876	>	Volume = 335,
5877	>	Year = 2004}
5878
5879		@article{Reddy2006,
5880		Abstract = {An overview on the recent developments in the field of liquid crystalline
#	Line 5694 \| Line 5892
5892		Author = {R. A. Reddy and C. Tschierske},
5893		Issn = {0959-9428},
5894		Journal = {Journal of Materials Chemistry},
5895	<	Number = {10},
5895	>	Number = 10,
5896		Pages = {907-961},
5897		Title = {Bent-core liquid crystals: polar order, superstructural chirality and spontaneous desymmetrisation in soft matter systems},
5898		Uri = {<Go to ISI>://000235990500001},
5899	<	Volume = {16},
5900	<	Year = {2006}}
5899	>	Volume = 16,
5900	>	Year = 2006}
5901
5902		@article{Reich1999,
5903		Abstract = {Backward error analysis has become an important tool for understanding
#	Line 5729 \| Line 5927
5927		Issn = {0036-1429},
5928		Journal = {Siam Journal on Numerical Analysis},
5929		Month = {Sep 8},
5930	<	Number = {5},
5930	>	Number = 5,
5931		Pages = {1549-1570},
5932		Title = {Backward error analysis for numerical integrators},
5933		Uri = {<Go to ISI>://000082650600010},
5934	<	Volume = {36},
5935	<	Year = {1999}}
5934	>	Volume = 36,
5935	>	Year = 1999}
5936
5937		@article{Ros2005,
5938		Abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
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5947		Author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
5948		Issn = {0959-9428},
5949		Journal = {Journal of Materials Chemistry},
5950	<	Number = {48},
5950	>	Number = 48,
5951		Pages = {5093-5098},
5952		Title = {Banana-shaped liquid crystals: a new field to explore},
5953		Uri = {<Go to ISI>://000233775500001},
5954	<	Volume = {15},
5955	<	Year = {2005}}
5954	>	Volume = 15,
5955	>	Year = 2005}
5956
5957		@article{Roux1991,
5958		Abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
#	Line 5782 \| Line 5980
5980		Issn = {0022-3654},
5981		Journal = {Journal of Physical Chemistry},
5982		Month = {Jun 13},
5983	<	Number = {12},
5983	>	Number = 12,
5984		Pages = {4856-4868},
5985		Title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
5986		Uri = {<Go to ISI>://A1991FR75600049},
5987	<	Volume = {95},
5988	<	Year = {1991}}
5987	>	Volume = 95,
5988	>	Year = 1991}
5989
5990		@article{Roy2005,
5991		Abstract = {A vast majority of compounds with bent core or banana shaped molecules
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6004		Issn = {1292-8941},
6005		Journal = {European Physical Journal E},
6006		Month = {Nov},
6007	<	Number = {3},
6007	>	Number = 3,
6008		Pages = {253-258},
6009		Title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases in banana shaped molecules},
6010		Uri = {<Go to ISI>://000233363300002},
6011	<	Volume = {18},
6012	<	Year = {2005}}
6011	>	Volume = 18,
6012	>	Year = 2005}
6013
6014		@article{Ryckaert1977,
6015		Annote = {Cz253 Times Cited:3680 Cited References Count:7},
6016		Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
6017		Issn = {0021-9991},
6018		Journal = {Journal of Computational Physics},
6019	<	Number = {3},
6019	>	Number = 3,
6020		Pages = {327-341},
6021		Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes},
6022		Uri = {<Go to ISI>://A1977CZ25300007},
6023	<	Volume = {23},
6024	<	Year = {1977}}
6023	>	Volume = 23,
6024	>	Year = 1977}
6025
6026		@article{Sagui1999,
6027		Abstract = {Current computer simulations of biomolecules typically make use of
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6046		Pages = {155-179},
6047		Title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic effects},
6048		Uri = {<Go to ISI>://000081271400008},
6049	<	Volume = {28},
6050	<	Year = {1999}}
6049	>	Volume = 28,
6050	>	Year = 1999}
6051
6052		@article{Sandu1999,
