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3
4	–	@ARTICLE{2003,
5	–	author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez
6	–	and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez},
7	–	title = {Calculation of the solution properties of flexible macromolecules:
8	–	methods and applications},
9	–	journal = {European Biophysics Journal with Biophysics Letters},
10	–	year = {2003},
11	–	volume = {32},
12	–	pages = {477-486},
13	–	number = {5},
14	–	month = {Aug},
15	–	abstract = {While the prediction of hydrodynamic properties of rigid particles
16	–	is nowadays feasible using simple and efficient computer programs,
17	–	the calculation of such properties and, in general, the dynamic
18	–	behavior of flexible macromolecules has not reached a similar situation.
19	–	Although the theories are available, usually the computational work
20	–	is done using solutions specific for each problem. We intend to
21	–	develop computer programs that would greatly facilitate the task
22	–	of predicting solution behavior of flexible macromolecules. In this
23	–	paper, we first present an overview of the two approaches that are
24	–	most practical: the Monte Carlo rigid-body treatment, and the Brownian
25	–	dynamics simulation technique. The Monte Carlo procedure is based
26	–	on the calculation of properties for instantaneous conformations
27	–	of the macromolecule that are regarded as if they were instantaneously
28	–	rigid. We describe how a Monte Carlo program can be interfaced to
29	–	the programs in the HYDRO suite for rigid particles, and provide
30	–	an example of such calculation, for a hypothetical particle: a protein
31	–	with two domains connected by a flexible linker. We also describe
32	–	briefly the essentials of Brownian dynamics, and propose a general
33	–	mechanical model that includes several kinds of intramolecular interactions,
34	–	such as bending, internal rotation, excluded volume effects, etc.
35	–	We provide an example of the application of this methodology to
36	–	the dynamics of a semiflexible, wormlike DNA.},
37	–	annote = {724XK Times Cited:6 Cited References Count:64},
38	–	issn = {0175-7571},
39	–	uri = {<Go to ISI>://000185513400011},
40	–	}
4
5	<	@ARTICLE{Alakent2005,
43	<	author = {B. Alakent and M. C. Camurdan and P. Doruker},
44	<	title = {Hierarchical structure of the energy landscape of proteins revisited
45	<	by time series analysis. II. Investigation of explicit solvent effects},
46	<	journal = {Journal of Chemical Physics},
47	<	year = {2005},
48	<	volume = {123},
49	<	pages = {-},
50	<	number = {14},
51	<	month = {Oct 8},
52	<	abstract = {Time series analysis tools are employed on the principal modes obtained
53	<	from the C-alpha trajectories from two independent molecular-dynamics
54	<	simulations of alpha-amylase inhibitor (tendamistat). Fluctuations
55	<	inside an energy minimum (intraminimum motions), transitions between
56	<	minima (interminimum motions), and relaxations in different hierarchical
57	<	energy levels are investigated and compared with those encountered
58	<	in vacuum by using different sampling window sizes and intervals.
59	<	The low-frequency low-indexed mode relationship, established in
60	<	vacuum, is also encountered in water, which shows the reliability
61	<	of the important dynamics information offered by principal components
62	<	analysis in water. It has been shown that examining a short data
63	<	collection period (100 ps) may result in a high population of overdamped
64	<	modes, while some of the low-frequency oscillations (< 10 cm(-1))
65	<	can be captured in water by using a longer data collection period
66	<	(1200 ps). Simultaneous analysis of short and long sampling window
67	<	sizes gives the following picture of the effect of water on protein
68	<	dynamics. Water makes the protein lose its memory: future conformations
69	<	are less dependent on previous conformations due to the lowering
70	<	of energy barriers in hierarchical levels of the energy landscape.
71	<	In short-time dynamics (< 10 ps), damping factors extracted from
72	<	time series model parameters are lowered. For tendamistat, the friction
73	<	coefficient in the Langevin equation is found to be around 40-60
74	<	cm(-1) for the low-indexed modes, compatible with literature. The
75	<	fact that water has increased the friction and that on the other
76	<	hand has lubrication effect at first sight contradicts. However,
77	<	this comes about because water enhances the transitions between
78	<	minima and forces the protein to reduce its already inherent inability
79	<	to maintain oscillations observed in vacuum. Some of the frequencies
80	<	lower than 10 cm(-1) are found to be overdamped, while those higher
81	<	than 20 cm(-1) are slightly increased. As for the long-time dynamics
82	<	in water, it is found that random-walk motion is maintained for
83	<	approximately 200 ps (about five times of that in vacuum) in the
84	<	low-indexed modes, showing the lowering of energy barriers between
85	<	the higher-level minima.},
86	<	annote = {973OH Times Cited:1 Cited References Count:33},
87	<	issn = {0021-9606},
88	<	uri = {<Go to ISI>://000232532000064},
89	<	}
5	>	%% Created for Xiuquan Sun at 2008-02-12 16:53:41 -0500
6
91	–	@ARTICLE{Allison1991,
92	–	author = {S. A. Allison},
93	–	title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application
94	–	to Polarized Dynamic Light-Scattering},
95	–	journal = {Macromolecules},
96	–	year = {1991},
97	–	volume = {24},
98	–	pages = {530-536},
99	–	number = {2},
100	–	month = {Jan 21},
101	–	abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
102	–	of rigid macromolecules. It is applied to polarized dynamic light
103	–	scattering from rodlike sturctures and from a model of a DNA fragment
104	–	(762 base pairs). A number of rod cases are examined in which the
105	–	translational anisotropy is increased form zero to a large value.
106	–	Simulated first cumulants as well as amplitudes and lifetimes of
107	–	the dynamic form factor are compared with predictions of analytic
108	–	theories and found to be in very good agreement with them. For DNA
109	–	fragments 762 base pairs in length or longer, translational anisotropy
110	–	does not contribute significantly to dynamic light scattering. In
111	–	a comparison of rigid and flexible simulations on semistiff models
112	–	of this fragment, it is shown directly that flexing contributes
113	–	to the faster decay processes probed by light scattering and that
114	–	the flexible model studies are in good agreement with experiment.},
115	–	annote = {Eu814 Times Cited:8 Cited References Count:32},
116	–	issn = {0024-9297},
117	–	uri = {<Go to ISI>://A1991EU81400029},
118	–	}
7
8	<	@ARTICLE{Auerbach2005,
121	<	author = {A. Auerbach},
122	<	title = {Gating of acetylcholine receptor channels: Brownian motion across
123	<	a broad transition state},
124	<	journal = {Proceedings of the National Academy of Sciences of the United States
125	<	of America},
126	<	year = {2005},
127	<	volume = {102},
128	<	pages = {1408-1412},
129	<	number = {5},
130	<	month = {Feb 1},
131	<	abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
132	<	stable #closed# and #open# conformations. In patch clamp recordings,
133	<	diliganded AChR gating appears to be a simple, two-state reaction.
134	<	However, mutagenesis studies indicate that during gating dozens
135	<	of residues across the protein move asynchronously and are organized
136	<	into rigid body gating domains (#blocks#). Moreover, there is an
137	<	upper limit to the apparent channel opening rate constant. These
138	<	observations suggest that the gating reaction has a broad, corrugated
139	<	transition state region, with the maximum opening rate reflecting,
140	<	in part, the mean first-passage time across this ensemble. Simulations
141	<	reveal that a flat, isotropic energy profile for the transition
142	<	state can account for many of the essential features of AChR gating.
143	<	With this mechanism, concerted, local structural transitions that
144	<	occur on the broad transition state ensemble give rise to fractional
145	<	measures of reaction progress (Phi values) determined by rate-equilibrium
146	<	free energy relationship analysis. The results suggest that the
147	<	coarse-grained AChR gating conformational change propagates through
148	<	the protein with dynamics that are governed by the Brownian motion
149	<	of individual gating blocks.},
150	<	annote = {895QF Times Cited:9 Cited References Count:33},
151	<	issn = {0027-8424},
152	<	uri = {<Go to ISI>://000226877300030},
153	<	}
8	>	%% Saved with string encoding Western (ASCII)
9
155	–	@ARTICLE{Banerjee2004,
156	–	author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
157	–	title = {Solution of quantum Langevin equation: Approximations, theoretical
158	–	and numerical aspects},
159	–	journal = {Journal of Chemical Physics},
160	–	year = {2004},
161	–	volume = {120},
162	–	pages = {8960-8972},
163	–	number = {19},
164	–	month = {May 15},
165	–	abstract = {Based on a coherent state representation of noise operator and an
166	–	ensemble averaging procedure using Wigner canonical thermal distribution
167	–	for harmonic oscillators, a generalized quantum Langevin equation
168	–	has been recently developed [Phys. Rev. E 65, 021109 (2002); 66,
169	–	051106 (2002)] to derive the equations of motion for probability
170	–	distribution functions in c-number phase-space. We extend the treatment
171	–	to explore several systematic approximation schemes for the solutions
172	–	of the Langevin equation for nonlinear potentials for a wide range
173	–	of noise correlation, strength and temperature down to the vacuum
174	–	limit. The method is exemplified by an analytic application to harmonic
175	–	oscillator for arbitrary memory kernel and with the help of a numerical
176	–	calculation of barrier crossing, in a cubic potential to demonstrate
177	–	the quantum Kramers' turnover and the quantum Arrhenius plot. (C)
178	–	2004 American Institute of Physics.},
179	–	annote = {816YY Times Cited:8 Cited References Count:35},
180	–	issn = {0021-9606},
181	–	uri = {<Go to ISI>://000221146400009},
182	–	}
10
11	<	@ARTICLE{Barth1998,
185	<	author = {E. Barth and T. Schlick},
186	<	title = {Overcoming stability limitations in biomolecular dynamics. I. Combining
187	<	force splitting via extrapolation with Langevin dynamics in LN},
188	<	journal = {Journal of Chemical Physics},
189	<	year = {1998},
190	<	volume = {109},
191	<	pages = {1617-1632},
192	<	number = {5},
193	<	month = {Aug 1},
194	<	abstract = {We present an efficient new method termed LN for propagating biomolecular
195	<	dynamics according to the Langevin equation that arose fortuitously
196	<	upon analysis of the range of harmonic validity of our normal-mode
197	<	scheme LIN. LN combines force linearization with force splitting
198	<	techniques and disposes of LIN'S computationally intensive minimization
199	<	(anharmonic correction) component. Unlike the competitive multiple-timestepping
200	<	(MTS) schemes today-formulated to be symplectic and time-reversible-LN
201	<	merges the slow and fast forces via extrapolation rather than impulses;
202	<	the Langevin heat bath prevents systematic energy drifts. This combination
203	<	succeeds in achieving more significant speedups than these MTS methods
204	<	which are Limited by resonance artifacts to an outer timestep less
205	<	than some integer multiple of half the period of the fastest motion
206	<	(around 4-5 fs for biomolecules). We show that LN achieves very
207	<	good agreement with small-timestep solutions of the Langevin equation
208	<	in terms of thermodynamics (energy means and variances), geometry,
209	<	and dynamics (spectral densities) for two proteins in vacuum and
210	<	a large water system. Significantly, the frequency of updating the
211	<	slow forces extends to 48 fs or more, resulting in speedup factors
212	<	exceeding 10. The implementation of LN in any program that employs
213	<	force-splitting computations is straightforward, with only partial
214	<	second-derivative information required, as well as sparse Hessian/vector
215	<	multiplication routines. The linearization part of LN could even
216	<	be replaced by direct evaluation of the fast components. The application
217	<	of LN to biomolecular dynamics is well suited for configurational
218	<	sampling, thermodynamic, and structural questions. (C) 1998 American
219	<	Institute of Physics.},
220	<	annote = {105HH Times Cited:29 Cited References Count:49},
221	<	issn = {0021-9606},
222	<	uri = {<Go to ISI>://000075066300006},
223	<	}
11	>	@string{acp = {Adv. Chem. Phys.}}
12
13	<	@ARTICLE{Batcho2001,
226	<	author = {P. F. Batcho and T. Schlick},
227	<	title = {Special stability advantages of position-Verlet over velocity-Verlet
228	<	in multiple-time step integration},
229	<	journal = {Journal of Chemical Physics},
230	<	year = {2001},
231	<	volume = {115},
232	<	pages = {4019-4029},
233	<	number = {9},
234	<	month = {Sep 1},
235	<	abstract = {We present an analysis for a simple two-component harmonic oscillator
236	<	that compares the use of position-Verlet to velocity-Verlet for
237	<	multiple-time step integration. The numerical stability analysis
238	<	based on the impulse-Verlet splitting shows that position-Verlet
239	<	has enhanced stability, in terms of the largest allowable time step,
240	<	for cases where an ample separation of time scales exists. Numerical
241	<	investigations confirm the advantages of the position-Verlet scheme
242	<	when used for the fastest time scales of the system. Applications
243	<	to a biomolecule. a solvated protein, for both Newtonian and Langevin
244	<	dynamics echo these trends over large outer time-step regimes. (C)
245	<	2001 American Institute of Physics.},
246	<	annote = {469KV Times Cited:6 Cited References Count:30},
247	<	issn = {0021-9606},
248	<	uri = {<Go to ISI>://000170813800005},
249	<	}
250	<
251	<	@ARTICLE{Beard2003,
252	<	author = {D. A. Beard and T. Schlick},
253	<	title = {Unbiased rotational moves for rigid-body dynamics},
254	<	journal = {Biophysical Journal},
255	<	year = {2003},
256	<	volume = {85},
257	<	pages = {2973-2976},
258	<	number = {5},
259	<	month = {Nov 1},
260	<	abstract = {We introduce an unbiased protocol for performing rotational moves
261	<	in rigid-body dynamics simulations. This approach - based on the
262	<	analytic solution for the rotational equations of motion for an
263	<	orthogonal coordinate system at constant angular velocity - removes
264	<	deficiencies that have been largely ignored in Brownian dynamics
265	<	simulations, namely errors for finite rotations that result from
266	<	applying the noncommuting rotational matrices in an arbitrary order.
267	<	Our algorithm should thus replace standard approaches to rotate
268	<	local coordinate frames in Langevin and Brownian dynamics simulations.},
269	<	annote = {736UA Times Cited:0 Cited References Count:11},
270	<	issn = {0006-3495},
271	<	uri = {<Go to ISI>://000186190500018},
272	<	}
13	>	@string{ccp5 = {CCP5 Information Quarterly}}
14
15	<	@ARTICLE{Beloborodov1998,
275	<	author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev},
276	<	title = {Effect of coupling between rotational and translational Brownian
277	<	motions on NMR spin relaxation: Consideration using green function
278	<	of rigid body diffusion},
279	<	journal = {Journal of Magnetic Resonance},
280	<	year = {1998},
281	<	volume = {132},
282	<	pages = {328-329},
283	<	number = {2},
284	<	month = {Jun},
285	<	abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
286	<	Biopolymers 33, 409-436, 1993), it was analytically shown that coupling
287	<	between translation and rotation diffusion degrees of freedom does
288	<	not affect the correlation functions relevant to the NMR intramolecular
289	<	relaxation. It follows that spectral densities usually used for
290	<	the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37,
291	<	647-654, 1962) can be regarded as exact in respect to the rotation-translation
292	<	coupling for the spin system connected with a rigid body. (C) 1998
293	<	Academic Press.},
294	<	annote = {Zu605 Times Cited:2 Cited References Count:6},
295	<	issn = {1090-7807},
296	<	uri = {<Go to ISI>://000074214800017},
297	<	}
15	>	@string{cp = {Chem. Phys.}}
16
17	<	@ARTICLE{Berkov2005,
300	<	author = {D. V. Berkov and N. L. Gorn},
301	<	title = {Stochastic dynamic simulations of fast remagnetization processes:
302	<	recent advances and applications},
303	<	journal = {Journal of Magnetism and Magnetic Materials},
304	<	year = {2005},
305	<	volume = {290},
306	<	pages = {442-448},
307	<	month = {Apr},
308	<	abstract = {Numerical simulations of fast remagnetization processes using stochastic
309	<	dynamics are widely used to study various magnetic systems. In this
310	<	paper, we first address several crucial methodological problems
311	<	of such simulations: (i) the influence of finite-element discretization
312	<	on simulated dynamics, (ii) choice between Ito and Stratonovich
313	<	stochastic calculi by the solution of micromagnetic stochastic equations
314	<	of motion and (iii) non-trivial correlation properties of the random
315	<	(thermal) field. Next, we discuss several examples to demonstrate
316	<	the great potential of the Langevin dynamics for studying fast remagnetization
317	<	processes in technically relevant applications: we present numerical
318	<	analysis of equilibrium magnon spectra in patterned structures,
319	<	study thermal noise effects on the magnetization dynamics of nanoelements
320	<	in pulsed fields and show some results for a remagnetization dynamics
321	<	induced by a spin-polarized current. (c) 2004 Elsevier B.V. All
322	<	rights reserved.},
323	<	annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
324	<	issn = {0304-8853},
325	<	uri = {<Go to ISI>://000228837600109},
326	<	}
17	>	@string{cpl = {Chem. Phys. Lett.}}
18
19	<	@ARTICLE{Berkov2005a,
329	<	author = {D. V. Berkov and N. L. Gorn},
330	<	title = {Magnetization precession due to a spin-polarized current in a thin
331	<	nanoelement: Numerical simulation study},
332	<	journal = {Physical Review B},
333	<	year = {2005},
334	<	volume = {72},
335	<	pages = {-},
336	<	number = {9},
337	<	month = {Sep},
338	<	abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
339	<	formalism) of magnetization oscillations driven by a spin-polarized
340	<	current through a thin elliptical nanoelement is presented. We show
341	<	that a sophisticated micromagnetic model, where a polycrystalline
342	<	structure of a nanoelement is taken into account, can explain qualitatively
343	<	all most important features of the magnetization oscillation spectra
344	<	recently observed experimentally [S. I. Kiselev , Nature 425, 380
345	<	(2003)], namely, existence of several equidistant spectral bands,
346	<	sharp onset and abrupt disappearance of magnetization oscillations
347	<	with increasing current, absence of the out-of-plane regime predicted
348	<	by a macrospin model, and the relation between frequencies of so-called
349	<	small-angle and quasichaotic oscillations. However, a quantitative
350	<	agreement with experimental results (especially concerning the frequency
351	<	of quasichaotic oscillations) could not be achieved in the region
352	<	of reasonable parameter values, indicating that further model refinement
353	<	is necessary for a complete understanding of the spin-driven magnetization
354	<	precession even in this relatively simple experimental situation.},
355	<	annote = {969IT Times Cited:2 Cited References Count:55},
356	<	issn = {1098-0121},
357	<	uri = {<Go to ISI>://000232228500058},
358	<	}
19	>	@string{jacs = {J. Am. Chem. Soc.}}
20
21	<	@ARTICLE{Berkov2002,
361	<	author = {D. V. Berkov and N. L. Gorn and P. Gornert},
362	<	title = {Magnetization dynamics in nanoparticle systems: Numerical simulation
363	<	using Langevin dynamics},
364	<	journal = {Physica Status Solidi a-Applied Research},
365	<	year = {2002},
366	<	volume = {189},
367	<	pages = {409-421},
368	<	number = {2},
369	<	month = {Feb 16},
370	<	abstract = {We report on recent progress achieved by the development of numerical
371	<	methods based on the stochastic (Langevin) dynamics applied to systems
372	<	of interacting magnetic nanoparticles. The method enables direct
373	<	simulations of the trajectories of magnetic moments taking into
374	<	account (i) all relevant interactions, (ii) precession dynamics,
375	<	and (iii) temperature fluctuations included via the random (thermal)
376	<	field. We present several novel results obtained using new methods
377	<	developed for the solution of the Langevin equations. In particular,
378	<	we have investigated magnetic nanodots and disordered granular systems
379	<	of single-domain magnetic particles. For the first case we have
380	<	calculated the spectrum and the spatial distribution of spin excitations.
381	<	For the second system the complex ac susceptibility chi(omega, T)
382	<	for various particle concentrations and particle anisotropies were
383	<	computed and compared with numerous experimental results.},
384	<	annote = {526TF Times Cited:4 Cited References Count:37},
385	<	issn = {0031-8965},
386	<	uri = {<Go to ISI>://000174145200026},
387	<	}
21	>	@string{jcc = {J. Comp. Chem.}}
22
23	<	@ARTICLE{Bernal1980,
390	<	author = {J.M. Bernal and J. G. {de la Torre}},
391	<	title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules
392	<	with Arbitrary Shape},
393	<	journal = {Biopolymers},
394	<	year = {1980},
395	<	volume = {19},
396	<	pages = {751-766},
397	<	}
23	>	@string{jcop = {J. Comp. Phys.}}
24
25	<	@ARTICLE{Brunger1984,
400	<	author = {A. Brunger and C. L. Brooks and M. Karplus},
401	<	title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations
402	<	of St2 Water},
403	<	journal = {Chemical Physics Letters},
404	<	year = {1984},
405	<	volume = {105},
406	<	pages = {495-500},
407	<	number = {5},
408	<	annote = {Sm173 Times Cited:143 Cited References Count:22},
409	<	issn = {0009-2614},
410	<	uri = {<Go to ISI>://A1984SM17300007},
411	<	}
25	>	@string{jcp = {J. Chem. Phys.}}
26
27	<	@ARTICLE{Chin2004,
414	<	author = {S. A. Chin},
415	<	title = {Dynamical multiple-time stepping methods for overcoming resonance
416	<	instabilities},
417	<	journal = {Journal of Chemical Physics},
418	<	year = {2004},
419	<	volume = {120},
420	<	pages = {8-13},
421	<	number = {1},
422	<	month = {Jan 1},
423	<	abstract = {Current molecular dynamics simulations of biomolecules using multiple
424	<	time steps to update the slowly changing force are hampered by instabilities
425	<	beginning at time steps near the half period of the fastest vibrating
426	<	mode. These #resonance# instabilities have became a critical barrier
427	<	preventing the long time simulation of biomolecular dynamics. Attempts
428	<	to tame these instabilities by altering the slowly changing force
429	<	and efforts to damp them out by Langevin dynamics do not address
430	<	the fundamental cause of these instabilities. In this work, we trace
431	<	the instability to the nonanalytic character of the underlying spectrum
432	<	and show that a correct splitting of the Hamiltonian, which renders
433	<	the spectrum analytic, restores stability. The resulting Hamiltonian
434	<	dictates that in addition to updating the momentum due to the slowly
435	<	changing force, one must also update the position with a modified
436	<	mass. Thus multiple-time stepping must be done dynamically. (C)
437	<	2004 American Institute of Physics.},
438	<	annote = {757TK Times Cited:1 Cited References Count:22},
439	<	issn = {0021-9606},
440	<	uri = {<Go to ISI>://000187577400003},
441	<	}
27	>	@string{jml = {J. Mol. Liq.}}
28
29	<	@ARTICLE{Cui2003,
444	<	author = {B. X. Cui and M. Y. Shen and K. F. Freed},
445	<	title = {Folding and misfolding of the papillomavirus E6 interacting peptide
446	<	E6ap},
447	<	journal = {Proceedings of the National Academy of Sciences of the United States
448	<	of America},
449	<	year = {2003},
450	<	volume = {100},
451	<	pages = {7087-7092},
452	<	number = {12},
453	<	month = {Jun 10},
454	<	abstract = {All-atom Langevin dynamics simulations have been performed to study
455	<	the folding pathways of the 18-residue binding domain fragment E6ap
456	<	of the human papillomavirus E6 interacting peptide. Six independent
457	<	folding trajectories, with a total duration of nearly 2 mus, all
458	<	lead to the same native state in which the E6ap adopts a fluctuating
459	<	a-helix structure in the central portion (Ser-4-Leu-13) but with
460	<	very flexible N and C termini. Simulations starting from different
461	<	core configurations exhibit the E6ap folding dynamics as either
462	<	a two- or three-state folder with an intermediate misfolded state.
463	<	The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13)
464	<	is well conserved in the native-state structure but absent in the
465	<	intermediate structure, suggesting that the leucine core is not
466	<	only essential for the binding activity of E6ap but also important
467	<	for the stability of the native structure. The free energy landscape
468	<	reveals a significant barrier between the basins separating the
469	<	native and misfolded states. We also discuss the various underlying
470	<	forces that drive the peptide into its native state.},
471	<	annote = {689LC Times Cited:3 Cited References Count:48},
472	<	issn = {0027-8424},
473	<	uri = {<Go to ISI>://000183493500037},
474	<	}
29	>	@string{jpc = {J. Phys. Chem.}}
30
31	<	@ARTICLE{Denisov2003,
477	<	author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou},
478	<	title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
479	<	journal = {Physical Review B},
480	<	year = {2003},
481	<	volume = {67},
482	<	pages = {-},
483	<	number = {1},
484	<	month = {Jan 1},
485	<	abstract = {We study the slow phase of thermally activated magnetic relaxation
486	<	in finite two-dimensional ensembles of dipolar interacting ferromagnetic
487	<	nanoparticles whose easy axes of magnetization are perpendicular
488	<	to the distribution plane. We develop a method to numerically simulate
489	<	the magnetic relaxation for the case that the smallest heights of
490	<	the potential barriers between the equilibrium directions of the
491	<	nanoparticle magnetic moments are much larger than the thermal energy.
492	<	Within this framework, we analyze in detail the role that the correlations
493	<	of the nanoparticle magnetic moments and the finite size of the
494	<	nanoparticle ensemble play in magnetic relaxation.},
495	<	annote = {642XH Times Cited:11 Cited References Count:31},
496	<	issn = {1098-0121},
497	<	uri = {<Go to ISI>://000180830400056},
498	<	}
31	>	@string{jpca = {J. Phys. Chem. A}}
32
33	<	@ARTICLE{Derreumaux1998,
34	<	author = {P. Derreumaux and T. Schlick},
35	<	title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
503	<	journal = {Biophysical Journal},
504	<	year = {1998},
505	<	volume = {74},
506	<	pages = {72-81},
507	<	number = {1},
508	<	month = {Jan},
509	<	abstract = {To explore the origin of the large-scale motion of triosephosphate
510	<	isomerase's flexible loop (residues 166 to 176) at the active site,
511	<	several simulation protocols are employed both for the free enzyme
512	<	in vacuo and for the free enzyme with some solvent modeling: high-temperature
513	<	Langevin dynamics simulations, sampling by a #dynamics##driver#
514	<	approach, and potential-energy surface calculations. Our focus is
515	<	on obtaining the energy barrier to the enzyme's motion and establishing
516	<	the nature of the loop movement. Previous calculations did not determine
517	<	this energy barrier and the effect of solvent on the barrier. High-temperature
518	<	molecular dynamics simulations and crystallographic studies have
519	<	suggested a rigid-body motion with two hinges located at both ends
520	<	of the loop; Brownian dynamics simulations at room temperature pointed
521	<	to a very flexible behavior. The present simulations and analyses
522	<	reveal that although solute/solvent hydrogen bonds play a crucial
523	<	role in lowering the energy along the pathway, there still remains
524	<	a high activation barrier, This finding clearly indicates that,
525	<	if the loop opens and closes in the absence of a substrate at standard
526	<	conditions (e.g., room temperature, appropriate concentration of
527	<	isomerase), the time scale for transition is not in the nanosecond
528	<	but rather the microsecond range. Our results also indicate that
529	<	in the context of spontaneous opening in the free enzyme, the motion
530	<	is of rigid-body type and that the specific interaction between
531	<	residues Ala(176) and Tyr(208) plays a crucial role in the loop
532	<	opening/closing mechanism.},
533	<	annote = {Zl046 Times Cited:30 Cited References Count:29},
534	<	issn = {0006-3495},
535	<	uri = {<Go to ISI>://000073393400009},
536	<	}
33	>	@string{jpcb = {J. Phys. Chem. B}}
34	>
35	>	@string{mp = {Mol. Phys.}}
36
37	<	@ARTICLE{Edwards2005,
539	<	author = {S. A. Edwards and D. R. M. Williams},
540	<	title = {Stretching a single diblock copolymer in a selective solvent: Langevin
541	<	dynamics simulations},
542	<	journal = {Macromolecules},
543	<	year = {2005},
544	<	volume = {38},
545	<	pages = {10590-10595},
546	<	number = {25},
547	<	month = {Dec 13},
548	<	abstract = {Using the Langevin dynamics technique, we have carried out simulations
549	<	of a single-chain flexible diblock copolymer. The polymer consists
550	<	of two blocks of equal length, one very poorly solvated and the
551	<	other close to theta-conditions. We study what happens when such
552	<	a polymer is stretched, for a range of different stretching speeds,
553	<	and correlate our observations with features in the plot of force
554	<	vs extension. We find that at slow speeds this force profile does
555	<	not increase monotonically, in disagreement with earlier predictions,
556	<	and that at high speeds there is a strong dependence on which end
557	<	of the polymer is pulled, as well as a high level of hysteresis.},
558	<	annote = {992EC Times Cited:0 Cited References Count:13},
559	<	issn = {0024-9297},
560	<	uri = {<Go to ISI>://000233866200035},
561	<	}
37	>	@string{pams = {Proc. Am. Math Soc.}}
38
39	<	@ARTICLE{Ermak1978,
564	<	author = {D. L. Ermak and J. A. Mccammon},
565	<	title = {Brownian Dynamics with Hydrodynamic Interactions},
566	<	journal = {Journal of Chemical Physics},
567	<	year = {1978},
568	<	volume = {69},
569	<	pages = {1352-1360},
570	<	number = {4},
571	<	annote = {Fp216 Times Cited:785 Cited References Count:42},
572	<	issn = {0021-9606},
573	<	uri = {<Go to ISI>://A1978FP21600004},
574	<	}
39	>	@string{pccp = {Phys. Chem. Chem. Phys.}}
40
41	<	@ARTICLE{Fernandes2002,
577	<	author = {M. X. Fernandes and J. G. {de la Torre}},
578	<	title = {Brownian dynamics simulation of rigid particles of arbitrary shape
579	<	in external fields},
580	<	journal = {Biophysical Journal},
581	<	year = {2002},
582	<	volume = {83},
583	<	pages = {3039-3048},
584	<	number = {6},
585	<	month = {Dec},
586	<	abstract = {We have developed a Brownian dynamics simulation algorithm to generate
587	<	Brownian trajectories of an isolated, rigid particle of arbitrary
588	<	shape in the presence of electric fields or any other external agents.
589	<	Starting from the generalized diffusion tensor, which can be calculated
590	<	with the existing HYDRO software, the new program BROWNRIG (including
591	<	a case-specific subprogram for the external agent) carries out a
592	<	simulation that is analyzed later to extract the observable dynamic
593	<	properties. We provide a variety of examples of utilization of this
594	<	method, which serve as tests of its performance, and also illustrate
595	<	its applicability. Examples include free diffusion, transport in
596	<	an electric field, and diffusion in a restricting environment.},
597	<	annote = {633AD Times Cited:2 Cited References Count:43},
598	<	issn = {0006-3495},
599	<	uri = {<Go to ISI>://000180256300012},
600	<	}
41	>	@string{pnas = {Proc. Natl. Acad. Sci. USA}}
42
43	<	@ARTICLE{Gelin1999,
603	<	author = {M. F. Gelin},
604	<	title = {Inertial effects in the Brownian dynamics with rigid constraints},
605	<	journal = {Macromolecular Theory and Simulations},
606	<	year = {1999},
607	<	volume = {8},
608	<	pages = {529-543},
609	<	number = {6},
610	<	month = {Nov},
611	<	abstract = {To investigate the influence of inertial effects on the dynamics of
612	<	an assembly of beads subjected to rigid constraints and placed in
613	<	a buffer medium, a convenient method to introduce suitable generalized
614	<	coordinates is presented. Without any restriction on the nature
615	<	of the soft forces involved (both stochastic and deterministic),
616	<	pertinent Langevin equations are derived. Provided that the Brownian
617	<	forces are Gaussian and Markovian, the corresponding Fokker-Planck
618	<	equation (FPE) is obtained in the complete phase space of generalized
619	<	coordinates and momenta. The correct short time behavior for correlation
620	<	functions (CFs) of generalized coordinates is established, and the
621	<	diffusion equation with memory (DEM) is deduced from the FPE in
622	<	the high friction Limit. The DEM is invoked to perform illustrative
623	<	calculations in two dimensions of the orientational CFs for once
624	<	broken nonrigid rods immobilized on a surface. These calculations
625	<	reveal that the CFs under certain conditions exhibit an oscillatory
626	<	behavior, which is irreproducible within the standard diffusion
627	<	equation. Several methods are considered for the approximate solution
628	<	of the DEM, and their application to three dimensional DEMs is discussed.},
629	<	annote = {257MM Times Cited:2 Cited References Count:82},
630	<	issn = {1022-1344},
631	<	uri = {<Go to ISI>://000083785700002},
632	<	}
43	>	@string{pr = {Phys. Rev.}}
44
45	<	@ARTICLE{Gray2003,
635	<	author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and
636	<	B. Kuhlman and C. A. Rohl and D. Baker},
637	<	title = {Protein-protein docking with simultaneous optimization of rigid-body
638	<	displacement and side-chain conformations},
639	<	journal = {Journal of Molecular Biology},
640	<	year = {2003},
641	<	volume = {331},
642	<	pages = {281-299},
643	<	number = {1},
644	<	month = {Aug 1},
645	<	abstract = {Protein-protein docking algorithms provide a means to elucidate structural
646	<	details for presently unknown complexes. Here, we present and evaluate
647	<	a new method to predict protein-protein complexes from the coordinates
648	<	of the unbound monomer components. The method employs a low-resolution,
649	<	rigid-body, Monte Carlo search followed by simultaneous optimization
650	<	of backbone displacement and side-chain conformations using Monte
651	<	Carlo minimization. Up to 10(5) independent simulations are carried
652	<	out, and the resulting #decoys# are ranked using an energy function
653	<	dominated by van der Waals interactions, an implicit solvation model,
654	<	and an orientation-dependent hydrogen bonding potential. Top-ranking
655	<	decoys are clustered to select the final predictions. Small-perturbation
656	<	studies reveal the formation of binding funnels in 42 of 54 cases
657	<	using coordinates derived from the bound complexes and in 32 of
658	<	54 cases using independently determined coordinates of one or both
659	<	monomers. Experimental binding affinities correlate with the calculated
660	<	score function and explain the predictive success or failure of
661	<	many targets. Global searches using one or both unbound components
662	<	predict at least 25% of the native residue-residue contacts in 28
663	<	of the 32 cases where binding funnels exist. The results suggest
664	<	that the method may soon be useful for generating models of biologically
665	<	important complexes from the structures of the isolated components,
666	<	but they also highlight the challenges that must be met to achieve
667	<	consistent and accurate prediction of protein-protein interactions.
668	<	(C) 2003 Elsevier Ltd. All rights reserved.},
669	<	annote = {704QL Times Cited:48 Cited References Count:60},
670	<	issn = {0022-2836},
671	<	uri = {<Go to ISI>://000184351300022},
672	<	}
45	>	@string{pra = {Phys. Rev. A}}
46
47	<	@ARTICLE{Hao1993,
675	<	author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga},
676	<	title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic
677	<	Trypsin-Inhibitor Studied by Computer-Simulations},
678	<	journal = {Biochemistry},
679	<	year = {1993},
680	<	volume = {32},
681	<	pages = {9614-9631},
682	<	number = {37},
683	<	month = {Sep 21},
684	<	abstract = {A new procedure for studying the folding and unfolding of proteins,
685	<	with an application to bovine pancreatic trypsin inhibitor (BPTI),
686	<	is reported. The unfolding and refolding of the native structure
687	<	of the protein are characterized by the dimensions of the protein,
688	<	expressed in terms of the three principal radii of the structure
689	<	considered as an ellipsoid. A dynamic equation, describing the variations
690	<	of the principal radii on the unfolding path, and a numerical procedure
691	<	to solve this equation are proposed. Expanded and distorted conformations
692	<	are refolded to the native structure by a dimensional-constraint
693	<	energy minimization procedure. A unique and reproducible unfolding
694	<	pathway for an intermediate of BPTI lacking the [30,51] disulfide
695	<	bond is obtained. The resulting unfolded conformations are extended;
696	<	they contain near-native local structure, but their longest principal
697	<	radii are more than 2.5 times greater than that of the native structure.
698	<	The most interesting finding is that the majority of expanded conformations,
699	<	generated under various conditions, can be refolded closely to the
700	<	native structure, as measured by the correct overall chain fold,
701	<	by the rms deviations from the native structure of only 1.9-3.1
702	<	angstrom, and by the energy differences of about 10 kcal/mol from
703	<	the native structure. Introduction of the [30,51] disulfide bond
704	<	at this stage, followed by minimization, improves the closeness
705	<	of the refolded structures to the native structure, reducing the
706	<	rms deviations to 0.9-2.0 angstrom. The unique refolding of these
707	<	expanded structures over such a large conformational space implies
708	<	that the folding is strongly dictated by the interactions in the
709	<	amino acid sequence of BPTI. The simulations indicate that, under
710	<	conditions that favor a compact structure as mimicked by the volume
711	<	constraints in our algorithm; the expanded conformations have a
712	<	strong tendency to move toward the native structure; therefore,
713	<	they probably would be favorable folding intermediates. The results
714	<	presented here support a general model for protein folding, i.e.,
715	<	progressive formation of partially folded structural units, followed
716	<	by collapse to the compact native structure. The general applicability
717	<	of the procedure is also discussed.},
718	<	annote = {Ly294 Times Cited:27 Cited References Count:57},
719	<	issn = {0006-2960},
720	<	uri = {<Go to ISI>://A1993LY29400014},
721	<	}
47	>	@string{prb = {Phys. Rev. B}}
48
49	<	@ARTICLE{Hinsen2000,
724	<	author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel
725	<	and G. R. Kneller},
726	<	title = {Harmonicity in slow protein dynamics},
727	<	journal = {Chemical Physics},
728	<	year = {2000},
729	<	volume = {261},
730	<	pages = {25-37},
731	<	number = {1-2},
732	<	month = {Nov 1},
733	<	abstract = {The slow dynamics of proteins around its native folded state is usually
734	<	described by diffusion in a strongly anharmonic potential. In this
735	<	paper, we try to understand the form and origin of the anharmonicities,
736	<	with the principal aim of gaining a better understanding of the
737	<	principal motion types, but also in order to develop more efficient
738	<	numerical methods for simulating neutron scattering spectra of large
739	<	proteins. First, we decompose a molecular dynamics (MD) trajectory
740	<	of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water
741	<	into three contributions that we expect to be independent: the global
742	<	motion of the residues, the rigid-body motion of the sidechains
743	<	relative to the backbone, and the internal deformations of the sidechains.
744	<	We show that they are indeed almost independent by verifying the
745	<	factorization of the incoherent intermediate scattering function.
746	<	Then, we show that the global residue motions, which include all
747	<	large-scale backbone motions, can be reproduced by a simple harmonic
748	<	model which contains two contributions: a short-time vibrational
749	<	term, described by a standard normal mode calculation in a local
750	<	minimum, and a long-time diffusive term, described by Brownian motion
751	<	in an effective harmonic potential. The potential and the friction
752	<	constants were fitted to the MD data. The major anharmonic contribution
753	<	to the incoherent intermediate scattering function comes from the
754	<	rigid-body diffusion of the sidechains. This model can be used to
755	<	calculate scattering functions for large proteins and for long-time
756	<	scales very efficiently, and thus provides a useful complement to
757	<	MD simulations, which are best suited for detailed studies on smaller
758	<	systems or for shorter time scales. (C) 2000 Elsevier Science B.V.
759	<	All rights reserved.},
760	<	annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31},
761	<	issn = {0301-0104},
762	<	uri = {<Go to ISI>://000090121700003},
763	<	}
49	>	@string{pre = {Phys. Rev. E}}
50
51	<	@ARTICLE{Izaguirre2001,
52	<	author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
53	<	title = {Langevin stabilization of molecular dynamics},
54	<	journal = {Journal of Chemical Physics},
55	<	year = {2001},
56	<	volume = {114},
57	<	pages = {2090-2098},
58	<	number = {5},
59	<	month = {Feb 1},
60	<	abstract = {In this paper we show the possibility of using very mild stochastic
61	<	damping to stabilize long time step integrators for Newtonian molecular
62	<	dynamics. More specifically, stable and accurate integrations are
63	<	obtained for damping coefficients that are only a few percent of
64	<	the natural decay rate of processes of interest, such as the velocity
779	<	autocorrelation function. Two new multiple time stepping integrators,
780	<	Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are
781	<	introduced in this paper. Both use the mollified impulse method
782	<	for the Newtonian term. LM uses a discretization of the Langevin
783	<	equation that is exact for the constant force, and BBK-M uses the
784	<	popular Brunger-Brooks-Karplus integrator (BBK). These integrators,
785	<	along with an extrapolative method called LN, are evaluated across
786	<	a wide range of damping coefficient values. When large damping coefficients
787	<	are used, as one would for the implicit modeling of solvent molecules,
788	<	the method LN is superior, with LM closely following. However, with
789	<	mild damping of 0.2 ps(-1), LM produces the best results, allowing
790	<	long time steps of 14 fs in simulations containing explicitly modeled
791	<	flexible water. With BBK-M and the same damping coefficient, time
792	<	steps of 12 fs are possible for the same system. Similar results
793	<	are obtained for a solvated protein-DNA simulation of estrogen receptor
794	<	ER with estrogen response element ERE. A parallel version of BBK-M
795	<	runs nearly three times faster than the Verlet-I/r-RESPA (reversible
796	<	reference system propagator algorithm) when using the largest stable
797	<	time step on each one, and it also parallelizes well. The computation
798	<	of diffusion coefficients for flexible water and ER/ERE shows that
799	<	when mild damping of up to 0.2 ps-1 is used the dynamics are not
800	<	significantly distorted. (C) 2001 American Institute of Physics.},
801	<	annote = {397CQ Times Cited:14 Cited References Count:36},
802	<	issn = {0021-9606},
803	<	uri = {<Go to ISI>://000166676100020},
804	<	}
51	>	@string{prl = {Phys. Rev. Lett.}}
52	>
53	>	@string{rmp = {Rev. Mod. Phys.}}
54	>
55	>
56	>	@book{Schlick2002,
57	>	Address = {Secaucus, NJ, USA},
58	>	Author = {Tamar Schlick},
59	>	Date-Added = {2008-02-12 16:52:19 -0500},
60	>	Date-Modified = {2008-02-12 16:53:15 -0500},
61	>	Isbn = {038795404X},
62	>	Publisher = {Springer-Verlag New York, Inc.},
63	>	Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
64	>	Year = {2002}}
65
66	<	@ARTICLE{Klimov1997,
67	<	author = {D. K. Klimov and D. Thirumalai},
68	<	title = {Viscosity dependence of the folding rates of proteins},
69	<	journal = {Physical Review Letters},
70	<	year = {1997},
71	<	volume = {79},
72	<	pages = {317-320},
73	<	number = {2},
74	<	month = {Jul 14},
75	<	abstract = {The viscosity (eta) dependence of the folding rates for four sequences
76	<	(the native state of three sequences is a beta sheet, while the
77	<	fourth forms an alpha helix) is calculated for off-lattice models
818	<	of proteins. Assuming that the dynamics is given by the Langevin
819	<	equation, we show that the folding rates increase linearly at low
820	<	viscosities eta, decrease as 1/eta at large eta, and have a maximum
821	<	at intermediate values. The Kramers' theory of barrier crossing
822	<	provides a quantitative fit of the numerical results. By mapping
823	<	the simulation results to real proteins we estimate that for optimized
824	<	sequences the time scale for forming a four turn alpha-helix topology
825	<	is about 500 ns, whereas for beta sheet it is about 10 mu s.},
826	<	annote = {Xk293 Times Cited:77 Cited References Count:17},
827	<	issn = {0031-9007},
828	<	uri = {<Go to ISI>://A1997XK29300035},
829	<	}
66	>	@misc{Chun:2000fj,
67	>	Abstract = {A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5- to 30-fold over atomistic simulations have been realized in various applications of the method. (C) 2000 John Wiley \& Sons, Inc.},
68	>	Author = {Chun, HM and Padilla, CE and Chin, DN and Watanabe, M and Karlov, VI and Alper, HE and Soosaar, K and Blair, KB and Becker, OM and Caves, LSD and Nagle, R and Haney, DN and Farmer, BL},
69	>	Date-Added = {2008-01-22 10:38:33 -0500},
70	>	Date-Modified = {2008-01-22 10:38:49 -0500},
71	>	Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
72	>	Note = {Journal of Computational Chemistry},
73	>	Pages = {159-184},
74	>	Timescited = {0},
75	>	Title = {MBO(N)D: A multibody method for long-time molecular dynamics simulations},
76	>	Volume = {21},
77	>	Year = {2000}}
78
79	<	@ARTICLE{Liwo2005,
80	<	author = {A. Liwo and M. Khalili and H. A. Scheraga},
81	<	title = {Ab initio simulations of protein folding pathways by molecular dynamics
82	<	with the united-residue (UNRES) model of polypeptide chains},
83	<	journal = {Febs Journal},
84	<	year = {2005},
85	<	volume = {272},
86	<	pages = {359-360},
87	<	month = {Jul},
88	<	annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
89	<	issn = {1742-464X},
90	<	uri = {<Go to ISI>://000234826102043},
91	<	}
79	>	@article{Fogolari:1996lr,
80	>	Abstract = {In an effort to reduce the number of degrees of freedom necessary to describe a polypeptide chain we analyze the statistical behavior of polypeptide chains when represented as C alpha chains, C alpha chains with C beta atoms attached, and C alpha chains with rotational ellipsoids as models of side chains. A statistical analysis on a restricted data set of 75 unrelated protein structures is performed. The comparison of the database distributions with those obtained by model calculation on very short polypeptide stretches allows the dissection of local versus nonlocal features of the distributions. The database distribution of the bend angles of polypeptide chains of pseudo bonded C alpha atoms spans a restricted range of values and shows a bimodal structure. On the other hand, the torsion angles of the C alpha chain may assume almost all possible values. The distribution is bimodal, but with a much broader probability distribution than for bend angles. The C alpha - C beta vectors may be taken as representative of the orientation of the lateral chain, as the direction of the bond is close to the direction of the vector joining C alpha to the ad hoc defined center of the "steric mass" of the side chain. Interestingly, both the bend angle defined by C alpha i-C alpha i+1-C beta i+1 and the torsional angle offset of the pseudo-dihedral C alpha i-C alpha i+1-C alpha i+2-C beta i+2 with respect to C alpha i-C alpha i+1-C alpha i+2-C alpha i+3 span a limited range of values. The latter results show that it is possible to give a more realistic representation of polypeptide chains without introducing additional degrees of freedom, i.e., by just adding to the C alpha chain a C beta with given side-chain properties. However, a more realistic description of side chains may be attained by modeling side chains as rotational ellipsoids that have roughly the same orientation and steric hindrance. To this end, we define the steric mass of an atom as proportional to its van der Waals volume and we calculate the side-chain inertia ellipsoid assuming that the steric mass of each atom is uniformly distributed within its van der Waals volume. Finally, we define the rotational ellipsoid representing the side chain as the uniform density ellipsoid possessing the same rotationally averaged inertia tensor of the side chain. The statistics of ellipsoid parameters support the possibility of representing a side chain via an ellipsoid, independently of the local conformation. To make this description useful for molecular modeling we describe ellipsoid-ellipsoid interactions via a Lennard-Jones potential that preserves the repulsive core of the interacting ellipsoids and takes into account their mutual orientation. Tests are performed for two different forms of the interaction potential on a set of high-resolution protein structures. Results are encouraging, in view of the drastic simplifications that were introduced.},
81	>	Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.},
82	>	Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
83	>	Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
84	>	Da = {19960924},
85	>	Date-Added = {2008-01-22 10:19:04 -0500},
86	>	Date-Modified = {2008-01-22 10:19:09 -0500},
87	>	Dcom = {19960924},
88	>	Edat = {1996/03/01},
89	>	Issn = {0006-3495 (Print)},
90	>	Jid = {0370626},
91	>	Journal = {Biophys J},
92	>	Jt = {Biophysical journal},
93	>	Language = {eng},
94	>	Lr = {20071115},
95	>	Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; *Models, Molecular; Molecular Structure; Peptides/*chemistry; *Protein Conformation; Software; Thermodynamics},
96	>	Mhda = {1996/03/01 00:01},
97	>	Number = {3},
98	>	Own = {NLM},
99	>	Pages = {1183--1197},
100	>	Pl = {UNITED STATES},
101	>	Pmid = {8785277},
102	>	Pst = {ppublish},
103	>	Pt = {Journal Article},
104	>	Pubm = {Print},
105	>	Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)},
106	>	Sb = {IM},
107	>	So = {Biophys J. 1996 Mar;70(3):1183-97. },
108	>	Stat = {MEDLINE},
109	>	Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.},
110	>	Volume = {70},
111	>	Year = {1996}}
112
113	<	@ARTICLE{Mielke2004,
114	<	author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen
115	<	and C. J. Benham},
116	<	title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian
117	<	dynamics study},
118	<	journal = {Journal of Chemical Physics},
119	<	year = {2004},
120	<	volume = {121},
121	<	pages = {8104-8112},
122	<	number = {16},
123	<	month = {Oct 22},
124	<	abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
125	<	DNA can potentially induce long-range structural deformations integral
858	<	to mechanisms of biological significance in both prokaryotes and
859	<	eukaryotes. In this paper, we introduce a dynamic computer model
860	<	for investigating this phenomenon. Duplex DNA is represented as
861	<	a chain of hydrodynamic beads interacting through potentials of
862	<	linearly elastic stretching, bending, and twisting, as well as excluded
863	<	volume. The chain, linear when relaxed, is looped to form two open
864	<	but topologically constrained subdomains. This permits the dynamic
865	<	introduction of torsional stress via a centrally applied torque.
866	<	We simulate by Brownian dynamics the 100 mus response of a 477-base
867	<	pair B-DNA template to the localized torque generated by the prokaryotic
868	<	transcription ensemble. Following a sharp rise at early times, the
869	<	distributed twist assumes a nearly constant value in both subdomains,
870	<	and a succession of supercoiling deformations occurs as superhelical
871	<	stress is increasingly partitioned to writhe. The magnitude of writhe
872	<	surpasses that of twist before also leveling off when the structure
873	<	reaches mechanical equilibrium with the torsional load. Superhelicity
874	<	is simultaneously right handed in one subdomain and left handed
875	<	in the other, as predicted by the #transcription-induced##twin-supercoiled-domain#
876	<	model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84,
877	<	7024 (1987)]. The properties of the chain at the onset of writhing
878	<	agree well with predictions from theory, and the generated stress
879	<	is ample for driving secondary structural transitions in physiological
880	<	DNA. (C) 2004 American Institute of Physics.},
881	<	annote = {861ZF Times Cited:3 Cited References Count:34},
882	<	issn = {0021-9606},
883	<	uri = {<Go to ISI>://000224456500064},
884	<	}
113	>	@inbook{Ramachandran1996,
114	>	Address = {Providence, Rhode Island},
115	>	Author = {GOMATHI RAMACHANDRAN AND TAMAR SCHLICK},
116	>	Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
117	>	Date-Added = {2008-01-22 10:03:42 -0500},
118	>	Date-Modified = {2008-01-22 10:06:57 -0500},
119	>	Editor = {P. M. Pardalos and D. Shalloway and G. Xue},
120	>	Pages = {215-231},
121	>	Publisher = {American Mathematical Society},
122	>	Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
123	>	Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
124	>	Volume = {23},
125	>	Year = {1996}}
126
127	<	@ARTICLE{Naess2001,
128	<	author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter},
129	<	title = {Brownian dynamics simulation of rigid bodies and segmented polymer
130	<	chains. Use of Cartesian rotation vectors as the generalized coordinates
131	<	describing angular orientations},
132	<	journal = {Physica A},
133	<	year = {2001},
134	<	volume = {294},
135	<	pages = {323-339},
136	<	number = {3-4},
137	<	month = {May 15},
138	<	abstract = {The three Eulerian angles constitute the classical choice of generalized
139	<	coordinates used to describe the three degrees of rotational freedom
140	<	of a rigid body, but it has long been known that this choice yields
141	<	singular equations of motion. The latter is also true when Eulerian
142	<	angles are used in Brownian dynamics analyses of the angular orientation
143	<	of single rigid bodies and segmented polymer chains. Starting from
144	<	kinetic theory we here show that by instead employing the three
145	<	components of Cartesian rotation vectors as the generalized coordinates
146	<	describing angular orientation, no singularity appears in the configuration
147	<	space diffusion equation and the associated Brownian dynamics algorithm.
148	<	The suitability of Cartesian rotation vectors in Brownian dynamics
149	<	simulations of segmented polymer chains with spring-like or ball-socket
150	<	joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.},
151	<	annote = {433TA Times Cited:7 Cited References Count:19},
152	<	issn = {0378-4371},
153	<	uri = {<Go to ISI>://000168774800005},
154	<	}
155	<
156	<	@ARTICLE{Noguchi2002,
157	<	author = {H. Noguchi and M. Takasu},
158	<	title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
159	<	journal = {Physical Review E},
160	<	year = {2002},
161	<	volume = {65},
162	<	pages = {-},
163	<	number = {5},
164	<	month = {may},
165	<	abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
166	<	forces using a Brownian dynamics simulation. Two nanoparticles,
167	<	which interact repulsively with amphiphilic molecules, are put inside
168	<	a vesicle. The position of one nanoparticle is fixed, and the other
169	<	is moved by a constant force as in optical-trapping experiments.
170	<	First, the pulled vesicle stretches into a pear or tube shape. Then
171	<	the inner monolayer in the tube-shaped region is deformed, and a
172	<	cylindrical structure is formed between two vesicles. After stretching
173	<	the cylindrical region, fission occurs near the moved vesicle. Soon
174	<	after this the cylindrical region shrinks. The trapping force similar
175	<	to 100 pN is needed to induce the formation of the cylindrical structure
176	<	and fission.},
177	<	annote = {Part 1 568PX Times Cited:5 Cited References Count:39},
178	<	issn = {1063-651X},
179	<	uri = {<Go to ISI>://000176552300084},
180	<	}
181	<
182	<	@ARTICLE{Noguchi2001,
183	<	author = {H. Noguchi and M. Takasu},
184	<	title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
185	<	journal = {Journal of Chemical Physics},
186	<	year = {2001},
187	<	volume = {115},
188	<	pages = {9547-9551},
189	<	number = {20},
190	<	month = {Nov 22},
191	<	abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
192	<	simulation. Amphiphilic molecules spontaneously form vesicles with
193	<	a bilayer structure. Two vesicles come into contact and form a stalk
194	<	intermediate, in which a necklike structure only connects the outer
195	<	monolayers, as predicted by the stalk hypothesis. We have found
196	<	a new pathway of pore opening from stalks at high temperature: the
197	<	elliptic stalk bends and contact between the ends of the arc-shaped
198	<	stalk leads to pore opening. On the other hand, we have clarified
199	<	that the pore-opening process at low temperature agrees with the
200	<	modified stalk model: a pore is induced by contact between the inner
201	<	monolayers inside the stalk. (C) 2001 American Institute of Physics.},
202	<	annote = {491UW Times Cited:48 Cited References Count:25},
203	<	issn = {0021-9606},
204	<	uri = {<Go to ISI>://000172129300049},
205	<	}
206	<
207	<	@ARTICLE{Palacios1998,
208	<	author = {J. L. Garcia-Palacios and F. J. Lazaro},
209	<	title = {Langevin-dynamics study of the dynamical properties of small magnetic
210	<	particles},
211	<	journal = {Physical Review B},
212	<	year = {1998},
213	<	volume = {58},
214	<	pages = {14937-14958},
215	<	number = {22},
216	<	month = {Dec 1},
217	<	abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
218	<	magnetic moment is numerically solved (properly observing the customary
219	<	interpretation of it as a Stratonovich stochastic differential equation),
220	<	in order to study the dynamics of magnetic nanoparticles. The corresponding
221	<	Langevin-dynamics approach allows for the study of the fluctuating
222	<	trajectories of individual magnetic moments, where we have encountered
223	<	remarkable phenomena in the overbarrier rotation process, such as
224	<	crossing-back or multiple crossing of the potential barrier, rooted
225	<	in the gyromagnetic nature of the system. Concerning averaged quantities,
226	<	we study the linear dynamic response of the archetypal ensemble
227	<	of noninteracting classical magnetic moments with axially symmetric
228	<	magnetic anisotropy. The results are compared with different analytical
229	<	expressions used to model the relaxation of nanoparticle ensembles,
230	<	assessing their accuracy. It has been found that, among a number
231	<	of heuristic expressions for the linear dynamic susceptibility,
232	<	only the simple formula proposed by Shliomis and Stepanov matches
233	<	the coarse features of the susceptibility reasonably. By comparing
234	<	the numerical results with the asymptotic formula of Storonkin {Sov.
235	<	Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]},
236	<	the effects of the intra-potential-well relaxation modes on the
237	<	low-temperature longitudinal dynamic response have been assessed,
238	<	showing their relatively small reflection in the susceptibility
239	<	curves but their dramatic influence on the phase shifts. Comparison
240	<	of the numerical results with the exact zero-damping expression
241	<	for the transverse susceptibility by Garanin, Ishchenko, and Panina
242	<	{Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242
243	<	(1990)]}, reveals a sizable contribution of the spread of the precession
244	<	frequencies of the magnetic moment in the anisotropy field to the
245	<	dynamic response at intermediate-to-high temperatures. [S0163-1829
246	<	(98)00446-9].},
247	<	annote = {146XW Times Cited:66 Cited References Count:45},
248	<	issn = {0163-1829},
249	<	uri = {<Go to ISI>://000077460000052},
250	<	}
251	<
252	<	@ARTICLE{Pastor1988,
253	<	author = {R. W. Pastor and B. R. Brooks and A. Szabo},
254	<	title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
255	<	journal = {Molecular Physics},
256	<	year = {1988},
257	<	volume = {65},
258	<	pages = {1409-1419},
259	<	number = {6},
260	<	month = {Dec 20},
261	<	annote = {T1302 Times Cited:61 Cited References Count:26},
262	<	issn = {0026-8976},
263	<	uri = {<Go to ISI>://A1988T130200011},
264	<	}
265	<
266	<	@ARTICLE{Recio2004,
267	<	author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
268	<	title = {Identification of protein-protein interaction sites from docking
269	<	energy landscapes},
270	<	journal = {Journal of Molecular Biology},
271	<	year = {2004},
272	<	volume = {335},
273	<	pages = {843-865},
274	<	number = {3},
275	<	month = {Jan 16},
276	<	abstract = {Protein recognition is one of the most challenging and intriguing
277	<	problems in structural biology. Despite all the available structural,
278	<	sequence and biophysical information about protein-protein complexes,
279	<	the physico-chemical patterns, if any, that make a protein surface
280	<	likely to be involved in protein-protein interactions, remain elusive.
281	<	Here, we apply protein docking simulations and analysis of the interaction
282	<	energy landscapes to identify protein-protein interaction sites.
283	<	The new protocol for global docking based on multi-start global
284	<	energy optimization of an allatom model of the ligand, with detailed
285	<	receptor potentials and atomic solvation parameters optimized in
286	<	a training set of 24 complexes, explores the conformational space
287	<	around the whole receptor without restrictions. The ensembles of
288	<	the rigid-body docking solutions generated by the simulations were
289	<	subsequently used to project the docking energy landscapes onto
290	<	the protein surfaces. We found that highly populated low-energy
291	<	regions consistently corresponded to actual binding sites. The procedure
292	<	was validated on a test set of 21 known protein-protein complexes
293	<	not used in the training set. As much as 81% of the predicted high-propensity
294	<	patch residues were located correctly in the native interfaces.
295	<	This approach can guide the design of mutations on the surfaces
296	<	of proteins, provide geometrical details of a possible interaction,
297	<	and help to annotate protein surfaces in structural proteomics.
298	<	(C) 2003 Elsevier Ltd. All rights reserved.},
299	<	annote = {763GQ Times Cited:21 Cited References Count:59},
300	<	issn = {0022-2836},
301	<	uri = {<Go to ISI>://000188066900016},
302	<	}
303	<
304	<	@ARTICLE{Sandu1999,
305	<	author = {A. Sandu and T. Schlick},
306	<	title = {Masking resonance artifacts in force-splitting methods for biomolecular
307	<	simulations by extrapolative Langevin dynamics},
308	<	journal = {Journal of Computational Physics},
309	<	year = {1999},
310	<	volume = {151},
311	<	pages = {74-113},
312	<	number = {1},
313	<	month = {May 1},
314	<	abstract = {Numerical resonance artifacts have become recognized recently as a
315	<	limiting factor to increasing the timestep in multiple-timestep
316	<	(MTS) biomolecular dynamics simulations. At certain timesteps correlated
317	<	to internal motions (e.g., 5 fs, around half the period of the fastest
318	<	bond stretch, T-min), visible inaccuracies or instabilities can
319	<	occur. Impulse-MTS schemes are vulnerable to these resonance errors
320	<	since large energy pulses are introduced to the governing dynamics
321	<	equations when the slow forces are evaluated. We recently showed
322	<	that such resonance artifacts can be masked significantly by applying
323	<	extrapolative splitting to stochastic dynamics. Theoretical and
324	<	numerical analyses of force-splitting integrators based on the Verlet
325	<	discretization are reported here for linear models to explain these
326	<	observations and to suggest how to construct effective integrators
327	<	for biomolecular dynamics that balance stability with accuracy.
328	<	Analyses for Newtonian dynamics demonstrate the severe resonance
329	<	patterns of the Impulse splitting, with this severity worsening
330	<	with the outer timestep. Delta t: Constant Extrapolation is generally
331	<	unstable, but the disturbances do not grow with Delta t. Thus. the
332	<	stochastic extrapolative combination can counteract generic instabilities
333	<	and largely alleviate resonances with a sufficiently strong Langevin
334	<	heat-bath coupling (gamma), estimates for which are derived here
335	<	based on the fastest and slowest motion periods. These resonance
336	<	results generally hold for nonlinear test systems: a water tetramer
337	<	and solvated protein. Proposed related approaches such as Extrapolation/Correction
338	<	and Midpoint Extrapolation work better than Constant Extrapolation
339	<	only for timesteps less than T-min/2. An effective extrapolative
340	<	stochastic approach for biomolecules that balances long-timestep
341	<	stability with good accuracy for the fast subsystem is then applied
342	<	to a biomolecule using a three-class partitioning: the medium forces
343	<	are treated by Midpoint Extrapolation via position Verlet, and the
344	<	slow forces are incorporated by Constant Extrapolation. The resulting
345	<	algorithm (LN) performs well on a solvated protein system in terms
346	<	of thermodynamic properties and yields an order of magnitude speedup
347	<	with respect to single-timestep Langevin trajectories. Computed
348	<	spectral density functions also show how the Newtonian modes can
349	<	be approximated by using a small gamma in the range Of 5-20 ps(-1).
350	<	(C) 1999 Academic Press.},
351	<	annote = {194FM Times Cited:14 Cited References Count:32},
352	<	issn = {0021-9991},
353	<	uri = {<Go to ISI>://000080181500004},
354	<	}
355	<
356	<	@ARTICLE{Shen2002,
357	<	author = {M. Y. Shen and K. F. Freed},
358	<	title = {Long time dynamics of met-enkephalin: Comparison of explicit and
359	<	implicit solvent models},
360	<	journal = {Biophysical Journal},
361	<	year = {2002},
362	<	volume = {82},
363	<	pages = {1791-1808},
364	<	number = {4},
365	<	month = {Apr},
366	<	abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
367	<	structure and receptor docking mechanism are still not well understood.
368	<	The conformational dynamics of this neuron peptide in liquid water
369	<	are studied here by using all-atom molecular dynamics (MID) and
370	<	implicit water Langevin dynamics (LD) simulations with AMBER potential
371	<	functions and the three-site transferable intermolecular potential
372	<	(TIP3P) model for water. To achieve the same simulation length in
373	<	physical time, the full MID simulations require 200 times as much
374	<	CPU time as the implicit water LID simulations. The solvent hydrophobicity
375	<	and dielectric behavior are treated in the implicit solvent LD simulations
376	<	by using a macroscopic solvation potential, a single dielectric
377	<	constant, and atomic friction coefficients computed using the accessible
378	<	surface area method with the TIP3P model water viscosity as determined
379	<	here from MID simulations for pure TIP3P water. Both the local and
380	<	the global dynamics obtained from the implicit solvent LD simulations
381	<	agree very well with those from the explicit solvent MD simulations.
382	<	The simulations provide insights into the conformational restrictions
383	<	that are associated with the bioactivity of the opiate peptide dermorphin
384	<	for the delta-receptor.},
385	<	annote = {540MH Times Cited:36 Cited References Count:45},
386	<	issn = {0006-3495},
387	<	uri = {<Go to ISI>://000174932400010},
388	<	}
389	<
390	<	@ARTICLE{Shillcock2005,
391	<	author = {J. C. Shillcock and R. Lipowsky},
392	<	title = {Tension-induced fusion of bilayer membranes and vesicles},
393	<	journal = {Nature Materials},
394	<	year = {2005},
395	<	volume = {4},
396	<	pages = {225-228},
397	<	number = {3},
398	<	month = {Mar},
399	<	annote = {901QJ Times Cited:9 Cited References Count:23},
400	<	issn = {1476-1122},
401	<	uri = {<Go to ISI>://000227296700019},
402	<	}
403	<
404	<	@ARTICLE{Skeel2002,
405	<	author = {R. D. Skeel and J. A. Izaguirre},
406	<	title = {An impulse integrator for Langevin dynamics},
407	<	journal = {Molecular Physics},
408	<	year = {2002},
409	<	volume = {100},
410	<	pages = {3885-3891},
411	<	number = {24},
412	<	month = {Dec 20},
413	<	abstract = {The best simple method for Newtonian molecular dynamics is indisputably
414	<	the leapfrog Stormer-Verlet method. The appropriate generalization
415	<	to simple Langevin dynamics is unclear. An analysis is presented
416	<	comparing an 'impulse method' (kick; fluctuate; kick), the 1982
417	<	method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus
418	<	(BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen
419	<	methods can be implemented as efficiently as the BBK method. Other
420	<	considerations suggest that the impulse method is the best basic
421	<	method for simple Langevin dynamics, with the van Gunsteren-Berendsen
422	<	method a close contender.},
423	<	annote = {633RX Times Cited:8 Cited References Count:22},
424	<	issn = {0026-8976},
425	<	uri = {<Go to ISI>://000180297200014},
426	<	}
427	<
428	<	@ARTICLE{Skeel1997,
429	<	author = {R. D. Skeel and G. H. Zhang and T. Schlick},
430	<	title = {A family of symplectic integrators: Stability, accuracy, and molecular
431	<	dynamics applications},
432	<	journal = {Siam Journal on Scientific Computing},
433	<	year = {1997},
434	<	volume = {18},
435	<	pages = {203-222},
436	<	number = {1},
437	<	month = {Jan},
438	<	abstract = {The following integration methods for special second-order ordinary
439	<	differential equations are studied: leapfrog, implicit midpoint,
440	<	trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all
441	<	are members, or equivalent to members, of a one-parameter family
442	<	of schemes. Some methods have more than one common form, and we
443	<	discuss a systematic enumeration of these forms. We also present
444	<	a stability and accuracy analysis based on the idea of ''modified
445	<	equations'' and a proof of symplecticness. It follows that Cowell-Numerov
446	<	and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic.
447	<	A different interpretation of the values used by these integrators
448	<	leads to higher accuracy and better energy conservation. Hence,
449	<	we suggest that the straightforward analysis of energy conservation
450	<	is misleading.},
451	<	annote = {We981 Times Cited:30 Cited References Count:35},
452	<	issn = {1064-8275},
453	<	uri = {<Go to ISI>://A1997WE98100012},
454	<	}
455	<
456	<	@ARTICLE{Tao2005,
457	<	author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont
458	<	and W. J. Briels},
459	<	title = {Brownian dynamics simulations of the self- and collective rotational
460	<	diffusion coefficients of rigid long thin rods},
461	<	journal = {Journal of Chemical Physics},
462	<	year = {2005},
463	<	volume = {122},
464	<	pages = {-},
465	<	number = {24},
466	<	month = {Jun 22},
467	<	abstract = {Recently a microscopic theory for the dynamics of suspensions of long
468	<	thin rigid rods was presented, confirming and expanding the well-known
469	<	theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon,
470	<	Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here
471	<	this theory is put to the test by comparing it against computer
472	<	simulations. A Brownian dynamics simulation program was developed
473	<	to follow the dynamics of the rods, with a length over a diameter
474	<	ratio of 60, on the Smoluchowski time scale. The model accounts
475	<	for excluded volume interactions between rods, but neglects hydrodynamic
476	<	interactions. The self-rotational diffusion coefficients D-r(phi)
477	<	of the rods were calculated by standard methods and by a new, more
478	<	efficient method based on calculating average restoring torques.
479	<	Collective decay of orientational order was calculated by means
480	<	of equilibrium and nonequilibrium simulations. Our results show
481	<	that, for the currently accessible volume fractions, the decay times
482	<	in both cases are virtually identical. Moreover, the observed decay
483	<	of diffusion coefficients with volume fraction is much quicker than
484	<	predicted by the theory, which is attributed to an oversimplification
485	<	of dynamic correlations in the theory. (c) 2005 American Institute
486	<	of Physics.},
487	<	annote = {943DN Times Cited:3 Cited References Count:26},
488	<	issn = {0021-9606},
489	<	uri = {<Go to ISI>://000230332400077},
490	<	}
491	<
492	<	@ARTICLE{Tuckerman1992,
493	<	author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
494	<	title = {Reversible Multiple Time Scale Molecular-Dynamics},
495	<	journal = {Journal of Chemical Physics},
496	<	year = {1992},
497	<	volume = {97},
498	<	pages = {1990-2001},
499	<	number = {3},
500	<	month = {Aug 1},
501	<	abstract = {The Trotter factorization of the Liouville propagator is used to generate
502	<	new reversible molecular dynamics integrators. This strategy is
503	<	applied to derive reversible reference system propagator algorithms
504	<	(RESPA) that greatly accelerate simulations of systems with a separation
505	<	of time scales or with long range forces. The new algorithms have
506	<	all of the advantages of previous RESPA integrators but are reversible,
507	<	and more stable than those methods. These methods are applied to
508	<	a set of paradigmatic systems and are shown to be superior to earlier
509	<	methods. It is shown how the new RESPA methods are related to predictor-corrector
510	<	integrators. Finally, we show how these methods can be used to accelerate
511	<	the integration of the equations of motion of systems with Nose
512	<	thermostats.},
513	<	annote = {Je891 Times Cited:680 Cited References Count:19},
514	<	issn = {0021-9606},
515	<	uri = {<Go to ISI>://A1992JE89100044},
516	<	}
517	<
127	>	@article{FIXMAN:1986lr,
128	>	Author = {FIXMAN, M},
129	>	Date-Added = {2008-01-22 09:59:29 -0500},
130	>	Date-Modified = {2008-01-22 09:59:35 -0500},
131	>	Journal = {Macromolecules},
132	>	Pages = {1204-1207},
133	>	Timescited = {0},
134	>	Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION},
135	>	Volume = {19},
136	>	Year = {1986}}
137	>
138	>	@article{Berendsen87,
139	>	Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
140	>	Date-Added = {2008-01-22 09:53:15 -0500},
141	>	Date-Modified = {2008-01-22 09:53:15 -0500},
142	>	Journal = jpc,
143	>	Pages = {6269-6271},
144	>	Title = {The Missing Term in Effective Pair Potentials},
145	>	Volume = 91,
146	>	Year = 1987}
147	>
148	>	@incollection{Berendsen81,
149	>	Address = {Dordrecht},
150	>	Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
151	>	Booktitle = {Intermolecular Forces},
152	>	Date-Added = {2008-01-22 09:52:49 -0500},
153	>	Date-Modified = {2008-01-22 09:52:49 -0500},
154	>	Editor = {B. Pullman},
155	>	Pages = {331-342},
156	>	Publisher = {Reidel},
157	>	Title = {Simple Point Charge Water},
158	>	Year = 1981}
159	>
160	>	@article{Stillinger74,
161	>	Author = {F.~H. Stillinger and A. Rahman},
162	>	Date-Added = {2008-01-22 09:51:43 -0500},
163	>	Date-Modified = {2008-01-22 09:51:43 -0500},
164	>	Journal = jcp,
165	>	Number = 4,
166	>	Pages = {1545-1557},
167	>	Title = {Improved simulation of liquid water by molecular dynamics},
168	>	Volume = 60,
169	>	Year = 1974}
170	>
171	>	@article{Torre:1983lr,
172	>	Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
173	>	Date-Added = {2008-01-11 16:16:43 -0500},
174	>	Date-Modified = {2008-01-11 16:16:43 -0500},
175	>	Journal = {The Journal of Chemical Physics},
176	>	Journal1 = {The Journal of Chemical Physics},
177	>	Journal2 = {J. Chem. Phys.},
178	>	Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
179	>	Number = 5,
180	>	Pages = {2454--2460},
181	>	Publisher = {AIP},
182	>	Title = {Effects from bead size and hydrodynamic interactions on the translational and rotational coefficients of macromolecular bead models},
183	>	Ty = {JOUR},
184	>	Url = {http://link.aip.org/link/?JCP/79/2454/1},
185	>	Volume = 79,
186	>	Year = 1983,
187	>	Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}}
188	>
189	>	@article{PhysRev.119.53,
190	>	Author = {Favro, L. Dale},
191	>	Date-Added = {2008-01-09 16:57:02 -0500},
192	>	Date-Modified = {2008-01-09 16:57:02 -0500},
193	>	Doi = {10.1103/PhysRev.119.53},
194	>	Journal = {Phys. Rev.},
195	>	Month = {Jul},
196	>	Number = 1,
197	>	Numpages = 9,
198	>	Pages = {53--62},
199	>	Publisher = {American Physical Society},
200	>	Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body},
201	>	Volume = 119,
202	>	Year = 1960,
203	>	Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}}
204	>
205	>	@article{hess:209,
206	>	Author = {Berk Hess},
207	>	Date-Added = {2008-01-08 16:41:06 -0500},
208	>	Date-Modified = {2008-01-08 16:41:06 -0500},
209	>	Doi = {10.1063/1.1421362},
210	>	Journal = {The Journal of Chemical Physics},
211	>	Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
212	>	Number = 1,
213	>	Pages = {209-217},
214	>	Publisher = {AIP},
215	>	Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
216	>	Url = {http://link.aip.org/link/?JCP/116/209/1},
217	>	Volume = 116,
218	>	Year = 2002,
219	>	Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
220	>	Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}}
221	>
222	>	@article{Garcia-de-la-Torre:1997qy,
223	>	Abstract = {Single-valued hydrodynamic coefficients of a rigid particle can be calculated from existing theories and computer programs for either bead models or ellipsoids. Starting from these coefficients, we review the procedures for the calculation of complex solution properties depending on rotational diffusion, such as the decays of electric birefringence and fluorescence anisotropy. We also describe the calculation of the scattering from factor of bead models. The hydrodynamic coefficients and solution properties can be combined to give universal, shape-dependent functions, which were initially intended for ellipsoidal particles, and are extended here for the most general case. We have implemented all three developments in a new computer program. SOLPRO, for calculation of SOLution PROperties, which can be linked to existing software for bead models or ellipsoids.},
224	>	Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es},
225	>	Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE},
226	>	Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E},
227	>	Da = 19970709,
228	>	Date-Added = {2008-01-08 15:45:31 -0500},
229	>	Date-Modified = {2008-01-08 15:46:57 -0500},
230	>	Dcom = 19970709,
231	>	Edat = {1997/01/01},
232	>	Issn = {0175-7571 (Print)},
233	>	Jid = 8409413,
234	>	Journal = {Eur Biophys J},
235	>	Jt = {European biophysics journal : EBJ},
236	>	Keywords = {Birefringence; Fluorescence Polarization; Humans; Immunoglobulin G/chemistry; Models, Structural; *Protein Conformation; Proteins/*chemistry; Scattering, Radiation; *Software; Ultracentrifugation/methods},
237	>	Language = {eng},
238	>	Lr = 20061115,
239	>	Mhda = {1997/01/01 00:01},
240	>	Number = {5-6},
241	>	Own = {NLM},
242	>	Pages = {361--372},
243	>	Pl = {GERMANY},
244	>	Pmid = 9213556,
245	>	Pst = {ppublish},
246	>	Pt = {Journal Article; Research Support, Non-U.S. Gov't},
247	>	Pubm = {Print},
248	>	Rn = {0 (Immunoglobulin G); 0 (Proteins)},
249	>	Sb = {IM},
250	>	So = {Eur Biophys J. 1997;25(5-6):361-72.},
251	>	Stat = {MEDLINE},
252	>	Title = {SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.},
253	>	Volume = 25,
254	>	Year = 1997}
255	>
256	>	@article{Ravichandran:1999fk,
257	>	Abstract = {Detailed molecular dynamics simulations of the rotational and the translational motions of Gay-Berne ellipsoids in a sea of Lennard-Jones spheres have been carried out. It is found that while the translational motion of an ellipsoid is isotropic at low density, it becomes increasingly anisotropic with density until the ratio of the parallel to the perpendicular diffusion coefficients becomes nearly equal to the value of the aspect ratio at high density. The latter is in agreement with the prediction of Navier-Stokes hydrodynamics with slip boundary condition. The product of the translational diffusion coefficient and the rotational correlation time also attains a hydrodynamic-like density independent behavior only at high density. The reorientational correlation function becomes nonexponential at high density and low temperature where it also develops a slow decay. The perpendicular component of the velocity time correlation function exhibits a clear double minimum, only at high density, which becomes more pronounced as the aspect ratio is increased. (C) 1999 American Institute of Physics. [S0021-9606(99)51440-2].},
258	>	Author = {Ravichandran, S and Bagchi, B},
259	>	Date-Added = {2008-01-08 15:24:48 -0500},
260	>	Date-Modified = {2008-01-08 15:25:41 -0500},
261	>	Journal = {Journal of Chemical Physics},
262	>	Pages = {7505-7511},
263	>	Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
264	>	Volume = 111,
265	>	Year = 1999}
266	>
267	>	@article{TANG:1993lr,
268	>	Abstract = {Translational friction coefficients of hard prolate ellipsoids (having aspect ratios of 1-10) have been calculated by solving the linearized Navier-Stokes equations of hydrodynamics, using the method of Faxen's theorem. When the stick boundary condition was used, the present results reproduce the famous work of Lamb. The new information derived from this study arises from the analysis of the friction under the influence of the slip hydrodynamic boundary condition. It was found that the slip friction perpendicular to the long axis of the prolate ellipsoid increases monotonically with aspect ratio, whereas the parallel component of the friction decreases monotonically to an apparent limiting value. The ratio f(perpendicular to)/f(parallel to) of friction coefficients perpendicular and parallel to the long axis of the particle, calculated using slip hydrodynamics, scales roughly as the aspect ratio of the ellipsoid, in accord with the findings from an Enskog (uncorrelated binary collision) kinetic theory of hard ellipsoids and from the estimate derived from molecular dynamics. In contrast, f(perpendicular to)/f(parallel to) derived by means of stick hydrodynamics shows a weak dependence on the aspect ratio and disagrees with kinetic theory and molecular dynamics findings.},
269	>	Author = {TANG, SA and EVANS, GT},
270	>	Date-Added = {2008-01-08 15:23:42 -0500},
271	>	Date-Modified = {2008-01-08 15:24:09 -0500},
272	>	Journal = {Molecular Physics},
273	>	Pages = {1443-1457},
274	>	Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
275	>	Volume = 80,
276	>	Year = 1993}
277	>
278	>	@article{Schmidt:2003kx,
279	>	Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a spherical solute in a dense fluid of spherical solvent particles. The size and mass of the solute particle are related in such a way that we can naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that as long as the solute radius is interpreted as an effective hydrodynamic radius, the Stokes-Einstein law with slip boundary conditions is satisfied as the Brownian limit is approached (specifically, when the solute is roughly 100 times more massive than the solvent particles). In contrast, the Stokes-Einstein law is not satisfied for a tagged particle of the neat solvent. We also find that in the Brownian limit the amplitude of the long-time tail of the solute's velocity autocorrelation function is in good agreement with theoretical hydrodynamic predictions. When the solvent density is substantially lower than the triple density, the Stokes-Einstein law is no longer satisfied, and the amplitude of the long-time tail is not in good agreement with theoretical predictions, signaling the breakdown of hydrodynamics. (C) 2003 American Institute of Physics.},
280	>	Author = {Schmidt, JR and Skinner, JL},
281	>	Date-Added = {2008-01-08 15:12:53 -0500},
282	>	Date-Modified = {2008-01-08 15:13:21 -0500},
283	>	Doi = {DOI 10.1063/1.1610442},
284	>	Journal = {Journal of Chemical Physics},
285	>	Pages = {8062-8068},
286	>	Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
287	>	Volume = 119,
288	>	Year = 2003,
289	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}
290	>
291	>	@article{Schmidt:2004fj,
292	>	Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a variety of solutes in a dense fluid of spherical solvent particles. We explore the effects of surface roughness of the solute on the resulting hydrodynamic boundary condition as we naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that when the solute and solvent interact through a purely repulsive isotropic potential, in the Brownian limit the Stokes-Einstein law is satisfied with slip boundary conditions. However, when surface roughness is introduced through an anisotropic solute-solvent interaction potential, we find that the Stokes-Einstein law is satisfied with stick boundary conditions. In addition, when the attractive strength of a short-range isotropic solute-solvent potential is increased, the solute becomes dressed with solvent particles, making it effectively rough, and so stick boundary conditions are again recovered.},
293	>	Author = {Schmidt, JR and Skinner, JL},
294	>	Date-Added = {2008-01-08 15:12:53 -0500},
295	>	Date-Modified = {2008-01-08 15:13:20 -0500},
296	>	Doi = {DOI 10.1021/jp037185r},
297	>	Journal = {Journal of Physical Chemistry B},
298	>	Pages = {6767-6771},
299	>	Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
300	>	Volume = 108,
301	>	Year = 2004,
302	>	Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}}
303	>
304	>	@article{Klein01,
305	>	Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
306	>	Date-Added = {2008-01-08 14:58:56 -0500},
307	>	Date-Modified = {2008-01-08 14:58:56 -0500},
308	>	Journal = {J. Phys. Chem. B},
309	>	Pages = {4464-4470},
310	>	Title = {A Coarse Grain Model for Phospholipid Simulations},
311	>	Volume = 105,
312	>	Year = 2001}
313	>
314	>	@article{Berardi98,
315	>	Author = {R. Berardi and C. Fava and C. Zannoni},
316	>	Date-Added = {2008-01-08 14:58:56 -0500},
317	>	Date-Modified = {2008-01-08 14:58:56 -0500},
318	>	Journal = cpl,
319	>	Pages = {8-14},
320	>	Title = {A Gay-Berne potential for dissimilar biaxial particles},
321	>	Volume = 297,
322	>	Year = 1998}
323	>
324	>	@article{Hura00,
325	>	Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
326	>	Date-Added = {2008-01-08 14:58:56 -0500},
327	>	Date-Modified = {2008-01-08 14:58:56 -0500},
328	>	Journal = {J. Chem. Phys.},
329	>	Pages = {9140-9148},
330	>	Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
331	>	Volume = 113,
332	>	Year = 2000}
333	>
334	>	@article{Peker93,
335	>	Author = {A. Peker and W.~L. Johnson},
336	>	Date-Added = {2008-01-08 14:58:56 -0500},
337	>	Date-Modified = {2008-01-08 14:58:56 -0500},
338	>	Journal = {Appl. Phys. Lett.},
339	>	Pages = {2342-2344},
340	>	Title = {A highly processable metallic-glass - $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
341	>	Volume = 63,
342	>	Year = 1993}
343	>
344	>	@article{Raphael2000,
345	>	Author = {Robert M. Raphael and Aleksander S. Popel and William E. Brownell},
346	>	Date-Added = {2008-01-08 14:58:56 -0500},
347	>	Date-Modified = {2008-01-08 14:58:56 -0500},
348	>	Journal = bj,
349	>	Pages = {2844-2862},
350	>	Title = {A Membrane Bending Model of Outer Hair Cell Electromotility},
351	>	Volume = 78,
352	>	Year = 2000}
353	>
354	>	@article{Heimburg00,
355	>	Author = {Thomas Heimburg},
356	>	Date-Added = {2008-01-08 14:58:56 -0500},
357	>	Date-Modified = {2008-01-08 14:58:56 -0500},
358	>	Journal = bj,
359	>	Pages = {1154-1165},
360	>	Title = {A Model for the Lipid Pretransition: Coupling of Ripple Formation with the Chain-Melting Transition},
361	>	Volume = 78,
362	>	Year = 2000}
363	>
364	>	@article{Tieleman98,
365	>	Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
366	>	Date-Added = {2008-01-08 14:58:56 -0500},
367	>	Date-Modified = {2008-01-08 14:58:56 -0500},
368	>	Journal = {Biophys. J.},
369	>	Pages = {2786-2801},
370	>	Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
371	>	Volume = 74,
372	>	Year = 1998}
373	>
374	>	@article{Soper86,
375	>	Author = {A.~K. Soper and M.~G. Phillips},
376	>	Date-Added = {2008-01-08 14:58:56 -0500},
377	>	Date-Modified = {2008-01-08 14:58:56 -0500},
378	>	Journal = cp,
379	>	Number = 1,
380	>	Pages = {47-60},
381	>	Title = {A new determination of the structure of water at 298K},
382	>	Volume = 107,
383	>	Year = 1986}
384	>
385	>	@article{Laflamme96,
386	>	Author = {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
387	>	Date-Added = {2008-01-08 14:58:56 -0500},
388	>	Date-Modified = {2008-01-08 14:58:56 -0500},
389	>	Journal = prl,
390	>	Pages = 77,
391	>	Title = {A perfect quantum error correcting code: 5 bit code correcting a general 1 qubit error to encode 1 qubit of information},
392	>	Volume = 98,
393	>	Year = 1996}
394	>
395	>	@article{Solomon86,
396	>	Author = {H. Solomon and H. Weiner},
397	>	Date-Added = {2008-01-08 14:58:56 -0500},
398	>	Date-Modified = {2008-01-08 14:58:56 -0500},
399	>	Journal = {Comm. Statistics A},
400	>	Pages = {2571-2607},
401	>	Title = {A REVIEW OF THE PACKING PROBLEM},
402	>	Volume = 15,
403	>	Year = 1986}
404	>
405	>	@article{Cornell95,
406	>	Author = {W.~D. Cornell and P. Cieplak and C.~I. Bayly and I.~R. Gould and K.~M. {Merz, Jr.} and D.~M. Ferguson and D.~C. Spellmeyer and T. Fox and J.~W. Caldwell and P.~A. Kollman},
407	>	Date-Added = {2008-01-08 14:58:56 -0500},
408	>	Date-Modified = {2008-01-08 14:58:56 -0500},
409	>	Journal = jacs,
410	>	Pages = {5179-5197},
411	>	Title = {A second generation force field for the simulation of proteins and nucleic acids},
412	>	Volume = 117,
413	>	Year = 1995}
414	>
415	>	@article{Finnis84,
416	>	Author = {M.~W Finnis and J.~E. Sinclair},
417	>	Date-Added = {2008-01-08 14:58:56 -0500},
418	>	Date-Modified = {2008-01-08 14:58:56 -0500},
419	>	Journal = {Phil. Mag. A},
420	>	Pages = {45-55},
421	>	Title = {A Simple Empirical N-Body Potential for Transition-Metals},
422	>	Volume = 50,
423	>	Year = 1984}
424	>
425	>	@article{Bratko85,
426	>	Author = {D. Bratko and L. Blum and A. Luzar},
427	>	Date-Added = {2008-01-08 14:58:56 -0500},
428	>	Date-Modified = {2008-01-08 14:58:56 -0500},
429	>	Journal = jcp,
430	>	Number = 12,
431	>	Pages = {6367-6370},
432	>	Title = {A simple model for the intermolecular potential of water},
433	>	Volume = 83,
434	>	Year = 1985}
435	>
436	>	@article{Essmann95,
437	>	Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
438	>	Date-Added = {2008-01-08 14:58:56 -0500},
439	>	Date-Modified = {2008-01-08 14:58:56 -0500},
440	>	Journal = {J. Chem. Phys.},
441	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf},
442	>	Number = 19,
443	>	Pages = {8577-8593},
444	>	Title = {A smooth particle mesh Ewald method},
445	>	Volume = 103,
446	>	Year = 1995}
447	>
448	>	@article{Ricci94,
449	>	Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
450	>	Date-Added = {2008-01-08 14:58:56 -0500},
451	>	Date-Modified = {2008-01-08 14:58:56 -0500},
452	>	Journal = jcp,
453	>	Pages = 9164,
454	>	Title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
455	>	Volume = 101,
456	>	Year = 1994}
457	>
458	>	@article{Tan03,
459	>	Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks and T. Ichiye},
460	>	Date-Added = {2008-01-08 14:58:56 -0500},
461	>	Date-Modified = {2008-01-08 14:58:56 -0500},
462	>	Journal = cpl,
463	>	Pages = {646-652},
464	>	Title = {A temperature of maximum density in soft sticky dipole water},
465	>	Volume = 376,
466	>	Year = 2003}
467	>
468	>	@article{Stillinger95,
469	>	Author = {F.~H. Stillinger},
470	>	Date-Added = {2008-01-08 14:58:56 -0500},
471	>	Date-Modified = {2008-01-08 14:58:56 -0500},
472	>	Journal = {Science},
473	>	Pages = {1935-1939},
474	>	Title = {A Topographic View of Supercooled Liquids and Glass Formation},
475	>	Volume = 267,
476	>	Year = 1995}
477	>
478	>	@article{Shlesinger99,
479	>	Author = {M.~F. Shlesinger and J. Klafter and G. Zumofen},
480	>	Date-Added = {2008-01-08 14:58:56 -0500},
481	>	Date-Modified = {2008-01-08 14:58:56 -0500},
482	>	Journal = {Am. J. Phys.},
483	>	Pages = {1253-1259},
484	>	Title = {Above, below, and beyond Brownian motion},
485	>	Volume = 67,
486	>	Year = 1999}
487	>
488	>	@article{Karasawa89,
489	>	Author = {N. Karasawa and W.~A. {Goddard III}},
490	>	Date-Added = {2008-01-08 14:58:56 -0500},
491	>	Date-Modified = {2008-01-08 14:58:57 -0500},
492	>	Journal = {J. Phys. Chem.},
493	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf},
494	>	Pages = {7320-7327},
495	>	Title = {Acceleration of Convergence for Lattice Sums},
496	>	Volume = 93,
497	>	Year = 1989}
498	>
499	>	@article{Petersen95,
500	>	Author = {H.~G. Petersen},
501	>	Date-Added = {2008-01-08 14:58:56 -0500},
502	>	Date-Modified = {2008-01-08 14:58:57 -0500},
503	>	Journal = {J. Chem. Phys.},
504	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
505	>	Month = {September},
506	>	Number = 9,
507	>	Pages = {3668-3679},
508	>	Title = {Accuracy and efficiency of the particle mesh Ewald method},
509	>	Volume = 103,
510	>	Year = 1995}
511	>
512	>	@article{Duncan06,
513	>	Author = {Peter D. Duncan and Philip J. Camp},
514	>	Date-Added = {2008-01-08 14:58:56 -0500},
515	>	Date-Modified = {2008-01-08 14:58:57 -0500},
516	>	Journal = prl,
517	>	Pages = 107202,
518	>	Title = {Aggregation Kinetics and the Nature of Phase Separation in Two-Dimensional Dipolar Fluids},
519	>	Volume = 97,
520	>	Year = 2006}
521	>
522	>	@article{Shor94,
523	>	Author = {P.W. Shor},
524	>	Date-Added = {2008-01-08 14:58:56 -0500},
525	>	Date-Modified = {2008-01-08 14:58:57 -0500},
526	>	Journal = {Proceedings of the 35th Annual Symposium on Foundations of Computer Science},
527	>	Pages = {124-134},
528	>	Title = {Algorithms for quantum computation: discrete logarithms and factoring},
529	>	Year = 1994}
530	>
531	>	@article{Tsonchev04II,
532	>	Author = {Stefan Tsonchev and Alessandro Troisi and George C. Schatz and Mark A. Ratner},
533	>	Date-Added = {2008-01-08 14:58:56 -0500},
534	>	Date-Modified = {2008-01-08 14:58:57 -0500},
535	>	Journal = jpcB,
536	>	Pages = {15278-15284},
537	>	Title = {All-Atom Numerical Studies of Self-Assembly of Zwitterionic Peptide Amphiphiles},
538	>	Volume = 108,
539	>	Year = 2004}
540	>
541	>	@article{Johnson89,
542	>	Author = {R.~A. Johnson},
543	>	Date-Added = {2008-01-08 14:58:56 -0500},
544	>	Date-Modified = {2008-01-08 14:58:57 -0500},
545	>	Journal = prb,
546	>	Number = 17,
547	>	Pages = 12554,
548	>	Title = {Alloy models with the embedded-atom method},
549	>	Volume = 39,
550	>	Year = 1989}
551	>
552	>	@article{Pandit03,
553	>	Author = {Sagar A. Pandit and David Bostick and Max L. Berkowitz},
554	>	Date-Added = {2008-01-08 14:58:56 -0500},
555	>	Date-Modified = {2008-01-08 14:58:57 -0500},
556	>	Journal = jcp,
557	>	Number = 4,
558	>	Pages = {2199-2205},
559	>	Title = {An algorithm to describe molecular scale rugged surfaces and its application to the study of a water/lipid bilayer interface},
560	>	Volume = 119,
561	>	Year = 2003}
562	>
563	>	@article{Chang90,
564	>	Author = {Y.-T. Chang and W.~H. Miller},
565	>	Date-Added = {2008-01-08 14:58:56 -0500},
566	>	Date-Modified = {2008-01-08 14:58:57 -0500},
567	>	Journal = jpc,
568	>	Pages = {5884-5888},
569	>	Title = {An Empirical Valence Bond Model for Constructing Global Potential Energy Surfaces for Chemical Reactions of Polyatomic Molecular Systems},
570	>	Volume = 94,
571	>	Year = 1990}
572	>
573	>	@incollection{Zannoni94,
574	>	Author = {C. Zannoni},
575	>	Booktitle = {The Molecular Dynamics of Liquid Crstals},
576	>	Chapter = 6,
577	>	Date-Added = {2008-01-08 14:58:56 -0500},
578	>	Date-Modified = {2008-01-08 14:58:57 -0500},
579	>	Editor = {G.~R. Luckhurst and C.~A. Veracini},
580	>	Pages = {139-169},
581	>	Publisher = {Kluwer Academic Publishers},
582	>	Title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
583	>	Year = 1994}
584	>
585	>	@article{Sparrman2003,
586	>	Author = {Tobias Sparrman and Per-Olof Westlund},
587	>	Date-Added = {2008-01-08 14:58:56 -0500},
588	>	Date-Modified = {2008-01-08 14:58:57 -0500},
589	>	Journal = pccp,
590	>	Pages = {2114-2121},
591	>	Title = {An NMR line shape and relaxation analysis of heavy water powder spectra of the $L_\alpha$, $L_{\beta'}$ and $P_{\beta'}$ phases in the DPPC/water system},
592	>	Volume = 5,
593	>	Year = 2003}
594	>
595	>	@article{Cascales98,
596	>	Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and {Garc\'{i}a de la Torre}, Jose},
597	>	Date-Added = {2008-01-08 14:58:56 -0500},
598	>	Date-Modified = {2008-01-08 14:58:57 -0500},
599	>	Journal = {J. Phys. Chem. B},
600	>	Pages = {625-631},
601	>	Title = {Anaesthetic mechanism on a model biological membrane: A molecular dynamics simulation study},
602	>	Volume = 102,
603	>	Year = 1998}
604	>
605	>	@inbook{Fowles99,
606	>	Author = {G.~R. Fowles and G.~L. Cassiday},
607	>	Chapter = 10,
608	>	Date-Added = {2008-01-08 14:58:56 -0500},
609	>	Date-Modified = {2008-01-08 14:58:57 -0500},
610	>	Edition = {6th},
611	>	Publisher = {Saunders College Publishing},
612	>	Title = {Analytical Mechanics},
613	>	Year = 1999}
614	>
615	>	@article{Mason01,
616	>	Author = {P. C. Mason and J. F. Nagle and R. M. Epand and J. Katsaras},
617	>	Date-Added = {2008-01-08 14:58:56 -0500},
618	>	Date-Modified = {2008-01-08 14:58:57 -0500},
619	>	Journal = pre,
620	>	Number = 030902,
621	>	Pages = {1-4},
622	>	Title = {Anomalous Swelling in Phospholipid bilayers is not coupled to the formation of a ripple phase},
623	>	Volume = 63,
624	>	Year = 2001}
625	>
626	>	@article{Forester97,
627	>	Author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
628	>	Date-Added = {2008-01-08 14:58:56 -0500},
629	>	Date-Modified = {2008-01-08 14:58:57 -0500},
630	>	Journal = {J. Chem. Soc. - Faraday Transactions},
631	>	Pages = {613-619},
632	>	Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
633	>	Volume = 93,
634	>	Year = 1997}
635	>
636	>	@article{Lu97,
637	>	Author = {J. Lu and J.~A. Szpunar},
638	>	Date-Added = {2008-01-08 14:58:56 -0500},
639	>	Date-Modified = {2008-01-08 14:58:57 -0500},
640	>	Journal = {Phil. Mag. A},
641	>	Pages = {1057-1066},
642	>	Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
643	>	Volume = 75,
644	>	Year = 1997}
645	>
646	>	@inproceedings{Gotze89,
647	>	Address = {Amsterdam},
648	>	Author = {W. G{\"{o}}tze},
649	>	Booktitle = {Liquids, Freezing and Glass Transitions},
650	>	Date-Added = {2008-01-08 14:58:56 -0500},
651	>	Date-Modified = {2008-01-08 14:58:57 -0500},
652	>	Editor = {J.~P. Hansen and D. Levesque and J. Zinn-Justin},
653	>	Pages = {287-503},
654	>	Publisher = {North-Holland},
655	>	Title = {Aspects of Structural Glass Transitions},
656	>	Volume = {I},
657	>	Year = 1989}
658	>
659	>	@article{Lewis91,
660	>	Author = {L.~J. Lewis},
661	>	Date-Added = {2008-01-08 14:58:56 -0500},
662	>	Date-Modified = {2008-01-08 14:58:57 -0500},
663	>	Journal = prb,
664	>	Pages = {4245-4254},
665	>	Title = {Atomic dynamics through the glass transition},
666	>	Volume = 44,
667	>	Year = 1991}
668	>
669	>	@article{Tartaglino02,
670	>	Author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
671	>	Date-Added = {2008-01-08 14:58:56 -0500},
672	>	Date-Modified = {2008-01-08 14:58:57 -0500},
673	>	Journal = prb,
674	>	Pages = 241406,
675	>	Title = {Bending strain-driven modification of surface resconstructions: Au(111)},
676	>	Volume = 65,
677	>	Year = 2002}
678	>
679	>	@article{Klafter96,
680	>	Author = {J. Klafter and M. Shlesinger and G. Zumofen},
681	>	Date-Added = {2008-01-08 14:58:56 -0500},
682	>	Date-Modified = {2008-01-08 14:58:57 -0500},
683	>	Journal = {Physics Today},
684	>	Pages = {33-39},
685	>	Title = {Beyond Brownian Motion},
686	>	Volume = 49,
687	>	Year = 1996}
688	>
689	>	@article{Roberts95,
690	>	Author = {J.~E. Roberts and J. Schnitker},
691	>	Date-Added = {2008-01-08 14:58:56 -0500},
692	>	Date-Modified = {2008-01-08 14:58:57 -0500},
693	>	Journal = {J. Phys. Chem.},
694	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
695	>	Pages = {1322-1331},
696	>	Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
697	>	Volume = 99,
698	>	Year = 1995}
699	>
700	>	@article{Ayton02,
701	>	Author = {G. Ayton and G.~A. Voth},
702	>	Date-Added = {2008-01-08 14:58:56 -0500},
703	>	Date-Modified = {2008-01-08 14:58:57 -0500},
704	>	Journal = {Biophys. J.},
705	>	Pages = {3357-3370},
706	>	Title = {Bridging Microscopic and Mesoscopic Simulations of Lipid Bilayers},
707	>	Volume = 83,
708	>	Year = 2002}
709	>
710	>	@article{ChoiYim97,
711	>	Author = {H. Choi-Yim and W.~L. Johnson},
712	>	Date-Added = {2008-01-08 14:58:56 -0500},
713	>	Date-Modified = {2008-01-08 14:58:57 -0500},
714	>	Journal = {Appl. Phys. Lett.},
715	>	Pages = {3808-3810},
716	>	Title = {Bulk metallic glass matrix composites},
717	>	Volume = 71,
718	>	Year = 1997}
719	>
720	>	@article{Rabani97,
721	>	Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
722	>	Date-Added = {2008-01-08 14:58:56 -0500},
723	>	Date-Modified = {2008-01-08 14:58:57 -0500},
724	>	Journal = {J. Chem. Phys.},
725	>	Pages = {6867-6876},
726	>	Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: Cage correlations},
727	>	Volume = 107,
728	>	Year = 1997}
729	>
730	>	@article{Gezelter97,
731	>	Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
732	>	Date-Added = {2008-01-08 14:58:56 -0500},
733	>	Date-Modified = {2008-01-08 14:58:57 -0500},
734	>	Journal = jcp,
735	>	Pages = 4618,
736	>	Title = {Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?},
737	>	Volume = 107,
738	>	Year = 1997}
739	>
740	>	@article{Hoover85,
741	>	Author = {W.~G. Hoover},
742	>	Date-Added = {2008-01-08 14:58:56 -0500},
743	>	Date-Modified = {2008-01-08 14:58:57 -0500},
744	>	Journal = pra,
745	>	Pages = 1695,
746	>	Title = {Canonical dynamics: Equilibrium phase-space distributions},
747	>	Volume = 31,
748	>	Year = 1985}
749	>
750	>	@article{Wigner55,
751	>	Author = {E.~P. Wigner},
752	>	Date-Added = {2008-01-08 14:58:56 -0500},
753	>	Date-Modified = {2008-01-08 14:58:57 -0500},
754	>	Journal = {Annals of Mathematics},
755	>	Pages = {548-564},
756	>	Title = {Characteristic Vectors of Bordered Matrices with Infinite Dimensions},
757	>	Volume = 62,
758	>	Year = 1955}
759	>
760	>	@article{Katsaras00,
761	>	Author = {J. Katsaras and S. Tristram-Nagle and Y. Liu and R. L. Headrick and E.Fontes and P. C. Mason and J. F. Nagle},
762	>	Date-Added = {2008-01-08 14:58:56 -0500},
763	>	Date-Modified = {2008-01-08 14:58:57 -0500},
764	>	Journal = pre,
765	>	Number = 5,
766	>	Pages = {5668-5677},
767	>	Title = {Clarification of the ripple phase of lecithin bilayer using fully hydrated, aligned samples},
768	>	Volume = 61,
769	>	Year = 2000}
770	>
771	>	@article{NorbertKucerka06012006,
772	>	Abstract = {X-ray data are presented for the benchmark dipalmitoylphosphatidylcholine lipid bilayer in the most biologically relevant state in which the bilayers are fully hydrated and in the fluid (liquid-crystalline) phase. Form factors F(qz) are obtained from a combination of two sample preparations, oriented stacks of bilayers for qz extending to 0.85 A-1 and unilamellar vesicles for smaller qz. Modeling obtains the electron density profile and values for the area per molecule, for the locations of the component groups, and for the different types of thicknesses of the bilayer, such as the hydrocarbon thickness and the steric thickness.