6053		Abstract = {Numerical resonance artifacts have become recognized recently as a
#	Line 5894 \| Line 6092
6092		Issn = {0021-9991},
6093		Journal = {Journal of Computational Physics},
6094		Month = {May 1},
6095	<	Number = {1},
6095	>	Number = 1,
6096		Pages = {74-113},
6097		Title = {Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics},
6098		Uri = {<Go to ISI>://000080181500004},
6099	<	Volume = {151},
6100	<	Year = {1999}}
6099	>	Volume = 151,
6100	>	Year = 1999}
6101
6102		@article{Sasaki2004,
6103		Abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
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6111		Author = {Y. Sasaki and R. Shukla and B. D. Smith},
6112		Issn = {1477-0520},
6113		Journal = {Organic \& Biomolecular Chemistry},
6114	<	Number = {2},
6114	>	Number = 2,
6115		Pages = {214-219},
6116		Title = {Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases},
6117		Uri = {<Go to ISI>://000187843800012},
6118	<	Volume = {2},
6119	<	Year = {2004}}
6118	>	Volume = 2,
6119	>	Year = 2004}
6120
6121		@article{Satoh1996,
6122		Abstract = {The effects of dipole-dipole interaction on mesophase formation are
#	Line 5937 \| Line 6135
6135		Pages = {99-104},
6136		Title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect of terminal dipole moment on mesophase formation},
6137		Uri = {<Go to ISI>://A1996UQ97500017},
6138	<	Volume = {255},
6139	<	Year = {1996}}
6138	>	Volume = 255,
6139	>	Year = 1996}
6140
6141		@article{Schaps1999,
6142		Annote = {163EC Times Cited:0 Cited References Count:0},
#	Line 5946 \| Line 6144
6144		Issn = {1044-789X},
6145		Journal = {Dr Dobbs Journal},
6146		Month = {Mar},
6147	<	Number = {3},
6147	>	Number = 3,
6148		Pages = {84-+},
6149		Title = {Compiler construction with ANTLR and Java - Tools for building tools},
6150		Uri = {<Go to ISI>://000078389200023},
6151	<	Volume = {24},
6152	<	Year = {1999}}
6151	>	Volume = 24,
6152	>	Year = 1999}
6153
6154		@article{Shen2002,
6155		Abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
#	Line 5978 \| Line 6176
6176		Issn = {0006-3495},
6177		Journal = {Biophysical Journal},
6178		Month = {Apr},
6179	<	Number = {4},
6179	>	Number = 4,
6180		Pages = {1791-1808},
6181		Title = {Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models},
6182		Uri = {<Go to ISI>://000174932400010},
6183	<	Volume = {82},
6184	<	Year = {2002}}
6183	>	Volume = 82,
6184	>	Year = 2002}
6185
6186		@article{Shillcock2005,
6187		Annote = {901QJ Times Cited:9 Cited References Count:23},
#	Line 5991 \| Line 6189
6189		Issn = {1476-1122},
6190		Journal = {Nature Materials},
6191		Month = {Mar},
6192	<	Number = {3},
6192	>	Number = 3,
6193		Pages = {225-228},
6194		Title = {Tension-induced fusion of bilayer membranes and vesicles},
6195		Uri = {<Go to ISI>://000227296700019},
6196	<	Volume = {4},
6197	<	Year = {2005}}
6196	>	Volume = 4,
6197	>	Year = 2005}
6198
6199		@article{Shimada1993,
6200		Abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
#	Line 6021 \| Line 6219
6219		Issn = {0192-8651},
6220		Journal = {Journal of Computational Chemistry},
6221		Month = {Jul},
6222	<	Number = {7},
6222	>	Number = 7,
6223		Pages = {867-878},
6224		Title = {Efficient Calculations of Coulombic Interactions in Biomolecular Simulations with Periodic Boundary-Conditions},
6225		Uri = {<Go to ISI>://A1993LH16400011},
6226	<	Volume = {14},
6227	<	Year = {1993}}
6226	>	Volume = 14,
6227	>	Year = 1993}
6228
6229		@article{Skeel2002,
6230		Abstract = {The best simple method for Newtonian molecular dynamics is indisputably
#	Line 6044 \| Line 6242
6242		Issn = {0026-8976},
6243		Journal = {Molecular Physics},
6244		Month = {Dec 20},
6245	<	Number = {24},