773	>	},
774	>	Author = {Kucerka, Norbert and Tristram-Nagle, Stephanie and Nagle, John F.},
775	>	Date-Added = {2008-01-08 14:58:56 -0500},
776	>	Date-Modified = {2008-01-08 14:58:57 -0500},
777	>	Doi = {10.1529/biophysj.106.086017},
778	>	Eprint = {http://www.biophysj.org/cgi/reprint/90/11/L83.pdf},
779	>	Journal = {Biophys. J.},
780	>	Number = 11,
781	>	Pages = {L83-85},
782	>	Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}},
783	>	Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
784	>	Volume = 90,
785	>	Year = 2006,
786	>	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
787	>	Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017}}
788	>
789	>	@article{deJoannis06,
790	>	Author = {J. de~Joannis and F.~Y. Jiang and J.~T. Kindt},
791	>	Date-Added = {2008-01-08 14:58:56 -0500},
792	>	Date-Modified = {2008-01-08 14:58:57 -0500},
793	>	Journal = {Langmuir},
794	>	Pages = {998-1005},
795	>	Title = {Coarse-Grained Model Simulations of Mixed-Lipid Systems: Composition and Line Tension of a Stabilized Bilayer Edge},
796	>	Volume = 22,
797	>	Year = 2006}
798	>
799	>	@article{Keyes98,
800	>	Author = {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher},
801	>	Date-Added = {2008-01-08 14:58:56 -0500},
802	>	Date-Modified = {2008-01-08 14:58:57 -0500},
803	>	Journal = jcp,
804	>	Pages = {4693-4694},
805	>	Title = {Comment on a critique of the instantaneous normal mode (INM) approach to diffusion (J. Chem. Phys. {\bf 107}, 4618 (1997))},
806	>	Volume = 109,
807	>	Year = 1998}
808	>
809	>	@article{Jorgensen83,
810	>	Author = {W.~L. Jorgensen and J. Chandrasekhar and J.~D. Madura and R.~W. Impey and M.~L. Klein},
811	>	Date-Added = {2008-01-08 14:58:56 -0500},
812	>	Date-Modified = {2008-01-08 14:58:57 -0500},
813	>	Journal = jcp,
814	>	Pages = {926-935},
815	>	Title = {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER},
816	>	Volume = 79,
817	>	Year = 1983}
818	>
819	>	@book{Warshel91,
820	>	Address = {New York},
821	>	Author = {Arieh Warshel},
822	>	Date-Added = {2008-01-08 14:58:56 -0500},
823	>	Date-Modified = {2008-01-08 14:58:57 -0500},
824	>	Publisher = {Wiley},
825	>	Title = {Computer modeling of chemical reactions in enzymes and solutions},
826	>	Year = 1991}
827	>
828	>	@article{Kushick76,
829	>	Author = {J. Kushick and B.~J. Berne},
830	>	Date-Added = {2008-01-08 14:58:56 -0500},
831	>	Date-Modified = {2008-01-08 14:58:57 -0500},
832	>	Journal = jcp,
833	>	Pages = {1362-1367},
834	>	Title = {Computer Simulation of anisotropic molecular fluids},
835	>	Volume = 64,
836	>	Year = 1976}
837	>
838	>	@article{Luckhurst90,
839	>	Author = {G.~R. Luckhurst and R.~A. Stephens and R.~W. Phippen},
840	>	Date-Added = {2008-01-08 14:58:56 -0500},
841	>	Date-Modified = {2008-01-08 14:58:57 -0500},
842	>	Journal = {Liquid Crystals},
843	>	Pages = {451-464},
844	>	Title = {Computer simulation studies of anisotropic systems {XIX}. Mesophases formed by the Gay-Berne model mesogen},
845	>	Volume = 8,
846	>	Year = 1990}
847	>
848	>	@article{Kubica02,
849	>	Author = {Krystian Kubica},
850	>	Date-Added = {2008-01-08 14:58:56 -0500},
851	>	Date-Modified = {2008-01-08 14:58:57 -0500},
852	>	Journal = {Computers and Chemistry},
853	>	Pages = {351-356},
854	>	Title = {Computer Simulation studies on significance of Lipid Polar Head Oreintation},
855	>	Volume = 26,
856	>	Year = 2002}
857	>
858	>	@article{Seifert97,
859	>	Author = {Udo Seifert},
860	>	Date-Added = {2008-01-08 14:58:56 -0500},
861	>	Date-Modified = {2008-01-08 14:58:57 -0500},
862	>	Journal = {Adv. Phys.},
863	>	Number = 1,
864	>	Pages = {13-137},
865	>	Title = {Configurations of fluid membranes and vesicles},
866	>	Volume = 46,
867	>	Year = 1997}
868	>
869	>	@article{Angelani98,
870	>	Author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
871	>	Date-Added = {2008-01-08 14:58:56 -0500},
872	>	Date-Modified = {2008-01-08 14:58:57 -0500},
873	>	Journal = prl,
874	>	Number = 21,
875	>	Pages = {4648-4651},
876	>	Title = {Connected Network of Minima as a Model Glass: Long Time Dynamics},
877	>	Volume = 81,
878	>	Year = 1998}
879	>
880	>	@article{Duwez60,
881	>	Author = {P. Duwez and R.~H. Willens and W. {Klement~Jr.}},
882	>	Date-Added = {2008-01-08 14:58:56 -0500},
883	>	Date-Modified = {2008-01-08 14:58:57 -0500},
884	>	Journal = {J. Appl. Phys.},
885	>	Pages = {1136-1137},
886	>	Title = {Continuous Series of Metastable Solid Solutions in Silver-Copper Alloys},
887	>	Volume = 31,
888	>	Year = 1960}
889	>
890	>	@article{Zhu2005,
891	>	Author = {Xiaoliang Zhu and F. Tavazza and D.~P. Landau},
892	>	Date-Added = {2008-01-08 14:58:56 -0500},
893	>	Date-Modified = {2008-01-08 14:58:57 -0500},
894	>	Journal = prb,
895	>	Pages = 104102,
896	>	Title = {Critical behavior of an elastic Ising antiferromagnet at constant pressure},
897	>	Volume = 72,
898	>	Year = 2005}
899	>
900	>	@article{Zhu2006,
901	>	Author = {Xiaoliang Zhu and D.~P. Landau},
902	>	Date-Added = {2008-01-08 14:58:56 -0500},
903	>	Date-Modified = {2008-01-08 14:58:58 -0500},
904	>	Journal = prb,
905	>	Pages = 064115,
906	>	Title = {Critical behavior of an elastic Ising model on a stacked triangular net at constant volume},
907	>	Volume = 73,
908	>	Year = 2006}
909	>
910	>	@article{Kolafa92,
911	>	Author = {J. Kolafa and J.~W. Perram},
912	>	Date-Added = {2008-01-08 14:58:56 -0500},
913	>	Date-Modified = {2008-01-08 14:58:58 -0500},
914	>	Journal = {Mol. Simul.},
915	>	Pages = {351-368},
916	>	Title = {Cutoff Errors in the Ewald. Summation Formulae for Point Charge Systems},
917	>	Volume = 9,
918	>	Year = 1992}
919	>
920	>	@article{Tlusty00,
921	>	Author = {T. Tlusty and S.~A. Safran},
922	>	Date-Added = {2008-01-08 14:58:56 -0500},
923	>	Date-Modified = {2008-01-08 14:58:58 -0500},
924	>	Journal = {Science},
925	>	Pages = {1328-1331},
926	>	Title = {Defect-Induced Phase Separation in Dipolar Fluids},
927	>	Volume = 290,
928	>	Year = 2000}
929	>
930	>	@article{Seung1988,
931	>	Author = {Seung, H. S. and Nelson, David R.},
932	>	Date-Added = {2008-01-08 14:58:56 -0500},
933	>	Date-Modified = {2008-01-08 14:58:58 -0500},
934	>	Doi = {10.1103/PhysRevA.38.1005},
935	>	Journal = {Phys. Rev. A},
936	>	Month = {Jul},
937	>	Number = 2,
938	>	Numpages = 13,
939	>	Pages = {1005--1018},
940	>	Publisher = {American Physical Society},
941	>	Title = {Defects in flexible membranes with crystalline order},
942	>	Volume = 38,
943	>	Year = 1988,
944	>	Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005}}
945	>
946	>	@article{Monroe95,
947	>	Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
948	>	Date-Added = {2008-01-08 14:58:56 -0500},
949	>	Date-Modified = {2008-01-08 14:58:58 -0500},
950	>	Journal = prl,
951	>	Pages = 4714,
952	>	Title = {Demonstration of a fundamental quantum logic gate},
953	>	Volume = 75,
954	>	Year = 1995}
955	>
956	>	@article{Parkhurst75a,
957	>	Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
958	>	Date-Added = {2008-01-08 14:58:56 -0500},
959	>	Date-Modified = {2008-01-08 14:58:58 -0500},
960	>	Journal = jcp,
961	>	Number = 6,
962	>	Pages = {2698-2704},
963	>	Title = {Dense liquids. I. The effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
964	>	Volume = 63,
965	>	Year = 1975}
966	>
967	>	@article{Parkhurst75b,
968	>	Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
969	>	Date-Added = {2008-01-08 14:58:56 -0500},
970	>	Date-Modified = {2008-01-08 14:58:58 -0500},
971	>	Journal = jcp,
972	>	Number = 6,
973	>	Pages = {2705-2709},
974	>	Title = {Dense liquids. II. The effect of density and temperature on viscosity of tetramethylsilane and benzene},
975	>	Volume = 63,
976	>	Year = 1975}
977	>
978	>	@article{Rodgers88,
979	>	Author = {G.~J. Rodgers and A. Bray},
980	>	Date-Added = {2008-01-08 14:58:56 -0500},
981	>	Date-Modified = {2008-01-08 14:58:58 -0500},
982	>	Journal = {Phys. Rev. B},
983	>	Pages = 355703562,
984	>	Title = {Density of States of a Sparse Random Matrix},
985	>	Volume = 37,
986	>	Year = 1988}
987	>
988	>	@article{Rodgers90,
989	>	Author = {G.~J. Rodgers and C. {De Dominicis}},
990	>	Date-Added = {2008-01-08 14:58:56 -0500},
991	>	Date-Modified = {2008-01-08 14:58:58 -0500},
992	>	Journal = {J. Phys. A: Math. Gen.},
993	>	Pages = {1567-1573},
994	>	Title = {Density of states of sparse random matrices},
995	>	Volume = 23,
996	>	Year = 1990}
997	>
998	>	@article{Ewald21,
999	>	Author = {P.~P. Ewald},
1000	>	Date-Added = {2008-01-08 14:58:56 -0500},
1001	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1002	>	Journal = {Ann. Physik},
1003	>	Pages = {253-287},
1004	>	Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
1005	>	Volume = 64,
1006	>	Year = 1921}
1007	>
1008	>	@article{Zwanzig88,
1009	>	Author = {R. Zwanzig},
1010	>	Date-Added = {2008-01-08 14:58:56 -0500},
1011	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1012	>	Journal = {Proc. Natl. Acad. Sci. USA},
1013	>	Pages = 2029,
1014	>	Title = {Diffusion in rough potential},
1015	>	Volume = 85,
1016	>	Year = 1988}
1017	>
1018	>	@article{Madan90,
1019	>	Author = {B. Madan and T. Keyes and G. Seeley},
1020	>	Date-Added = {2008-01-08 14:58:56 -0500},
1021	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1022	>	Journal = jcp,
1023	>	Pages = {7565-7569},
1024	>	Title = {Diffusion in supercooled liquids via normal mode analysis},
1025	>	Volume = 92,
1026	>	Year = 1990}
1027	>
1028	>	@article{Gaukel98,
1029	>	Author = {C. Gaukel and H.~R. Schober},
1030	>	Date-Added = {2008-01-08 14:58:56 -0500},
1031	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1032	>	Journal = {Solid State Comm.},
1033	>	Pages = {1-5},
1034	>	Title = {Diffusion Mechanisms in under-cooled Binary Metal Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$},
1035	>	Volume = 107,
1036	>	Year = 1998}
1037	>
1038	>	@article{Semmler98,
1039	>	Author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
1040	>	Date-Added = {2008-01-08 14:58:56 -0500},
1041	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1042	>	Journal = {Langmuir},
1043	>	Pages = {5127-5132},
1044	>	Title = {Diffusional Deposition of Charged Latex Particles on Water-Solid Interfaces at Low Ionic Strength},
1045	>	Volume = 14,
1046	>	Year = 1998}
1047	>
1048	>	@article{Rabani99,
1049	>	Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
1050	>	Date-Added = {2008-01-08 14:58:56 -0500},
1051	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1052	>	Journal = prl,
1053	>	Pages = 3649,
1054	>	Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
1055	>	Volume = 82,
1056	>	Year = 1999}
1057	>
1058	>	@article{Ngai81,
1059	>	Author = {K.~L. Ngai and F.-S. Liu},
1060	>	Date-Added = {2008-01-08 14:58:56 -0500},
1061	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1062	>	Journal = prb,
1063	>	Pages = {1049-1065},
1064	>	Title = {Dispersive diffusion transport and noise, time-dependent diffusion coefficient, generalized Einstein-Nernst relation, and dispersive diffusion-controlled unimolecular and bimolecular reactions},
1065	>	Volume = 24,
1066	>	Year = 1981}
1067	>
1068	>	@book{Berne90,
1069	>	Address = {Malabar, Florida},
1070	>	Author = {B.~J. Berne and R. Pecora},
1071	>	Date-Added = {2008-01-08 14:58:56 -0500},
1072	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1073	>	Publisher = {Robert E. Krieger Publishing Company, Inc.},
1074	>	Title = {Dynamic Light Scattering},
1075	>	Year = 1990}
1076	>
1077	>	@article{Essmann99,
1078	>	Author = {U. Essmann and M.~L. Berkowitz},
1079	>	Date-Added = {2008-01-08 14:58:56 -0500},
1080	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1081	>	Journal = {Biophys. J.},
1082	>	Pages = {2081-2089},
1083	>	Title = {Dynamical properties of phospholipid bilayers from computer simulation},
1084	>	Volume = 76,
1085	>	Year = 1999}
1086	>
1087	>	@article{Stillinger83,
1088	>	Author = {F.~H. Stillinger and T.~A. Weber},
1089	>	Date-Added = {2008-01-08 14:58:56 -0500},
1090	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1091	>	Journal = pra,
1092	>	Number = 4,
1093	>	Pages = {2408-2416},
1094	>	Title = {Dynamics of structural transitions in liquids},
1095	>	Volume = 28,
1096	>	Year = 1983}
1097	>
1098	>	@article{Hunenberger99b,
1099	>	Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
1100	>	Date-Added = {2008-01-08 14:58:56 -0500},
1101	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1102	>	Journal = {Biophys. Chem.},
1103	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
1104	>	Pages = {69-88},
1105	>	Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
1106	>	Volume = 78,
1107	>	Year = 1999}
1108	>
1109	>	@article{Spohr97,
1110	>	Author = {E. Spohr},
1111	>	Date-Added = {2008-01-08 14:58:56 -0500},
1112	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1113	>	Journal = {J. Chem. Phys.},
1114	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
1115	>	Number = 16,
1116	>	Pages = {6342-6348},
1117	>	Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
1118	>	Volume = 107,
1119	>	Year = 1997}
1120	>
1121	>	@article{Marrink01b,
1122	>	Author = {S.~J. Marrink and A.~E. Mark},
1123	>	Date-Added = {2008-01-08 14:58:56 -0500},
1124	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1125	>	Journal = {Journal of Physical Chemistry B},
1126	>	Pages = {6122-6127},
1127	>	Title = {Effect of undulations on surface tension in simulated bilayers},
1128	>	Volume = 105,
1129	>	Year = 2001}
1130	>
1131	>	@article{Tu98,
1132	>	Author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf},
1133	>	Date-Added = {2008-01-08 14:58:56 -0500},
1134	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1135	>	Journal = {Biophys. J.},
1136	>	Pages = {2123-2134},
1137	>	Title = {Effects of anesthetics on the structure of a phospholipid bilayer: Molecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine},
1138	>	Volume = 75,
1139	>	Year = 1998}
1140	>
1141	>	@article{Billing75,
1142	>	Author = {G.~D. Billing},
1143	>	Date-Added = {2008-01-08 14:58:56 -0500},
1144	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1145	>	Journal = cpl,
1146	>	Pages = 391,
1147	>	Title = {ehrenfest},
1148	>	Volume = 30,
1149	>	Year = 1975}
1150	>
1151	>	@article{Khorunzhy97,
1152	>	Author = {A. Khorunzhy and G.~J. Rodgers},
1153	>	Date-Added = {2008-01-08 14:58:56 -0500},
1154	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1155	>	Journal = {J. Math. Phys.},
1156	>	Pages = {3300-3320},
1157	>	Title = {Eigenvalue distribution of large dilute random matrices},
1158	>	Volume = 38,
1159	>	Year = 1997}
1160	>
1161	>	@article{Onsager36,
1162	>	Author = {L. Onsager},
1163	>	Date-Added = {2008-01-08 14:58:56 -0500},
1164	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1165	>	Journal = jacs,
1166	>	Pages = {1486-1493},
1167	>	Title = {Electric Moments of Molecules in Liquids},
1168	>	Volume = 58,
1169	>	Year = 1936}
1170	>
1171	>	@article{Petrov2006,
1172	>	Author = {A.~G. Petrov},
1173	>	Date-Added = {2008-01-08 14:58:56 -0500},
1174	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1175	>	Journal = {Anal. Chim. Acta},
1176	>	Pages = {70-83},
1177	>	Title = {Electricity and mechanics of biomembrane systems: Flexoelectricity in living membranes},
1178	>	Year = 2006}
1179	>
1180	>	@article{Reinot97,
1181	>	Author = {T. Reinot and J.~M. Hayes and G.~J. Small},
1182	>	Date-Added = {2008-01-08 14:58:56 -0500},
1183	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1184	>	Journal = jcp,
1185	>	Pages = {457-466},
1186	>	Title = {Electronic dephasing and electron-phonon coupling of aluminum phthalocyanine tetrasulphonate in hyperquenched and annealed glassy films of ethanol and methanol over a broad temperature range},
1187	>	Volume = 106,
1188	>	Year = 1997}
1189	>
1190	>	@article{Banhart92,
1191	>	Author = {J. Banhart and H. Ebert and R. Kuentzler and J. Voitl\"{a}nder},
1192	>	Date-Added = {2008-01-08 14:58:56 -0500},
1193	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1194	>	Journal = prb,
1195	>	Pages = {9968-9975},
1196	>	Title = {Electronic properties of single-phased metastable Ag-Cu alloys},
1197	>	Volume = 46,
1198	>	Year = 1992}
1199	>
1200	>	@article{Saiz02,
1201	>	Author = {L. Saiz and M. Klein},
1202	>	Date-Added = {2008-01-08 14:58:56 -0500},
1203	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1204	>	Journal = jcp,
1205	>	Number = 7,
1206	>	Pages = {3052-3057},
1207	>	Title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
1208	>	Volume = 116,
1209	>	Year = 2002}
1210	>
1211	>	@article{deLeeuw79,
1212	>	Author = {S.~W. {de Leeuw} and J.~W. Perram},
1213	>	Date-Added = {2008-01-08 14:58:56 -0500},
1214	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1215	>	Journal = {Mol. Phys.},
1216	>	Pages = {1313-1327},
1217	>	Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices},
1218	>	Volume = 37,
1219	>	Year = 1979}
1220	>
1221	>	@article{Heyes81,
1222	>	Author = {D.~M. Heyes},
1223	>	Date-Added = {2008-01-08 14:58:56 -0500},
1224	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1225	>	Journal = {J. Chem. Phys.},
1226	>	Keywords = {Empty Keywords},
1227	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
1228	>	Number = 3,
1229	>	Pages = {1924-1929},
1230	>	Title = {Electrostatic potentials and fields in infinite point charge lattices},
1231	>	Volume = 74,
1232	>	Year = 1981}
1233	>
1234	>	@article{Tsonchev04,
1235	>	Author = {Stefan Tsonchev and George C. Schatz and Mark A. Ratner},
1236	>	Date-Added = {2008-01-08 14:58:56 -0500},
1237	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1238	>	Journal = jpcB,
1239	>	Pages = {8817-8822},
1240	>	Title = {Electrostatically-Directed Self-Assembly of Cylindrical Peptide Amphiphile Nanostructures},
1241	>	Volume = 108,
1242	>	Year = 2004}
1243	>
1244	>	@article{Tobias01,
1245	>	Author = {D.~J. Tobias},
1246	>	Date-Added = {2008-01-08 14:58:56 -0500},
1247	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1248	>	Journal = {Curr. Opin. Struct. Biol.},
1249	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
1250	>	Pages = {253-261},
1251	>	Title = {Electrostatics calculations: recent methodological advances and applications to membranes},
1252	>	Volume = 11,
1253	>	Year = 2001}
1254	>
1255	>	@article{Arnold02,
1256	>	Author = {A. Arnold and J. {de Joannis} and C. Holm},
1257	>	Date-Added = {2008-01-08 14:58:56 -0500},
1258	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1259	>	Doi = {10.1063/1.149195},
1260	>	Journal = {J. Chem. Phys.},
1261	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Arnold_SlabElectrostatics_02.pdf},
1262	>	Number = 6,
1263	>	Pages = {2496-2502},
1264	>	Title = {Electrostatics in periodic slab geometries. I},
1265	>	Volume = 117,
1266	>	Year = 2002,
1267	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1268	>
1269	>	@article{deJoannis02,
1270	>	Author = {J. {de Joannis} and A. Arnold and C. Holm},
1271	>	Date-Added = {2008-01-08 14:58:56 -0500},
1272	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1273	>	Doi = {10.1063/1.149195},
1274	>	Journal = {J. Chem. Phys.},
1275	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf},
1276	>	Number = 6,
1277	>	Pages = {2503-2512},
1278	>	Title = {Electrostatics in periodic slab geometries. II},
1279	>	Volume = 117,
1280	>	Year = 2002,
1281	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}}
1282	>
1283	>	@article{Barenco95,
1284	>	Author = {A. Barenco and C.~H. Bennett and R. Cleve and D.~P. DiVincenzo and N. Margolus and P. Shor and T. Sleator and J.~A. Smolin and H. Weinfurter},
1285	>	Date-Added = {2008-01-08 14:58:56 -0500},
1286	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1287	>	Journal = {Phys. Rev. A},
1288	>	Pages = {3457-3467},
1289	>	Title = {elementary gates for quantum computation},
1290	>	Volume = 52,
1291	>	Year = 1995}
1292	>
1293	>	@article{Perram96,
1294	>	Author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and J.~L. Lebowitz},
1295	>	Date-Added = {2008-01-08 14:58:56 -0500},
1296	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1297	>	Journal = pre,
1298	>	Pages = {6565-6572},
1299	>	Title = {Ellipsoid contact potential: Theory and relation to overlap potentials},
1300	>	Volume = 54,
1301	>	Year = 1996}
1302	>
1303	>	@article{Daw84,
1304	>	Author = {M.~S. Daw and M.~I. Baskes},
1305	>	Date-Added = {2008-01-08 14:58:56 -0500},
1306	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1307	>	Journal = prb,
1308	>	Number = 12,
1309	>	Pages = {6443-6453},
1310	>	Title = {Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals},
1311	>	Volume = 29,
1312	>	Year = 1984}
1313	>
1314	>	@article{Foiles86,
1315	>	Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
1316	>	Date-Added = {2008-01-08 14:58:56 -0500},
1317	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1318	>	Journal = prb,
1319	>	Number = 12,
1320	>	Pages = 7983,
1321	>	Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1322	>	Volume = 33,
1323	>	Year = 1986}
1324	>
1325	>	@article{Zahn02,
1326	>	Author = {D. Zahn and B. Schilling and S.~M. Kast},
1327	>	Date-Added = {2008-01-08 14:58:56 -0500},
1328	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1329	>	Journal = {J. Phys. Chem. B},
1330	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
1331	>	Number = 41,
1332	>	Pages = {10725-10732},
1333	>	Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
1334	>	Volume = 106,
1335	>	Year = 2002}
1336	>
1337	>	@article{Metropolis53,
1338	>	Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
1339	>	Date-Added = {2008-01-08 14:58:56 -0500},
1340	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1341	>	Journal = {J. Chem. Phys.},
1342	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Metropolis_MCCalculations_53.pdf},
1343	>	Pages = {1087-1092},
1344	>	Title = {Equation of State Calculations by Fast Computing Machines},
1345	>	Volume = 21,
1346	>	Year = 1953}
1347	>
1348	>	@article{Parry76,
1349	>	Author = {D.~E. Parry},
1350	>	Date-Added = {2008-01-08 14:58:56 -0500},
1351	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1352	>	Journal = {Surf. Sci.},
1353	>	Pages = 195,
1354	>	Title = {Errata: The electrostatic potential in the surface region of an ionic crystal},
1355	>	Volume = 54,
1356	>	Year = 1976}
1357	>
1358	>	@article{Steane96,
1359	>	Author = {A.~M. Steane},
1360	>	Date-Added = {2008-01-08 14:58:56 -0500},
1361	>	Date-Modified = {2008-01-08 14:58:58 -0500},
1362	>	Journal = prl,
1363	>	Pages = {793-797},
1364	>	Title = {Error correcting codes in quantum theory},
1365	>	Volume = 77,
1366	>	Year = 1996}
1367	>
1368	>	@article{Todorova2004,
1369	>	Author = {L. Todorova and T. Angelov and Y. Marinov and A.~G. Petrov},
1370	>	Date-Added = {2008-01-08 14:58:56 -0500},
1371	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1372	>	Journal = {J. Mat. Sci. Mat. Elect.},
1373	>	Pages = {817-818},
1374	>	Title = {Evidence of flexoelectricity in polymer-dispersed liquid crystals},
1375	>	Volume = 14,
1376	>	Year = 2004}
1377	>
1378	>	@article{Hunenberger99a,
1379	>	Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
1380	>	Date-Added = {2008-01-08 14:58:56 -0500},
1381	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1382	>	Journal = {J. Chem. Phys.},
1383	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
1384	>	Number = 4,
1385	>	Pages = {1856-1872},
1386	>	Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study},
1387	>	Volume = 110,
1388	>	Year = 1999}
1389	>
1390	>	@article{Rhee89,
1391	>	Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
1392	>	Date-Added = {2008-01-08 14:58:56 -0500},
1393	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1394	>	Journal = {Phys. Rev. B},
1395	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
1396	>	Number = 1,
1397	>	Pages = {36-42},
1398	>	Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions},
1399	>	Volume = 40,
1400	>	Year = 1989}
1401	>
1402	>	@article{Yeh99,
1403	>	Author = {I.-C. Yeh and M.~L. Berkowitz},
1404	>	Date-Added = {2008-01-08 14:58:56 -0500},
1405	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1406	>	Journal = {J. Chem. Phys.},
1407	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
1408	>	Number = 7,
1409	>	Pages = {3155-3162},
1410	>	Title = {Ewald summation for systems with slab geometry},
1411	>	Volume = 111,
1412	>	Year = 1999}
1413	>
1414	>	@article{Brodka04,
1415	>	Author = {A. Br\'{o}dka},
1416	>	Date-Added = {2008-01-08 14:58:56 -0500},
1417	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1418	>	Doi = {10.1016/j.cplett.2004.10.086},
1419	>	Journal = {Chem. Phys. Lett.},
1420	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf},
1421	>	Pages = {62-67},
1422	>	Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
1423	>	Volume = 400,
1424	>	Year = 2004,
1425	>	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086}}
1426	>
1427	>	@article{Chuang98,
1428	>	Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
1429	>	Date-Added = {2008-01-08 14:58:56 -0500},
1430	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1431	>	Journal = prl,
1432	>	Pages = {3408-3411},
1433	>	Title = {Experimental Implementation of Fast Quantum Searching},
1434	>	Volume = 80,
1435	>	Year = 1998}
1436	>
1437	>	@article{Banerjee02,
1438	>	Author = {Srilekha Banerjee},
1439	>	Date-Added = {2008-01-08 14:58:56 -0500},
1440	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1441	>	Journal = {Physica A},
1442	>	Pages = {89-100},
1443	>	Title = {Exploring the Ripple Phase of Biomembranes},
1444	>	Volume = 308,
1445	>	Year = 2002}
1446	>
1447	>	@article{Bannerjee02,
1448	>	Author = {S. Bannerjee},
1449	>	Date-Added = {2008-01-08 14:58:56 -0500},
1450	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1451	>	Journal = {Physica A},
1452	>	Pages = {89-100},
1453	>	Title = {Exploring the ripple phase of biomembranes},
1454	>	Volume = 308,
1455	>	Year = 2002}
1456	>
1457	>	@article{Cleaver96,
1458	>	Author = {Douglas J. Cleaver and Christopher M. Care and Michael P. Allen and Maureen P. Neal},
1459	>	Date-Added = {2008-01-08 14:58:56 -0500},
1460	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1461	>	Journal = pre,
1462	>	Number = 1,
1463	>	Pages = {559-567},
1464	>	Title = {Extension and generalization of the Gay-Berne potential},
1465	>	Volume = 54,
1466	>	Year = 1996}
1467	>
1468	>	@article{Plimpton95,
1469	>	Author = {S. Plimpton},
1470	>	Date-Added = {2008-01-08 14:58:56 -0500},
1471	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1472	>	Journal = {J. Comp. Phys.},
1473	>	Pages = {1-19},
1474	>	Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
1475	>	Volume = 117,
1476	>	Year = 1995}
1477	>
1478	>	@article{Ayton97,
1479	>	Author = {G. Ayton and M. J. P. Gingras and G. N. Patey},
1480	>	Date-Added = {2008-01-08 14:58:56 -0500},
1481	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1482	>	Journal = pre,
1483	>	Number = 1,
1484	>	Pages = {562-570},
1485	>	Title = {Ferroelectric and dipolar glass phases of noncrystalline systems},
1486	>	Volume = 56,
1487	>	Year = 1997}
1488	>
1489	>	@article{Benninger:2005qy,
1490	>	Abstract = {The plasma membrane of cells is an ordered environment, giving rise to anisotropic orientation and restricted motion of molecules and proteins residing in the membrane. At the same time as being an organized matrix of defined structure, the cell membrane is heterogeneous and dynamic. Here we present a method where we use fluorescence imaging of linear dichroism to measure the orientation of molecules relative to the cell membrane. By detecting linear dichroism as well as fluorescence anisotropy, the orientation parameters are separated from dynamic properties such as rotational diffusion and homo energy transfer (energy migration). The sensitivity of the technique is enhanced by using two-photon excitation for higher photo-selection compared to single photon excitation. We show here that we can accurately image lipid organization in whole cell membranes and in delicate structures such as membrane nanotubes connecting two cells. The speed of our wide-field imaging system makes it possible to image changes in orientation and anisotropy occurring on a subsecond timescale. This is demonstrated by time-lapse studies showing that cholesterol depletion rapidly disrupts the orientation of a fluorophore located within the hydrophobic region of the cell membrane but not of a surface bound probe. This is consistent with cholesterol having an important role in stabilizing and ordering the lipid tails within the plasma membrane. },
1491	>	Annote = {10.1529/biophysj.104.050096},
1492	>	Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.},
1493	>	Date-Added = {2008-01-08 14:58:56 -0500},
1494	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1495	>	Journal = {Biophysical Journal},
1496	>	Journal1 = {Biophys. J.},
1497	>	Number = 1,
1498	>	Pages = {609--622},
1499	>	Title = {Fluorescence Imaging of Two-Photon Linear Dichroism: Cholesterol Depletion Disrupts Molecular Orientation in Cell Membranes},
1500	>	Ty = {JOUR},
1501	>	Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
1502	>	Volume = 88,
1503	>	Year = 2005,
1504	>	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609}}
1505	>
1506	>	@inbook{Blumen86,
1507	>	Address = {Amsterdam},
1508	>	Author = {A. Blumen and J. Klafter and G. Zumofen},
1509	>	Chapter = {Reactions in Disordered Media Modelled by Fractals},
1510	>	Date-Added = {2008-01-08 14:58:56 -0500},
1511	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1512	>	Editor = {Luciano Peitronero and E. Tosatti},
1513	>	Pages = 399,
1514	>	Publisher = {North-Holland},
1515	>	Series = {International Symposium on Fractals in Physics},
1516	>	Title = {Fractals in Physics},
1517	>	Year = 1986}
1518	>
1519	>	@article{Marland1979,
1520	>	Author = {L.~G. Marland and D.~D. Betts},
1521	>	Date-Added = {2008-01-08 14:58:56 -0500},
1522	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1523	>	Journal = prl,
1524	>	Number = 21,
1525	>	Pages = {1618-1621},
1526	>	Title = {Frustration Effect in Quantum Spin Systems},
1527	>	Volume = 43,
1528	>	Year = 1979}
1529	>
1530	>	@article{Berne72,
1531	>	Author = {B.~J. Berne and P. Pechukas},
1532	>	Date-Added = {2008-01-08 14:58:56 -0500},
1533	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1534	>	Journal = jcp,
1535	>	Pages = {4213-4216},
1536	>	Title = {Gaussian Model Potentials for Molecular Interactions},
1537	>	Volume = 56,
1538	>	Year = 1972}
1539	>
1540	>	@article{Golubkov06,
1541	>	Author = {Pavel A. Golubkov and Rengyu Ren},
1542	>	Date-Added = {2008-01-08 14:58:56 -0500},
1543	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1544	>	Journal = jcp,
1545	>	Pages = 064103,
1546	>	Title = {Generalized coarse-grained model based on point multipole and Gay-Berne potentials},
1547	>	Volume = 125,
1548	>	Year = 2006}
1549	>
1550	>	@article{Harden2006,
1551	>	Author = {J. Harden and B. Mbanga and N. Eber and K. Fodor-Csorba and S. Sprunt and J. T. Gleeson and A. Jakli},
1552	>	Date-Added = {2008-01-08 14:58:56 -0500},
1553	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1554	>	Eid = 157802,
1555	>	Journal = {Physical Review Letters},
1556	>	Number = 15,
1557	>	Numpages = 4,
1558	>	Pages = 157802,
1559	>	Publisher = {APS},
1560	>	Title = {Giant Flexoelectricity of Bent-Core Nematic Liquid Crystals},
1561	>	Volume = 97,
1562	>	Year = 2006}
1563	>
1564	>	@article{Dzugutov92,
1565	>	Author = {M. Dzugutov},
1566	>	Date-Added = {2008-01-08 14:58:56 -0500},
1567	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1568	>	Journal = pra,
1569	>	Pages = {R2984-R2987},
1570	>	Title = {Glass formation in a simple monatomic liquid with icosahedral inherent local order},
1571	>	Volume = 46,
1572	>	Year = 1992}
1573	>
1574	>	@article{Calderbank96,
1575	>	Author = {A.~R. Calderbank and P.~W. Shor},
1576	>	Date-Added = {2008-01-08 14:58:56 -0500},
1577	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1578	>	Journal = {Phys. Rev. A},
1579	>	Pages = {1098-1105},
1580	>	Title = {Good quantum error-correcting codes exist},
1581	>	Volume = 54,
1582	>	Year = 1996}
1583	>
1584	>	@article{Carraro1993,
1585	>	Author = {Carlo Carraro and David R. Nelson},
1586	>	Date-Added = {2008-01-08 14:58:56 -0500},
1587	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1588	>	Journal = pre,
1589	>	Number = 4,
1590	>	Pages = {3082-3090},
1591	>	Title = {Grain-boundary buckling and spin-glass models of disorder in membranes},
1592	>	Volume = 48,
1593	>	Year = 1993}
1594	>
1595	>	@article{Stillinger82,
1596	>	Author = {F.~H. Stillinger and T.~A. Weber},
1597	>	Date-Added = {2008-01-08 14:58:56 -0500},
1598	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1599	>	Journal = pra,
1600	>	Number = 2,
1601	>	Pages = {978-989},
1602	>	Title = {Hidden structure in liquids},
1603	>	Volume = 25,
1604	>	Year = 1982}
1605	>
1606	>	@article{Little96,
1607	>	Author = {H.~J. Little},
1608	>	Date-Added = {2008-01-08 14:58:56 -0500},
1609	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1610	>	Journal = {Pharmacology \& Therapeutics},
1611	>	Pages = {37-58},
1612	>	Title = {How has molecular pharmacology contributed to our understanding of the mechanism(s) of general anesthesia?},
1613	>	Volume = 69,
1614	>	Year = 1996}
1615	>
1616	>	@article{Roberts94,
1617	>	Author = {J.~E. Roberts and J. Schnitker},
1618	>	Date-Added = {2008-01-08 14:58:56 -0500},
1619	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1620	>	Journal = {J. Chem. Phys.},
1621	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
1622	>	Number = 6,
1623	>	Pages = {5024-5031},
1624	>	Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
1625	>	Volume = 101,
1626	>	Year = 1994}
1627	>
1628	>	@article{Stillinger85,
1629	>	Author = {F.~H. Stillinger and T.~A. Weber},
1630	>	Date-Added = {2008-01-08 14:58:56 -0500},
1631	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1632	>	Journal = jcp,
1633	>	Number = 9,
1634	>	Pages = {4767-4775},
1635	>	Title = {Inherent structure theory of liquids in the hard-sphere limit},
1636	>	Volume = 83,
1637	>	Year = 1985}
1638	>
1639	>	@article{Kast03,
1640	>	Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
1641	>	Date-Added = {2008-01-08 14:58:56 -0500},
1642	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1643	>	Journal = {Chem. Phys. Lett.},
1644	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
1645	>	Pages = {398-404},
1646	>	Title = {Integral equation theory for correcting truncation errors in molecular simulations},
1647	>	Volume = 367,
1648	>	Year = 2003}
1649	>
1650	>	@article{Ayton01,
1651	>	Author = {Gary Ayton and Scott G. Bardenhagen and Patrick McMurty and Deborah Sulsky and Gregory A. Voth},
1652	>	Date-Added = {2008-01-08 14:58:56 -0500},
1653	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1654	>	Journal = jcp,
1655	>	Number = 15,
1656	>	Pages = {6913-6924},
1657	>	Title = {Interfacing continuum and molecular dynamics: An application to lipid bilayers},
1658	>	Volume = 114,
1659	>	Year = 2001}
1660	>
1661	>	@inbook{Voter95b,
1662	>	Author = {A.~F. Voter},
1663	>	Chapter = 4,
1664	>	Date-Added = {2008-01-08 14:58:56 -0500},
1665	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1666	>	Editor = {J.~H. Westbrook and R.~L. Fleischer},
1667	>	Pages = 77,
1668	>	Publisher = {John Wiley and Sons Ltd},
1669	>	Title = {Intermetallic Compounds: Principles and Practice},
1670	>	Volume = 1,
1671	>	Year = 1995}
1672	>
1673	>	@article{Truhlar78,
1674	>	Author = {Donald G. Truhlar},
1675	>	Date-Added = {2008-01-08 14:58:56 -0500},
1676	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1677	>	Journal = {J. Chem. Ed.},
1678	>	Pages = 309,
1679	>	Title = {Interpretation of the Activation Energy},
1680	>	Volume = 55,
1681	>	Year = 1978}
1682	>
1683	>	@book{Chandler87,
1684	>	Author = {David Chandler},
1685	>	Date-Added = {2008-01-08 14:58:56 -0500},
1686	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1687	>	Publisher = {Oxford University Press},
1688	>	Title = {Introduction to Modern Statistical Mechanics},
1689	>	Year = 1987}
1690	>
1691	>	@article{Keshavamurthy94,
1692	>	Author = {S. Keshavamurthy and W.~H. Miller},
1693	>	Date-Added = {2008-01-08 14:58:56 -0500},
1694	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1695	>	Journal = cpl,
1696	>	Pages = 189,
1697	>	Title = {ivr},
1698	>	Volume = 218,
1699	>	Year = 1994}
1700	>
1701	>	@article{Luty95,
1702	>	Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
1703	>	Date-Added = {2008-01-08 14:58:56 -0500},
1704	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1705	>	Journal = {J. Chem. Phys.},
1706	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
1707	>	Number = 8,
1708	>	Pages = {3014-3021},
1709	>	Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
1710	>	Volume = 103,
1711	>	Year = 1995}
1712	>
1713	>	@article{Wan94,
1714	>	Author = {Yi. Wan and R.~M. Stratt},
1715	>	Date-Added = {2008-01-08 14:58:56 -0500},
1716	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1717	>	Journal = jcp,
1718	>	Pages = {5123-5138},
1719	>	Title = {Liquid theory for the instantaneous normal modes of a liquid},
1720	>	Volume = 100,
1721	>	Year = 1994}
1722	>
1723	>	@article{Sutton90,
1724	>	Author = {A.~P. Sutton and J. Chen},
1725	>	Date-Added = {2008-01-08 14:58:56 -0500},
1726	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1727	>	Journal = {Phil. Mag. Lett.},
1728	>	Pages = {139-146},
1729	>	Title = {Long-Range $\mbox{Finnis Sinclair}$ Potentials},
1730	>	Volume = 61,
1731	>	Year = 1990}
1732	>
1733	>	@article{Bassolino95,
1734	>	Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
1735	>	Date-Added = {2008-01-08 14:58:56 -0500},
1736	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1737	>	Journal = {J. Am. Chem. Soc.},
1738	>	Pages = {4118-4129},
1739	>	Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
1740	>	Volume = 117,
1741	>	Year = 1995}
1742	>
1743	>	@article{Lindahl00,
1744	>	Author = {E. Lindahl and O. Edholm},
1745	>	Date-Added = {2008-01-08 14:58:56 -0500},
1746	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1747	>	Journal = {Biophysical Journal},
1748	>	Month = {July},
1749	>	Pages = {426-433},
1750	>	Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
1751	>	Volume = 79,
1752	>	Year = 2000}
1753	>
1754	>	@article{Gezelter99,
1755	>	Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
1756	>	Date-Added = {2008-01-08 14:58:56 -0500},
1757	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1758	>	Journal = jcp,
1759	>	Pages = 3444,
1760	>	Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
1761	>	Volume = 110,
1762	>	Year = 1999}
1763	>
1764	>	@article{Sun97b,
1765	>	Author = {X. Sun and W.~H. Miller},
1766	>	Date-Added = {2008-01-08 14:58:56 -0500},
1767	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1768	>	Journal = jcp,
1769	>	Pages = 916,
1770	>	Title = {Mixed semiclassical-classical approaches to the dynamics of complex molecular systems},
1771	>	Year = 1997}
1772	>
1773	>	@article{Goldstein88,
1774	>	Author = {Raymond E. Goldstein and Stanislas Leibler},
1775	>	Date-Added = {2008-01-08 14:58:56 -0500},
1776	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1777	>	Journal = prl,
1778	>	Number = 19,
1779	>	Pages = {2213-2216},
1780	>	Title = {Model for Lamellar Phases of Interacting Lipid Membranes},
1781	>	Volume = 61,
1782	>	Year = 1988,
1783	>	Bdsk-File-1 = {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}}
1784	>
1785	>	@article{Daw89,
1786	>	Author = {Murray~S. Daw},
1787	>	Date-Added = {2008-01-08 14:58:56 -0500},
1788	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1789	>	Journal = {Physical Review B},
1790	>	Pages = {7441-7452},
1791	>	Title = {Model of metallic cohesion: The embedded-atom method},
1792	>	Volume = 39,
1793	>	Year = 1989}
1794	>
1795	>	@article{Heyes77,
1796	>	Author = {D.~M. Heyes and M. Barber and J.~H.~R. Clarke},
1797	>	Date-Added = {2008-01-08 14:58:56 -0500},
1798	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1799	>	Journal = {J. Chem. Soc., Faraday Trans. II},
1800	>	Number = 7,
1801	>	Pages = {1485-1496},
1802	>	Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride},
1803	>	Volume = 73,
1804	>	Year = 1977}
1805	>
1806	>	@article{Vuilleumier97,
1807	>	Author = {Rodolphe Vuilleumier and Daniel Borgis},
1808	>	Date-Added = {2008-01-08 14:58:56 -0500},
1809	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1810	>	Journal = jpc,
1811	>	Title = {Molecular Dynamics of an excess proton in water using a non-additive valence bond force field},
1812	>	Volume = {in press},
1813	>	Year = 1997}
1814	>
1815	>	@article{Nina02,
1816	>	Author = {M. Nina and T. Simonson},
1817	>	Date-Added = {2008-01-08 14:58:56 -0500},
1818	>	Date-Modified = {2008-01-08 14:58:59 -0500},
1819	>	Journal = {J. Phys. Chem. B},
1820	>	Pages = {3696-3705},
1821	>	Title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments},
1822	>	Volume = 106,
1823	>	Year = 2002}
1824	>
1825	>	@article{Heller93,
1826	>	Author = {H. Heller and M. Schaefer and K. Schulten},
1827	>	Date-Added = {2008-01-08 14:58:56 -0500},
1828	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1829	>	Journal = jpc,
1830	>	Pages = {8343-8360},
1831	>	Title = {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200 LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES},
1832	>	Volume = 97,
1833	>	Year = 1993}
1834	>
1835	>	@article{Smondyrev99,
1836	>	Author = {A.~M. Smondyrev and M.~L. Berkowitz},
1837	>	Date-Added = {2008-01-08 14:58:56 -0500},
1838	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1839	>	Journal = {Biophysical Journal},
1840	>	Pages = {2472-2478},
1841	>	Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1842	>	Volume = 76,
1843	>	Year = 1999}
1844	>
1845	>	@article{Marrink02,
1846	>	Author = {S.~J. Marrink and D.~P. Teileman},
1847	>	Date-Added = {2008-01-08 14:58:56 -0500},
1848	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1849	>	Journal = {Biophysical Journal},
1850	>	Pages = {2386-2392},
1851	>	Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1852	>	Volume = 83,
1853	>	Year = 2002}
1854	>
1855	>	@article{Marrink03,
1856	>	Author = {S.~J. Marrink and A.~E. Mark},
1857	>	Date-Added = {2008-01-08 14:58:56 -0500},
1858	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1859	>	Journal = {J. Am. Chem. Soc.},
1860	>	Pages = {15233-15242},
1861	>	Title = {Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
1862	>	Volume = 125,
1863	>	Year = 2003}
1864	>
1865	>	@article{Tieleman96,
1866	>	Author = {D. P. Tieleman and H. J. C. Berendsen},
1867	>	Date-Added = {2008-01-08 14:58:56 -0500},
1868	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1869	>	Journal = jcp,
1870	>	Number = 11,
1871	>	Pages = {4871-4880},
1872	>	Title = {Molecular Dynamics Simulations of a Fully Hydrated Dipalmitoylphosphatidylcholine Bilayer with Different Macroscopic Boundary Conditions and Parameters},
1873	>	Volume = 105,
1874	>	Year = 1996}
1875	>
1876	>	@article{Venable93,
1877	>	Author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and R.~W. Pastor},
1878	>	Date-Added = {2008-01-08 14:58:56 -0500},
1879	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1880	>	Journal = {Science},
1881	>	Pages = {223-226},
1882	>	Title = {Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: An Investigation of Membrane Fluidity},
1883	>	Volume = 262,
1884	>	Year = 1993}
1885	>
1886	>	@article{Weber00,
1887	>	Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
1888	>	Date-Added = {2008-01-08 14:58:56 -0500},
1889	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1890	>	Doi = {10.1021/jp9937757},
1891	>	Journal = {J. Phys. Chem. B},
1892	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
1893	>	Number = 15,
1894	>	Pages = {3668-3675},
1895	>	Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
1896	>	Volume = 104,
1897	>	Year = 2000,
1898	>	Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757}}
1899	>
1900	>	@article{Venable00,
1901	>	Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
1902	>	Date-Added = {2008-01-08 14:58:56 -0500},
1903	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1904	>	Journal = jcp,
1905	>	Number = 10,
1906	>	Pages = {4822-4832},
1907	>	Title = {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
1908	>	Volume = 112,
1909	>	Year = 2000}
1910	>
1911	>	@article{Patra03,
1912	>	Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
1913	>	Date-Added = {2008-01-08 14:58:56 -0500},
1914	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1915	>	Journal = {Biophysical Journal},
1916	>	Pages = {3636-3645},
1917	>	Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
1918	>	Volume = 84,
1919	>	Year = 2003}
1920	>
1921	>	@article{Jiang04,
1922	>	Author = {F.~Y. Jiang and Y. Bouret and J.~T. Kindt},
1923	>	Date-Added = {2008-01-08 14:58:56 -0500},
1924	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1925	>	Journal = {Biophys. J.},
1926	>	Pages = {182-192},
1927	>	Title = {Molecular Dynamics Simulations of the Lipid Bilayer Edge},
1928	>	Volume = 87,
1929	>	Year = 2004}
1930	>
1931	>	@article{Rahman71,
1932	>	Author = {A. Rahman and F.~H. Stillinger},
1933	>	Date-Added = {2008-01-08 14:58:56 -0500},
1934	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1935	>	Journal = {J. Chem. Phys.},
1936	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
1937	>	Month = {October},
1938	>	Number = 7,
1939	>	Pages = {3336-3359},
1940	>	Title = {Molecular Dynamics Study of Liquid Water},
1941	>	Volume = 55,
1942	>	Year = 1971}
1943	>
1944	>	@article{Sum03,
1945	>	Author = {A.~K. Sum and J.~J. de~Pablo},
1946	>	Date-Added = {2008-01-08 14:58:56 -0500},
1947	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1948	>	Journal = {Biophysical Journal},
1949	>	Pages = {3636-3645},
1950	>	Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
1951	>	Volume = 85,
1952	>	Year = 2003}
1953	>
1954	>	@article{deVries05,
1955	>	Author = {A.~H. de~Vries and S. Yefimov and A.~E. Mark and S.~J. Marrink},
1956	>	Date-Added = {2008-01-08 14:58:56 -0500},
1957	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1958	>	Journal = pnas,
1959	>	Number = 15,
1960	>	Pages = {5392-5396},
1961	>	Title = {Molecular structure of the lecithin ripple phase},
1962	>	Volume = 102,
1963	>	Year = 2005}
1964	>
1965	>	@article{Sok92,
1966	>	Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
1967	>	Date-Added = {2008-01-08 14:58:56 -0500},
1968	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1969	>	Journal = {J. Chem. Phys.},
1970	>	Pages = {4699-4704},
1971	>	Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
1972	>	Volume = 96,
1973	>	Year = 1992}
1974	>
1975	>	@article{Qi99,
1976	>	Author = {Y. Qi and T. \c{C}a\v{g}in and Y. Kimura and W.~A. {Goddard III}},
1977	>	Date-Added = {2008-01-08 14:58:56 -0500},
1978	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1979	>	Journal = prb,
1980	>	Number = 5,
1981	>	Pages = {3527-3533},
1982	>	Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ and $\mbox{Cu-Ni}$},
1983	>	Volume = 59,
1984	>	Year = 1999}
1985	>
1986	>	@article{Berardi99,
1987	>	Author = {R. Berardi and S. Orlandi and C. Zannoni},
1988	>	Date-Added = {2008-01-08 14:58:56 -0500},
1989	>	Date-Modified = {2008-01-08 14:59:00 -0500},
1990	>	Journal = {Int. J. Mod. Phys. C},
1991	>	Pages = {477-484},
1992	>	Title = {Monte Carlo simulations of rod-like Gay-Berne mesogens with transverse dipoles},
1993	>	Volume = 10,
1994	>	Year = 1999}
1995	>
1996	>	@article{Barker73,
1997	>	Author = {J.~A. Barker and R.~O. Watts},
1998	>	Date-Added = {2008-01-08 14:58:56 -0500},
1999	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2000	>	Journal = {Mol. Phys.},
2001	>	Pages = {789-792},
2002	>	Title = {Monte Carlo studies of the dielectric properties of water-like models},
2003	>	Volume = 26,
2004	>	Year = 1973}
2005	>
2006	>	@article{Brush66,
2007	>	Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
2008	>	Date-Added = {2008-01-08 14:58:56 -0500},
2009	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2010	>	Journal = {J. Chem. Phys.},
2011	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
2012	>	Month = {September},
2013	>	Number = 6,
2014	>	Pages = {2102-2118},
2015	>	Title = {Monte Carlo Study of a One-Component Plasma. I},
2016	>	Volume = 45,
2017	>	Year = 1966}
2018	>
2019	>	@article{Tenchov2001,
2020	>	Author = {Boris Tenchov and Rumiana Koynova and Gert Rapp},
2021	>	Date-Added = {2008-01-08 14:58:56 -0500},
2022	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2023	>	Journal = bj,
2024	>	Pages = {1873-1890},
2025	>	Title = {New Ordered Metastable Phases between the Gel and Subgel Phases in Hydrated Phospholipids},
2026	>	Volume = 80,
2027	>	Year = 2001}
2028	>
2029	>	@article{Steinbach94,
2030	>	Author = {P.~J. Steinbach and B.~R. Brooks},
2031	>	Date-Added = {2008-01-08 14:58:56 -0500},
2032	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2033	>	Doi = {10.1002/jcc.540150702},
2034	>	Journal = {J. Comput. Chem.},
2035	>	Number = 7,
2036	>	Pages = {667-683},
2037	>	Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
2038	>	Volume = 15,
2039	>	Year = 1994,
2040	>	Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150702}}
2041	>
2042	>	@article{McKinnon92,
2043	>	Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
2044	>	Date-Added = {2008-01-08 14:58:56 -0500},
2045	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2046	>	Journal = jpc,
2047	>	Pages = {10497-10506},
2048	>	Title = {Nonequilibrium Molecular Dynamics Simulation of Oxygen Diffusion through Hexadecane Monolayers with Varying Concentrations of Cholesterol},
2049	>	Volume = 96,
2050	>	Year = 1992}
2051	>
2052	>	@article{Moore94,
2053	>	Author = {P. Moore and T. Keyes},
2054	>	Date-Added = {2008-01-08 14:58:56 -0500},
2055	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2056	>	Journal = jcp,
2057	>	Pages = 6709,
2058	>	Title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: Velocity Correlation Functions and Self-Diffusion Constants},
2059	>	Volume = 100,
2060	>	Year = 1994}
2061	>
2062	>	@article{Madan91,
2063	>	Author = {B. Madan and T. Keyes and G. Seeley},
2064	>	Date-Added = {2008-01-08 14:58:56 -0500},
2065	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2066	>	Journal = jcp,
2067	>	Pages = {6762-6769},
2068	>	Title = {Normal mode analysis of the velocity correlation function in supercooled liquids},
2069	>	Volume = 94,
2070	>	Year = 1991}
2071	>
2072	>	@article{Seeley89,
2073	>	Author = {G. Seeley and T. Keyes},
2074	>	Date-Added = {2008-01-08 14:58:56 -0500},
2075	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2076	>	Journal = jcp,
2077	>	Pages = {5581-5586},
2078	>	Title = {Normal-mode analysis of liquid-state dynamics},
2079	>	Volume = 91,
2080	>	Year = 1989}
2081	>
2082	>	@article{Sengupta00,
2083	>	Author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
2084	>	Date-Added = {2008-01-08 14:58:56 -0500},
2085	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2086	>	Journal = {Europhysics Letters},
2087	>	Number = 6,
2088	>	Pages = {722-728},
2089	>	Title = {Novel structural Features of the ripple phase of phospholipids},
2090	>	Volume = 49,
2091	>	Year = 2000}
2092	>
2093	>	@article{Nitzan95,
2094	>	Author = {G.~V. Vijayadamodar and A. Nitzan},
2095	>	Date-Added = {2008-01-08 14:58:56 -0500},
2096	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2097	>	Journal = jcp,
2098	>	Pages = {2169-2177},
2099	>	Title = {On the application of instantaneous normal mode analysis to long time dynamics of liquids},
2100	>	Volume = 103,
2101	>	Year = 1995}
2102	>
2103	>	@article{Bonnier93,
2104	>	Author = {B. Bonnier and M. Hontebeyrie and C. Meyers},
2105	>	Date-Added = {2008-01-08 14:58:56 -0500},
2106	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2107	>	Journal = {Physica A},
2108	>	Pages = {1-10},
2109	>	Title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING D-DIMENSIONAL CUBES},
2110	>	Volume = 198,
2111	>	Year = 1993}
2112	>
2113	>	@article{Zwanzig83,
2114	>	Author = {R. Zwanzig},
2115	>	Date-Added = {2008-01-08 14:58:56 -0500},
2116	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2117	>	Journal = jcp,
2118	>	Pages = {4507-4508},
2119	>	Title = {On the relation between self-diffusion and viscosity of liquids},
2120	>	Volume = 79,
2121	>	Year = 1983}
2122	>
2123	>	@article{Klafter86,
2124	>	Author = {J. Klafter and M.~F. Shlesinger},
2125	>	Date-Added = {2008-01-08 14:58:56 -0500},
2126	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2127	>	Journal = {Proc. Natl. Acad. Sci. USA},
2128	>	Pages = {848-851},
2129	>	Title = {On the relationship among three theories of relaxation in disordered systems},
2130	>	Volume = 83,
2131	>	Year = 1986}
2132	>
2133	>	@article{Norberg00,
2134	>	Author = {J. Norberg and L. Nilsson},
2135	>	Date-Added = {2008-01-08 14:58:56 -0500},
2136	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2137	>	Journal = {Biophysical Journal},
2138	>	Pages = {1537-1553},
2139	>	Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
2140	>	Volume = 79,
2141	>	Year = 2000}
2142	>
2143	>	@article{Shlesinger84,
2144	>	Author = {M.~F. Shlesinger and E.~W. Montroll},
2145	>	Date-Added = {2008-01-08 14:58:56 -0500},
2146	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2147	>	Journal = {Proc. Natl. Acad. Sci. USA},
2148	>	Pages = {1280-1283},
2149	>	Title = {On the Williams-Watts function of dielectric relaxation},
2150	>	Volume = 81,
2151	>	Year = 1984}
2152	>
2153	>	@incollection{Jorgensen98a,
2154	>	Address = {New York},
2155	>	Author = {W.~L. Jorgensen},
2156	>	Booktitle = {The Encyclopedia of Computational Chemistry},
2157	>	Date-Added = {2008-01-08 14:58:56 -0500},
2158	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2159	>	Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
2160	>	Pages = {1986-1989},
2161	>	Publisher = {John Wiley \& Sons},
2162	>	Title = {OPLS Force Fields},
2163	>	Volume = 3,
2164	>	Year = 1998}
2165	>
2166	>	@article{Jones56,
2167	>	Author = {R.~E. Jones and D.~H. Templeton},
2168	>	Date-Added = {2008-01-08 14:58:56 -0500},
2169	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2170	>	Journal = {J. Chem. Phys.},
2171	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
2172	>	Number = 5,
2173	>	Pages = {1062-1063},
2174	>	Title = {Optimum Atomic Shape for Bertaut Series},
2175	>	Volume = 25,
2176	>	Year = 1956}
2177	>
2178	>	@article{Renard1966,
2179	>	Author = {R\'emi Renard and Carl W. Garland},
2180	>	Date-Added = {2008-01-08 14:58:56 -0500},
2181	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2182	>	Journal = jcp,
2183	>	Number = 3,
2184	>	Pages = {1125-1129},
2185	>	Title = {Order-Disorder Phenomena. II. Elastic Constants of a Two-Dimensional Ising Model},
2186	>	Volume = 44,
2187	>	Year = 1966}
2188	>
2189	>	@article{Jiang2006,
2190	>	Author = {Ying Jiang and Thorsten Emig},
2191	>	Date-Added = {2008-01-08 14:58:56 -0500},
2192	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2193	>	Journal = prb,
2194	>	Pages = 104452,
2195	>	Title = {Ordering of geometrically frustrated classical and quantum triangular Ising magnets},
2196	>	Volume = 73,
2197	>	Year = 2006}
2198	>
2199	>	@article{Alper95,
2200	>	Author = {H.~E. Alper and T.~R. Stouch},
2201	>	Date-Added = {2008-01-08 14:58:56 -0500},
2202	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2203	>	Journal = {J. Phys. Chem.},
2204	>	Pages = {5724-5731},
2205	>	Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
2206	>	Volume = 99,
2207	>	Year = 1995}
2208	>
2209	>	@article{Weis92,
2210	>	Author = {J. J. Weis and D. Levesque and G. J. Zarragoicoechea},
2211	>	Date-Added = {2008-01-08 14:58:56 -0500},
2212	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2213	>	Journal = prl,
2214	>	Number = 6,
2215	>	Pages = {913-916},
2216	>	Title = {Orientational Order in Simple Dipolar Liquid-Crystal Models},
2217	>	Volume = 69,
2218	>	Year = 1992}
2219	>
2220	>	@article{Wei92,
2221	>	Author = {Dongqing Wei and G. N. Patey},
2222	>	Date-Added = {2008-01-08 14:58:56 -0500},
2223	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2224	>	Journal = prl,
2225	>	Number = 13,
2226	>	Pages = {2043-2045},
2227	>	Title = {Orientational Order in Simple Dipolar Liquids: Computer Simulation of a Ferroeletric Nematic Phase},
2228	>	Volume = 68,
2229	>	Year = 1992}
2230	>
2231	>	@article{Ayton95,
2232	>	Author = {G. Ayton and M.~J.~P. Gingras and G.~N. Patey},
2233	>	Date-Added = {2008-01-08 14:58:56 -0500},
2234	>	Date-Modified = {2008-01-08 14:59:00 -0500},
2235	>	Journal = prl,
2236	>	Number = 12,
2237	>	Pages = {2360-2363},
2238	>	Title = {Orientational Ordering in Spatially Disordered Dipolar System},
2239	>	Volume = 75,
2240	>	Year = 1995}
2241	>
2242	>	@article{Darden93,
2243	>	Author = {T. Darden and D. York and L. Pedersen},
2244	>	Date-Added = {2008-01-08 14:58:56 -0500},
2245	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2246	>	Journal = {J. Chem. Phys.},
2247	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_ParticleMeshEwald_93.pdf},
2248	>	Number = 12,
2249	>	Pages = {10089-10092},
2250	>	Title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
2251	>	Volume = 98,
2252	>	Year = 1993}
2253	>
2254	>	@book{Mazur97,
2255	>	Address = {New Jersey},
2256	>	Author = {Eric Mazur},
2257	>	Date-Added = {2008-01-08 14:58:56 -0500},
2258	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2259	>	Publisher = {Prentice Hall},
2260	>	Title = {Peer Instruction: A User's Manual},
2261	>	Year = 1997}
2262	>
2263	>	@article{Boyer95,
2264	>	Author = {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
2265	>	Date-Added = {2008-01-08 14:58:56 -0500},
2266	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2267	>	Journal = jcp,
2268	>	Pages = 1607,
2269	>	Title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL ADSORPTION},
2270	>	Volume = 103,
2271	>	Year = 1995}
2272	>
2273	>	@article{Chakrabarti92,
2274	>	Author = {A.~C. Chakrabarti and D.~W. Deamer},
2275	>	Date-Added = {2008-01-08 14:58:56 -0500},
2276	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2277	>	Journal = {Biochimica et Biophysica Acta},
2278	>	Pages = {171-177},
2279	>	Title = {PERMEABILITY OF LIPID BILAYERS TO AMINO-ACIDS AND PHOSPHATE},
2280	>	Volume = 1111,
2281	>	Year = 1992}
2282	>
2283	>	@article{Paula96,
2284	>	Author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and T.~H. Haines and D.~W. Deamer},
2285	>	Date-Added = {2008-01-08 14:58:56 -0500},
2286	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2287	>	Journal = {Biophys. J.},
2288	>	Pages = {339-348},
2289	>	Title = {Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness},
2290	>	Volume = 70,
2291	>	Year = 1996}
2292	>
2293	>	@article{Kranenburg2005,
2294	>	Author = {Marieke Kranenburg and Berend Smit},
2295	>	Date-Added = {2008-01-08 14:58:56 -0500},
2296	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2297	>	Journal = jpcb,
2298	>	Pages = {6553-6563},
2299	>	Title = {Phase Behavior of Model Lipid Bilayers},
2300	>	Volume = 109,
2301	>	Year = 2005}
2302	>
2303	>	@article{Stevens95,
2304	>	Author = {M.~J. Stevens and G.~S. Grest},
2305	>	Date-Added = {2008-01-08 14:58:56 -0500},
2306	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2307	>	Journal = {Physical Review E},
2308	>	Number = 6,
2309	>	Pages = {5976-5983},
2310	>	Title = {Phase coexistence of a Stockmayer fluid in an aplied field},
2311	>	Volume = 51,
2312	>	Year = 1995}
2313	>
2314	>	@book{Cevc87,
2315	>	Address = {New York},
2316	>	Author = {Gregor Cevc and Derek Marsh},
2317	>	Date-Added = {2008-01-08 14:58:56 -0500},
2318	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2319	>	Publisher = {Wiley-Interscience},
2320	>	Title = {Phospholipid Bilayers},
2321	>	Year = 1980}
2322	>
2323	>	@article{Smith82,
2324	>	Author = {W. Smith},
2325	>	Date-Added = {2008-01-08 14:58:56 -0500},
2326	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2327	>	Journal = {CCP5 Quarterly},
2328	>	Pages = {13-25},
2329	>	Title = {Point multipoles in the Ewald summation},
2330	>	Volume = 4,
2331	>	Year = 1982}
2332	>
2333	>	@article{Meyer96,
2334	>	Author = {H. W. Meyer},
2335	>	Date-Added = {2008-01-08 14:58:56 -0500},
2336	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2337	>	Journal = {Biochim. Biophys. Acta.},
2338	>	Pages = {221-245},
2339	>	Title = {Pretansition-Ripples in Bilayers of Dipalmitoylphosphatidylcholine: Undulation or Periodic Segments? A Freeze-Fracture Study},
2340	>	Volume = 1302,
2341	>	Year = 1996}
2342	>
2343	>	@article{Klafter94,
2344	>	Author = {J. Klafter and G. Zumofen},
2345	>	Date-Added = {2008-01-08 14:58:56 -0500},
2346	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2347	>	Journal = jpc,
2348	>	Pages = {7366-7370},
2349	>	Title = {Probability Distributions for Continuous-Time Random Walks with Long Tails},
2350	>	Volume = 98,
2351	>	Year = 1994}
2352	>
2353	>	@article{Pasterny00,
2354	>	Author = {K. Pasterny and E. Gwozdz and A. Brodka},
2355	>	Date-Added = {2008-01-08 14:58:56 -0500},
2356	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2357	>	Journal = {J. Mol. Liq.},
2358	>	Pages = {173-184},
2359	>	Title = {Properties of a model liquid crystal: Polar Gay-Berne particles},
2360	>	Volume = 85,
2361	>	Year = 2000}
2362	>
2363	>	@article{Mazur92,
2364	>	Author = {E. Mazur},
2365	>	Date-Added = {2008-01-08 14:58:56 -0500},
2366	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2367	>	Journal = {Optics and Photonics News},
2368	>	Pages = 38,
2369	>	Title = {Qualitative vs. Quantititative Thinking: Are we teaching the right thing?},
2370	>	Volume = 3,
2371	>	Year = 1992}
2372	>
2373	>	@article{Lent93,
2374	>	Author = {C.~S. Lent and P.~D. Tougaw and W.~Porod and G.~H. Bernstein},
2375	>	Date-Added = {2008-01-08 14:58:56 -0500},
2376	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2377	>	Journal = {Nanotechnology},
2378	>	Pages = {49-57},
2379	>	Title = {Quantum Cellular Automata},
2380	>	Volume = 4,
2381	>	Year = 1993}
2382	>
2383	>	@article{Grover97,
2384	>	Author = {L.~K. Grover},
2385	>	Date-Added = {2008-01-08 14:58:56 -0500},
2386	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2387	>	Journal = prl,
2388	>	Pages = {4709-4712},
2389	>	Title = {Quantum computers can search arbitrarily large databases by a single query},
2390	>	Volume = 79,
2391	>	Year = 1997}
2392	>
2393	>	@article{Belonoshko00,
2394	>	Author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and B. Johansson},
2395	>	Date-Added = {2008-01-08 14:58:56 -0500},
2396	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2397	>	Journal = prb,
2398	>	Pages = {3838-3844},
2399	>	Title = {Quasi ab initio molecular dynamic study of Cu melting},
2400	>	Volume = 61,
2401	>	Year = 2000}
2402	>
2403	>	@article{Tavares02,
2404	>	Author = {J.~M. Tavares and J.~J. Weis and M.~M. Telo da Gama},
2405	>	Date-Added = {2008-01-08 14:58:56 -0500},
2406	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2407	>	Journal = pre,
2408	>	Pages = 061201,
2409	>	Title = {Quasi-two-dimensional dipolar fluid at low densities: Monte Carlo simulations and theory},
2410	>	Volume = 65,
2411	>	Year = 2002}
2412	>
2413	>	@article{Evans93,
2414	>	Author = {J.~W. Evans},
2415	>	Date-Added = {2008-01-08 14:58:56 -0500},
2416	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2417	>	Journal = rmp,
2418	>	Pages = {1281-1329},
2419	>	Title = {Random and Cooperative Sequential Adsorption},
2420	>	Volume = 65,
2421	>	Year = 1993}
2422	>
2423	>	@article{Viot92a,
2424	>	Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
2425	>	Date-Added = {2008-01-08 14:58:56 -0500},
2426	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2427	>	Journal = jpc,
2428	>	Pages = {5212-5218},
2429	>	Title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
2430	>	Volume = 97,
2431	>	Year = 1992}
2432	>
2433	>	@article{Kawata01,
2434	>	Author = {M. Kawata and M. Mikami},
2435	>	Date-Added = {2008-01-08 14:58:56 -0500},
2436	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2437	>	Journal = {Chem. Phys. Lett.},
2438	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Kawata_Rapid2DEwald_01.pdf},
2439	>	Pages = {157-164},
2440	>	Title = {Rapid calculation of two-dimensional Ewald summation},
2441	>	Volume = 340,
2442	>	Year = 2001}
2443	>
2444	>	@inproceedings{Barker80,
2445	>	Author = {J.~A. Barker},
2446	>	Booktitle = {The problem of long-range forces in the computer simulation of condensed matter},
2447	>	Date-Added = {2008-01-08 14:58:56 -0500},
2448	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2449	>	Editor = {D. Ceperley},
2450	>	Pages = {45-6},
2451	>	Series = {NRCC Workshop Proceedings},
2452	>	Title = {Reaction field method for polar fluids},
2453	>	Volume = 9,
2454	>	Year = 1980}
2455	>
2456	>	@article{Blumen83,
2457	>	Author = {A. Blumen and J. Klafter and G. Zumofen},
2458	>	Date-Added = {2008-01-08 14:58:56 -0500},
2459	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2460	>	Journal = {Phys. Rev. B},
2461	>	Pages = {3429-3435},
2462	>	Title = {Recombination in amorphous materials as a continuous-time random-walk problem},
2463	>	Volume = 27,
2464	>	Year = 1983}
2465	>
2466	>	@article{Rabani00,
2467	>	Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
2468	>	Date-Added = {2008-01-08 14:58:56 -0500},
2469	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2470	>	Journal = prl,
2471	>	Pages = 467,
2472	>	Title = {Reply to `Comment on ``Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using th eCage Correlation Function'' '},
2473	>	Volume = 85,
2474	>	Year = 2000}
2475	>
2476	>	@article{Gezelter95,
2477	>	Author = {J.~D. Gezelter and W.~H. Miller},
2478	>	Date-Added = {2008-01-08 14:58:56 -0500},
2479	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2480	>	Journal = jcp,
2481	>	Pages = {7868-7876},
2482	>	Title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE RATE OF KETENE ISOMERIZATION},
2483	>	Volume = 103,
2484	>	Year = 1995}
2485	>
2486	>	@article{Gezelter98,
2487	>	Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
2488	>	Date-Added = {2008-01-08 14:58:56 -0500},
2489	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2490	>	Journal = jcp,
2491	>	Pages = 4695,
2492	>	Title = {Response to 'Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion'},
2493	>	Volume = 109,
2494	>	Year = 1998}
2495	>
2496	>	@article{Leidy02,
2497	>	Author = {Chad Leidy and Thomas Kaasgaard and John H. Crowe and Ole G. Mouritsen and Kent J\o gensen},
2498	>	Date-Added = {2008-01-08 14:58:56 -0500},
2499	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2500	>	Journal = bj,
2501	>	Pages = {2625-2633},
2502	>	Title = {Ripples and the Formation of Anisotropic Lipid Domains: Imaging Two-Component Supported Double Bilayers by Atomic Force Microscopy},
2503	>	Volume = 83,
2504	>	Year = 2002}
2505	>
2506	>	@article{Viot92b,
2507	>	Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
2508	>	Date-Added = {2008-01-08 14:58:56 -0500},
2509	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2510	>	Journal = {Physica A},
2511	>	Pages = {248-252},
2512	>	Title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION OF VERY ELONGATED PARTICLES},
2513	>	Volume = 191,
2514	>	Year = 1992}
2515	>
2516	>	@article{Viot92c,
2517	>	Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
2518	>	Date-Added = {2008-01-08 14:58:56 -0500},
2519	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2520	>	Journal = {Physica A},
2521	>	Pages = {248-252},
2522	>	Title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC PARTICLES},
2523	>	Volume = 191,
2524	>	Year = 1992}
2525	>
2526	>	@article{Pearlman95,
2527	>	Author = {David~A. Pearlman and David~A. Case and James~W. Caldwell and Wilson~S. Ross and Thomas~E. Cheatham~III and Steve DeBolt and David Ferguson and George Seibel and Peter Kollman},
2528	>	Date-Added = {2008-01-08 14:58:56 -0500},
2529	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2530	>	Journal = {Computer Physics Communications},
2531	>	Pages = {1-41},
2532	>	Title = {{\sc amber}, a package of computer programs for applying molecular mechanics. normal mode analysis, molecular dynamics, and free energy calculations to simulate the structural and energetic properties of molecules},
2533	>	Volume = 91,
2534	>	Year = 1995}
2535	>
2536	>	@article{Brooks83,
2537	>	Author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States and S. Swaminathan and M. Karplus},
2538	>	Date-Added = {2008-01-08 14:58:56 -0500},
2539	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2540	>	Journal = {J. Comp. Chem.},
2541	>	Pages = {187-217},
2542	>	Title = {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
2543	>	Volume = 4,
2544	>	Year = 1983}
2545	>
2546	>	@incollection{MacKerell98,
2547	>	Address = {New York},
2548	>	Author = {A.~D. {MacKerell, Jr.} and B. Brooks and C.~L. {Brooks III} and L. Nilsson and B. Roux and Y. Won and and M. Karplus},
2549	>	Booktitle = {The Encyclopedia of Computational Chemistry},
2550	>	Date-Added = {2008-01-08 14:58:56 -0500},
2551	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2552	>	Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
2553	>	Pages = {271-277},
2554	>	Publisher = {John Wiley \& Sons},
2555	>	Title = {{\sc charmm}: The Energy Function and Its Parameterization with an Overview of the Program},
2556	>	Volume = 1,
2557	>	Year = 1998}
2558	>
2559	>	@article{Li01,
2560	>	Author = {Z. Li and M. Lieberman and W. Hill},
2561	>	Date-Added = {2008-01-08 14:58:56 -0500},
2562	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2563	>	Journal = {Langmuir},
2564	>	Pages = {4887-4894},
2565	>	Title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine Monolayers: umbrella vs. octopus design strategies for formation of oriented {\sc sam}s},
2566	>	Volume = 17,
2567	>	Year = 2001}
2568	>
2569	>	@article{Shor95,
2570	>	Author = {P.~W. Shor},
2571	>	Date-Added = {2008-01-08 14:58:56 -0500},
2572	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2573	>	Journal = {Phys. Rev. A},
2574	>	Pages = {2493-2496},
2575	>	Title = {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY},
2576	>	Volume = 52,
2577	>	Year = 1995}
2578	>
2579	>	@article{Spath96,
2580	>	Author = {B.~W. Spath and W.~H. Miller},
2581	>	Date-Added = {2008-01-08 14:58:56 -0500},
2582	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2583	>	Journal = jcp,
2584	>	Pages = 95,
2585	>	Title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION PROBABILITIES},
2586	>	Volume = 104,
2587	>	Year = 1996}
2588	>
2589	>	@article{Sun97a,
2590	>	Author = {X. Sun and W.~H. Miller},
2591	>	Date-Added = {2008-01-08 14:58:56 -0500},
2592	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2593	>	Journal = jcp,
2594	>	Pages = 6346,
2595	>	Title = {Semiclassical initial value representation for electronically nonadiabatic molecular dynamics},
2596	>	Volume = 106,
2597	>	Year = 1997}
2598	>
2599	>	@article{Gomez03,
2600	>	Author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom},
2601	>	Date-Added = {2008-01-08 14:58:56 -0500},
2602	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2603	>	Journal = {Eur. Biophys. J.},
2604	>	Pages = {217-227},
2605	>	Title = {Setting up and optimization of membrane protein simulations},
2606	>	Volume = 31,
2607	>	Year = 2002}
2608	>
2609	>	@article{Stillinger98,
2610	>	Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
2611	>	Date-Added = {2008-01-08 14:58:56 -0500},
2612	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2613	>	Journal = {Nature},
2614	>	Pages = {554-557},
2615	>	Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
2616	>	Volume = 393,
2617	>	Year = 1998}
2618	>
2619	>	@article{Anheuser94,
2620	>	Author = {K. Anheuser and J.P. Northover},
2621	>	Date-Added = {2008-01-08 14:58:56 -0500},
2622	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2623	>	Journal = {Brit. Num. J.},
2624	>	Pages = 22,
2625	>	Title = {Silver plating of Roman and Celtic coins from Britan - a technical study},
2626	>	Volume = 64,
2627	>	Year = 1994}
2628	>
2629	>	@article{Feynman82,
2630	>	Author = {R.~P. Feynman},
2631	>	Date-Added = {2008-01-08 14:58:56 -0500},
2632	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2633	>	Journal = {Int. J. Theor. Phys.},
2634	>	Pages = {467-488},
2635	>	Title = {Simulating physics with computers},
2636	>	Volume = 21,
2637	>	Year = 1982}
2638	>
2639	>	@article{deLeeuw80,
2640	>	Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
2641	>	Date-Added = {2008-01-08 14:58:56 -0500},
2642	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2643	>	Journal = {Proc. R. Soc. London Ser. A},
2644	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
2645	>	Number = 1752,
2646	>	Pages = {27-56},
2647	>	Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
2648	>	Volume = 373,
2649	>	Year = 1980}
2650	>
2651	>	@article{Ercolessi88,
2652	>	Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
2653	>	Date-Added = {2008-01-08 14:58:56 -0500},
2654	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2655	>	Journal = {Philosophical Magazine A},
2656	>	Pages = {213-226},
2657	>	Title = {Simulation of Gold in the Glue Model.},
2658	>	Volume = 58,
2659	>	Year = 1988}
2660	>
2661	>	@article{Marrink01a,
2662	>	Author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
2663	>	Date-Added = {2008-01-08 14:58:56 -0500},
2664	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2665	>	Journal = jacs,
2666	>	Pages = {8638-8639},
2667	>	Title = {Simulations of the Spontaneous Aggregation of Phospholipids into Bilayers},
2668	>	Volume = 123,
2669	>	Year = 2001}
2670	>
2671	>	@article{Liu96b,
2672	>	Author = {Y. Liu and T. Ichiye},
2673	>	Date-Added = {2008-01-08 14:58:56 -0500},
2674	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2675	>	Journal = jpc,
2676	>	Pages = {2723-2730},
2677	>	Title = {Soft sticky dipole potential for liquid water: a new model},
2678	>	Volume = 100,
2679	>	Year = 1996}
2680	>
2681	>	@article{Brannigan04a,
2682	>	Author = {G. Brannigan and F.~L.~H. Brown},
2683	>	Date-Added = {2008-01-08 14:58:56 -0500},
2684	>	Date-Modified = {2008-01-08 14:59:01 -0500},
2685	>	Journal = jcp,
2686	>	Number = 2,
2687	>	Pages = {1059-1071},
2688	>	Title = {Solvent-free simulations of fluid membrane bilayers},
2689	>	Volume = 120,
2690	>	Year = 2004}
2691	>
2692	>	@article{Tolman20,
2693	>	Author = {R. C. Tolman},
2694	>	Date-Added = {2008-01-08 14:58:56 -0500},
2695	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2696	>	Journal = jacs,
2697	>	Pages = 2506,
2698	>	Title = {Statistical Mechanics Applied to Chemical Kinetics},
2699	>	Volume = 42,
2700	>	Year = 1920}
2701	>
2702	>	@book{Tolman27,
2703	>	Address = {New York},
2704	>	Author = {R. C. Tolman},
2705	>	Date-Added = {2008-01-08 14:58:56 -0500},
2706	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2707	>	Pages = {260-270},
2708	>	Publisher = {Chemical Catalog Co.},
2709	>	Title = {Statistical Mechanics with Applications to Physics and Chemistry},
2710	>	Year = 1927}
2711	>
2712	>	@book{Safran94,
2713	>	Address = {Reading, MA},
2714	>	Author = {S.~A. Safran},
2715	>	Date-Added = {2008-01-08 14:58:56 -0500},
2716	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2717	>	Publisher = {Addison-Wesley},
2718	>	Title = {Statistical Thermodynamics of Surfaces, Interfaces, and Membranes},
2719	>	Year = 1994}
2720	>
2721	>	@article{McCullough90,
2722	>	Author = {W. Scott McCullough and H. L. Scott},
2723	>	Date-Added = {2008-01-08 14:58:56 -0500},
2724	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2725	>	Journal = prl,
2726	>	Number = 7,
2727	>	Pages = {931-934},
2728	>	Title = {Statistical-Mechanial Theory of the Ripple Phase of Lipid Bilayers},
2729	>	Volume = 65,
2730	>	Year = 1990}
2731	>
2732	>	@article{Duncan04,
2733	>	Author = {Peter D. Duncan and Philip J. Camp},
2734	>	Date-Added = {2008-01-08 14:58:56 -0500},
2735	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2736	>	Journal = jcp,
2737	>	Number = 22,
2738	>	Pages = {11322-11331},
2739	>	Title = {Structure and dynamics in monolayer of dipolar spheres},
2740	>	Volume = 121,
2741	>	Year = 2004}
2742	>
2743	>	@article{Pomes96,
2744	>	Author = {R. Pomes and B. Roux},
2745	>	Date-Added = {2008-01-08 14:58:56 -0500},
2746	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2747	>	Journal = {Biophys. J.},
2748	>	Pages = {19-39},
2749	>	Title = {Structure and dynamics of a proton wire: A theoretical study of H+ translocation along the single-file water chain in the gramicidin a channel},
2750	>	Volume = 71,
2751	>	Year = 1996}
2752	>
2753	>	@article{NorbertKucerka04012005,
2754	>	Abstract = {Quantitative structures of the fully hydrated fluid phases of dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) were obtained at 30{degrees}C. Data for the relative form factors F(qz) for DMPC were obtained using a combination of four methods. 1), Volumetric data provided F(0). 2), Diffuse x-ray scattering from oriented stacks of bilayers provided relative form factors |F(qz)| for high qz, 0.22 < qz < 0.8 A-1. 3), X-ray scattering from extruded unilamellar vesicles with diameter 600 A provided |F(qz)| for low qz, 0.1 < qz < 0.3 A-1. 4), Previous measurements using a liquid crystallographic x-ray method provided |F(2{pi}h/D)| for h = 1 and 2 for a range of nearly fully hydrated D-spacings. The data from method 4 overlap and validate the new unilamellar vesicles data for DMPC, so method 4 is not required for DLPC or future studies. We used hybrid electron density models to obtain structural results from these form factors. Comparison of the model electron density profiles with that of gel phase DMPC provides areas per lipid A, 60.6 {+/-} 0.5 A2 for DMPC and 63.2 {+/-} 0.5 A2 for DLPC. Constraints on the model provided by volume measurements and component volumes obtained from simulations put the electron density profiles {rho}(z) and the corresponding form factors F(qz) on absolute scales. Various thicknesses, such as the hydrophobic thickness and the steric thickness, are obtained and compared to literature values.