6245	>	Number = 24,
6246		Pages = {3885-3891},
6247		Title = {An impulse integrator for Langevin dynamics},
6248		Uri = {<Go to ISI>://000180297200014},
6249	<	Volume = {100},
6250	<	Year = {2002}}
6249	>	Volume = 100,
6250	>	Year = 2002}
6251
6252		@article{Skeel1997,
6253		Abstract = {The following integration methods for special second-order ordinary
#	Line 6070 \| Line 6268
6268		Issn = {1064-8275},
6269		Journal = {Siam Journal on Scientific Computing},
6270		Month = {Jan},
6271	<	Number = {1},
6271	>	Number = 1,
6272		Pages = {203-222},
6273		Title = {A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications},
6274		Uri = {<Go to ISI>://A1997WE98100012},
6275	<	Volume = {18},
6276	<	Year = {1997}}
6275	>	Volume = 18,
6276	>	Year = 1997}
6277
6278		@article{Tao2005,
6279		Abstract = {Recently a microscopic theory for the dynamics of suspensions of long
#	Line 6103 \| Line 6301
6301		Issn = {0021-9606},
6302		Journal = {Journal of Chemical Physics},
6303		Month = {Jun 22},
6304	<	Number = {24},
6304	>	Number = 24,
6305		Pages = {-},
6306		Title = {Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods},
6307		Uri = {<Go to ISI>://000230332400077},
6308	<	Volume = {122},
6309	<	Year = {2005}}
6308	>	Volume = 122,
6309	>	Year = 2005}
6310
6311		@book{Tolman1979,
6312		Address = {New York},
6313		Author = {R.~C. Tolman},
6314	<	Chapter = {2},
6314	>	Chapter = 2,
6315		Pages = {19-22},
6316		Publisher = {Dover Publications, Inc.},
6317		Title = {The Principles of Statistical Mechanics},
6318	<	Year = {1979}}
6318	>	Year = 1979}
6319
6320		@article{Tu1995,
6321		Abstract = {We report a constant pressure and temperature molecular dynamics simulation
#	Line 6144 \| Line 6342
6342		Issn = {0006-3495},
6343		Journal = {Biophysical Journal},
6344		Month = {Dec},
6345	<	Number = {6},
6345	>	Number = 6,
6346		Pages = {2558-2562},
6347		Title = {Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer},
6348		Uri = {<Go to ISI>://A1995TV01800037},
6349	<	Volume = {69},
6350	<	Year = {1995}}
6349	>	Volume = 69,
6350	>	Year = 1995}
6351
6352		@article{Tuckerman1992,
6353		Abstract = {The Trotter factorization of the Liouville propagator is used to generate
#	Line 6169 \| Line 6367
6367		Issn = {0021-9606},
6368		Journal = {Journal of Chemical Physics},
6369		Month = {Aug 1},
6370	<	Number = {3},
6370	>	Number = 3,
6371		Pages = {1990-2001},
6372		Title = {Reversible Multiple Time Scale Molecular-Dynamics},
6373		Uri = {<Go to ISI>://A1992JE89100044},
6374	<	Volume = {97},
6375	<	Year = {1992}}
6374	>	Volume = 97,
6375	>	Year = 1992}
6376
6377		@book{Varadarajan1974,
6378		Address = {New York},
6379		Author = {V.S. Varadarajan},
6380		Publisher = {Prentice-Hall},
6381		Title = {Lie groups, Lie algebras, and their representations},
6382	<	Year = {1974}}
6382	>	Year = 1974}
6383
6384		@article{Vincent1995,
6385		Abstract = {We have implemented a portable parallel version of the macromolecular
#	Line 6203 \| Line 6401
6401		Issn = {0192-8651},
6402		Journal = {Journal of Computational Chemistry},
6403		Month = {Nov},
6404	<	Number = {11},
6404	>	Number = 11,
6405		Pages = {1420-1427},
6406		Title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing Interface Standard},
6407		Uri = {<Go to ISI>://A1995TA40300009},
6408	<	Volume = {16},
6409	<	Year = {1995}}
6408	>	Volume = 16,
6409	>	Year = 1995}
6410
6411		@article{Wegener1979,
6412		Author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
6413		Journal = {Proc. Natl. Acad. Sci.},
6414	<	Number = {12},
6414	>	Number = 12,
6415		Pages = {6356-6360},
6416		Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
6417	<	Volume = {76},
6418	<	Year = {1979}}