2755	>	},
2756	>	Author = {Kucerka, Norbert and Liu, Yufeng and Chu, Nanjun and Petrache, Horia I. and Tristram-Nagle, Stephanie and Nagle, John F.},
2757	>	Date-Added = {2008-01-08 14:58:56 -0500},
2758	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2759	>	Doi = {10.1529/biophysj.104.056606},
2760	>	Eprint = {http://www.biophysj.org/cgi/reprint/88/4/2626.pdf},
2761	>	Journal = {Biophys. J.},
2762	>	Number = 4,
2763	>	Pages = {2626-2637},
2764	>	Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}},
2765	>	Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2766	>	Volume = 88,
2767	>	Year = 2005,
2768	>	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
2769	>	Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606}}
2770	>
2771	>	@article{Lenz07,
2772	>	Author = {Olaf Lenz and Friederike Schmid},
2773	>	Date-Added = {2008-01-08 14:58:56 -0500},
2774	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2775	>	Journal = prl,
2776	>	Number = 5,
2777	>	Pages = 058104,
2778	>	Title = {Structure of Symmetric and Asymmetric "Ripple" Phases in Lipid Bilayers},
2779	>	Volume = 98,
2780	>	Year = 2007}
2781	>
2782	>	@article{Sun96,
2783	>	Author = {W. J. Sun and S. Tristram-Nagle and R. M. Suter and J. F. Nagle},
2784	>	Date-Added = {2008-01-08 14:58:56 -0500},
2785	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2786	>	Journal = pnas,
2787	>	Pages = {7008-7012},
2788	>	Title = {Structure of the Ripple Phase in Lecithin Bilayers},
2789	>	Volume = 93,
2790	>	Year = 1996}
2791	>
2792	>	@article{Sengupta03,
2793	>	Author = {Kheya Sengupta and V. A. Raghunathan and John Katsaras},
2794	>	Date-Added = {2008-01-08 14:58:56 -0500},
2795	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2796	>	Journal = pre,
2797	>	Number = 031710,
2798	>	Pages = {1-12},
2799	>	Title = {Structure of the Ripple Phase of Phospholipid Multibilayers},
2800	>	Volume = 68,
2801	>	Year = 2003}
2802	>
2803	>	@article{Liu92,
2804	>	Author = {R.~S. Liu and D.~W. Qi and S. Wang},
2805	>	Date-Added = {2008-01-08 14:58:56 -0500},
2806	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2807	>	Journal = prb,
2808	>	Pages = {451-453},
2809	>	Title = {Subpeaks of structure factors for rapidly quenched metals},
2810	>	Volume = 45,
2811	>	Year = 1992}
2812	>
2813	>	@article{Ediger96,
2814	>	Author = {M.D. Ediger and C.A. Angell and Sidney R. Nagel},
2815	>	Date-Added = {2008-01-08 14:58:56 -0500},
2816	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2817	>	Journal = jpc,
2818	>	Pages = 13200,
2819	>	Title = {Supercooled Liquids and Glasses},
2820	>	Volume = 100,
2821	>	Year = 1996}
2822	>
2823	>	@article{Janiak79,
2824	>	Author = {M.~J. Janiak and D.~M. Small and G.~G. Shipley},
2825	>	Date-Added = {2008-01-08 14:58:56 -0500},
2826	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2827	>	Journal = {J. Biol. Chem.},
2828	>	Pages = {6068-6078},
2829	>	Title = {Temperature and Compositional Dependence of the Structure of Hydrated Dimyristoyl Lecithin},
2830	>	Volume = 254,
2831	>	Year = 1979}
2832	>
2833	>	@article{Kaasgaard03,
2834	>	Author = {Thomas Kaasgaard and Chad Leidy and John H. Crowe and Ole G. Mouritsen and Kent J{\o}rgensen},
2835	>	Date-Added = {2008-01-08 14:58:56 -0500},
2836	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2837	>	Journal = bj,
2838	>	Number = 1,
2839	>	Pages = {350-360},
2840	>	Title = {Temperature-Controlled Structure and Kinetics of Ripple Phases in One- and Two-Component Supported Lipid Bilayers},
2841	>	Volume = 85,
2842	>	Year = 2003}
2843	>
2844	>	@article{Holz00,
2845	>	Author = {M. Holz and S.~R. Heil and A. Sacco},
2846	>	Date-Added = {2008-01-08 14:58:56 -0500},
2847	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2848	>	Journal = {Phys. Chem. Chem. Phys.},
2849	>	Pages = {4740-4742},
2850	>	Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1${\sc h} {\sc nmr pfg} measurements},
2851	>	Volume = 2,
2852	>	Year = 2000}
2853	>
2854	>	@article{Kob95a,
2855	>	Author = {W. Kob and H.~C. Andersen},
2856	>	Date-Added = {2008-01-08 14:58:56 -0500},
2857	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2858	>	Journal = pre,
2859	>	Pages = {4626-4641},
2860	>	Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures: The van Hove corraltion function},
2861	>	Volume = 51,
2862	>	Year = 1995}
2863	>
2864	>	@article{Kob95b,
2865	>	Author = {W. Kob and H.~C. Andersen},
2866	>	Date-Added = {2008-01-08 14:58:56 -0500},
2867	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2868	>	Journal = pre,
2869	>	Pages = {4134-4153},
2870	>	Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures. II. Intermediate scattering function and dynamic susceptibility},
2871	>	Volume = 52,
2872	>	Year = 1995}
2873	>
2874	>	@article{Adams79,
2875	>	Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills},
2876	>	Date-Added = {2008-01-08 14:58:56 -0500},
2877	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2878	>	Journal = {Mol. Phys.},
2879	>	Number = 2,
2880	>	Pages = {387-400},
2881	>	Title = {The computer simulation of polar liquids},
2882	>	Volume = 38,
2883	>	Year = 1979}
2884	>
2885	>	@article{Pense92,
2886	>	Author = {A. W. Pense},
2887	>	Date-Added = {2008-01-08 14:58:56 -0500},
2888	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2889	>	Journal = {Mat. Char.},
2890	>	Pages = 213,
2891	>	Title = {The Decline and Fall of the Roman Denarius},
2892	>	Volume = 29,
2893	>	Year = 1992}
2894	>
2895	>	@article{Weber84,
2896	>	Author = {T.~A. Weber and F.~H. Stillinger},
2897	>	Date-Added = {2008-01-08 14:58:56 -0500},
2898	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2899	>	Journal = jcp,
2900	>	Number = 6,
2901	>	Pages = {2742-2746},
2902	>	Title = {The effect of density on the inherent structure in liquids},
2903	>	Volume = 80,
2904	>	Year = 1984}
2905	>
2906	>	@article{Teixeira00,
2907	>	Author = {P~I~C Teixeira and J~M Tavares and M~M Telo da Gama},
2908	>	Date-Added = {2008-01-08 14:58:56 -0500},
2909	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2910	>	Journal = {J. Phys.: Condens. Matter},
2911	>	Pages = {R411-R434},
2912	>	Title = {The effect of dipolar forces on the structure and thermodynamics of classical fluids},
2913	>	Volume = 12,
2914	>	Year = 2000}
2915	>
2916	>	@article{Parry75,
2917	>	Author = {D.~E. Parry},
2918	>	Date-Added = {2008-01-08 14:58:56 -0500},
2919	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2920	>	Journal = {Surf. Sci.},
2921	>	Pages = {433-440},
2922	>	Title = {The electrostatic potential in the surface region of an ionic crystal},
2923	>	Volume = 49,
2924	>	Year = 1975}
2925	>
2926	>	@article{Daw93,
2927	>	Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes},
2928	>	Date-Added = {2008-01-08 14:58:56 -0500},
2929	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2930	>	Journal = {Mat. Sci. Rep.},
2931	>	Pages = {251-310},
2932	>	Title = {The embededd-atom method},
2933	>	Volume = 9,
2934	>	Year = 1993}
2935	>
2936	>	@article{Stratt95,
2937	>	Author = {R.~M. Stratt},
2938	>	Date-Added = {2008-01-08 14:58:56 -0500},
2939	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2940	>	Journal = {Acc. Chem. Res.},
2941	>	Pages = {201-207},
2942	>	Title = {The instantaneous normal modes of liquids},
2943	>	Volume = 28,
2944	>	Year = 1995}
2945	>
2946	>	@article{Copeland80,
2947	>	Author = {B. R. Copeland and H. M. McConnell},
2948	>	Date-Added = {2008-01-08 14:58:56 -0500},
2949	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2950	>	Journal = {Biochim. Biophys. Acta.},
2951	>	Pages = {95-109},
2952	>	Title = {The Rippled Structure in Bilayer Membranes of Phosphatidylcholine and Binary Mixture of Phosphatidylcholine and Cholesterol},
2953	>	Volume = 599,
2954	>	Year = 1980}
2955	>
2956	>	@article{Bembenek96,
2957	>	Author = {S.~D. Bembenek and B.~B. Laird},
2958	>	Date-Added = {2008-01-08 14:58:56 -0500},
2959	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2960	>	Journal = jcp,
2961	>	Pages = 5199,
2962	>	Title = {The role of localization in glasses and supercooled liquids},
2963	>	Volume = 104,
2964	>	Year = 1996}
2965	>
2966	>	@article{Andrea83,
2967	>	Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
2968	>	Date-Added = {2008-01-08 14:58:56 -0500},
2969	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2970	>	Journal = {J. Chem. Phys.},
2971	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
2972	>	Number = 9,
2973	>	Pages = {4576-4584},
2974	>	Title = {The role of long ranged forces in determining the structure and properties of liquid water},
2975	>	Volume = 79,
2976	>	Year = 1983}
2977	>
2978	>	@article{Brannigan04b,
2979	>	Author = {G. Brannigan and A.~C. Tamboli and F.~L.~H. Brown},
2980	>	Date-Added = {2008-01-08 14:58:56 -0500},
2981	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2982	>	Journal = jcp,
2983	>	Key = 121,
2984	>	Pages = {3259-3271},
2985	>	Title = {The role of molecular shape in bilayer elasticity and phase behavior},
2986	>	Volume = 7,
2987	>	Year = 2004}
2988	>
2989	>	@article{Buchner92,
2990	>	Author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt},
2991	>	Date-Added = {2008-01-08 14:58:56 -0500},
2992	>	Date-Modified = {2008-01-08 14:59:02 -0500},
2993	>	Journal = jcp,
2994	>	Pages = {8522-8535},
2995	>	Title = {The short-time dynamics of molecular liquids. Instantaneous-normal-mode theory},
2996	>	Volume = 97,
2997	>	Year = 1992}
2998	>
2999	>	@article{Liu96a,
3000	>	Author = {Y. Liu and T. Ichiye},
3001	>	Date-Added = {2008-01-08 14:58:56 -0500},
3002	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3003	>	Journal = {Chem. Phys. Lett.},
3004	>	Pages = {334-340},
3005	>	Title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
3006	>	Volume = 256,
3007	>	Year = 1996}
3008	>
3009	>	@article{Holm05,
3010	>	Author = {C. Holm and J.-J. Weis},
3011	>	Date-Added = {2008-01-08 14:58:56 -0500},
3012	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3013	>	Journal = {Curr. Opin. Colloid Interface Sci.},
3014	>	Pages = {133-140},
3015	>	Title = {The structure of ferrofluids: A status report},
3016	>	Volume = 10,
3017	>	Year = 2005}
3018	>
3019	>	@article{Luttinger46,
3020	>	Author = {J. M. Luttinger and L. Tisza},
3021	>	Date-Added = {2008-01-08 14:58:56 -0500},
3022	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3023	>	Journal = {Physical Review},
3024	>	Number = 11,
3025	>	Pages = {954-964},
3026	>	Title = {Theory of Dipole Interaction in Crystals},
3027	>	Volume = 70,
3028	>	Year = 1946}
3029	>
3030	>	@article{Toulouse1977,
3031	>	Author = {G. Toulouse},
3032	>	Date-Added = {2008-01-08 14:58:56 -0500},
3033	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3034	>	Journal = {Commun. Phys.},
3035	>	Number = 4,
3036	>	Pages = {115-119},
3037	>	Title = {Theory of Frustration Effect in Spin-Glasses. I.},
3038	>	Volume = 2,
3039	>	Year = 1977}
3040	>
3041	>	@article{Carlson87,
3042	>	Author = {J.~M. Carlson and J.~P. Sethna},
3043	>	Date-Added = {2008-01-08 14:58:56 -0500},
3044	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3045	>	Journal = pra,
3046	>	Number = 7,
3047	>	Pages = 3359,
3048	>	Title = {Theory of ripple phase in hydrated phospholipid bilayers},
3049	>	Volume = 36,
3050	>	Year = 1987}
3051	>
3052	>	@article{Lubensky93,
3053	>	Author = {T. C. Lubensky and F. C. MacKintosh},
3054	>	Date-Added = {2008-01-08 14:58:56 -0500},
3055	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3056	>	Journal = prl,
3057	>	Number = 10,
3058	>	Pages = {1565-1568},
3059	>	Title = {Theory of ``Ripple'' Phases of Lipid Bilayers},
3060	>	Volume = 71,
3061	>	Year = 1993}
3062	>
3063	>	@book{Hansen86,
3064	>	Address = {London},
3065	>	Author = {J.~P. Hansen and I.~R. McDonald},
3066	>	Chapter = 7,
3067	>	Date-Added = {2008-01-08 14:58:56 -0500},
3068	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3069	>	Pages = {199-206},
3070	>	Publisher = {Academic Press},
3071	>	Title = {Theory of Simple Liquids},
3072	>	Year = 1986}
3073	>
3074	>	@article{Marder84,
3075	>	Author = {M. Marder and H.~L. Frisch and J.~S. Langer and H.~M. McConnell},
3076	>	Date-Added = {2008-01-08 14:58:56 -0500},
3077	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3078	>	Journal = pnas,
3079	>	Pages = {6559-6561},
3080	>	Title = {Theory of the intermediate rippled phase of phospholipid bilayers},
3081	>	Volume = 81,
3082	>	Year = 1984}
3083	>
3084	>	@book{Tobias90,
3085	>	Address = {Tucson},
3086	>	Author = {Sheila Tobias},
3087	>	Date-Added = {2008-01-08 14:58:56 -0500},
3088	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3089	>	Publisher = {Research Corp.},
3090	>	Title = {They're not Dumb. They're Different: Stalking the Second Tier},
3091	>	Year = 1990}
3092	>
3093	>	@article{Tao91,
3094	>	Author = {R. Tao and J. M. Sun},
3095	>	Date-Added = {2008-01-08 14:58:56 -0500},
3096	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3097	>	Journal = prl,
3098	>	Number = 3,
3099	>	Pages = {398-401},
3100	>	Title = {Three-Dimensional Structure of Induced Electrorheological Solid},
3101	>	Volume = 67,
3102	>	Year = 1991}
3103	>
3104	>	@article{Bratko95,
3105	>	Author = {L. Blum and F. Vericat and D. Bratko},
3106	>	Date-Added = {2008-01-08 14:58:56 -0500},
3107	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3108	>	Journal = jcp,
3109	>	Number = 3,
3110	>	Pages = {1461-1462},
3111	>	Title = {Towards an analytical model of water: The octupolar model},
3112	>	Volume = 102,
3113	>	Year = 1995}
3114	>
3115	>	@article{Martin98,
3116	>	Author = {M. Martin and J.~I. Siepmann},
3117	>	Date-Added = {2008-01-08 14:58:56 -0500},
3118	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3119	>	Journal = jpcB,
3120	>	Pages = {2569-2577},
3121	>	Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes},
3122	>	Volume = 102,
3123	>	Year = 1998}
3124	>
3125	>	@article{Misbah98,
3126	>	Author = {C. Misbah and J. Duplat and B. Houchmandzadeh},
3127	>	Date-Added = {2008-01-08 14:58:56 -0500},
3128	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3129	>	Journal = prl,
3130	>	Number = 20,
3131	>	Pages = {4598-4601},
3132	>	Title = {Transition to Ripple Phases in Hydrated Amphiphiles},
3133	>	Volume = 80,
3134	>	Year = 1998}
3135	>
3136	>	@article{Alemany98,
3137	>	Author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego},
3138	>	Date-Added = {2008-01-08 14:58:56 -0500},
3139	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3140	>	Journal = jcp,
3141	>	Pages = {5175-5176},
3142	>	Title = {Transport coefficients of liquid transition metals: A computer simulation study using the embedded atom model},
3143	>	Volume = 109,
3144	>	Year = 1998}
3145	>
3146	>	@article{Born12,
3147	>	Author = {M. Born and Th. Von~Karman},
3148	>	Date-Added = {2008-01-08 14:58:56 -0500},
3149	>	Date-Modified = {2008-01-08 14:59:02 -0500},
3150	>	Journal = {Physik Z.},
3151	>	Number = {297-309},
3152	>	Title = {Uber Schwingungen in Raumgittern},
3153	>	Volume = 13,
3154	>	Year = 1912}
3155	>
3156	>	@incollection{Angell85,
3157	>	Address = {Springfield, VA},
3158	>	Author = {C.~A. Angell},
3159	>	Booktitle = {Relaxations in Complex Systems},
3160	>	Date-Added = {2008-01-08 14:58:56 -0500},
3161	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3162	>	Editor = {K.~Ngai and G.~B. Wright},
3163	>	Pages = 1,
3164	>	Publisher = {National Technical Information Service, U.S. Department of Commerce},
3165	>	Title = {unknown},
3166	>	Year = 1985}
3167	>
3168	>	@article{Ribeiro98,
3169	>	Author = {M.~C.~C. Ribeiro and P.~A. Madden},
3170	>	Date-Added = {2008-01-08 14:58:56 -0500},
3171	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3172	>	Journal = jcp,
3173	>	Pages = {3256-3263},
3174	>	Title = {Unstable Modes in Ionic Melts},
3175	>	Volume = 108,
3176	>	Year = 1998}
3177	>
3178	>	@article{Mutz1991,
3179	>	Author = {Mutz, M. and Bensimon, D. and Brienne, M. J.},
3180	>	Date-Added = {2008-01-08 14:58:56 -0500},
3181	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3182	>	Doi = {10.1103/PhysRevLett.67.923},
3183	>	Journal = {Phys. Rev. Lett.},
3184	>	Month = {Aug},
3185	>	Number = 7,
3186	>	Numpages = 3,
3187	>	Pages = {923--926},
3188	>	Publisher = {American Physical Society},
3189	>	Title = {Wrinkling transition in partially polymerized vesicles},
3190	>	Volume = 67,
3191	>	Year = 1991,
3192	>	Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923}}
3193	>
3194	>	@article{Wendt78,
3195	>	Author = {H. Wendt and F.~F. Abraham},
3196	>	Date-Added = {2008-01-08 14:58:56 -0500},
3197	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3198	>	Journal = prl,
3199	>	Pages = 1244,
3200	>	Volume = 41,
3201	>	Year = 1978}
3202	>
3203	>	@unpublished{Truhlar00,
3204	>	Author = {D.~G. Truhlar and A. Kohen},
3205	>	Date-Added = {2008-01-08 14:58:56 -0500},
3206	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3207	>	Note = {private correspondence},
3208	>	Year = 2000}
3209	>
3210	>	@article{Dwyer1977,
3211	>	Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
3212	>	Date-Added = {2008-01-08 14:58:56 -0500},
3213	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3214	>	Journal = {Surf. Sci.},
3215	>	Pages = 617,
3216	>	Volume = 64,
3217	>	Year = 1977}
3218	>
3219	>	@article{Macritche78,
3220	>	Author = {F. MacRitche},
3221	>	Date-Added = {2008-01-08 14:58:56 -0500},
3222	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3223	>	Journal = {Adv. Protein Chem.},
3224	>	Pages = 283,
3225	>	Volume = 32,
3226	>	Year = 1978}
3227	>
3228	>	@article{Feder80,
3229	>	Author = {J. Feder},
3230	>	Date-Added = {2008-01-08 14:58:56 -0500},
3231	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3232	>	Journal = {J. Theor. Biol.},
3233	>	Pages = 237,
3234	>	Volume = 87,
3235	>	Year = 1980}
3236	>
3237	>	@article{Ramsden93,
3238	>	Author = {J.~J. Ramsden},
3239	>	Date-Added = {2008-01-08 14:58:56 -0500},
3240	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3241	>	Journal = prl,
3242	>	Pages = 295,
3243	>	Volume = 71,
3244	>	Year = 1993}
3245	>
3246	>	@article{Egelhoff89,
3247	>	Author = {W.~F. Egelhoff and I. Jacob},
3248	>	Date-Added = {2008-01-08 14:58:56 -0500},
3249	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3250	>	Journal = prl,
3251	>	Pages = 921,
3252	>	Volume = 62,
3253	>	Year = 1989}
3254	>
3255	>	@article{Dobson1987,
3256	>	Author = {B.~W. Dobson},
3257	>	Date-Added = {2008-01-08 14:58:56 -0500},
3258	>	Date-Modified = {2008-01-08 14:59:03 -0500},
3259	>	Journal = prb,
3260	>	Pages = 1068,
3261	>	Volume = 36,
3262	>	Year = 1987}
3263	>
3264	>	@article{Davis:1969uq,
3265	>	Abstract = { Exact solutions of the Stokes equations are derived for the case of two unequal spheres slowly rotating or translating perpendicular to their line of centers in a quiescent, unbounded viscous fluid, following Wakiya[16]. Numerical results are presented for the force and torque coefficients for size ratios from 1[middle dot]0 to 10[middle dot]0, and separations down to 0[middle dot]001 times the radius of the smaller.},
3266	>	Author = {Davis, M. H.},
3267	>	Date-Added = {2008-01-08 14:57:14 -0500},
3268	>	Date-Modified = {2008-01-08 14:57:14 -0500},
3269	>	Journal = {Chemical Engineering Science},
3270	>	Number = 12,
3271	>	Pages = {1769--1776},
3272	>	Title = {The slow translation and rotation of two unequal spheres in a viscous fluid},
3273	>	Ty = {JOUR},
3274	>	Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
3275	>	Volume = 24,
3276	>	Year = 1969,
3277	>	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}}
3278	>
3279	>	@article{Stimson:1926qy,
3280	>	Author = {Stimson, M and Jeffery, GB},
3281	>	Date-Added = {2008-01-08 14:51:23 -0500},
3282	>	Date-Modified = {2008-01-08 14:51:35 -0500},
3283	>	Journal = {Proceedings of the Royal Society of London Series A-Containing Papers of a Mathematical and Physical Character},
3284	>	Pages = {110-116},
3285	>	Title = {The motion of two spheres in a viscous fluid},
3286	>	Volume = 111,
3287	>	Year = 1926}
3288	>
3289	>	@article{Orlandi:2006fk,
3290	>	Abstract = {Liquid crystal phases formed by bent-shaped (or {\tt{}"{}}banana{\tt{}"{}}) molecules are currently of great interest. Here we investigate by Monte Carlo computer simulations the phases formed by rigid banana molecules modeled combining three Gay-Berne sites and containing either one central or two lateral and transversal dipoles. We show that changing the dipole position and orientation has a profound effect on the mesophase stability and molecular organization. In particular, we find a uniaxial nematic phase only for off-center dipolar models and tilted phases only for the one with terminal dipoles.},
3291	>	Address = {Dipartimento di Chimica Fisica e Inorganica, and INSTM, Universita di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.},
3292	>	Au = {Orlandi, S and Berardi, R and Steltzer, J and Zannoni, C},
3293	>	Author = {Orlandi, Silvia and Berardi, Roberto and Steltzer, Joachim and Zannoni, Claudio},
3294	>	Da = 20060407,
3295	>	Date-Added = {2008-01-08 14:47:56 -0500},
3296	>	Date-Modified = {2008-01-08 14:48:06 -0500},
3297	>	Dcom = 20070727,
3298	>	Doi = {10.1063/1.2176622},
3299	>	Edat = {2006/04/08 09:00},
3300	>	Issn = {0021-9606 (Print)},
3301	>	Jid = 0375360,
3302	>	Journal = {J Chem Phys},
3303	>	Jt = {The Journal of chemical physics},
3304	>	Language = {eng},
3305	>	Mhda = {2006/04/08 09:01},
3306	>	Number = 12,
3307	>	Own = {NLM},
3308	>	Pages = 124907,
3309	>	Pl = {United States},
3310	>	Pmid = 16599725,
3311	>	Pst = {ppublish},
3312	>	Pt = {Journal Article},
3313	>	Pubm = {Print},
3314	>	So = {J Chem Phys. 2006 Mar 28;124(12):124907.},
3315	>	Stat = {PubMed-not-MEDLINE},
3316	>	Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.},
3317	>	Volume = 124,
3318	>	Year = 2006,
3319	>	Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}}
3320	>
3321	>	@article{sun:031602,
3322	>	Author = {Xiuquan Sun and J. Daniel Gezelter},
3323	>	Date-Added = {2008-01-08 14:42:33 -0500},
3324	>	Date-Modified = {2008-01-08 14:42:33 -0500},
3325	>	Doi = {10.1103/PhysRevE.75.031602},
3326	>	Eid = 031602,
3327	>	Journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)},
3328	>	Keywords = {lattice theory; membranes},
3329	>	Number = 3,
3330	>	Numpages = 7,
3331	>	Pages = 031602,
3332	>	Publisher = {APS},
3333	>	Title = {Spontaneous corrugation of dipolar membranes},
3334	>	Url = {http://link.aps.org/abstract/PRE/v75/e031602},
3335	>	Volume = 75,
3336	>	Year = 2007,
3337	>	Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602},
3338	>	Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}}
3339	>
3340	>	@article{Ortega:2007lr,
3341	>	Abstract = {The equivalent radius for any solution property is the radius of a spherical particle having the same value of solution property as that of the macromolecule under consideration. Equivalent radii for different properties present a dependence on size and shape that are more similar than the values of the properties themselves. Furthermore, the ratios of equivalent radii of two properties depend on the conformation (shape or flexibility), but not on the absolute sizes. We define equivalent radii and their ratios, and describe their evaluation for some common models of rigid and flexible macromolecules. Using radii and ratios, we have devised procedures to fit macromolecular models to experimental properties, allowing the determination of the model parameters. Using these quantities, we can construct target functions for an equilibrated, unbiased optimization. The procedures, which have been implemented in public-domain computer programs, are illustrated for rigid, globular proteins, and the rodlike tobacco mosaic virus, and for semiflexible, wormlike heparin molecules.},
3342	>	Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.},
3343	>	Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3344	>	Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
3345	>	Da = 20070813,
3346	>	Date-Added = {2008-01-08 14:38:03 -0500},
3347	>	Date-Modified = {2008-01-08 14:38:49 -0500},
3348	>	Dcom = 20071017,
3349	>	Dep = 20070724,
3350	>	Doi = {10.1021/bm700473f},
3351	>	Edat = {2007/07/25 09:00},
3352	>	Issn = {1525-7797 (Print)},
3353	>	Jid = 100892849,
3354	>	Journal = {Biomacromolecules},
3355	>	Jt = {Biomacromolecules},
3356	>	Keywords = {Computer Simulation; Heparin/chemistry; Macromolecular Substances/*chemistry; *Models, Chemical; *Models, Molecular; Molecular Conformation; Particle Size; Protein Conformation; Proteins/chemistry; Software; Solutions},
3357	>	Language = {eng},
3358	>	Mhda = {2007/10/18 09:00},
3359	>	Number = 8,
3360	>	Own = {NLM},
3361	>	Pages = {2464--2475},
3362	>	Phst = {2007/07/24 {$[$}aheadofprint{$]$}},
3363	>	Pl = {United States},
3364	>	Pmid = 17645309,
3365	>	Pst = {ppublish},
3366	>	Pt = {Journal Article; Research Support, Non-U.S. Gov't},
3367	>	Pubm = {Print-Electronic},
3368	>	Rn = {0 (Macromolecular Substances); 0 (Proteins); 0 (Solutions); 9005-49-6 (Heparin)},
3369	>	Sb = {IM},
3370	>	So = {Biomacromolecules. 2007 Aug;8(8):2464-75. Epub 2007 Jul 24.},
3371	>	Stat = {MEDLINE},
3372	>	Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.},
3373	>	Volume = 8,
3374	>	Year = 2007,
3375	>	Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}}
3376	>
3377	>	@article{Torre2003,
3378	>	Abstract = {While the prediction of hydrodynamic properties of rigid particles
3379	>	is nowadays feasible using simple and efficient computer programs,
3380	>	the calculation of such properties and, in general, the dynamic
3381	>	behavior of flexible macromolecules has not reached a similar situation.
3382	>	Although the theories are available, usually the computational work
3383	>	is done using solutions specific for each problem. We intend to
3384	>	develop computer programs that would greatly facilitate the task
3385	>	of predicting solution behavior of flexible macromolecules. In this
3386	>	paper, we first present an overview of the two approaches that are
3387	>	most practical: the Monte Carlo rigid-body treatment, and the Brownian
3388	>	dynamics simulation technique. The Monte Carlo procedure is based
3389	>	on the calculation of properties for instantaneous conformations
3390	>	of the macromolecule that are regarded as if they were instantaneously
3391	>	rigid. We describe how a Monte Carlo program can be interfaced to
3392	>	the programs in the HYDRO suite for rigid particles, and provide
3393	>	an example of such calculation, for a hypothetical particle: a protein
3394	>	with two domains connected by a flexible linker. We also describe
3395	>	briefly the essentials of Brownian dynamics, and propose a general
3396	>	mechanical model that includes several kinds of intramolecular interactions,
3397	>	such as bending, internal rotation, excluded volume effects, etc.
3398	>	We provide an example of the application of this methodology to
3399	>	the dynamics of a semiflexible, wormlike DNA.},
3400	>	Annote = {724XK Times Cited:6 Cited References Count:64},
3401	>	Author = {{Garc\'{i}a de la Torre}, Jose and H. E. Sanchez and A. Ortega and J. G. Hernandez and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez},
3402	>	Issn = {0175-7571},
3403	>	Journal = {European Biophysics Journal with Biophysics Letters},
3404	>	Month = {Aug},
3405	>	Number = 5,
3406	>	Pages = {477-486},
3407	>	Title = {Calculation of the solution properties of flexible macromolecules: methods and applications},
3408	>	Uri = {<Go to ISI>://000185513400011},
3409	>	Volume = 32,
3410	>	Year = 2003}
3411	>
3412	>	@article{Alakent2005,
3413	>	Abstract = {Time series analysis tools are employed on the principal modes obtained
3414	>	from the C-alpha trajectories from two independent molecular-dynamics
3415	>	simulations of alpha-amylase inhibitor (tendamistat). Fluctuations
3416	>	inside an energy minimum (intraminimum motions), transitions between
3417	>	minima (interminimum motions), and relaxations in different hierarchical
3418	>	energy levels are investigated and compared with those encountered
3419	>	in vacuum by using different sampling window sizes and intervals.
3420	>	The low-frequency low-indexed mode relationship, established in
3421	>	vacuum, is also encountered in water, which shows the reliability
3422	>	of the important dynamics information offered by principal components
3423	>	analysis in water. It has been shown that examining a short data
3424	>	collection period (100 ps) may result in a high population of overdamped
3425	>	modes, while some of the low-frequency oscillations (< 10 cm(-1))
3426	>	can be captured in water by using a longer data collection period
3427	>	(1200 ps). Simultaneous analysis of short and long sampling window
3428	>	sizes gives the following picture of the effect of water on protein
3429	>	dynamics. Water makes the protein lose its memory: future conformations
3430	>	are less dependent on previous conformations due to the lowering
3431	>	of energy barriers in hierarchical levels of the energy landscape.
3432	>	In short-time dynamics (< 10 ps), damping factors extracted from
3433	>	time series model parameters are lowered. For tendamistat, the friction
3434	>	coefficient in the Langevin equation is found to be around 40-60
3435	>	cm(-1) for the low-indexed modes, compatible with literature. The
3436	>	fact that water has increased the friction and that on the other
3437	>	hand has lubrication effect at first sight contradicts. However,
3438	>	this comes about because water enhances the transitions between
3439	>	minima and forces the protein to reduce its already inherent inability
3440	>	to maintain oscillations observed in vacuum. Some of the frequencies
3441	>	lower than 10 cm(-1) are found to be overdamped, while those higher
3442	>	than 20 cm(-1) are slightly increased. As for the long-time dynamics
3443	>	in water, it is found that random-walk motion is maintained for
3444	>	approximately 200 ps (about five times of that in vacuum) in the
3445	>	low-indexed modes, showing the lowering of energy barriers between
3446	>	the higher-level minima.},
3447	>	Annote = {973OH Times Cited:1 Cited References Count:33},
3448	>	Author = {B. Alakent and M. C. Camurdan and P. Doruker},
3449	>	Issn = {0021-9606},
3450	>	Journal = {Journal of Chemical Physics},
3451	>	Month = {Oct 8},
3452	>	Number = 14,
3453	>	Pages = {-},
3454	>	Title = {Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects},
3455	>	Uri = {<Go to ISI>://000232532000064},
3456	>	Volume = 123,
3457	>	Year = 2005}
3458	>
3459	>	@book{Alexander1987,
3460	>	Address = {New York},
3461	>	Author = {C. Alexander},
3462	>	Publisher = {Oxford University Press},
3463	>	Title = {A Pattern Language: Towns, Buildings, Construction},
3464	>	Year = 1987}
3465	>
3466	>	@book{Allen1987,
3467	>	Address = {New York},
3468	>	Author = {M.~P. Allen and D.~J. Tildesley},
3469	>	Publisher = {Oxford University Press},
3470	>	Title = {Computer Simulations of Liquids},
3471	>	Year = 1987}
3472	>
3473	>	@article{Allison1991,
3474	>	Abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
3475	>	of rigid macromolecules. It is applied to polarized dynamic light
3476	>	scattering from rodlike sturctures and from a model of a DNA fragment
3477	>	(762 base pairs). A number of rod cases are examined in which the
3478	>	translational anisotropy is increased form zero to a large value.
3479	>	Simulated first cumulants as well as amplitudes and lifetimes of
3480	>	the dynamic form factor are compared with predictions of analytic
3481	>	theories and found to be in very good agreement with them. For DNA
3482	>	fragments 762 base pairs in length or longer, translational anisotropy
3483	>	does not contribute significantly to dynamic light scattering. In
3484	>	a comparison of rigid and flexible simulations on semistiff models
3485	>	of this fragment, it is shown directly that flexing contributes
3486	>	to the faster decay processes probed by light scattering and that
3487	>	the flexible model studies are in good agreement with experiment.},
3488	>	Annote = {Eu814 Times Cited:8 Cited References Count:32},
3489	>	Author = {S. A. Allison},
3490	>	Issn = {0024-9297},
3491	>	Journal = {Macromolecules},
3492	>	Month = {Jan 21},
3493	>	Number = 2,
3494	>	Pages = {530-536},
3495	>	Title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application to Polarized Dynamic Light-Scattering},
3496	>	Uri = {<Go to ISI>://A1991EU81400029},
3497	>	Volume = 24,
3498	>	Year = 1991}
3499	>
3500	>	@article{Andersen1983,
3501	>	Annote = {Rq238 Times Cited:559 Cited References Count:14},
3502	>	Author = {H. C. Andersen},
3503	>	Issn = {0021-9991},
3504	>	Journal = {Journal of Computational Physics},
3505	>	Number = 1,
3506	>	Pages = {24-34},
3507	>	Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
3508	>	Uri = {<Go to ISI>://A1983RQ23800002},
3509	>	Volume = 52,
3510	>	Year = 1983}
3511	>
3512	>	@article{Auerbach2005,
3513	>	Abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
3514	>	stable #closed# and #open# conformations. In patch clamp recordings,
3515	>	diliganded AChR gating appears to be a simple, two-state reaction.
3516	>	However, mutagenesis studies indicate that during gating dozens
3517	>	of residues across the protein move asynchronously and are organized
3518	>	into rigid body gating domains (#blocks#). Moreover, there is an
3519	>	upper limit to the apparent channel opening rate constant. These
3520	>	observations suggest that the gating reaction has a broad, corrugated
3521	>	transition state region, with the maximum opening rate reflecting,
3522	>	in part, the mean first-passage time across this ensemble. Simulations
3523	>	reveal that a flat, isotropic energy profile for the transition
3524	>	state can account for many of the essential features of AChR gating.
3525	>	With this mechanism, concerted, local structural transitions that
3526	>	occur on the broad transition state ensemble give rise to fractional
3527	>	measures of reaction progress (Phi values) determined by rate-equilibrium
3528	>	free energy relationship analysis. The results suggest that the
3529	>	coarse-grained AChR gating conformational change propagates through
3530	>	the protein with dynamics that are governed by the Brownian motion
3531	>	of individual gating blocks.},
3532	>	Annote = {895QF Times Cited:9 Cited References Count:33},
3533	>	Author = {A. Auerbach},
3534	>	Issn = {0027-8424},
3535	>	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
3536	>	Month = {Feb 1},
3537	>	Number = 5,
3538	>	Pages = {1408-1412},
3539	>	Title = {Gating of acetylcholine receptor channels: Brownian motion across a broad transition state},
3540	>	Uri = {<Go to ISI>://000226877300030},
3541	>	Volume = 102,
3542	>	Year = 2005}
3543	>
3544	>	@article{Baber1995,
3545	>	Abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
3546	>	on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine
3547	>	membranes in the liquid crystalline phase was investigated using
3548	>	H-2 NMR. Upon the addition of the anesthetics, the first five methylene
3549	>	units near the interface generally show a very small increase in
3550	>	segmental order, while segments deeper within the bilayer show a
3551	>	small decrease in segmental order. From the H-2 NMR results, the
3552	>	chain length for the perdeuterated palmitoyl chain in the absence
3553	>	of anesthetic was found to be 12.35 Angstrom. Upon the addition
3554	>	of halothane enflurane, or isoflurane, the acyl chain undergoes
3555	>	slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively,
3556	>	at 50 mol % anesthetic. A simple model was used to estimate the
3557	>	relative amounts of anesthetic located near the interface and deeper
3558	>	in the bilayer hydrocarbon region, and only a slight preference
3559	>	for an interfacial location was observed. Intermolecular H-1-H-1
3560	>	nuclear Overhauser effects (NOEs) were measured between phospholipid
3561	>	and halothane protons. These NOEs are consistent with the intramembrane
3562	>	location of the anesthetics suggested by the H-2 NMR data. In addition,
3563	>	the NOE data indicate that anesthetics prefer the interfacial and
3564	>	hydrocarbon regions of the membrane and are not found in high concentrations
3565	>	in the phospholipid headgroup.},
3566	>	Annote = {Qz716 Times Cited:38 Cited References Count:37},
3567	>	Author = {J. Baber and J. F. Ellena and D. S. Cafiso},
3568	>	Issn = {0006-2960},
3569	>	Journal = {Biochemistry},
3570	>	Month = {May 16},
3571	>	Number = 19,
3572	>	Pages = {6533-6539},
3573	>	Title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
3574	>	Uri = {<Go to ISI>://A1995QZ71600035},
3575	>	Volume = 34,
3576	>	Year = 1995}
3577	>
3578	>	@article{Banerjee2004,
3579	>	Abstract = {Based on a coherent state representation of noise operator and an
3580	>	ensemble averaging procedure using Wigner canonical thermal distribution
3581	>	for harmonic oscillators, a generalized quantum Langevin equation
3582	>	has been recently developed [Phys. Rev. E 65, 021109 (2002); 66,
3583	>	051106 (2002)] to derive the equations of motion for probability
3584	>	distribution functions in c-number phase-space. We extend the treatment
3585	>	to explore several systematic approximation schemes for the solutions
3586	>	of the Langevin equation for nonlinear potentials for a wide range
3587	>	of noise correlation, strength and temperature down to the vacuum
3588	>	limit. The method is exemplified by an analytic application to harmonic
3589	>	oscillator for arbitrary memory kernel and with the help of a numerical
3590	>	calculation of barrier crossing, in a cubic potential to demonstrate
3591	>	the quantum Kramers' turnover and the quantum Arrhenius plot. (C)
3592	>	2004 American Institute of Physics.},
3593	>	Annote = {816YY Times Cited:8 Cited References Count:35},
3594	>	Author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
3595	>	Issn = {0021-9606},
3596	>	Journal = {Journal of Chemical Physics},
3597	>	Month = {May 15},
3598	>	Number = 19,
3599	>	Pages = {8960-8972},
3600	>	Title = {Solution of quantum Langevin equation: Approximations, theoretical and numerical aspects},
3601	>	Uri = {<Go to ISI>://000221146400009},
3602	>	Volume = 120,
3603	>	Year = 2004}
3604	>
3605	>	@article{Barojas1973,
3606	>	Author = {J. Barojas and D. Levesque},
3607	>	Journal = {Phys. Rev. A},
3608	>	Pages = {1092-1105},
3609	>	Title = {Simulation of Diatomic Homonuclear Liquids},
3610	>	Volume = 7,
3611	>	Year = 1973}
3612	>
3613	>	@article{Barth1998,
3614	>	Abstract = {We present an efficient new method termed LN for propagating biomolecular
3615	>	dynamics according to the Langevin equation that arose fortuitously
3616	>	upon analysis of the range of harmonic validity of our normal-mode
3617	>	scheme LIN. LN combines force linearization with force splitting
3618	>	techniques and disposes of LIN'S computationally intensive minimization
3619	>	(anharmonic correction) component. Unlike the competitive multiple-timestepping
3620	>	(MTS) schemes today-formulated to be symplectic and time-reversible-LN
3621	>	merges the slow and fast forces via extrapolation rather than impulses;
3622	>	the Langevin heat bath prevents systematic energy drifts. This combination
3623	>	succeeds in achieving more significant speedups than these MTS methods
3624	>	which are Limited by resonance artifacts to an outer timestep less
3625	>	than some integer multiple of half the period of the fastest motion
3626	>	(around 4-5 fs for biomolecules). We show that LN achieves very
3627	>	good agreement with small-timestep solutions of the Langevin equation
3628	>	in terms of thermodynamics (energy means and variances), geometry,
3629	>	and dynamics (spectral densities) for two proteins in vacuum and
3630	>	a large water system. Significantly, the frequency of updating the
3631	>	slow forces extends to 48 fs or more, resulting in speedup factors
3632	>	exceeding 10. The implementation of LN in any program that employs
3633	>	force-splitting computations is straightforward, with only partial
3634	>	second-derivative information required, as well as sparse Hessian/vector
3635	>	multiplication routines. The linearization part of LN could even
3636	>	be replaced by direct evaluation of the fast components. The application
3637	>	of LN to biomolecular dynamics is well suited for configurational
3638	>	sampling, thermodynamic, and structural questions. (C) 1998 American
3639	>	Institute of Physics.},
3640	>	Annote = {105HH Times Cited:29 Cited References Count:49},
3641	>	Author = {E. Barth and T. Schlick},
3642	>	Issn = {0021-9606},
3643	>	Journal = {Journal of Chemical Physics},
3644	>	Month = {Aug 1},
3645	>	Number = 5,
3646	>	Pages = {1617-1632},
3647	>	Title = {Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN},
3648	>	Uri = {<Go to ISI>://000075066300006},
3649	>	Volume = 109,
3650	>	Year = 1998}
3651	>
3652	>	@article{Batcho2001,
3653	>	Abstract = {We present an analysis for a simple two-component harmonic oscillator
3654	>	that compares the use of position-Verlet to velocity-Verlet for
3655	>	multiple-time step integration. The numerical stability analysis
3656	>	based on the impulse-Verlet splitting shows that position-Verlet
3657	>	has enhanced stability, in terms of the largest allowable time step,
3658	>	for cases where an ample separation of time scales exists. Numerical
3659	>	investigations confirm the advantages of the position-Verlet scheme
3660	>	when used for the fastest time scales of the system. Applications
3661	>	to a biomolecule. a solvated protein, for both Newtonian and Langevin
3662	>	dynamics echo these trends over large outer time-step regimes. (C)
3663	>	2001 American Institute of Physics.},
3664	>	Annote = {469KV Times Cited:6 Cited References Count:30},
3665	>	Author = {P. F. Batcho and T. Schlick},
3666	>	Issn = {0021-9606},
3667	>	Journal = {Journal of Chemical Physics},
3668	>	Month = {Sep 1},
3669	>	Number = 9,
3670	>	Pages = {4019-4029},
3671	>	Title = {Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration},
3672	>	Uri = {<Go to ISI>://000170813800005},
3673	>	Volume = 115,
3674	>	Year = 2001}
3675	>
3676	>	@article{Bates2005,
3677	>	Abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
3678	>	can exhibit the elusive biaxial nematic phase, we have developed
3679	>	a generic simulation model for such systems. This contains the features
3680	>	of the molecule that are essential to its liquid crystal behavior,
3681	>	namely the anisotropies of the two arms and the angle between them.
3682	>	The behavior of the model has been investigated using Monte Carlo
3683	>	simulations for a wide range of these structural parameters. This
3684	>	allows us to establish the relationship between the V-shaped molecule
3685	>	and its ability to form a biaxial nematic phase. Of particular importance
3686	>	are the criteria of geometry and the relative anisotropy necessary
3687	>	for the system to exhibit a Landau point, at which the biaxial nematic
3688	>	is formed directly from the isotropic phase. The simulations have
3689	>	also been used to determine the orientational order parameters for
3690	>	a selection of molecular axes. These are especially important because
3691	>	they reveal the phase symmetry and are connected to the experimental
3692	>	determination of this. The simulation results show that, whereas
3693	>	some positions are extremely sensitive to the phase biaxiality,
3694	>	others are totally blind to this.},
3695	>	Annote = {Part 1 988LQ Times Cited:0 Cited References Count:38},
3696	>	Author = {M. A. Bates and G. R. Luckhurst},
3697	>	Issn = {1539-3755},
3698	>	Journal = {Physical Review E},
3699	>	Month = {Nov},
3700	>	Number = 5,
3701	>	Pages = {-},
3702	>	Title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation study},
3703	>	Uri = {<Go to ISI>://000233603100030},
3704	>	Volume = 72,
3705	>	Year = 2005}
3706	>
3707	>	@article{Beard2003,
3708	>	Abstract = {We introduce an unbiased protocol for performing rotational moves
3709	>	in rigid-body dynamics simulations. This approach - based on the
3710	>	analytic solution for the rotational equations of motion for an
3711	>	orthogonal coordinate system at constant angular velocity - removes
3712	>	deficiencies that have been largely ignored in Brownian dynamics
3713	>	simulations, namely errors for finite rotations that result from
3714	>	applying the noncommuting rotational matrices in an arbitrary order.
3715	>	Our algorithm should thus replace standard approaches to rotate
3716	>	local coordinate frames in Langevin and Brownian dynamics simulations.},
3717	>	Annote = {736UA Times Cited:0 Cited References Count:11},
3718	>	Author = {D. A. Beard and T. Schlick},
3719	>	Issn = {0006-3495},
3720	>	Journal = {Biophysical Journal},
3721	>	Month = {Nov 1},
3722	>	Number = 5,
3723	>	Pages = {2973-2976},
3724	>	Title = {Unbiased rotational moves for rigid-body dynamics},
3725	>	Uri = {<Go to ISI>://000186190500018},
3726	>	Volume = 85,
3727	>	Year = 2003}
3728	>
3729	>	@article{Beloborodov1998,
3730	>	Abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
3731	>	Biopolymers 33, 409-436, 1993), it was analytically shown that coupling
3732	>	between translation and rotation diffusion degrees of freedom does
3733	>	not affect the correlation functions relevant to the NMR intramolecular
3734	>	relaxation. It follows that spectral densities usually used for
3735	>	the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37,
3736	>	647-654, 1962) can be regarded as exact in respect to the rotation-translation
3737	>	coupling for the spin system connected with a rigid body. (C) 1998
3738	>	Academic Press.},
3739	>	Annote = {Zu605 Times Cited:2 Cited References Count:6},
3740	>	Author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev},
3741	>	Issn = {1090-7807},
3742	>	Journal = {Journal of Magnetic Resonance},
3743	>	Month = {Jun},
3744	>	Number = 2,
3745	>	Pages = {328-329},
3746	>	Title = {Effect of coupling between rotational and translational Brownian motions on NMR spin relaxation: Consideration using green function of rigid body diffusion},
3747	>	Uri = {<Go to ISI>://000074214800017},
3748	>	Volume = 132,
3749	>	Year = 1998}
3750	>
3751	>	@article{Berardi1996,
3752	>	Abstract = {We demonstrate that the overall molecular dipole organization in a
3753	>	smectic liquid crystal formed of polar molecules can be strongly
3754	>	influenced by the position of the dipole in the molecule. We study
3755	>	by large scale Monte Carlo simulations systems of attractive-repulsive
3756	>	''Gay-Berne'' elongated ellipsoids with an axial dipole at the center
3757	>	or near the end of the molecule and we show that monolayer smectic
3758	>	liquid crystals and modulated antiferroelectric bilayer stripe domains
3759	>	similar to the experimentally observed ''antiphase'' structures
3760	>	are obtained in the two cases.},
3761	>	Annote = {Vn637 Times Cited:49 Cited References Count:26},
3762	>	Author = {R. Berardi and S. Orlandi and C. Zannoni},
3763	>	Issn = {0009-2614},
3764	>	Journal = {Chemical Physics Letters},
3765	>	Month = {Oct 18},
3766	>	Number = 3,
3767	>	Pages = {357-362},
3768	>	Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
3769	>	Uri = {<Go to ISI>://A1996VN63700023},
3770	>	Volume = 261,
3771	>	Year = 1996}
3772	>
3773	>	@article{Berkov2005,
3774	>	Abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
3775	>	formalism) of magnetization oscillations driven by a spin-polarized
3776	>	current through a thin elliptical nanoelement is presented. We show
3777	>	that a sophisticated micromagnetic model, where a polycrystalline
3778	>	structure of a nanoelement is taken into account, can explain qualitatively
3779	>	all most important features of the magnetization oscillation spectra
3780	>	recently observed experimentally [S. I. Kiselev , Nature 425, 380
3781	>	(2003)], namely, existence of several equidistant spectral bands,
3782	>	sharp onset and abrupt disappearance of magnetization oscillations
3783	>	with increasing current, absence of the out-of-plane regime predicted
3784	>	by a macrospin model, and the relation between frequencies of so-called
3785	>	small-angle and quasichaotic oscillations. However, a quantitative
3786	>	agreement with experimental results (especially concerning the frequency
3787	>	of quasichaotic oscillations) could not be achieved in the region
3788	>	of reasonable parameter values, indicating that further model refinement
3789	>	is necessary for a complete understanding of the spin-driven magnetization
3790	>	precession even in this relatively simple experimental situation.},
3791	>	Annote = {969IT Times Cited:2 Cited References Count:55},
3792	>	Author = {D. V. Berkov and N. L. Gorn},
3793	>	Issn = {1098-0121},
3794	>	Journal = {Physical Review B},
3795	>	Month = {Sep},
3796	>	Number = 9,
3797	>	Pages = {-},
3798	>	Title = {Magnetization precession due to a spin-polarized current in a thin nanoelement: Numerical simulation study},
3799	>	Uri = {<Go to ISI>://000232228500058},
3800	>	Volume = 72,
3801	>	Year = 2005}
3802	>
3803	>	@article{Berkov2005a,
3804	>	Abstract = {Numerical simulations of fast remagnetization processes using stochastic
3805	>	dynamics are widely used to study various magnetic systems. In this
3806	>	paper, we first address several crucial methodological problems
3807	>	of such simulations: (i) the influence of finite-element discretization
3808	>	on simulated dynamics, (ii) choice between Ito and Stratonovich
3809	>	stochastic calculi by the solution of micromagnetic stochastic equations
3810	>	of motion and (iii) non-trivial correlation properties of the random
3811	>	(thermal) field. Next, we discuss several examples to demonstrate
3812	>	the great potential of the Langevin dynamics for studying fast remagnetization
3813	>	processes in technically relevant applications: we present numerical
3814	>	analysis of equilibrium magnon spectra in patterned structures,
3815	>	study thermal noise effects on the magnetization dynamics of nanoelements
3816	>	in pulsed fields and show some results for a remagnetization dynamics
3817	>	induced by a spin-polarized current. (c) 2004 Elsevier B.V. All
3818	>	rights reserved.},
3819	>	Annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
3820	>	Author = {D. V. Berkov and N. L. Gorn},
3821	>	Issn = {0304-8853},
3822	>	Journal = {Journal of Magnetism and Magnetic Materials},
3823	>	Month = {Apr},
3824	>	Pages = {442-448},
3825	>	Title = {Stochastic dynamic simulations of fast remagnetization processes: recent advances and applications},
3826	>	Uri = {<Go to ISI>://000228837600109},
3827	>	Volume = 290,
3828	>	Year = 2005}
3829	>
3830	>	@article{Berkov2002,
3831	>	Abstract = {We report on recent progress achieved by the development of numerical
3832	>	methods based on the stochastic (Langevin) dynamics applied to systems
3833	>	of interacting magnetic nanoparticles. The method enables direct
3834	>	simulations of the trajectories of magnetic moments taking into
3835	>	account (i) all relevant interactions, (ii) precession dynamics,
3836	>	and (iii) temperature fluctuations included via the random (thermal)
3837	>	field. We present several novel results obtained using new methods
3838	>	developed for the solution of the Langevin equations. In particular,
3839	>	we have investigated magnetic nanodots and disordered granular systems
3840	>	of single-domain magnetic particles. For the first case we have
3841	>	calculated the spectrum and the spatial distribution of spin excitations.
3842	>	For the second system the complex ac susceptibility chi(omega, T)
3843	>	for various particle concentrations and particle anisotropies were
3844	>	computed and compared with numerous experimental results.},
3845	>	Annote = {526TF Times Cited:4 Cited References Count:37},
3846	>	Author = {D. V. Berkov and N. L. Gorn and P. Gornert},
3847	>	Issn = {0031-8965},
3848	>	Journal = {Physica Status Solidi a-Applied Research},
3849	>	Month = {Feb 16},
3850	>	Number = 2,
3851	>	Pages = {409-421},
3852	>	Title = {Magnetization dynamics in nanoparticle systems: Numerical simulation using Langevin dynamics},
3853	>	Uri = {<Go to ISI>://000174145200026},
3854	>	Volume = 189,
3855	>	Year = 2002}
3856	>
3857	>	@article{Bernal1980,
3858	>	Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose},
3859	>	Journal = {Biopolymers},
3860	>	Pages = {751-766},
3861	>	Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape},
3862	>	Volume = 19,
3863	>	Year = 1980}
3864	>
3865	>	@article{Brenner1967,
3866	>	Author = {H. Brenner},
3867	>	Journal = {J. Collid. Int. Sci.},
3868	>	Pages = {407-436},
3869	>	Title = {Coupling between the Translational and Rotational Brownian Motions of Rigid Particles of Arbitrary shape},
3870	>	Volume = 23,
3871	>	Year = 1967}
3872	>
3873	>	@article{Brooks1983,
3874	>	Annote = {Qp423 Times Cited:6414 Cited References Count:96},
3875	>	Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus},
3876	>	Issn = {0192-8651},
3877	>	Journal = {Journal of Computational Chemistry},
3878	>	Number = 2,
3879	>	Pages = {187-217},
3880	>	Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
3881	>	Uri = {<Go to ISI>://A1983QP42300010},
3882	>	Volume = 4,
3883	>	Year = 1983}
3884	>
3885	>	@article{Brunger1984,
3886	>	Annote = {Sm173 Times Cited:143 Cited References Count:22},
3887	>	Author = {A. Brunger and C. L. Brooks and M. Karplus},
3888	>	Issn = {0009-2614},
3889	>	Journal = {Chemical Physics Letters},
3890	>	Number = 5,
3891	>	Pages = {495-500},
3892	>	Title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations of St2 Water},
3893	>	Uri = {<Go to ISI>://A1984SM17300007},
3894	>	Volume = 105,
3895	>	Year = 1984}
3896	>
3897	>	@article{Budd1999,
3898	>	Abstract = {This paper examines a synthesis of adaptive mesh methods with the
3899	>	use of symmetry to study a partial differential equation. In particular,
3900	>	it considers methods which admit discrete self-similar solutions,
3901	>	examining the convergence of these to the true self-similar solution
3902	>	as well as their stability. Special attention is given to the nonlinear
3903	>	diffusion equation describing flow in a porous medium.},
3904	>	Annote = {199EE Times Cited:4 Cited References Count:14},
3905	>	Author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell},
3906	>	Issn = {1364-503X},
3907	>	Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
3908	>	Month = {Apr 15},
3909	>	Number = 1754,
3910	>	Pages = {1047-1077},
3911	>	Title = {Self-similar numerical solutions of the porous-medium equation using moving mesh methods},
3912	>	Uri = {<Go to ISI>://000080466800005},
3913	>	Volume = 357,
3914	>	Year = 1999}
3915	>
3916	>	@article{Camp1999,
3917	>	Abstract = {Fluids of hard bent-core molecules have been studied using theory
3918	>	and computer simulation. The molecules are composed of two hard
3919	>	spherocylinders, with length-to-breadth ratio L/D, joined by their
3920	>	ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20
3921	>	degrees, the simulations show isotropic, nematic, smectic, and solid
3922	>	phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic,
3923	>	and solid phases are in evidence, which suggests that there is a
3924	>	nematic-smectic-solid triple point at an angle in the range 20 degrees
3925	>	< gamma < 30 degrees. In all of the orientationally ordered fluid
3926	>	phases the order is purely uniaxial. For gamma = 10 degrees and
3927	>	20 degrees, at the studied densities, the solid is also uniaxially
3928	>	ordered, whilst for gamma = 30 degrees the solid layers are biaxially
3929	>	ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find
3930	>	no spontaneous orientational ordering. This is shown to be due to
3931	>	the interlocking of dimer pairs which precludes alignment. We find
3932	>	similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial
3933	>	nematic transition is predicted by Onsager theory. Simulations in
3934	>	the biaxial nematic phase show it to be at least mechanically stable
3935	>	with respect to the isotropic phase, however. We have compared the
3936	>	quasi-exact simulation results in the isotropic phase with the predicted
3937	>	equations of state from three theories: the virial expansion containing
3938	>	the second and third virial coefficients; the Parsons-Lee equation
3939	>	of state; an application of Wertheim's theory of associating fluids
3940	>	in the limit of infinite attractive association energy. For all
3941	>	of the molecule elongations and geometries we have simulated, the
3942	>	Wertheim theory proved to be the most accurate. Interestingly, the
3943	>	isotropic equation of state is virtually independent of the dimer
3944	>	bond angle-a feature that is also reflected in the lack of variation
3945	>	with angle of the calculated second and third virial coefficients.
3946	>	(C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].},
3947	>	Annote = {255TC Times Cited:24 Cited References Count:38},
3948	>	Author = {P. J. Camp and M. P. Allen and A. J. Masters},
3949	>	Issn = {0021-9606},
3950	>	Journal = {Journal of Chemical Physics},
3951	>	Month = {Dec 1},
3952	>	Number = 21,
3953	>	Pages = {9871-9881},
3954	>	Title = {Theory and computer simulation of bent-core molecules},
3955	>	Uri = {<Go to ISI>://000083685400056},
3956	>	Volume = 111,
3957	>	Year = 1999}
3958	>
3959	>	@article{Care2005,
3960	>	Abstract = {A review is presented of molecular and mesoscopic computer simulations
3961	>	of liquid crystalline systems. Molecular simulation approaches applied
3962	>	to such systems are described, and the key findings for bulk phase
3963	>	behaviour are reported. Following this, recently developed lattice
3964	>	Boltzmann approaches to the mesoscale modelling of nemato-dynanics
3965	>	are reviewed. This paper concludes with a discussion of possible
3966	>	areas for future development in this field.},
3967	>	Annote = {989TU Times Cited:2 Cited References Count:258},
3968	>	Author = {C. M. Care and D. J. Cleaver},
3969	>	Issn = {0034-4885},
3970	>	Journal = {Reports on Progress in Physics},
3971	>	Month = {Nov},
3972	>	Number = 11,
3973	>	Pages = {2665-2700},
3974	>	Title = {Computer simulation of liquid crystals},
3975	>	Uri = {<Go to ISI>://000233697600004},
3976	>	Volume = 68,
3977	>	Year = 2005}
3978	>
3979	>	@article{Carrasco1999,
3980	>	Abstract = {The hydrodynamic properties of rigid particles are calculated from
3981	>	models composed of spherical elements (beads) using theories developed
3982	>	by Kirkwood, Bloomfield, and their coworkers. Bead models have usually
3983	>	been built in such a way that the beads fill the volume occupied
3984	>	by the particles. Sometimes the beads are few and of varying sizes
3985	>	(bead models in the strict sense), and other times there are many
3986	>	small beads (filling models). Because hydrodynamic friction takes
3987	>	place at the molecular surface, another possibility is to use shell
3988	>	models, as originally proposed by Bloomfield. In this work, we have
3989	>	developed procedures to build models of the various kinds, and we
3990	>	describe the theory and methods for calculating their hydrodynamic
3991	>	properties, including approximate methods that may be needed to
3992	>	treat models with a very large number of elements. By combining
3993	>	the various possibilities of model building and hydrodynamic calculation,
3994	>	several strategies can be designed. We have made a quantitative
3995	>	comparison of the performance of the various strategies by applying
3996	>	them to some test cases, for which the properties are known a priori.
3997	>	We provide guidelines and computational tools for bead modeling.},
3998	>	Annote = {200TT Times Cited:46 Cited References Count:57},
3999	>	Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
4000	>	Issn = {0006-3495},
4001	>	Journal = {Biophysical Journal},
4002	>	Month = {Jun},
4003	>	Number = 6,
4004	>	Pages = {3044-3057},
4005	>	Title = {Hydrodynamic properties of rigid particles: Comparison of different modeling and computational procedures},
4006	>	Uri = {<Go to ISI>://000080556700016},
4007	>	Volume = 76,
4008	>	Year = 1999}
4009	>
4010	>	@article{Chandra1999,
4011	>	Abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
4012	>	are calculated by means of molecular dynamics simulations. Since
4013	>	this is not a simple point model, the forces and torques arising
4014	>	from the SSD potential are derived here. Simulations are carried
4015	>	out in the microcanonical ensemble employing the Ewald method for
4016	>	the electrostatic interactions. Various time correlation functions
4017	>	and dynamical quantities associated with the translational and rotational
4018	>	motion of water molecules are evaluated and compared with those
4019	>	of two other commonly used models of liquid water, namely the transferable
4020	>	intermolecular potential-three points (TIP3P) and simple point charge/extended
4021	>	(SPC/E) models, and also with experiments. The dynamical properties
4022	>	of the SSD water model are found to be in good agreement with the
4023	>	experimental results and appear to be better than the TIP3P and
4024	>	SPC/E models in most cases, as has been previously shown for its
4025	>	thermodynamic, structural, and dielectric properties. Also, molecular
4026	>	dynamics simulations of the SSD model are found to run much faster
4027	>	than TIP3P, SPC/E, and other multisite models. (C) 1999 American
4028	>	Institute of Physics. [S0021-9606(99)51430-X].},
4029	>	Annote = {221EN Times Cited:14 Cited References Count:66},
4030	>	Author = {A. Chandra and T. Ichiye},
4031	>	Issn = {0021-9606},
4032	>	Journal = {Journal of Chemical Physics},
4033	>	Month = {Aug 8},
4034	>	Number = 6,
4035	>	Pages = {2701-2709},
4036	>	Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations},
4037	>	Uri = {<Go to ISI>://000081711200038},
4038	>	Volume = 111,
4039	>	Year = 1999}
4040	>
4041	>	@article{Channell1990,
4042	>	Annote = {Dk631 Times Cited:152 Cited References Count:34},
4043	>	Author = {P. J. Channell and C. Scovel},
4044	>	Issn = {0951-7715},
4045	>	Journal = {Nonlinearity},
4046	>	Month = {may},
4047	>	Number = 2,
4048	>	Pages = {231-259},
4049	>	Title = {Symplectic Integration of Hamiltonian-Systems},
4050	>	Uri = {<Go to ISI>://A1990DK63100001},
4051	>	Volume = 3,
4052	>	Year = 1990}
4053	>
4054	>	@article{Chen2003,
4055	>	Abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
4056	>	equations and introduce a family of mixed methods from combinations
4057	>	of explicit Runge-Kutta methods. These methods have better stability
4058	>	behavior than traditional Runge-Kutta methods and generally extend
4059	>	the range of validity of the calculated solutions. These methods
4060	>	also give a way of determining if the numerical solutions are real
4061	>	or spurious. Emphasis is put on examples coming from mathematical
4062	>	models in ecology. (C) 2002 IMACS. Published by Elsevier Science
4063	>	B.V. All rights reserved.},
4064	>	Annote = {633ZD Times Cited:0 Cited References Count:9},
4065	>	Author = {B. Chen and F. Solis},
4066	>	Issn = {0168-9274},
4067	>	Journal = {Applied Numerical Mathematics},
4068	>	Month = {Jan},
4069	>	Number = {1-2},
4070	>	Pages = {21-30},
4071	>	Title = {Explicit mixed finite order Runge-Kutta methods},
4072	>	Uri = {<Go to ISI>://000180314200002},
4073	>	Volume = 44,
4074	>	Year = 2003}
4075	>
4076	>	@article{Cheung2004,
4077	>	Abstract = {Equilibrium molecular dynamics calculations have been performed for
4078	>	the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile
4079	>	(PCH5) using a fully atomistic model. Simulation data have been
4080	>	obtained for a series of temperatures in the nematic phase. The
4081	>	simulation data have been used to calculate the flexoelectric coefficients
4082	>	e(s) and e(b) using the linear response formalism of Osipov and
4083	>	Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr.
4084	>	31, 125 (1986)]. The temperature and order parameter dependence
4085	>	of e(s) and e(b) are examined, as are separate contributions from
4086	>	different intermolecular interactions. Values of e(s) and e(b) calculated
4087	>	from simulation are consistent with those found from experiment.
4088	>	(C) 2004 American Institute of Physics.},
4089	>	Annote = {866UM Times Cited:4 Cited References Count:61},
4090	>	Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
4091	>	Issn = {0021-9606},
4092	>	Journal = {Journal of Chemical Physics},
4093	>	Month = {Nov 8},
4094	>	Number = 18,
4095	>	Pages = {9131-9139},
4096	>	Title = {Calculation of flexoelectric coefficients for a nematic liquid crystal by atomistic simulation},
4097	>	Uri = {<Go to ISI>://000224798900053},
4098	>	Volume = 121,
4099	>	Year = 2004}
4100	>
4101	>	@article{Cheung2002,
4102	>	Abstract = {Equilibrium molecular dynamics calculations have been performed for
4103	>	the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile
4104	>	(PCH5) using a fully atomistic model. Simulation data has been obtained
4105	>	for a series of temperatures in the nematic phase. The rotational
4106	>	viscosity co-efficient gamma(1), has been calculated using the angular
4107	>	velocity correlation function of the nematic director, n, the mean
4108	>	squared diffusion of n and statistical mechanical methods based
4109	>	on the rotational diffusion co-efficient. We find good agreement
4110	>	between the first two methods and experimental values. (C) 2002
4111	>	Published by Elsevier Science B.V.},
4112	>	Annote = {547KF Times Cited:8 Cited References Count:31},
4113	>	Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
4114	>	Issn = {0009-2614},
4115	>	Journal = {Chemical Physics Letters},
4116	>	Month = {Apr 15},
4117	>	Number = {1-2},
4118	>	Pages = {140-146},
4119	>	Title = {Calculation of the rotational viscosity of a nematic liquid crystal},
4120	>	Uri = {<Go to ISI>://000175331000020},
4121	>	Volume = 356,
4122	>	Year = 2002}
4123	>
4124	>	@article{Chin2004,
4125	>	Abstract = {Current molecular dynamics simulations of biomolecules using multiple
4126	>	time steps to update the slowly changing force are hampered by instabilities
4127	>	beginning at time steps near the half period of the fastest vibrating
4128	>	mode. These #resonance# instabilities have became a critical barrier
4129	>	preventing the long time simulation of biomolecular dynamics. Attempts
4130	>	to tame these instabilities by altering the slowly changing force
4131	>	and efforts to damp them out by Langevin dynamics do not address
4132	>	the fundamental cause of these instabilities. In this work, we trace
4133	>	the instability to the nonanalytic character of the underlying spectrum
4134	>	and show that a correct splitting of the Hamiltonian, which renders
4135	>	the spectrum analytic, restores stability. The resulting Hamiltonian
4136	>	dictates that in addition to updating the momentum due to the slowly
4137	>	changing force, one must also update the position with a modified
4138	>	mass. Thus multiple-time stepping must be done dynamically. (C)
4139	>	2004 American Institute of Physics.},
4140	>	Annote = {757TK Times Cited:1 Cited References Count:22},
4141	>	Author = {S. A. Chin},
4142	>	Issn = {0021-9606},
4143	>	Journal = {Journal of Chemical Physics},
4144	>	Month = {Jan 1},
4145	>	Number = 1,
4146	>	Pages = {8-13},
4147	>	Title = {Dynamical multiple-time stepping methods for overcoming resonance instabilities},
4148	>	Uri = {<Go to ISI>://000187577400003},
4149	>	Volume = 120,
4150	>	Year = 2004}
4151	>
4152	>	@article{Cook2000,
4153	>	Abstract = {The Kirkwood correlation factor g(1) determines the preference for
4154	>	local parallel or antiparallel dipole association in the isotropic
4155	>	phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood
4156	>	factors greater than 1 have an enhanced effective dipole moment
4157	>	along the molecular long axis. This leads to higher values of Delta
4158	>	epsilon in the nematic phase. This paper describes state-of-the-art
4159	>	molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile
4160	>	(PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl)
4161	>	in the isotropic liquid phase using an all-atom force field and
4162	>	taking long range electrostatics into account using an Ewald summation.
4163	>	Using this methodology, PCH5 is seen to prefer antiparallel dipole
4164	>	alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel
4165	>	dipole alignment with a positive g(1); this is in accordance with
4166	>	experimental dielectric measurements. Analysis of the molecular
4167	>	dynamics trajectories allows an assessment of why these molecules
4168	>	behave differently.},
4169	>	Annote = {376BF Times Cited:10 Cited References Count:16},
4170	>	Author = {M. J. Cook and M. R. Wilson},
4171	>	Issn = {0267-8292},
4172	>	Journal = {Liquid Crystals},
4173	>	Month = {Dec},
4174	>	Number = 12,
4175	>	Pages = {1573-1583},
4176	>	Title = {Simulation studies of dipole correlation in the isotropic liquid phase},
4177	>	Uri = {<Go to ISI>://000165437800002},
4178	>	Volume = 27,
4179	>	Year = 2000}
4180	>
4181	>	@article{Cui2003,
4182	>	Abstract = {All-atom Langevin dynamics simulations have been performed to study
4183	>	the folding pathways of the 18-residue binding domain fragment E6ap
4184	>	of the human papillomavirus E6 interacting peptide. Six independent
4185	>	folding trajectories, with a total duration of nearly 2 mus, all
4186	>	lead to the same native state in which the E6ap adopts a fluctuating
4187	>	a-helix structure in the central portion (Ser-4-Leu-13) but with
4188	>	very flexible N and C termini. Simulations starting from different
4189	>	core configurations exhibit the E6ap folding dynamics as either
4190	>	a two- or three-state folder with an intermediate misfolded state.
4191	>	The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13)
4192	>	is well conserved in the native-state structure but absent in the
4193	>	intermediate structure, suggesting that the leucine core is not
4194	>	only essential for the binding activity of E6ap but also important
4195	>	for the stability of the native structure. The free energy landscape
4196	>	reveals a significant barrier between the basins separating the
4197	>	native and misfolded states. We also discuss the various underlying
4198	>	forces that drive the peptide into its native state.},
4199	>	Annote = {689LC Times Cited:3 Cited References Count:48},
4200	>	Author = {B. X. Cui and M. Y. Shen and K. F. Freed},
4201	>	Issn = {0027-8424},
4202	>	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
4203	>	Month = {Jun 10},
4204	>	Number = 12,
4205	>	Pages = {7087-7092},
4206	>	Title = {Folding and misfolding of the papillomavirus E6 interacting peptide E6ap},
4207	>	Uri = {<Go to ISI>://000183493500037},
4208	>	Volume = 100,
4209	>	Year = 2003}
4210	>
4211	>	@article{Denisov2003,
4212	>	Abstract = {We study the slow phase of thermally activated magnetic relaxation
4213	>	in finite two-dimensional ensembles of dipolar interacting ferromagnetic
4214	>	nanoparticles whose easy axes of magnetization are perpendicular
4215	>	to the distribution plane. We develop a method to numerically simulate
4216	>	the magnetic relaxation for the case that the smallest heights of
4217	>	the potential barriers between the equilibrium directions of the
4218	>	nanoparticle magnetic moments are much larger than the thermal energy.
4219	>	Within this framework, we analyze in detail the role that the correlations
4220	>	of the nanoparticle magnetic moments and the finite size of the
4221	>	nanoparticle ensemble play in magnetic relaxation.},
4222	>	Annote = {642XH Times Cited:11 Cited References Count:31},
4223	>	Author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou},
4224	>	Issn = {1098-0121},
4225	>	Journal = {Physical Review B},
4226	>	Month = {Jan 1},
4227	>	Number = 1,
4228	>	Pages = {-},
4229	>	Title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
4230	>	Uri = {<Go to ISI>://000180830400056},
4231	>	Volume = 67,
4232	>	Year = 2003}
4233	>
4234	>	@article{Derreumaux1998,
4235	>	Abstract = {To explore the origin of the large-scale motion of triosephosphate
4236	>	isomerase's flexible loop (residues 166 to 176) at the active site,
4237	>	several simulation protocols are employed both for the free enzyme
4238	>	in vacuo and for the free enzyme with some solvent modeling: high-temperature
4239	>	Langevin dynamics simulations, sampling by a #dynamics##driver#
4240	>	approach, and potential-energy surface calculations. Our focus is
4241	>	on obtaining the energy barrier to the enzyme's motion and establishing
4242	>	the nature of the loop movement. Previous calculations did not determine
4243	>	this energy barrier and the effect of solvent on the barrier. High-temperature
4244	>	molecular dynamics simulations and crystallographic studies have
4245	>	suggested a rigid-body motion with two hinges located at both ends
4246	>	of the loop; Brownian dynamics simulations at room temperature pointed
4247	>	to a very flexible behavior. The present simulations and analyses
4248	>	reveal that although solute/solvent hydrogen bonds play a crucial
4249	>	role in lowering the energy along the pathway, there still remains
4250	>	a high activation barrier, This finding clearly indicates that,
4251	>	if the loop opens and closes in the absence of a substrate at standard
4252	>	conditions (e.g., room temperature, appropriate concentration of
4253	>	isomerase), the time scale for transition is not in the nanosecond
4254	>	but rather the microsecond range. Our results also indicate that
4255	>	in the context of spontaneous opening in the free enzyme, the motion
4256	>	is of rigid-body type and that the specific interaction between
4257	>	residues Ala(176) and Tyr(208) plays a crucial role in the loop
4258	>	opening/closing mechanism.},
4259	>	Annote = {Zl046 Times Cited:30 Cited References Count:29},
4260	>	Author = {P. Derreumaux and T. Schlick},
4261	>	Issn = {0006-3495},
4262	>	Journal = {Biophysical Journal},
4263	>	Month = {Jan},
4264	>	Number = 1,
4265	>	Pages = {72-81},
4266	>	Title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
4267	>	Uri = {<Go to ISI>://000073393400009},
4268	>	Volume = 74,
4269	>	Year = 1998}
4270	>
4271	>	@article{Dullweber1997,
4272	>	Abstract = {Rigid body molecular models possess symplectic structure and time-reversal
4273	>	symmetry. Standard numerical integration methods destroy both properties,
4274	>	introducing nonphysical dynamical behavior such as numerically induced
4275	>	dissipative states and drift in the energy during long term simulations.
4276	>	This article describes the construction, implementation, and practical
4277	>	application of fast explicit symplectic-reversible integrators for
4278	>	multiple rigid body molecular simulations, These methods use a reduction
4279	>	to Euler equations for the free rigid body, together with a symplectic
4280	>	splitting technique. In every time step, the orientational dynamics
4281	>	of each rigid body is integrated by a sequence of planar rotations.
4282	>	Besides preserving the symplectic and reversible structures of the
4283	>	flow, this scheme accurately conserves the total angular momentum
4284	>	of a system of interacting rigid bodies. Excellent energy conservation
4285	>	fan be obtained relative to traditional methods, especially in long-time
4286	>	simulations. The method is implemented in a research code, ORIENT
4287	>	and compared with a quaternion/extrapolation scheme for the TIP4P
4288	>	model of water. Our experiments show that the symplectic-reversible
4289	>	scheme is far superior to the more traditional quaternion method.
4290	>	(C) 1997 American Institute of Physics.},
4291	>	Annote = {Ya587 Times Cited:35 Cited References Count:32},
4292	>	Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
4293	>	Issn = {0021-9606},
4294	>	Journal = {Journal of Chemical Physics},
4295	>	Month = {Oct 15},
4296	>	Number = 15,
4297	>	Pages = {5840-5851},
4298	>	Title = {Symplectic splitting methods for rigid body molecular dynamics},
4299	>	Uri = {<Go to ISI>://A1997YA58700024},
4300	>	Volume = 107,
4301	>	Year = 1997}
4302	>
4303	>	@book{Gamma1994,
4304	>	Address = {London},
4305	>	Author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
4306	>	Chapter = 7,
4307	>	Publisher = {Perason Education},
4308	>	Title = {Design Patterns: Elements of Reusable Object-Oriented Software},
4309	>	Year = 1994}
4310	>
4311	>	@article{Edwards2005,
4312	>	Abstract = {Using the Langevin dynamics technique, we have carried out simulations
4313	>	of a single-chain flexible diblock copolymer. The polymer consists
4314	>	of two blocks of equal length, one very poorly solvated and the
4315	>	other close to theta-conditions. We study what happens when such
4316	>	a polymer is stretched, for a range of different stretching speeds,
4317	>	and correlate our observations with features in the plot of force
4318	>	vs extension. We find that at slow speeds this force profile does
4319	>	not increase monotonically, in disagreement with earlier predictions,
4320	>	and that at high speeds there is a strong dependence on which end
4321	>	of the polymer is pulled, as well as a high level of hysteresis.},
4322	>	Annote = {992EC Times Cited:0 Cited References Count:13},
4323	>	Author = {S. A. Edwards and D. R. M. Williams},
4324	>	Issn = {0024-9297},
4325	>	Journal = {Macromolecules},
4326	>	Month = {Dec 13},
4327	>	Number = 25,
4328	>	Pages = {10590-10595},
4329	>	Title = {Stretching a single diblock copolymer in a selective solvent: Langevin dynamics simulations},
4330	>	Uri = {<Go to ISI>://000233866200035},
4331	>	Volume = 38,
4332	>	Year = 2005}
4333	>
4334	>	@article{Egberts1988,
4335	>	Annote = {Q0188 Times Cited:219 Cited References Count:43},
4336	>	Author = {E. Egberts and H. J. C. Berendsen},
4337	>	Issn = {0021-9606},
4338	>	Journal = {Journal of Chemical Physics},
4339	>	Month = {Sep 15},
4340	>	Number = 6,
4341	>	Pages = {3718-3732},
4342	>	Title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic Detail},
4343	>	Uri = {<Go to ISI>://A1988Q018800036},
4344	>	Volume = 89,
4345	>	Year = 1988}
4346	>
4347	>	@article{Ermak1978,
4348	>	Annote = {Fp216 Times Cited:785 Cited References Count:42},
4349	>	Author = {D. L. Ermak and J. A. Mccammon},
4350	>	Issn = {0021-9606},
4351	>	Journal = {Journal of Chemical Physics},
4352	>	Number = 4,
4353	>	Pages = {1352-1360},
4354	>	Title = {Brownian Dynamics with Hydrodynamic Interactions},
4355	>	Uri = {<Go to ISI>://A1978FP21600004},
4356	>	Volume = 69,
4357	>	Year = 1978}
4358	>
4359	>	@article{Evans1977,
4360	>	Annote = {Ds757 Times Cited:271 Cited References Count:18},
4361	>	Author = {D. J. Evans},
4362	>	Issn = {0026-8976},
4363	>	Journal = {Molecular Physics},
4364	>	Number = 2,
4365	>	Pages = {317-325},
4366	>	Title = {Representation of Orientation Space},
4367	>	Uri = {<Go to ISI>://A1977DS75700002},
4368	>	Volume = 34,
4369	>	Year = 1977}
4370	>
4371	>	@article{Fennell2004,
4372	>	Abstract = {The density maximum and temperature dependence of the self-diffusion
4373	>	constant were investigated for the soft sticky dipole (SSD) water
4374	>	model and two related reparametrizations of this single-point model.
4375	>	A combination of microcanonical and isobaric-isothermal molecular
4376	>	dynamics simulations was used to calculate these properties, both
4377	>	with and without the use of reaction field to handle long-range
4378	>	electrostatics. The isobaric-isothermal simulations of the melting
4379	>	of both ice-I-h and ice-I-c showed a density maximum near 260 K.
4380	>	In most cases, the use of the reaction field resulted in calculated
4381	>	densities which were significantly lower than experimental densities.
4382	>	Analysis of self-diffusion constants shows that the original SSD
4383	>	model captures the transport properties of experimental water very
4384	>	well in both the normal and supercooled liquid regimes. We also
4385	>	present our reparametrized versions of SSD for use both with the
4386	>	reaction field or without any long-range electrostatic corrections.
4387	>	These are called the SSD/RF and SSD/E models, respectively. These
4388	>	modified models were shown to maintain or improve upon the experimental
4389	>	agreement with the structural and transport properties that can
4390	>	be obtained with either the original SSD or the density-corrected
4391	>	version of the original model (SSD1). Additionally, a novel low-density
4392	>	ice structure is presented which appears to be the most stable ice
4393	>	structure for the entire SSD family. (C) 2004 American Institute
4394	>	of Physics.},
4395	>	Annote = {816YY Times Cited:5 Cited References Count:39},
4396	>	Author = {C. J. Fennell and J. D. Gezelter},
4397	>	Issn = {0021-9606},
4398	>	Journal = {Journal of Chemical Physics},
4399	>	Month = {May 15},
4400	>	Number = 19,
4401	>	Pages = {9175-9184},
4402	>	Title = {On the structural and transport properties of the soft sticky dipole and related single-point water models},
4403	>	Uri = {<Go to ISI>://000221146400032},
4404	>	Volume = 120,
4405	>	Year = 2004}
4406	>
4407	>	@article{Fernandes2002,
4408	>	Abstract = {We have developed a Brownian dynamics simulation algorithm to generate
4409	>	Brownian trajectories of an isolated, rigid particle of arbitrary
4410	>	shape in the presence of electric fields or any other external agents.