6417	>	Volume = 76,
6418	>	Year = 1979}
6419
6420		@article{Wilson2006,
6421		Author = {G.~V. Wilson},
6422		Journal = {American Scientist},
6423		Title = {Where's the Real Bottleneck in Scientific Computing?},
6424	<	Volume = {94},
6425	<	Year = {2006}}
6424	>	Volume = 94,
6425	>	Year = 2006}
6426
6427		@article{Withers2003,
6428		Abstract = {The effects of longitudinal quadrupole moments on the formation of
#	Line 6259 \| Line 6457
6457		Issn = {0021-9606},
6458		Journal = {Journal of Chemical Physics},
6459		Month = {Nov 15},
6460	<	Number = {19},
6460	>	Number = 19,
6461		Pages = {10209-10223},
6462		Title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne fluid},
6463		Uri = {<Go to ISI>://000186273200027},
6464	<	Volume = {119},
6465	<	Year = {2003}}
6464	>	Volume = 119,
6465	>	Year = 2003}
6466
6467		@article{Wolf1999,
6468		Abstract = {Based on a recent result showing that the net Coulomb potential in
#	Line 6293 \| Line 6491
6491		Issn = {0021-9606},
6492		Journal = {Journal of Chemical Physics},
6493		Month = {May 1},
6494	<	Number = {17},
6494	>	Number = 17,
6495		Pages = {8254-8282},
6496		Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r(-1) summation},
6497		Uri = {<Go to ISI>://000079913000008},
6498	<	Volume = {110},
6499	<	Year = {1999}}
6498	>	Volume = 110,
6499	>	Year = 1999}
6500
6501		@article{Yoshida1990,
6502		Annote = {Ej798 Times Cited:492 Cited References Count:9},
#	Line 6310 \| Line 6508
6508		Pages = {262-268},
6509		Title = {Construction of Higher-Order Symplectic Integrators},
6510		Uri = {<Go to ISI>://A1990EJ79800009},
6511	<	Volume = {150},
6512	<	Year = {1990}}
6511	>	Volume = 150,
6512	>	Year = 1990}
6513
6514		@article{Blum1972,
6515		Author = {L. Blum and A.~J. Torruella},
#	Line 6354 \| Line 6552
6552		Author = {M.W. Hirsch},
6553		Publisher = {Springer},
6554		Title = {Differential Topology},
6555	<	Year = {1997}}
6555	>	Year = 1997}
6556
6557		@book{Jost2002,
6558		Address = {Berlin},
6559		Author = {J. Jost},
6560		Publisher = {Springer-Verlag},
6561		Title = {Riemannian Geometry and Geometric Analysis},
6562	<	Year = {2002}}
6562	>	Year = 2002}
6563
6564		@book{McDuff1998,
6565		Address = {Oxford},
6566		Author = {D. McDuff and D. Salamon},
6567		Publisher = {Oxford Mathematical Monographs},
6568		Title = {Introduction to Symplectic Topology},
6569	<	Year = {1998}}
6569	>	Year = 1998}
6570
6571		@article{Matubayasi1999,
6572		Author = {N. Matubayasi and M. Nakahara},
#	Line 6432 \| Line 6630
6630		Title = {The Dynamics of Runge-Kutta Methods},
6631		Volume = 2,
6632		Year = 1992}
6633	+
6634	+	@article{HuseyinKaya07012005,
6635	+	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.
6636	+	},
6637	+	Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun},
6638	+	Doi = {10.1529/biophysj.104.057471},
6639	+	Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf},
6640	+	Journal = {Biophys. J.},
6641	+	Number = 1,
6642	+	Pages = {520-535},
6643	+	Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}},
6644	+	Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6645	+	Volume = 89,
6646	+	Year = 2005,
6647	+	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6648	+	Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}}

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Comparing trunk/langevin/langevin.bib (file contents): Revision 3310 by gezelter, Fri Jan 11 22:08:57 2008 UTC vs. Revision 3352 by gezelter, Fri Feb 29 22:02:46 2008 UTC

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Comparing trunk/langevin/langevin.bib (file contents):
Revision 3310 by gezelter, Fri Jan 11 22:08:57 2008 UTC vs.
Revision 3352 by gezelter, Fri Feb 29 22:02:46 2008 UTC