4411	>	Starting from the generalized diffusion tensor, which can be calculated
4412	>	with the existing HYDRO software, the new program BROWNRIG (including
4413	>	a case-specific subprogram for the external agent) carries out a
4414	>	simulation that is analyzed later to extract the observable dynamic
4415	>	properties. We provide a variety of examples of utilization of this
4416	>	method, which serve as tests of its performance, and also illustrate
4417	>	its applicability. Examples include free diffusion, transport in
4418	>	an electric field, and diffusion in a restricting environment.},
4419	>	Annote = {633AD Times Cited:2 Cited References Count:43},
4420	>	Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4421	>	Issn = {0006-3495},
4422	>	Journal = {Biophysical Journal},
4423	>	Month = {Dec},
4424	>	Number = 6,
4425	>	Pages = {3039-3048},
4426	>	Title = {Brownian dynamics simulation of rigid particles of arbitrary shape in external fields},
4427	>	Uri = {<Go to ISI>://000180256300012},
4428	>	Volume = 83,
4429	>	Year = 2002}
4430	>
4431	>	@book{Frenkel1996,
4432	>	Address = {New York},
4433	>	Author = {D. Frenkel and B. Smit},
4434	>	Publisher = {Academic Press},
4435	>	Title = {Understanding Molecular Simulation : From Algorithms to Applications},
4436	>	Year = 1996}
4437	>
4438	>	@article{Gay1981,
4439	>	Annote = {Lj347 Times Cited:482 Cited References Count:13},
4440	>	Author = {J. G. Gay and B. J. Berne},
4441	>	Issn = {0021-9606},
4442	>	Journal = {Journal of Chemical Physics},
4443	>	Number = 6,
4444	>	Pages = {3316-3319},
4445	>	Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
4446	>	Uri = {<Go to ISI>://A1981LJ34700029},
4447	>	Volume = 74,
4448	>	Year = 1981}
4449	>
4450	>	@article{Gelin1999,
4451	>	Abstract = {To investigate the influence of inertial effects on the dynamics of
4452	>	an assembly of beads subjected to rigid constraints and placed in
4453	>	a buffer medium, a convenient method to introduce suitable generalized
4454	>	coordinates is presented. Without any restriction on the nature
4455	>	of the soft forces involved (both stochastic and deterministic),
4456	>	pertinent Langevin equations are derived. Provided that the Brownian
4457	>	forces are Gaussian and Markovian, the corresponding Fokker-Planck
4458	>	equation (FPE) is obtained in the complete phase space of generalized
4459	>	coordinates and momenta. The correct short time behavior for correlation
4460	>	functions (CFs) of generalized coordinates is established, and the
4461	>	diffusion equation with memory (DEM) is deduced from the FPE in
4462	>	the high friction Limit. The DEM is invoked to perform illustrative
4463	>	calculations in two dimensions of the orientational CFs for once
4464	>	broken nonrigid rods immobilized on a surface. These calculations
4465	>	reveal that the CFs under certain conditions exhibit an oscillatory
4466	>	behavior, which is irreproducible within the standard diffusion
4467	>	equation. Several methods are considered for the approximate solution
4468	>	of the DEM, and their application to three dimensional DEMs is discussed.},
4469	>	Annote = {257MM Times Cited:2 Cited References Count:82},
4470	>	Author = {M. F. Gelin},
4471	>	Issn = {1022-1344},
4472	>	Journal = {Macromolecular Theory and Simulations},
4473	>	Month = {Nov},
4474	>	Number = 6,
4475	>	Pages = {529-543},
4476	>	Title = {Inertial effects in the Brownian dynamics with rigid constraints},
4477	>	Uri = {<Go to ISI>://000083785700002},
4478	>	Volume = 8,
4479	>	Year = 1999}
4480	>
4481	>	@article{Goetz1998,
4482	>	Author = {R. Goetz and R. Lipowsky},
4483	>	Journal = {Journal of Chemical Physics},
4484	>	Number = 17,
4485	>	Pages = 7397,
4486	>	Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
4487	>	Volume = 108,
4488	>	Year = 1998}
4489	>
4490	>	@book{Goldstein2001,
4491	>	Address = {San Francisco},
4492	>	Author = {H. Goldstein and C. Poole and J. Safko},
4493	>	Edition = {3rd},
4494	>	Publisher = {Addison Wesley},
4495	>	Title = {Classical Mechanics},
4496	>	Year = 2001}
4497	>
4498	>	@article{Gray2003,
4499	>	Abstract = {Protein-protein docking algorithms provide a means to elucidate structural
4500	>	details for presently unknown complexes. Here, we present and evaluate
4501	>	a new method to predict protein-protein complexes from the coordinates
4502	>	of the unbound monomer components. The method employs a low-resolution,
4503	>	rigid-body, Monte Carlo search followed by simultaneous optimization
4504	>	of backbone displacement and side-chain conformations using Monte
4505	>	Carlo minimization. Up to 10(5) independent simulations are carried
4506	>	out, and the resulting #decoys# are ranked using an energy function
4507	>	dominated by van der Waals interactions, an implicit solvation model,
4508	>	and an orientation-dependent hydrogen bonding potential. Top-ranking
4509	>	decoys are clustered to select the final predictions. Small-perturbation
4510	>	studies reveal the formation of binding funnels in 42 of 54 cases
4511	>	using coordinates derived from the bound complexes and in 32 of
4512	>	54 cases using independently determined coordinates of one or both
4513	>	monomers. Experimental binding affinities correlate with the calculated
4514	>	score function and explain the predictive success or failure of
4515	>	many targets. Global searches using one or both unbound components
4516	>	predict at least 25% of the native residue-residue contacts in 28
4517	>	of the 32 cases where binding funnels exist. The results suggest
4518	>	that the method may soon be useful for generating models of biologically
4519	>	important complexes from the structures of the isolated components,
4520	>	but they also highlight the challenges that must be met to achieve
4521	>	consistent and accurate prediction of protein-protein interactions.
4522	>	(C) 2003 Elsevier Ltd. All rights reserved.},
4523	>	Annote = {704QL Times Cited:48 Cited References Count:60},
4524	>	Author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and B. Kuhlman and C. A. Rohl and D. Baker},
4525	>	Issn = {0022-2836},
4526	>	Journal = {Journal of Molecular Biology},
4527	>	Month = {Aug 1},
4528	>	Number = 1,
4529	>	Pages = {281-299},
4530	>	Title = {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations},
4531	>	Uri = {<Go to ISI>://000184351300022},
4532	>	Volume = 331,
4533	>	Year = 2003}
4534	>
4535	>	@article{Greengard1994,
4536	>	Abstract = {Some of the recently developed fast summation methods that have arisen
4537	>	in scientific computing are described. These methods require an
4538	>	amount of work proportional to N or N log N to evaluate all pairwise
4539	>	interactions in an ensemble of N particles. Traditional methods,
4540	>	by contrast, require an amount of work proportional to N-2. AS a
4541	>	result, large-scale simulations can be carried out using only modest
4542	>	computer resources. In combination with supercomputers, it is possible
4543	>	to address questions that were previously out of reach. Problems
4544	>	from diffusion, gravitation, and wave propagation are considered.},
4545	>	Annote = {Pb499 Times Cited:99 Cited References Count:44},
4546	>	Author = {L. Greengard},
4547	>	Issn = {0036-8075},
4548	>	Journal = {Science},
4549	>	Month = {Aug 12},
4550	>	Number = 5174,
4551	>	Pages = {909-914},
4552	>	Title = {Fast Algorithms for Classical Physics},
4553	>	Uri = {<Go to ISI>://A1994PB49900031},
4554	>	Volume = 265,
4555	>	Year = 1994}
4556	>
4557	>	@article{Greengard1987,
4558	>	Annote = {L0498 Times Cited:899 Cited References Count:7},
4559	>	Author = {L. Greengard and V. Rokhlin},
4560	>	Issn = {0021-9991},
4561	>	Journal = {Journal of Computational Physics},
4562	>	Month = {Dec},
4563	>	Number = 2,
4564	>	Pages = {325-348},
4565	>	Title = {A Fast Algorithm for Particle Simulations},
4566	>	Uri = {<Go to ISI>://A1987L049800006},
4567	>	Volume = 73,
4568	>	Year = 1987}
4569	>
4570	>	@article{Hairer1997,
4571	>	Abstract = {Backward error analysis is a useful tool for the study of numerical
4572	>	approximations to ordinary differential equations. The numerical
4573	>	solution is formally interpreted as the exact solution of a perturbed
4574	>	differential equation, given as a formal and usually divergent series
4575	>	in powers of the step size. For a rigorous analysis, this series
4576	>	has to be truncated. In this article we study the influence of this
4577	>	truncation to the difference between the numerical solution and
4578	>	the exact solution of the perturbed differential equation. Results
4579	>	on the long-time behaviour of numerical solutions are obtained in
4580	>	this way. We present applications to the numerical phase portrait
4581	>	near hyperbolic equilibrium points, to asymptotically stable periodic
4582	>	orbits and Hopf bifurcation, and to energy conservation and approximation
4583	>	of invariant tori in Hamiltonian systems.},
4584	>	Annote = {Xj488 Times Cited:50 Cited References Count:19},
4585	>	Author = {E. Hairer and C. Lubich},
4586	>	Issn = {0029-599X},
4587	>	Journal = {Numerische Mathematik},
4588	>	Month = {Jun},
4589	>	Number = 4,
4590	>	Pages = {441-462},
4591	>	Title = {The life-span of backward error analysis for numerical integrators},
4592	>	Uri = {<Go to ISI>://A1997XJ48800002},
4593	>	Volume = 76,
4594	>	Year = 1997}
4595	>
4596	>	@article{Hao1993,
4597	>	Abstract = {A new procedure for studying the folding and unfolding of proteins,
4598	>	with an application to bovine pancreatic trypsin inhibitor (BPTI),
4599	>	is reported. The unfolding and refolding of the native structure
4600	>	of the protein are characterized by the dimensions of the protein,
4601	>	expressed in terms of the three principal radii of the structure
4602	>	considered as an ellipsoid. A dynamic equation, describing the variations
4603	>	of the principal radii on the unfolding path, and a numerical procedure
4604	>	to solve this equation are proposed. Expanded and distorted conformations
4605	>	are refolded to the native structure by a dimensional-constraint
4606	>	energy minimization procedure. A unique and reproducible unfolding
4607	>	pathway for an intermediate of BPTI lacking the [30,51] disulfide
4608	>	bond is obtained. The resulting unfolded conformations are extended;
4609	>	they contain near-native local structure, but their longest principal
4610	>	radii are more than 2.5 times greater than that of the native structure.
4611	>	The most interesting finding is that the majority of expanded conformations,
4612	>	generated under various conditions, can be refolded closely to the
4613	>	native structure, as measured by the correct overall chain fold,
4614	>	by the rms deviations from the native structure of only 1.9-3.1
4615	>	angstrom, and by the energy differences of about 10 kcal/mol from
4616	>	the native structure. Introduction of the [30,51] disulfide bond
4617	>	at this stage, followed by minimization, improves the closeness
4618	>	of the refolded structures to the native structure, reducing the
4619	>	rms deviations to 0.9-2.0 angstrom. The unique refolding of these
4620	>	expanded structures over such a large conformational space implies
4621	>	that the folding is strongly dictated by the interactions in the
4622	>	amino acid sequence of BPTI. The simulations indicate that, under
4623	>	conditions that favor a compact structure as mimicked by the volume
4624	>	constraints in our algorithm; the expanded conformations have a
4625	>	strong tendency to move toward the native structure; therefore,
4626	>	they probably would be favorable folding intermediates. The results
4627	>	presented here support a general model for protein folding, i.e.,
4628	>	progressive formation of partially folded structural units, followed
4629	>	by collapse to the compact native structure. The general applicability
4630	>	of the procedure is also discussed.},
4631	>	Annote = {Ly294 Times Cited:27 Cited References Count:57},
4632	>	Author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga},
4633	>	Issn = {0006-2960},
4634	>	Journal = {Biochemistry},
4635	>	Month = {Sep 21},
4636	>	Number = 37,
4637	>	Pages = {9614-9631},
4638	>	Title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic Trypsin-Inhibitor Studied by Computer-Simulations},
4639	>	Uri = {<Go to ISI>://A1993LY29400014},
4640	>	Volume = 32,
4641	>	Year = 1993}
4642	>
4643	>	@article{Hinsen2000,
4644	>	Abstract = {The slow dynamics of proteins around its native folded state is usually
4645	>	described by diffusion in a strongly anharmonic potential. In this
4646	>	paper, we try to understand the form and origin of the anharmonicities,
4647	>	with the principal aim of gaining a better understanding of the
4648	>	principal motion types, but also in order to develop more efficient
4649	>	numerical methods for simulating neutron scattering spectra of large
4650	>	proteins. First, we decompose a molecular dynamics (MD) trajectory
4651	>	of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water
4652	>	into three contributions that we expect to be independent: the global
4653	>	motion of the residues, the rigid-body motion of the sidechains
4654	>	relative to the backbone, and the internal deformations of the sidechains.
4655	>	We show that they are indeed almost independent by verifying the
4656	>	factorization of the incoherent intermediate scattering function.
4657	>	Then, we show that the global residue motions, which include all
4658	>	large-scale backbone motions, can be reproduced by a simple harmonic
4659	>	model which contains two contributions: a short-time vibrational
4660	>	term, described by a standard normal mode calculation in a local
4661	>	minimum, and a long-time diffusive term, described by Brownian motion
4662	>	in an effective harmonic potential. The potential and the friction
4663	>	constants were fitted to the MD data. The major anharmonic contribution
4664	>	to the incoherent intermediate scattering function comes from the
4665	>	rigid-body diffusion of the sidechains. This model can be used to
4666	>	calculate scattering functions for large proteins and for long-time
4667	>	scales very efficiently, and thus provides a useful complement to
4668	>	MD simulations, which are best suited for detailed studies on smaller
4669	>	systems or for shorter time scales. (C) 2000 Elsevier Science B.V.
4670	>	All rights reserved.},
4671	>	Annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31},
4672	>	Author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel and G. R. Kneller},
4673	>	Issn = {0301-0104},
4674	>	Journal = {Chemical Physics},
4675	>	Month = {Nov 1},
4676	>	Number = {1-2},
4677	>	Pages = {25-37},
4678	>	Title = {Harmonicity in slow protein dynamics},
4679	>	Uri = {<Go to ISI>://000090121700003},
4680	>	Volume = 261,
4681	>	Year = 2000}
4682	>
4683	>	@article{Ho1992,
4684	>	Abstract = {Evidence has been found for the existence water at the protein-lipid
4685	>	hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome
4686	>	C, using two related fluorescence spectroscopic approaches. The
4687	>	first approach exploited the fact that the presence of water in
4688	>	the excited state solvent cage of a fluorophore increases the rate
4689	>	of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl)
4690	>	phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores
4691	>	are located in the hydrophobic core of the lipid bilayer, the introduction
4692	>	of gramicidin reduced the fluorescence lifetime, indicative of an
4693	>	increased presence of water in the bilayer. Since a high protein:lipid
4694	>	ratio was used, the fluorophores were forced to be adjacent to the
4695	>	protein hydrophobic surface, hence the presence of water in this
4696	>	region could be inferred. Cholesterol is known to reduce the water
4697	>	content of lipid bilayers and this effect was maintained at the
4698	>	protein-lipid interface with both gramicidin and apocytochrome C,
4699	>	again suggesting hydration in this region. The second approach was
4700	>	to use the fluorescence enhancement induced by exchanging deuterium
4701	>	oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH,
4702	>	located in the lipid head group region, and of the gramicidin intrinsic
4703	>	tryptophans were greater in a D2O buffer compared with H2O, showing
4704	>	that the fluorophores were exposed to water in the bilayer at the
4705	>	protein-lipid interface. In the presence of cholesterol the fluorescence
4706	>	intensity ratio of D2O to H2O decreased, indicating a removal of
4707	>	water by the cholesterol, in keeping with the lifetime data. Altered
4708	>	hydration at the protein-lipid interface could affect conformation,
4709	>	thereby offering a new route by which membrane protein functioning
4710	>	may be modified.},
4711	>	Annote = {Ju251 Times Cited:55 Cited References Count:44},
4712	>	Author = {C. Ho and C. D. Stubbs},
4713	>	Issn = {0006-3495},
4714	>	Journal = {Biophysical Journal},
4715	>	Month = {Oct},
4716	>	Number = 4,
4717	>	Pages = {897-902},
4718	>	Title = {Hydration at the Membrane Protein-Lipid Interface},
4719	>	Uri = {<Go to ISI>://A1992JU25100002},
4720	>	Volume = 63,
4721	>	Year = 1992}
4722	>
4723	>	@book{Hockney1981,
4724	>	Address = {New York},
4725	>	Author = {R.W. Hockney and J.W. Eastwood},
4726	>	Publisher = {McGraw-Hill},
4727	>	Title = {Computer Simulation Using Particles},
4728	>	Year = 1981}
4729	>
4730	>	@article{Hoover1985,
4731	>	Annote = {Acr30 Times Cited:1809 Cited References Count:11},
4732	>	Author = {W. G. Hoover},
4733	>	Issn = {1050-2947},
4734	>	Journal = {Physical Review A},
4735	>	Number = 3,
4736	>	Pages = {1695-1697},
4737	>	Title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
4738	>	Uri = {<Go to ISI>://A1985ACR3000056},
4739	>	Volume = 31,
4740	>	Year = 1985}
4741	>
4742	>	@article{Huh2004,
4743	>	Abstract = {Racemic fluids of chiral calamitic molecules are investigated with
4744	>	molecular dynamics simulations. In particular, the phase behavior
4745	>	as a function of density is examined for eight racemates. The relationship
4746	>	between chiral discrimination and orientational order in the phase
4747	>	is explored. We find that the transition from the isotropic phase
4748	>	to a liquid crystal phase is accompanied by an increase in chiral
4749	>	discrimination, as measured by differences in radial distributions.
4750	>	Among ordered phases, discrimination is largest for smectic phases
4751	>	with a significant preference for heterochiral contact within the
4752	>	layers. (C) 2004 American Institute of Physics.},
4753	>	Annote = {870FJ Times Cited:0 Cited References Count:63},
4754	>	Author = {Y. Huh and N. M. Cann},
4755	>	Issn = {0021-9606},
4756	>	Journal = {Journal of Chemical Physics},
4757	>	Month = {Nov 22},
4758	>	Number = 20,
4759	>	Pages = {10299-10308},
4760	>	Title = {Discrimination in isotropic, nematic, and smectic phases of chiral calamitic molecules: A computer simulation study},
4761	>	Uri = {<Go to ISI>://000225042700059},
4762	>	Volume = 121,
4763	>	Year = 2004}
4764	>
4765	>	@article{Humphrey1996,
4766	>	Abstract = {VMD is a molecular graphics program designed for the display and analysis
4767	>	of molecular assemblies, in particular biopolymers such as proteins
4768	>	and nucleic acids. VMD can simultaneously display any number of
4769	>	structures using a wide variety of rendering styles and coloring
4770	>	methods. Molecules are displayed as one or more ''representations,''
4771	>	in which each representation embodies a particular rendering method
4772	>	and coloring scheme for a selected subset of atoms. The atoms displayed
4773	>	in each representation are chosen using an extensive atom selection
4774	>	syntax, which includes Boolean operators and regular expressions.
4775	>	VMD provides a complete graphical user interface for program control,
4776	>	as well as a text interface using the Tcl embeddable parser to allow
4777	>	for complex scripts with variable substitution, control loops, and
4778	>	function calls. Full session logging is supported, which produces
4779	>	a VMD command script for later playback. High-resolution raster
4780	>	images of displayed molecules may be produced by generating input
4781	>	scripts for use by a number of photorealistic image-rendering applications.
4782	>	VMD has also been expressly designed with the ability to animate
4783	>	molecular dynamics (MD) simulation trajectories, imported either
4784	>	from files or from a direct connection to a running MD simulation.
4785	>	VMD is the visualization component of MDScope, a set of tools for
4786	>	interactive problem solving in structural biology, which also includes
4787	>	the parallel MD program NAMD, and the MDCOMM software used to connect
4788	>	the visualization and simulation programs. VMD is written in C++,
4789	>	using an object-oriented design; the program, including source code
4790	>	and extensive documentation, is freely available via anonymous ftp
4791	>	and through the World Wide Web.},
4792	>	Annote = {Uh515 Times Cited:1418 Cited References Count:19},
4793	>	Author = {W. Humphrey and A. Dalke and K. Schulten},
4794	>	Issn = {0263-7855},
4795	>	Journal = {Journal of Molecular Graphics},
4796	>	Month = {Feb},
4797	>	Number = 1,
4798	>	Pages = {33-\&},
4799	>	Title = {VMD: Visual molecular dynamics},
4800	>	Uri = {<Go to ISI>://A1996UH51500005},
4801	>	Volume = 14,
4802	>	Year = 1996}
4803	>
4804	>	@article{Izaguirre2001,
4805	>	Abstract = {In this paper we show the possibility of using very mild stochastic
4806	>	damping to stabilize long time step integrators for Newtonian molecular
4807	>	dynamics. More specifically, stable and accurate integrations are
4808	>	obtained for damping coefficients that are only a few percent of
4809	>	the natural decay rate of processes of interest, such as the velocity
4810	>	autocorrelation function. Two new multiple time stepping integrators,
4811	>	Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are
4812	>	introduced in this paper. Both use the mollified impulse method
4813	>	for the Newtonian term. LM uses a discretization of the Langevin
4814	>	equation that is exact for the constant force, and BBK-M uses the
4815	>	popular Brunger-Brooks-Karplus integrator (BBK). These integrators,
4816	>	along with an extrapolative method called LN, are evaluated across
4817	>	a wide range of damping coefficient values. When large damping coefficients
4818	>	are used, as one would for the implicit modeling of solvent molecules,
4819	>	the method LN is superior, with LM closely following. However, with
4820	>	mild damping of 0.2 ps(-1), LM produces the best results, allowing
4821	>	long time steps of 14 fs in simulations containing explicitly modeled
4822	>	flexible water. With BBK-M and the same damping coefficient, time
4823	>	steps of 12 fs are possible for the same system. Similar results
4824	>	are obtained for a solvated protein-DNA simulation of estrogen receptor
4825	>	ER with estrogen response element ERE. A parallel version of BBK-M
4826	>	runs nearly three times faster than the Verlet-I/r-RESPA (reversible
4827	>	reference system propagator algorithm) when using the largest stable
4828	>	time step on each one, and it also parallelizes well. The computation
4829	>	of diffusion coefficients for flexible water and ER/ERE shows that
4830	>	when mild damping of up to 0.2 ps-1 is used the dynamics are not
4831	>	significantly distorted. (C) 2001 American Institute of Physics.},
4832	>	Annote = {397CQ Times Cited:14 Cited References Count:36},
4833	>	Author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
4834	>	Issn = {0021-9606},
4835	>	Journal = {Journal of Chemical Physics},
4836	>	Month = {Feb 1},
4837	>	Number = 5,
4838	>	Pages = {2090-2098},
4839	>	Title = {Langevin stabilization of molecular dynamics},
4840	>	Uri = {<Go to ISI>://000166676100020},
4841	>	Volume = 114,
4842	>	Year = 2001}
4843	>
4844	>	@article{Torre1977,
4845	>	Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield},
4846	>	Journal = {Biopolymers},
4847	>	Pages = {1747-1763},
4848	>	Title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
4849	>	Volume = 16,
4850	>	Year = 1977}
4851	>
4852	>	@article{Kale1999,
4853	>	Abstract = {Molecular dynamics programs simulate the behavior of biomolecular
4854	>	systems, leading to understanding of their functions. However, the
4855	>	computational complexity of such simulations is enormous. Parallel
4856	>	machines provide the potential to meet this computational challenge.
4857	>	To harness this potential, it is necessary to develop a scalable
4858	>	program. It is also necessary that the program be easily modified
4859	>	by application-domain programmers. The NAMD2 program presented in
4860	>	this paper seeks to provide these desirable features. It uses spatial
4861	>	decomposition combined with force decomposition to enhance scalability.
4862	>	It uses intelligent periodic load balancing, so as to maximally
4863	>	utilize the available compute power. It is modularly organized,
4864	>	and implemented using Charm++, a parallel C++ dialect, so as to
4865	>	enhance its modifiability. It uses a combination of numerical techniques
4866	>	and algorithms to ensure that energy drifts are minimized, ensuring
4867	>	accuracy in long running calculations. NAMD2 uses a portable run-time
4868	>	framework called Converse that also supports interoperability among
4869	>	multiple parallel paradigms. As a result, different components of
4870	>	applications can be written in the most appropriate parallel paradigms.
4871	>	NAMD2 runs on most parallel machines including workstation clusters
4872	>	and has yielded speedups in excess of 180 on 220 processors. This
4873	>	paper also describes the performance obtained on some benchmark
4874	>	applications. (C) 1999 Academic Press.},
4875	>	Annote = {194FM Times Cited:373 Cited References Count:51},
4876	>	Author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan and K. Schulten},
4877	>	Issn = {0021-9991},
4878	>	Journal = {Journal of Computational Physics},
4879	>	Month = {May 1},
4880	>	Number = 1,
4881	>	Pages = {283-312},
4882	>	Title = {NAMD2: Greater scalability for parallel molecular dynamics},
4883	>	Uri = {<Go to ISI>://000080181500013},
4884	>	Volume = 151,
4885	>	Year = 1999}
4886	>
4887	>	@article{Kane2000,
4888	>	Abstract = {The purpose of this work is twofold. First, we demonstrate analytically
4889	>	that the classical Newmark family as well as related integration
4890	>	algorithms are variational in the sense of the Veselov formulation
4891	>	of discrete mechanics. Such variational algorithms are well known
4892	>	to be symplectic and momentum preserving and to often have excellent
4893	>	global energy behaviour. This analytical result is verified through
4894	>	numerical examples and is believed to be one of the primary reasons
4895	>	that this class of algorithms performs so well. Second, we develop
4896	>	algorithms for mechanical systems with forcing, and in particular,
4897	>	for dissipative systems. In this case, we develop integrators that
4898	>	are based on a discretization of the Lagrange d'Alembert principle
4899	>	as well as on a variational formulation of dissipation. It is demonstrated
4900	>	that these types of structured integrators have good numerical behaviour
4901	>	in terms of obtaining the correct amounts by which the energy changes
4902	>	over the integration run. Copyright (C) 2000 John Wiley & Sons,
4903	>	Ltd.},
4904	>	Annote = {373CJ Times Cited:30 Cited References Count:41},
4905	>	Author = {C. Kane and J. E. Marsden and M. Ortiz and M. West},
4906	>	Issn = {0029-5981},
4907	>	Journal = {International Journal for Numerical Methods in Engineering},
4908	>	Month = {Dec 10},
4909	>	Number = 10,
4910	>	Pages = {1295-1325},
4911	>	Title = {Variational integrators and the Newmark algorithm for conservative and dissipative mechanical systems},
4912	>	Uri = {<Go to ISI>://000165270600004},
4913	>	Volume = 49,
4914	>	Year = 2000}
4915	>
4916	>	@article{Klimov1997,
4917	>	Abstract = {The viscosity (eta) dependence of the folding rates for four sequences
4918	>	(the native state of three sequences is a beta sheet, while the
4919	>	fourth forms an alpha helix) is calculated for off-lattice models
4920	>	of proteins. Assuming that the dynamics is given by the Langevin
4921	>	equation, we show that the folding rates increase linearly at low
4922	>	viscosities eta, decrease as 1/eta at large eta, and have a maximum
4923	>	at intermediate values. The Kramers' theory of barrier crossing
4924	>	provides a quantitative fit of the numerical results. By mapping
4925	>	the simulation results to real proteins we estimate that for optimized
4926	>	sequences the time scale for forming a four turn alpha-helix topology
4927	>	is about 500 ns, whereas for beta sheet it is about 10 mu s.},
4928	>	Annote = {Xk293 Times Cited:77 Cited References Count:17},
4929	>	Author = {D. K. Klimov and D. Thirumalai},
4930	>	Issn = {0031-9007},
4931	>	Journal = {Physical Review Letters},
4932	>	Month = {Jul 14},
4933	>	Number = 2,
4934	>	Pages = {317-320},
4935	>	Title = {Viscosity dependence of the folding rates of proteins},
4936	>	Uri = {<Go to ISI>://A1997XK29300035},
4937	>	Volume = 79,
4938	>	Year = 1997}
4939	>
4940	>	@article{Kol1997,
4941	>	Abstract = {Rigid-body molecular dynamics simulations typically are performed
4942	>	in a quaternion representation. The nonseparable form of the Hamiltonian
4943	>	in quaternions prevents the use of a standard leapfrog (Verlet)
4944	>	integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation
4945	>	methods are generally used, This is unfortunate since symplectic
4946	>	methods like Verlet exhibit superior energy conservation in long-time
4947	>	integrations. In this article, we describe an alternative method,
4948	>	which we call RSHAKE (for rotation-SHAKE), in which the entire rotation
4949	>	matrix is evolved (using the scheme of McLachlan and Scovel [J.
4950	>	Nonlin. Sci, 16 233 (1995)]) in tandem with the particle positions.
4951	>	We employ a fast approximate Newton solver to preserve the orthogonality
4952	>	of the rotation matrix. We test our method on a system of soft-sphere
4953	>	dipoles and compare with quaternion evolution using a 4th-order
4954	>	predictor-corrector integrator, Although the short-time error of
4955	>	the quaternion algorithm is smaller for fixed time step than that
4956	>	for RSHAKE, the quaternion scheme exhibits an energy drift which
4957	>	is not observed in simulations with RSHAKE, hence a fixed energy
4958	>	tolerance can be achieved by using a larger time step, The superiority
4959	>	of RSHAKE increases with system size. (C) 1997 American Institute
4960	>	of Physics.},
4961	>	Annote = {Xq332 Times Cited:11 Cited References Count:18},
4962	>	Author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
4963	>	Issn = {0021-9606},
4964	>	Journal = {Journal of Chemical Physics},
4965	>	Month = {Aug 15},
4966	>	Number = 7,
4967	>	Pages = {2580-2588},
4968	>	Title = {A symplectic method for rigid-body molecular simulation},
4969	>	Uri = {<Go to ISI>://A1997XQ33200046},
4970	>	Volume = 107,
4971	>	Year = 1997}
4972	>
4973	>	@article{Lansac2001,
4974	>	Abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
4975	>	class of mesogens. Many of the peculiar properties of nCB's (e.g.,
4976	>	the occurence of the partial bilayer smectic-A(d) phase) are thought
4977	>	to be a manifestation of short-range antiparallel association of
4978	>	neighboring molecules, resulting from strong dipole-dipole interactions
4979	>	between cyano groups. To test and extend existing models of microscopic
4980	>	ordering in nCB's, we carry out large-scale atomistic simulation
4981	>	studies of the microscopic structure and dynamics of the Sm-A(d)
4982	>	phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of
4983	>	thermodynamic, structural, and dynamical properties for this material,
4984	>	and make a detailed comparison of our results with experimental
4985	>	measurements in order to validate our molecular model. Semiquantitative
4986	>	agreement with experiment is found: the smectic layer spacing and
4987	>	mass density are well reproduced, translational diffusion constants
4988	>	are similar to experiment, but the orientational ordering of alkyl
4989	>	chains is overestimated. This simulation provides a detailed picture
4990	>	of molecular conformation, smectic layer structure, and intermolecular
4991	>	correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range
4992	>	antiparallel association of molecules arising from dipole-dipole
4993	>	interactions plays a dominant role in determining the molecular-scale
4994	>	structure of 8CB.},
4995	>	Annote = {Part 1 496QF Times Cited:10 Cited References Count:60},
4996	>	Author = {Y. Lansac and M. A. Glaser and N. A. Clark},
4997	>	Issn = {1063-651X},
4998	>	Journal = {Physical Review E},
4999	>	Month = {Nov},
5000	>	Number = 5,
5001	>	Pages = {-},
5002	>	Title = {Microscopic structure and dynamics of a partial bilayer smectic liquid crystal},
5003	>	Uri = {<Go to ISI>://000172406900063},
5004	>	Volume = 6405,
5005	>	Year = 2001}
5006	>
5007	>	@article{Lansac2003,
5008	>	Abstract = {Recently, a new class of smectic liquid crystal phases characterized
5009	>	by the spontaneous formation of macroscopic chiral domains from
5010	>	achiral bent-core molecules has been discovered. We have carried
5011	>	out Monte Carlo simulations of a minimal hard spherocylinder dimer
5012	>	model to investigate the role of excluded volume interactions in
5013	>	determining the phase behavior of bent-core materials and to probe
5014	>	the molecular origins of polar and chiral symmetry breaking. We
5015	>	present the phase diagram of hard spherocylinder dimers of length-diameter
5016	>	ratio of 5 as a function of pressure or density and dimer opening
5017	>	angle psi. With decreasing psi, a transition from a nonpolar to
5018	>	a polar smectic A phase is observed near psi=167degrees, and the
5019	>	nematic phase becomes thermodynamically unstable for psi<135degrees.
5020	>	Free energy calculations indicate that the antipolar smectic A (SmAP(A))
5021	>	phase is more stable than the polar smectic A phase (SmAP(F)). No
5022	>	chiral smectic or biaxial nematic phases were found.},
5023	>	Annote = {Part 1 646CM Times Cited:15 Cited References Count:38},
5024	>	Author = {Y. Lansac and P. K. Maiti and N. A. Clark and M. A. Glaser},
5025	>	Issn = {1063-651X},
5026	>	Journal = {Physical Review E},
5027	>	Month = {Jan},
5028	>	Number = 1,
5029	>	Pages = {-},
5030	>	Title = {Phase behavior of bent-core molecules},
5031	>	Uri = {<Go to ISI>://000181017300042},
5032	>	Volume = 67,
5033	>	Year = 2003}
5034	>
5035	>	@book{Leach2001,
5036	>	Address = {Harlow, England},
5037	>	Author = {A. Leach},
5038	>	Edition = {2nd},
5039	>	Publisher = {Pearson Educated Limited},
5040	>	Title = {Molecular Modeling: Principles and Applications},
5041	>	Year = 2001}
5042	>
5043	>	@article{Leimkuhler1999,
5044	>	Abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
5045	>	regularization and modified Sundman transformations are applied
5046	>	to simulate general perturbed Kepler motion and to compute classical
5047	>	trajectories of atomic systems (e.g. Rydberg atoms). The new family
5048	>	of reversible adaptive regularization methods also conserves angular
5049	>	momentum and exhibits superior energy conservation and numerical
5050	>	stability in long-time integrations. The schemes are appropriate
5051	>	for scattering, for astronomical calculations of escape time and
5052	>	long-term stability, and for classical and semiclassical studies
5053	>	of atomic dynamics. The components of an algorithm for trajectory
5054	>	calculations are described. Numerical experiments illustrate the
5055	>	effectiveness of the reversible approach.},
5056	>	Annote = {199EE Times Cited:11 Cited References Count:48},
5057	>	Author = {B. Leimkuhler},
5058	>	Issn = {1364-503X},
5059	>	Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
5060	>	Month = {Apr 15},
5061	>	Number = 1754,
5062	>	Pages = {1101-1133},
5063	>	Title = {Reversible adaptive regularization: perturbed Kepler motion and classical atomic trajectories},
5064	>	Uri = {<Go to ISI>://000080466800007},
5065	>	Volume = 357,
5066	>	Year = 1999}
5067	>
5068	>	@book{Leimkuhler2004,
5069	>	Address = {Cambridge},
5070	>	Author = {B. Leimkuhler and S. Reich},
5071	>	Publisher = {Cambridge University Press},
5072	>	Title = {Simulating Hamiltonian Dynamics},
5073	>	Year = 2004}
5074	>
5075	>	@article{Levelut1981,
5076	>	Annote = {Ml751 Times Cited:96 Cited References Count:16},
5077	>	Author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard and G. Sigaud},
5078	>	Issn = {1050-2947},
5079	>	Journal = {Physical Review A},
5080	>	Number = 4,
5081	>	Pages = {2180-2186},
5082	>	Title = {Number of Sa Phases},
5083	>	Uri = {<Go to ISI>://A1981ML75100057},
5084	>	Volume = 24,
5085	>	Year = 1981}
5086	>
5087	>	@article{Lieb1982,
5088	>	Annote = {Nu461 Times Cited:40 Cited References Count:28},
5089	>	Author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
5090	>	Issn = {0006-3002},
5091	>	Journal = {Biochimica Et Biophysica Acta},
5092	>	Number = 2,
5093	>	Pages = {388-398},
5094	>	Title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - Evidence from Raman-Scattering},
5095	>	Uri = {<Go to ISI>://A1982NU46100012},
5096	>	Volume = 688,
5097	>	Year = 1982}
5098	>
5099	>	@article{Link1997,
5100	>	Abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
5101	>	cores was found to have fluid layers that exhibit two spontaneous
5102	>	symmetry-breaking instabilities: polar molecular orientational ordering
5103	>	about the layer normal and molecular tilt. These instabilities combine
5104	>	to form a chiral layer structure with a handedness that depends
5105	>	on the sign of the tilt. The bulk states are either antiferroelectric-racemic,
5106	>	with the layer polar direction and handedness alternating in sign
5107	>	from layer to layer, or antiferroelectric-chiral, which is of uniform
5108	>	layer handedness. Both states exhibit an electric field-induced
5109	>	transition from antiferroelectric to ferroelectric.},
5110	>	Annote = {Yl002 Times Cited:407 Cited References Count:25},
5111	>	Author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A. Clark and E. Korblova and D. M. Walba},
5112	>	Issn = {0036-8075},
5113	>	Journal = {Science},
5114	>	Month = {Dec 12},
5115	>	Number = 5345,
5116	>	Pages = {1924-1927},
5117	>	Title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic phase of achiral molecules},
5118	>	Uri = {<Go to ISI>://A1997YL00200028},
5119	>	Volume = 278,
5120	>	Year = 1997}
5121	>
5122	>	@article{Liwo2005,
5123	>	Annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
5124	>	Author = {A. Liwo and M. Khalili and H. A. Scheraga},
5125	>	Issn = {1742-464X},
5126	>	Journal = {Febs Journal},
5127	>	Month = {Jul},
5128	>	Pages = {359-360},
5129	>	Title = {Ab initio simulations of protein folding pathways by molecular dynamics with the united-residue (UNRES) model of polypeptide chains},
5130	>	Uri = {<Go to ISI>://000234826102043},
5131	>	Volume = 272,
5132	>	Year = 2005}
5133	>
5134	>	@article{Luty1994,
5135	>	Abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
5136	>	for calculating electrostatic interactions in periodic molecular
5137	>	systems. A brief comparison of the theories shows that the methods
5138	>	are very similar differing mainly in the technique which is used
5139	>	to perform the ''k-space'' or mesh calculation. Because the PPPM
5140	>	utilizes the highly efficient numerical Fast Fourier Transform (FFT)
5141	>	method it requires significantly less computational effort than
5142	>	the Ewald method and scale's almost linearly with system size.},
5143	>	Annote = {Qf464 Times Cited:50 Cited References Count:20},
5144	>	Author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
5145	>	Issn = {0892-7022},
5146	>	Journal = {Molecular Simulation},
5147	>	Number = 1,
5148	>	Pages = {11-20},
5149	>	Title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
5150	>	Uri = {<Go to ISI>://A1994QF46400002},
5151	>	Volume = 14,
5152	>	Year = 1994}
5153	>
5154	>	@book{Marion1990,
5155	>	Address = {New York},
5156	>	Author = {J.~B. Marion},
5157	>	Edition = {2rd},
5158	>	Publisher = {Academic Press},
5159	>	Title = {Classical Dynamics of Particles and Systems},
5160	>	Year = 1990}
5161	>
5162	>	@article{Marrink1994,
5163	>	Abstract = {To obtain insight in the process of water permeation through a lipid
5164	>	membrane, we performed molecular dynamics simulations on a phospholipid
5165	>	(DPPC)/water system with atomic detail. Since the actual process
5166	>	of permeation is too slow to be studied directly, we deduced the
5167	>	permeation rate indirectly via computation of the free energy and
5168	>	diffusion rate profiles of a water molecule across the bilayer.
5169	>	We conclude that the permeation of water through a lipid membrane
5170	>	cannot be described adequately by a simple homogeneous solubility-diffusion
5171	>	model. Both the excess free energy and the diffusion rate strongly
5172	>	depend on the position in the membrane, as a result from the inhomogeneous
5173	>	nature of the membrane. The calculated excess free energy profile
5174	>	has a shallow slope and a maximum height of 26 kJ/mol. The diffusion
5175	>	rate is highest in the middle of the membrane where the lipid density
5176	>	is low. In the interfacial region almost all water molecules are
5177	>	bound by the lipid headgroups, and the diffusion turns out to be
5178	>	1 order of magnitude smaller. The total transport process is essentially
5179	>	determined by the free energy barrier. The rate-limiting step is
5180	>	the permeation through the dense part of the lipid tails, where
5181	>	the resistance is highest. We found a permeation rate of 7(+/-3)
5182	>	x 10(-2) cm/s at 350 K, comparable to experimental values for DPPC
5183	>	membranes, if corrected for the temperature of the simulation. Taking
5184	>	the inhomogeneity of the membrane into account, we define a new
5185	>	''four-region'' model which seems to be more realistic than the
5186	>	''two-phase'' solubility-diffusion model.},
5187	>	Annote = {Ng219 Times Cited:187 Cited References Count:25},
5188	>	Author = {S. J. Marrink and H. J. C. Berendsen},
5189	>	Issn = {0022-3654},
5190	>	Journal = {Journal of Physical Chemistry},
5191	>	Month = {Apr 14},
5192	>	Number = 15,
5193	>	Pages = {4155-4168},
5194	>	Title = {Simulation of Water Transport through a Lipid-Membrane},
5195	>	Uri = {<Go to ISI>://A1994NG21900040},
5196	>	Volume = 98,
5197	>	Year = 1994}
5198	>
5199	>	@article{Marrink2004,
5200	>	Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
5201	>	Journal = {J. Phys. Chem. B},
5202	>	Pages = {750-760},
5203	>	Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
5204	>	Volume = 108,
5205	>	Year = 2004}
5206	>
5207	>	@article{Marsden1998,
5208	>	Abstract = {This paper presents a geometric-variational approach to continuous
5209	>	and discrete mechanics and field theories. Using multisymplectic
5210	>	geometry, we show that the existence of the fundamental geometric
5211	>	structures as well as their preservation along solutions can be
5212	>	obtained directly from the variational principle. In particular,
5213	>	we prove that a unique multisymplectic structure is obtained by
5214	>	taking the derivative of an action function, and use this structure
5215	>	to prove covariant generalizations of conservation of symplecticity
5216	>	and Noether's theorem. Natural discretization schemes for PDEs,
5217	>	which have these important preservation properties, then follow
5218	>	by choosing a discrete action functional. In the case of mechanics,
5219	>	we recover the variational symplectic integrators of Veselov type,
5220	>	while for PDEs we obtain covariant spacetime integrators which conserve
5221	>	the corresponding discrete multisymplectic form as well as the discrete
5222	>	momentum mappings corresponding to symmetries. We show that the
5223	>	usual notion of symplecticity along an infinite-dimensional space
5224	>	of fields can be naturally obtained by making a spacetime split.
5225	>	All of the aspects of our method are demonstrated with a nonlinear
5226	>	sine-Gordon equation, including computational results and a comparison
5227	>	with other discretization schemes.},
5228	>	Annote = {154RH Times Cited:88 Cited References Count:36},
5229	>	Author = {J. E. Marsden and G. W. Patrick and S. Shkoller},
5230	>	Issn = {0010-3616},
5231	>	Journal = {Communications in Mathematical Physics},
5232	>	Month = {Dec},
5233	>	Number = 2,
5234	>	Pages = {351-395},
5235	>	Title = {Multisymplectic geometry, variational integrators, and nonlinear PDEs},
5236	>	Uri = {<Go to ISI>://000077902200006},
5237	>	Volume = 199,
5238	>	Year = 1998}
5239	>
5240	>	@article{Matthey2004,
5241	>	Abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
5242	>	of novel algorithms for molecular dynamics and related applications.
5243	>	Its flexibility is achieved primarily through the use of inheritance
5244	>	and design patterns (object-oriented programming): Performance is
5245	>	obtained by using templates that enable generation of efficient
5246	>	code for sections critical to performance (generic programming).
5247	>	The framework encapsulates important optimizations that can be used
5248	>	by developers, such as parallelism in the force computation. Its
5249	>	design is based on domain analysis of numerical integrators for
5250	>	molecular dynamics (MD) and of fast solvers for the force computation,
5251	>	particularly due to electrostatic interactions. Several new and
5252	>	efficient algorithms are implemented in PROTOMOL. Finally, it is
5253	>	shown that PROTOMOL'S sequential performance is excellent when compared
5254	>	to a leading MD program, and that it scales well for moderate number
5255	>	of processors. Binaries and source codes for Windows, Linux, Solaris,
5256	>	IRIX, HP-UX, and AIX platforms are available under open source license
5257	>	at http://protomol.sourceforge.net.},
5258	>	Annote = {860EP Times Cited:2 Cited References Count:52},
5259	>	Author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre},
5260	>	Issn = {0098-3500},
5261	>	Journal = {Acm Transactions on Mathematical Software},
5262	>	Month = {Sep},
5263	>	Number = 3,
5264	>	Pages = {237-265},
5265	>	Title = {ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics},
5266	>	Uri = {<Go to ISI>://000224325600001},
5267	>	Volume = 30,
5268	>	Year = 2004}
5269	>
5270	>	@article{McLachlan1993,
5271	>	Author = {R.~I McLachlan},
5272	>	Journal = {prl},
5273	>	Pages = {3043-3046},
5274	>	Title = {Explicit Lie-Poisson integration and the Euler equations},
5275	>	Volume = 71,
5276	>	Year = 1993}
5277	>
5278	>	@article{McLachlan1998,
5279	>	Abstract = {We give a survey and some new examples of generating functions for
5280	>	systems with symplectic structure, systems with a first integral,
5281	>	systems that preserve volume, and systems with symmetries and/or
5282	>	time-reversing symmetries. Both ODEs and maps are treated, and we
5283	>	discuss how generating functions may be used in the structure-preserving
5284	>	numerical integration of ODEs with the above properties.},
5285	>	Annote = {Yt049 Times Cited:7 Cited References Count:26},
5286	>	Author = {R. I. McLachlan and G. R. W. Quispel},
5287	>	Issn = {0167-2789},
5288	>	Journal = {Physica D},
5289	>	Month = {Jan 15},
5290	>	Number = {1-2},
5291	>	Pages = {298-309},
5292	>	Title = {Generating functions for dynamical systems with symmetries, integrals, and differential invariants},
5293	>	Uri = {<Go to ISI>://000071558900021},
5294	>	Volume = 112,
5295	>	Year = 1998}
5296	>
5297	>	@article{McLachlan1998a,
5298	>	Abstract = {We consider properties of flows, the relationships between them, and
5299	>	whether numerical integrators can be made to preserve these properties.
5300	>	This is done in the context of automorphisms and antiautomorphisms
5301	>	of a certain group generated by maps associated to vector fields.
5302	>	This new framework unifies several known constructions. We also
5303	>	use the concept of #covariance# of a numerical method with respect
5304	>	to a group of coordinate transformations. The main application is
5305	>	to explore the relationship between spatial symmetries, reversing
5306	>	symmetries, and time symmetry of flows and numerical integrators.},
5307	>	Annote = {Zc449 Times Cited:14 Cited References Count:33},
5308	>	Author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner},
5309	>	Issn = {0036-1429},
5310	>	Journal = {Siam Journal on Numerical Analysis},
5311	>	Month = {Apr},
5312	>	Number = 2,
5313	>	Pages = {586-599},
5314	>	Title = {Numerical integrators that preserve symmetries and reversing symmetries},
5315	>	Uri = {<Go to ISI>://000072580500010},
5316	>	Volume = 35,
5317	>	Year = 1998}
5318	>
5319	>	@article{McLachlan2005,
5320	>	Abstract = {In this paper we revisit the Moser-Veselov description of the free
5321	>	rigid body in body coordinates, which, in the 3 x 3 case, can be
5322	>	implemented as an explicit, second-order, integrable approximation
5323	>	of the continuous solution. By backward error analysis, we study
5324	>	the modified vector field which is integrated exactly by the discrete
5325	>	algorithm. We deduce that the discrete Moser-Veselov (DMV) is well
5326	>	approximated to higher order by time reparametrizations of the continuous
5327	>	equations (modified vector field). We use the modified vector field
5328	>	to scale the initial data of the DMV to improve the order of the
5329	>	approximation and show the equivalence of the DMV and the RATTLE
5330	>	algorithm. Numerical integration with these preprocessed initial
5331	>	data is several orders of magnitude more accurate than the original
5332	>	DMV and RATTLE approach.},
5333	>	Annote = {911NS Times Cited:0 Cited References Count:14},
5334	>	Author = {R. I. McLachlan and A. Zanna},
5335	>	Issn = {1615-3375},
5336	>	Journal = {Foundations of Computational Mathematics},
5337	>	Month = {Feb},
5338	>	Number = 1,
5339	>	Pages = {87-123},
5340	>	Title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
5341	>	Uri = {<Go to ISI>://000228011900003},
5342	>	Volume = 5,
5343	>	Year = 2005}
5344	>
5345	>	@article{Meineke2005,
5346	>	Abstract = {OOPSE is a new molecular dynamics simulation program that is capable
5347	>	of efficiently integrating equations of motion for atom types with
5348	>	orientational degrees of freedom (e.g. #sticky# atoms and point
5349	>	dipoles). Transition metals can also be simulated using the embedded
5350	>	atom method (EAM) potential included in the code. Parallel simulations
5351	>	are carried out using the force-based decomposition method. Simulations
5352	>	are specified using a very simple C-based meta-data language. A
5353	>	number of advanced integrators are included, and the basic integrator
5354	>	for orientational dynamics provides substantial improvements over
5355	>	older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.},
5356	>	Annote = {891CF Times Cited:1 Cited References Count:56},
5357	>	Author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and J. D. Gezelter},
5358	>	Issn = {0192-8651},
5359	>	Journal = {Journal of Computational Chemistry},
5360	>	Month = {Feb},
5361	>	Number = 3,
5362	>	Pages = {252-271},
5363	>	Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
5364	>	Uri = {<Go to ISI>://000226558200006},
5365	>	Volume = 26,
5366	>	Year = 2005}
5367	>
5368	>	@article{Melchionna1993,
5369	>	Abstract = {In this paper we write down equations of motion (following the approach
5370	>	pioneered by Hoover) for an exact isothermal-isobaric molecular
5371	>	dynamics simulation, and we extend them to multiple thermostating
5372	>	rates, to a shape-varying cell and to molecular systems, coherently
5373	>	with the previous 'extended system method'. An integration scheme
5374	>	is proposed together with a numerical illustration of the method.},
5375	>	Annote = {Kq355 Times Cited:172 Cited References Count:17},
5376	>	Author = {S. Melchionna and G. Ciccotti and B. L. Holian},
5377	>	Issn = {0026-8976},
5378	>	Journal = {Molecular Physics},
5379	>	Month = {Feb 20},
5380	>	Number = 3,
5381	>	Pages = {533-544},
5382	>	Title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
5383	>	Uri = {<Go to ISI>://A1993KQ35500002},
5384	>	Volume = 78,
5385	>	Year = 1993}
5386	>
5387	>	@article{Memmer2002,
5388	>	Abstract = {The phase behaviour of achiral banana-shaped molecules was studied
5389	>	by computer simulation. The banana-shaped molecules were described
5390	>	by model intermolecular interactions based on the Gay-Berne potential.
5391	>	The characteristic molecular structure was considered by joining
5392	>	two calamitic Gay-Berne particles through a bond to form a biaxial
5393	>	molecule of point symmetry group C-2v with a suitable bending angle.
5394	>	The dependence on temperature of systems of N=1024 rigid banana-shaped
5395	>	molecules with bending angle phi=140degrees has been studied by
5396	>	means of Monte Carlo simulations in the isobaric-isothermal ensemble
5397	>	(NpT). On cooling an isotropic system, two phase transitions characterized
5398	>	by phase transition enthalpy, entropy and relative volume change
5399	>	have been observed. For the first time by computer simulation of
5400	>	a many-particle system of banana-shaped molecules, at low temperature
5401	>	an untilted smectic phase showing a global phase biaxiality and
5402	>	a spontaneous local polarization in the layers, i.e. a local polar
5403	>	arrangement of the steric dipoles, with an antiferroelectric-like
5404	>	superstructure could be proven, a phase structure which recently
5405	>	has been discovered experimentally. Additionally, at intermediate
5406	>	temperature a nematic-like phase has been proved, whereas close
5407	>	to the transition to the smectic phase hints of a spontaneous achiral
5408	>	symmetry breaking have been determined. Here, in the absence of
5409	>	a layered structure a helical superstructure has been formed. All
5410	>	phases have been characterized by visual representations of selected
5411	>	configurations, scalar and pseudoscalar correlation functions, and
5412	>	order parameters.},
5413	>	Annote = {531HT Times Cited:12 Cited References Count:37},
5414	>	Author = {R. Memmer},
5415	>	Issn = {0267-8292},
5416	>	Journal = {Liquid Crystals},
5417	>	Month = {Apr},
5418	>	Number = 4,
5419	>	Pages = {483-496},
5420	>	Title = {Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study},
5421	>	Uri = {<Go to ISI>://000174410500001},
5422	>	Volume = 29,
5423	>	Year = 2002}
5424	>
5425	>	@article{Metropolis1949,
5426	>	Author = {N. Metropolis and S. Ulam},
5427	>	Journal = {J. Am. Stat. Ass.},
5428	>	Pages = {335-341},
5429	>	Title = {The $\mbox{Monte Carlo}$ Method},
5430	>	Volume = 44,
5431	>	Year = 1949}
5432	>
5433	>	@article{Mielke2004,
5434	>	Abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
5435	>	DNA can potentially induce long-range structural deformations integral
5436	>	to mechanisms of biological significance in both prokaryotes and
5437	>	eukaryotes. In this paper, we introduce a dynamic computer model
5438	>	for investigating this phenomenon. Duplex DNA is represented as
5439	>	a chain of hydrodynamic beads interacting through potentials of
5440	>	linearly elastic stretching, bending, and twisting, as well as excluded
5441	>	volume. The chain, linear when relaxed, is looped to form two open
5442	>	but topologically constrained subdomains. This permits the dynamic
5443	>	introduction of torsional stress via a centrally applied torque.
5444	>	We simulate by Brownian dynamics the 100 mus response of a 477-base
5445	>	pair B-DNA template to the localized torque generated by the prokaryotic
5446	>	transcription ensemble. Following a sharp rise at early times, the
5447	>	distributed twist assumes a nearly constant value in both subdomains,
5448	>	and a succession of supercoiling deformations occurs as superhelical
5449	>	stress is increasingly partitioned to writhe. The magnitude of writhe
5450	>	surpasses that of twist before also leveling off when the structure
5451	>	reaches mechanical equilibrium with the torsional load. Superhelicity
5452	>	is simultaneously right handed in one subdomain and left handed
5453	>	in the other, as predicted by the #transcription-induced##twin-supercoiled-domain#
5454	>	model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84,
5455	>	7024 (1987)]. The properties of the chain at the onset of writhing
5456	>	agree well with predictions from theory, and the generated stress
5457	>	is ample for driving secondary structural transitions in physiological
5458	>	DNA. (C) 2004 American Institute of Physics.},
5459	>	Annote = {861ZF Times Cited:3 Cited References Count:34},
5460	>	Author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen and C. J. Benham},
5461	>	Issn = {0021-9606},
5462	>	Journal = {Journal of Chemical Physics},
5463	>	Month = {Oct 22},
5464	>	Number = 16,
5465	>	Pages = {8104-8112},
5466	>	Title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study},
5467	>	Uri = {<Go to ISI>://000224456500064},
5468	>	Volume = 121,
5469	>	Year = 2004}
5470	>
5471	>	@article{Naess2001,
5472	>	Abstract = {The three Eulerian angles constitute the classical choice of generalized
5473	>	coordinates used to describe the three degrees of rotational freedom
5474	>	of a rigid body, but it has long been known that this choice yields
5475	>	singular equations of motion. The latter is also true when Eulerian
5476	>	angles are used in Brownian dynamics analyses of the angular orientation
5477	>	of single rigid bodies and segmented polymer chains. Starting from
5478	>	kinetic theory we here show that by instead employing the three
5479	>	components of Cartesian rotation vectors as the generalized coordinates
5480	>	describing angular orientation, no singularity appears in the configuration
5481	>	space diffusion equation and the associated Brownian dynamics algorithm.
5482	>	The suitability of Cartesian rotation vectors in Brownian dynamics
5483	>	simulations of segmented polymer chains with spring-like or ball-socket
5484	>	joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.},
5485	>	Annote = {433TA Times Cited:7 Cited References Count:19},
5486	>	Author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter},
5487	>	Issn = {0378-4371},
5488	>	Journal = {Physica A},
5489	>	Month = {May 15},
5490	>	Number = {3-4},
5491	>	Pages = {323-339},
5492	>	Title = {Brownian dynamics simulation of rigid bodies and segmented polymer chains. Use of Cartesian rotation vectors as the generalized coordinates describing angular orientations},
5493	>	Uri = {<Go to ISI>://000168774800005},
5494	>	Volume = 294,
5495	>	Year = 2001}
5496	>
5497	>	@article{Niori1996,
5498	>	Abstract = {The synthesis of a banana-shaped molecule is reported and it is found
5499	>	that the smectic phase which it forms is biaxial with the molecules
5500	>	packed in the best,direction into a layer. Because of this characteristic
5501	>	packing, spontaneous polarization appears parallel to the layer
5502	>	and switches on reversal of an applied electric field. This is the
5503	>	first obvious example of ferroelectricity in an achiral smectic
5504	>	phase and is ascribed to the C-2v symmetry of the molecular packing.},
5505	>	Annote = {Ux855 Times Cited:447 Cited References Count:18},
5506	>	Author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe},
5507	>	Issn = {0959-9428},
5508	>	Journal = {Journal of Materials Chemistry},
5509	>	Month = {Jul},
5510	>	Number = 7,
5511	>	Pages = {1231-1233},
5512	>	Title = {Distinct ferroelectric smectic liquid crystals consisting of banana shaped achiral molecules},
5513	>	Uri = {<Go to ISI>://A1996UX85500025},
5514	>	Volume = 6,
5515	>	Year = 1996}
5516	>
5517	>	@article{Noguchi2002,
5518	>	Abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
5519	>	forces using a Brownian dynamics simulation. Two nanoparticles,
5520	>	which interact repulsively with amphiphilic molecules, are put inside
5521	>	a vesicle. The position of one nanoparticle is fixed, and the other
5522	>	is moved by a constant force as in optical-trapping experiments.
5523	>	First, the pulled vesicle stretches into a pear or tube shape. Then
5524	>	the inner monolayer in the tube-shaped region is deformed, and a
5525	>	cylindrical structure is formed between two vesicles. After stretching
5526	>	the cylindrical region, fission occurs near the moved vesicle. Soon
5527	>	after this the cylindrical region shrinks. The trapping force similar
5528	>	to 100 pN is needed to induce the formation of the cylindrical structure
5529	>	and fission.},
5530	>	Annote = {Part 1 568PX Times Cited:5 Cited References Count:39},
5531	>	Author = {H. Noguchi and M. Takasu},
5532	>	Issn = {1063-651X},
5533	>	Journal = {Physical Review E},
5534	>	Month = {may},
5535	>	Number = 5,
5536	>	Pages = {-},
5537	>	Title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
5538	>	Uri = {<Go to ISI>://000176552300084},
5539	>	Volume = 65,
5540	>	Year = 2002}
5541	>
5542	>	@article{Noguchi2001,
5543	>	Abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
5544	>	simulation. Amphiphilic molecules spontaneously form vesicles with
5545	>	a bilayer structure. Two vesicles come into contact and form a stalk
5546	>	intermediate, in which a necklike structure only connects the outer
5547	>	monolayers, as predicted by the stalk hypothesis. We have found
5548	>	a new pathway of pore opening from stalks at high temperature: the
5549	>	elliptic stalk bends and contact between the ends of the arc-shaped
5550	>	stalk leads to pore opening. On the other hand, we have clarified
5551	>	that the pore-opening process at low temperature agrees with the
5552	>	modified stalk model: a pore is induced by contact between the inner
5553	>	monolayers inside the stalk. (C) 2001 American Institute of Physics.},
5554	>	Annote = {491UW Times Cited:48 Cited References Count:25},
5555	>	Author = {H. Noguchi and M. Takasu},
5556	>	Issn = {0021-9606},
5557	>	Journal = {Journal of Chemical Physics},
5558	>	Month = {Nov 22},
5559	>	Number = 20,
5560	>	Pages = {9547-9551},
5561	>	Title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
5562	>	Uri = {<Go to ISI>://000172129300049},
5563	>	Volume = 115,
5564	>	Year = 2001}
5565	>
5566	>	@book{Olver1986,
5567	>	Address = {New York},
5568	>	Author = {P.J. Olver},
5569	>	Publisher = {Springer},
5570	>	Title = {Applications of Lie groups to differential equatitons},
5571	>	Year = 1986}
5572	>
5573	>	@article{Omelyan1998,
5574	>	Abstract = {A revised version of the quaternion approach for numerical integration
5575	>	of the equations of motion for rigid polyatomic molecules is proposed.
5576	>	The modified approach is based on a formulation of the quaternion
5577	>	dynamics with constraints. This allows one to resolve the rigidity
5578	>	problem rigorously using constraint forces. It is shown that the
5579	>	procedure for preservation of molecular rigidity can be realized
5580	>	particularly simply within the Verlet algorithm in velocity form.
5581	>	We demonstrate that the method presented leads to an improved numerical
5582	>	stability with respect to the usual quaternion rescaling scheme
5583	>	and it is roughly as good as the cumbersome atomic-constraint technique.
5584	>	(C) 1998 American Institute of Physics.},
5585	>	Annote = {Yx279 Times Cited:12 Cited References Count:28},
5586	>	Author = {I. P. Omelyan},
5587	>	Issn = {0894-1866},
5588	>	Journal = {Computers in Physics},
5589	>	Month = {Jan-Feb},
5590	>	Number = 1,
5591	>	Pages = {97-103},
5592	>	Title = {On the numerical integration of motion for rigid polyatomics: The modified quaternion approach},
5593	>	Uri = {<Go to ISI>://000072024300025},
5594	>	Volume = 12,
5595	>	Year = 1998}
5596	>
5597	>	@article{Omelyan1998a,
5598	>	Abstract = {An algorithm for numerical integration of the rigid-body equations
5599	>	of motion is proposed. The algorithm uses the leapfrog scheme and
5600	>	the quantities involved are angular velocities and orientational
5601	>	variables that can be expressed in terms of either principal axes
5602	>	or quaternions. Due to specific features of the algorithm, orthonormality
5603	>	and unit norms of the orientational variables are integrals of motion,
5604	>	despite an approximate character of the produced trajectories. It
5605	>	is shown that the method presented appears to be the most efficient
5606	>	among all such algorithms known.},
5607	>	Annote = {101XL Times Cited:8 Cited References Count:22},
5608	>	Author = {I. P. Omelyan},
5609	>	Issn = {1063-651X},
5610	>	Journal = {Physical Review E},
5611	>	Month = {Jul},
5612	>	Number = 1,
5613	>	Pages = {1169-1172},
5614	>	Title = {Algorithm for numerical integration of the rigid-body equations of motion},
5615	>	Uri = {<Go to ISI>://000074893400151},
5616	>	Volume = 58,
5617	>	Year = 1998}
5618	>
5619	>	@article{Owren1992,
5620	>	Abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
5621	>	stages are considered. These methods are continuously differentiable
5622	>	if and only if one of the stages is the FSAL evaluation. A characterization
5623	>	of a subclass of these methods is developed for orders 3, 4, and
5624	>	5. It is shown how the free parameters of these methods can be used
5625	>	either to minimize the continuous truncation error coefficients
5626	>	or to maximize the stability region. As a representative for these
5627	>	methods the fifth-order method with minimized error coefficients
5628	>	is chosen, supplied with an error estimation method, and analysed
5629	>	by using the DETEST software. The results are compared with a similar
5630	>	implementation of the Dormand-Prince 5(4) pair with interpolant,
5631	>	showing a significant advantage in the new method for the chosen
5632	>	problems.},
5633	>	Annote = {Ju936 Times Cited:25 Cited References Count:20},
5634	>	Author = {B. Owren and M. Zennaro},
5635	>	Issn = {0196-5204},
5636	>	Journal = {Siam Journal on Scientific and Statistical Computing},
5637	>	Month = {Nov},
5638	>	Number = 6,
5639	>	Pages = {1488-1501},
5640	>	Title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
5641	>	Uri = {<Go to ISI>://A1992JU93600013},
5642	>	Volume = 13,
5643	>	Year = 1992}
5644	>
5645	>	@article{Palacios1998,
5646	>	Abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
5647	>	magnetic moment is numerically solved (properly observing the customary
5648	>	interpretation of it as a Stratonovich stochastic differential equation),
5649	>	in order to study the dynamics of magnetic nanoparticles. The corresponding
5650	>	Langevin-dynamics approach allows for the study of the fluctuating
5651	>	trajectories of individual magnetic moments, where we have encountered
5652	>	remarkable phenomena in the overbarrier rotation process, such as
5653	>	crossing-back or multiple crossing of the potential barrier, rooted
5654	>	in the gyromagnetic nature of the system. Concerning averaged quantities,
5655	>	we study the linear dynamic response of the archetypal ensemble
5656	>	of noninteracting classical magnetic moments with axially symmetric
5657	>	magnetic anisotropy. The results are compared with different analytical
5658	>	expressions used to model the relaxation of nanoparticle ensembles,
5659	>	assessing their accuracy. It has been found that, among a number
5660	>	of heuristic expressions for the linear dynamic susceptibility,
5661	>	only the simple formula proposed by Shliomis and Stepanov matches
5662	>	the coarse features of the susceptibility reasonably. By comparing
5663	>	the numerical results with the asymptotic formula of Storonkin {Sov.
5664	>	Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]},
5665	>	the effects of the intra-potential-well relaxation modes on the
5666	>	low-temperature longitudinal dynamic response have been assessed,
5667	>	showing their relatively small reflection in the susceptibility
5668	>	curves but their dramatic influence on the phase shifts. Comparison
5669	>	of the numerical results with the exact zero-damping expression
5670	>	for the transverse susceptibility by Garanin, Ishchenko, and Panina
5671	>	{Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242
5672	>	(1990)]}, reveals a sizable contribution of the spread of the precession
5673	>	frequencies of the magnetic moment in the anisotropy field to the
5674	>	dynamic response at intermediate-to-high temperatures. [S0163-1829
5675	>	(98)00446-9].},
5676	>	Annote = {146XW Times Cited:66 Cited References Count:45},
5677	>	Author = {J. L. Garcia-Palacios and F. J. Lazaro},
5678	>	Issn = {0163-1829},
5679	>	Journal = {Physical Review B},
5680	>	Month = {Dec 1},
5681	>	Number = 22,
5682	>	Pages = {14937-14958},
5683	>	Title = {Langevin-dynamics study of the dynamical properties of small magnetic particles},
5684	>	Uri = {<Go to ISI>://000077460000052},
5685	>	Volume = 58,
5686	>	Year = 1998}
5687	>
5688	>	@article{Parr1995,
5689	>	Abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
5690	>	often choose to write recursive-descent parsers by hand to obtain
5691	>	increased flexibility, better error handling, and ease of debugging.
5692	>	We introduce ANTLR, a public-domain parser generator that combines
5693	>	the flexibility of hand-coded parsing with the convenience of a
5694	>	parser generator, which is a component of PCCTS. ANTLR has many
5695	>	features that make it easier to use than other language tools. Most
5696	>	important, ANTLR provides predicates which let the programmer systematically
5697	>	direct the parse via arbitrary expressions using semantic and syntactic
5698	>	context; in practice, the use of predicates eliminates the need
5699	>	to hand-tweak the ANTLR output, even for difficult parsing problems.
5700	>	ANTLR also integrates the description of lexical and syntactic analysis,
5701	>	accepts LL(k) grammars for k > 1 with extended BNF notation, and
5702	>	can automatically generate abstract syntax trees. ANTLR is widely
5703	>	used, with over 1000 registered industrial and academic users in
5704	>	37 countries. It has been ported to many popular systems such as
5705	>	the PC, Macintosh, and a variety of UNIX platforms; a commercial
5706	>	C++ front-end has been developed as a result of one of our industrial
5707	>	collaborations.},
5708	>	Annote = {Rk104 Times Cited:19 Cited References Count:10},
5709	>	Author = {T. J. Parr and R. W. Quong},
5710	>	Issn = {0038-0644},
5711	>	Journal = {Software-Practice \& Experience},
5712	>	Month = {Jul},
5713	>	Number = 7,
5714	>	Pages = {789-810},
5715	>	Title = {Antlr - a Predicated-Ll(K) Parser Generator},
5716	>	Uri = {<Go to ISI>://A1995RK10400004},
5717	>	Volume = 25,
5718	>	Year = 1995}
5719	>
5720	>	@article{Pastor1988,
5721	>	Annote = {T1302 Times Cited:61 Cited References Count:26},
5722	>	Author = {R. W. Pastor and B. R. Brooks and A. Szabo},
5723	>	Issn = {0026-8976},
5724	>	Journal = {Molecular Physics},
5725	>	Month = {Dec 20},
5726	>	Number = 6,
5727	>	Pages = {1409-1419},
5728	>	Title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
5729	>	Uri = {<Go to ISI>://A1988T130200011},
5730	>	Volume = 65,
5731	>	Year = 1988}
5732	>
5733	>	@article{Pelzl1999,
5734	>	Annote = {220RC Times Cited:313 Cited References Count:49},
5735	>	Author = {G. Pelzl and S. Diele and W. Weissflog},
5736	>	Issn = {0935-9648},
5737	>	Journal = {Advanced Materials},
5738	>	Month = {Jul 5},
5739	>	Number = 9,
5740	>	Pages = {707-724},
5741	>	Title = {Banana-shaped compounds - A new field of liquid crystals},
5742	>	Uri = {<Go to ISI>://000081680400007},
5743	>	Volume = 11,
5744	>	Year = 1999}
5745	>
5746	>	@article{Perram1985,
5747	>	Annote = {Akb93 Times Cited:71 Cited References Count:12},
5748	>	Author = {J. W. Perram and M. S. Wertheim},
5749	>	Issn = {0021-9991},
5750	>	Journal = {Journal of Computational Physics},
5751	>	Number = 3,
5752	>	Pages = {409-416},
5753	>	Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function},
5754	>	Uri = {<Go to ISI>://A1985AKB9300008},
5755	>	Volume = 58,
5756	>	Year = 1985}
5757	>
5758	>	@article{Rotne1969,
5759	>	Author = {F. Perrin},
5760	>	Journal = {J. Chem. Phys.},
5761	>	Pages = {4831-4837},
5762	>	Title = {Variational treatment of hydrodynamic interaction in polymers},
5763	>	Volume = 50,
5764	>	Year = 1969}
5765	>
5766	>	@article{Perrin1936,
5767	>	Author = {F. Perrin},
5768	>	Journal = {J. Phys. Radium},
5769	>	Pages = {1-11},
5770	>	Title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation des fluorescences. Translation et diffusion de moleculese ellipsoidales},
5771	>	Volume = 7,
5772	>	Year = 1936}
5773	>
5774	>	@article{Perrin1934,
5775	>	Author = {F. Perrin},
5776	>	Journal = {J. Phys. Radium},
5777	>	Pages = {497-511},
5778	>	Title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour des molecules ellipsoidales},
5779	>	Volume = 5,
5780	>	Year = 1934}
5781	>
5782	>	@article{Petrache2000,
5783	>	Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
5784	>	Journal = {Biophysical Journal},
5785	>	Pages = {3172-3192},
5786	>	Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
5787	>	Volume = 79,
5788	>	Year = 2000}
5789	>
5790	>	@article{Petrache1998,
5791	>	Abstract = {X-ray diffraction data taken at high instrumental resolution were
5792	>	obtained for EPC and DMPC under various osmotic pressures, primarily
5793	>	at T = 30 degrees C. The headgroup thickness D-HH was obtained from
5794	>	relative electron density profiles. By using volumetric results
5795	>	and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4
5796	>	+/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The
5797	>	analysis also gives estimates for the areal compressibility K-A.
5798	>	The A(F) results lead to other structural results regarding membrane
5799	>	thickness and associated waters. Using the recently determined absolute
5800	>	electrons density profile of DPPC, the AF results also lead to absolute
5801	>	electron density profiles and absolute continuous transforms \F(q)\
5802	>	for EPC and DMPC, Limited measurements of temperature dependence
5803	>	show directly that fluctuations increase with increasing temperature
5804	>	and that a small decrease in bending modulus K-c accounts for the
5805	>	increased water spacing reported by Simon et al. (1995) Biophys.
5806	>	J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights
5807	>	reserved.},
5808	>	Annote = {130AT Times Cited:98 Cited References Count:39},
5809	>	Author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle},
5810	>	Issn = {0009-3084},
5811	>	Journal = {Chemistry and Physics of Lipids},
5812	>	Month = {Sep},
5813	>	Number = 1,
5814	>	Pages = {83-94},
5815	>	Title = {Fluid phase structure of EPC and DMPC bilayers},
5816	>	Uri = {<Go to ISI>://000076497600007},
5817	>	Volume = 95,
5818	>	Year = 1998}
5819	>
5820	>	@article{Powles1973,
5821	>	Author = {J.~G. Powles},
5822	>	Journal = {Advan. Phys.},
5823	>	Pages = {1-56},
5824	>	Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
5825	>	Volume = 22,
5826	>	Year = 1973}
5827	>
5828	>	@article{Recio2004,
5829	>	Abstract = {Protein recognition is one of the most challenging and intriguing
5830	>	problems in structural biology. Despite all the available structural,
5831	>	sequence and biophysical information about protein-protein complexes,
5832	>	the physico-chemical patterns, if any, that make a protein surface
5833	>	likely to be involved in protein-protein interactions, remain elusive.
5834	>	Here, we apply protein docking simulations and analysis of the interaction
5835	>	energy landscapes to identify protein-protein interaction sites.
5836	>	The new protocol for global docking based on multi-start global
5837	>	energy optimization of an allatom model of the ligand, with detailed
5838	>	receptor potentials and atomic solvation parameters optimized in
5839	>	a training set of 24 complexes, explores the conformational space
5840	>	around the whole receptor without restrictions. The ensembles of
5841	>	the rigid-body docking solutions generated by the simulations were
5842	>	subsequently used to project the docking energy landscapes onto
5843	>	the protein surfaces. We found that highly populated low-energy
5844	>	regions consistently corresponded to actual binding sites. The procedure
5845	>	was validated on a test set of 21 known protein-protein complexes
5846	>	not used in the training set. As much as 81% of the predicted high-propensity
5847	>	patch residues were located correctly in the native interfaces.
5848	>	This approach can guide the design of mutations on the surfaces
5849	>	of proteins, provide geometrical details of a possible interaction,
5850	>	and help to annotate protein surfaces in structural proteomics.
5851	>	(C) 2003 Elsevier Ltd. All rights reserved.},
5852	>	Annote = {763GQ Times Cited:21 Cited References Count:59},
5853	>	Author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
5854	>	Issn = {0022-2836},
5855	>	Journal = {Journal of Molecular Biology},
5856	>	Month = {Jan 16},
5857	>	Number = 3,
5858	>	Pages = {843-865},
5859	>	Title = {Identification of protein-protein interaction sites from docking energy landscapes},
5860	>	Uri = {<Go to ISI>://000188066900016},
5861	>	Volume = 335,
5862	>	Year = 2004}
5863	>
5864	>	@article{Reddy2006,
5865	>	Abstract = {An overview on the recent developments in the field of liquid crystalline
5866	>	bent-core molecules (so-called banana liquid crystals) is given.
5867	>	After some basic issues, dealing with general aspects of the systematisation
5868	>	of the mesophases, development of polar order and chirality in this
5869	>	class of LC systems and explaining some general structure-property
5870	>	relationships, we focus on fascinating new developments in this
5871	>	field, such as modulated, undulated and columnar phases, so-called
5872	>	B7 phases, phase biaxiality, ferroelectric and antiferroelectric
5873	>	polar order in smectic and columnar phases, amplification and switching
5874	>	of chirality and the spontaneous formation of superstructural and
5875	>	supramolecular chirality.},
5876	>	Annote = {021NS Times Cited:2 Cited References Count:316},
5877	>	Author = {R. A. Reddy and C. Tschierske},
5878	>	Issn = {0959-9428},
5879	>	Journal = {Journal of Materials Chemistry},
5880	>	Number = 10,
5881	>	Pages = {907-961},
5882	>	Title = {Bent-core liquid crystals: polar order, superstructural chirality and spontaneous desymmetrisation in soft matter systems},
5883	>	Uri = {<Go to ISI>://000235990500001},
5884	>	Volume = 16,
5885	>	Year = 2006}
5886	>
5887	>	@article{Reich1999,
5888	>	Abstract = {Backward error analysis has become an important tool for understanding
5889	>	the long time behavior of numerical integration methods. This is
5890	>	true in particular for the integration of Hamiltonian systems where
5891	>	backward error analysis can be used to show that a symplectic method
5892	>	will conserve energy over exponentially long periods of time. Such
5893	>	results are typically based on two aspects of backward error analysis:
5894	>	(i) It can be shown that the modified vector fields have some qualitative
5895	>	properties which they share with the given problem and (ii) an estimate
5896	>	is given for the difference between the best interpolating vector
5897	>	field and the numerical method. These aspects have been investigated
5898	>	recently, for example, by Benettin and Giorgilli in [J. Statist.
5899	>	Phys., 74 (1994), pp. 1117-1143], by Hairer in [Ann. Numer. Math.,
5900	>	1 (1994), pp. 107-132], and by Hairer and Lubich in [Numer. Math.,
5901	>	76 (1997), pp. 441-462]. In this paper we aim at providing a unifying
5902	>	framework and a simplification of the existing results and corresponding
5903	>	proofs. Our approach to backward error analysis is based on a simple
5904	>	recursive definition of the modified vector fields that does not
5905	>	require explicit Taylor series expansion of the numerical method
5906	>	and the corresponding flow maps as in the above-cited works. As
5907	>	an application we discuss the long time integration of chaotic Hamiltonian
5908	>	systems and the approximation of time averages along numerically
5909	>	computed trajectories.},
5910	>	Annote = {237HV Times Cited:43 Cited References Count:41},
5911	>	Author = {S. Reich},
5912	>	Issn = {0036-1429},
5913	>	Journal = {Siam Journal on Numerical Analysis},
5914	>	Month = {Sep 8},
5915	>	Number = 5,
5916	>	Pages = {1549-1570},
5917	>	Title = {Backward error analysis for numerical integrators},
5918	>	Uri = {<Go to ISI>://000082650600010},
5919	>	Volume = 36,
5920	>	Year = 1999}
5921	>
5922	>	@article{Ros2005,
5923	>	Abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
5924	>	mesogenic materials represent a bewitching and stimulating field
5925	>	of research that is interesting both academically and in terms of
5926	>	applications. Numerous topics are open to investigation in this
5927	>	area because of the rich phenomenology and new possibilities that
5928	>	these materials offer. The principal concepts in this area are reviewed
5929	>	along with recent results. In addition, new directions to stimulate
5930	>	further research activities are highlighted.},
5931	>	Annote = {990XA Times Cited:3 Cited References Count:72},
5932	>	Author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
5933	>	Issn = {0959-9428},
5934	>	Journal = {Journal of Materials Chemistry},
5935	>	Number = 48,
5936	>	Pages = {5093-5098},
5937	>	Title = {Banana-shaped liquid crystals: a new field to explore},
5938	>	Uri = {<Go to ISI>://000233775500001},
5939	>	Volume = 15,
5940	>	Year = 2005}
5941	>
5942	>	@article{Roux1991,
5943	>	Abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
5944	>	poly-(L,D)-alanine beta-helix, a model for the interior of the gramicidin
5945	>	channel. Because of the different dynamical regimes for the three
5946	>	species (high barrier for Na+, low barrier for K+, almost free diffusion
5947	>	for water), different methods are used to calculate the mobilities.
5948	>	By use of activated dynamics and a potential of mean force determined
5949	>	previously (Roux, B.; Karplus, M. Biophys. J. 1991, 59, 961), the
5950	>	barrier crossing rate of Na+ ion is determined. The motion of Na+
5951	>	at the transition state is controlled by local interactions and
5952	>	collisions with the neighboring carbonyls and the two nearest water
5953	>	molecules. There are significant deviations from transition-state
5954	>	theory; the transmission coefficient is equal to 0.11. The water
5955	>	and K+ motions are found to be well described by a diffusive model;
5956	>	the motion of K+ appears to be controlled by the diffusion of water.
5957	>	The time-dependent friction functions of Na+ and K+ ions in the
5958	>	periodic beta-helix are calculated and analyzed by using a generalized
5959	>	Langevin equation approach. Both Na+ and K+ suffer many rapid collisions,
5960	>	and their dynamics is overdamped and noninertial. Thus, the selectivity
5961	>	sequence of ions in the beta-helix is not influenced strongly by
5962	>	their masses.},
5963	>	Annote = {Fr756 Times Cited:97 Cited References Count:65},
5964	>	Author = {B. Roux and M. Karplus},
5965	>	Issn = {0022-3654},
5966	>	Journal = {Journal of Physical Chemistry},
5967	>	Month = {Jun 13},
5968	>	Number = 12,
5969	>	Pages = {4856-4868},
5970	>	Title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
5971	>	Uri = {<Go to ISI>://A1991FR75600049},
5972	>	Volume = 95,
5973	>	Year = 1991}
5974	>
5975	>	@article{Roy2005,
5976	>	Abstract = {A vast majority of compounds with bent core or banana shaped molecules
5977	>	exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased
5978	>	in a homologous series. The B-6 phase has an intercalated fluid
5979	>	lamellar structure with a layer spacing of half the molecular length.
5980	>	The B-1 phase has a two dimensionally periodic rectangular columnar
5981	>	structure. The B-2 phase has a monolayer fluid lamellar structure
5982	>	with molecules tilted with respect to the layer normal. Neglecting
5983	>	the tilt order of the molecules in the B-2 phase, we have developed
5984	>	a frustrated packing model to describe this phase sequence qualitatively.
5985	>	The model has some analogy with that of the frustrated smectics
5986	>	exhibited by highly polar rod like molecules.},
5987	>	Annote = {985FW Times Cited:0 Cited References Count:30},
5988	>	Author = {A. Roy and N. V. Madhusudana},
5989	>	Issn = {1292-8941},
5990	>	Journal = {European Physical Journal E},
5991	>	Month = {Nov},
5992	>	Number = 3,
5993	>	Pages = {253-258},
5994	>	Title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases in banana shaped molecules},
5995	>	Uri = {<Go to ISI>://000233363300002},
5996	>	Volume = 18,
5997	>	Year = 2005}
5998	>
5999	>	@article{Ryckaert1977,
6000	>	Annote = {Cz253 Times Cited:3680 Cited References Count:7},
6001	>	Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
6002	>	Issn = {0021-9991},
6003	>	Journal = {Journal of Computational Physics},
6004	>	Number = 3,
6005	>	Pages = {327-341},
6006	>	Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes},
6007	>	Uri = {<Go to ISI>://A1977CZ25300007},
6008	>	Volume = 23,
6009	>	Year = 1977}
6010	>
6011	>	@article{Sagui1999,
6012	>	Abstract = {Current computer simulations of biomolecules typically make use of
6013	>	classical molecular dynamics methods, as a very large number (tens
6014	>	to hundreds of thousands) of atoms are involved over timescales
6015	>	of many nanoseconds. The methodology for treating short-range bonded
6016	>	and van der Waals interactions has matured. However, long-range
6017	>	electrostatic interactions still represent a bottleneck in simulations.
6018	>	In this article, we introduce the basic issues for an accurate representation
6019	>	of the relevant electrostatic interactions. In spite of the huge
6020	>	computational time demanded by most biomolecular systems, it is
6021	>	no longer necessary to resort to uncontrolled approximations such
6022	>	as the use of cutoffs. In particular, we discuss the Ewald summation
6023	>	methods, the fast particle mesh methods, and the fast multipole
6024	>	methods. We also review recent efforts to understand the role of
6025	>	boundary conditions in systems with long-range interactions, and
6026	>	conclude with a short perspective on future trends.},
6027	>	Annote = {213KJ Times Cited:126 Cited References Count:73},
6028	>	Author = {C. Sagui and T. A. Darden},
6029	>	Issn = {1056-8700},
6030	>	Journal = {Annual Review of Biophysics and Biomolecular Structure},
6031	>	Pages = {155-179},
6032	>	Title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic effects},
6033	>	Uri = {<Go to ISI>://000081271400008},
6034	>	Volume = 28,
6035	>	Year = 1999}
6036	>
6037	>	@article{Sandu1999,
6038	>	Abstract = {Numerical resonance artifacts have become recognized recently as a
6039	>	limiting factor to increasing the timestep in multiple-timestep
6040	>	(MTS) biomolecular dynamics simulations. At certain timesteps correlated
6041	>	to internal motions (e.g., 5 fs, around half the period of the fastest
6042	>	bond stretch, T-min), visible inaccuracies or instabilities can
6043	>	occur. Impulse-MTS schemes are vulnerable to these resonance errors
6044	>	since large energy pulses are introduced to the governing dynamics
6045	>	equations when the slow forces are evaluated. We recently showed
6046	>	that such resonance artifacts can be masked significantly by applying
6047	>	extrapolative splitting to stochastic dynamics. Theoretical and
6048	>	numerical analyses of force-splitting integrators based on the Verlet
6049	>	discretization are reported here for linear models to explain these
6050	>	observations and to suggest how to construct effective integrators
6051	>	for biomolecular dynamics that balance stability with accuracy.
6052	>	Analyses for Newtonian dynamics demonstrate the severe resonance
6053	>	patterns of the Impulse splitting, with this severity worsening
6054	>	with the outer timestep. Delta t: Constant Extrapolation is generally
6055	>	unstable, but the disturbances do not grow with Delta t. Thus. the
6056	>	stochastic extrapolative combination can counteract generic instabilities
6057	>	and largely alleviate resonances with a sufficiently strong Langevin
6058	>	heat-bath coupling (gamma), estimates for which are derived here
6059	>	based on the fastest and slowest motion periods. These resonance
6060	>	results generally hold for nonlinear test systems: a water tetramer
6061	>	and solvated protein. Proposed related approaches such as Extrapolation/Correction
6062	>	and Midpoint Extrapolation work better than Constant Extrapolation
6063	>	only for timesteps less than T-min/2. An effective extrapolative
6064	>	stochastic approach for biomolecules that balances long-timestep
6065	>	stability with good accuracy for the fast subsystem is then applied
6066	>	to a biomolecule using a three-class partitioning: the medium forces
6067	>	are treated by Midpoint Extrapolation via position Verlet, and the
6068	>	slow forces are incorporated by Constant Extrapolation. The resulting
6069	>	algorithm (LN) performs well on a solvated protein system in terms
6070	>	of thermodynamic properties and yields an order of magnitude speedup
6071	>	with respect to single-timestep Langevin trajectories. Computed
6072	>	spectral density functions also show how the Newtonian modes can
6073	>	be approximated by using a small gamma in the range Of 5-20 ps(-1).
6074	>	(C) 1999 Academic Press.},
6075	>	Annote = {194FM Times Cited:14 Cited References Count:32},
6076	>	Author = {A. Sandu and T. Schlick},
6077	>	Issn = {0021-9991},
6078	>	Journal = {Journal of Computational Physics},
6079	>	Month = {May 1},
6080	>	Number = 1,
6081	>	Pages = {74-113},
6082	>	Title = {Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics},
6083	>	Uri = {<Go to ISI>://000080181500004},
6084	>	Volume = 151,
6085	>	Year = 1999}
6086	>
6087	>	@article{Sasaki2004,
6088	>	Abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
6089	>	groups are shown to facilitate the translocation of fluorescent
6090	>	phospholipid probes and endogenous phosphatidylserine across vesicle
6091	>	and erythrocyte cell membranes. The synthetic translocases appear
6092	>	to operate by binding to the phospholipid head groups and forming
6093	>	lipophilic supramolecular complexes which diffuse through the non-polar
6094	>	interior of the bilayer membrane.},
6095	>	Annote = {760PX Times Cited:8 Cited References Count:25},
6096	>	Author = {Y. Sasaki and R. Shukla and B. D. Smith},
6097	>	Issn = {1477-0520},
6098	>	Journal = {Organic \& Biomolecular Chemistry},
6099	>	Number = 2,
6100	>	Pages = {214-219},
6101	>	Title = {Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases},
6102	>	Uri = {<Go to ISI>://000187843800012},
6103	>	Volume = 2,
6104	>	Year = 2004}
6105	>
6106	>	@article{Satoh1996,
6107	>	Abstract = {The effects of dipole-dipole interaction on mesophase formation are
6108	>	investigated with a Monte Carlo simulation using the dipolar Gay-Berne
6109	>	potential. It is shown that the dipole moment at the end of a molecule
6110	>	causes a shift in the nematic-isotropic transition toward higher
6111	>	temperature and a spread of the temperature range of the nematic
6112	>	phase and that layer structures with various interdigitations are
6113	>	formed in the smectic phase.},
6114	>	Annote = {Uq975 Times Cited:32 Cited References Count:33},
6115	>	Author = {K. Satoh and S. Mita and S. Kondo},
6116	>	Issn = {0009-2614},
6117	>	Journal = {Chemical Physics Letters},
6118	>	Month = {Jun 7},
6119	>	Number = {1-3},
6120	>	Pages = {99-104},
6121	>	Title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect of terminal dipole moment on mesophase formation},
6122	>	Uri = {<Go to ISI>://A1996UQ97500017},
6123	>	Volume = 255,
6124	>	Year = 1996}
6125	>
6126	>	@article{Schaps1999,
6127	>	Annote = {163EC Times Cited:0 Cited References Count:0},
6128	>	Author = {G. L. Schaps},
6129	>	Issn = {1044-789X},
6130	>	Journal = {Dr Dobbs Journal},
6131	>	Month = {Mar},
6132	>	Number = 3,
6133	>	Pages = {84-+},
6134	>	Title = {Compiler construction with ANTLR and Java - Tools for building tools},
6135	>	Uri = {<Go to ISI>://000078389200023},
6136	>	Volume = 24,
6137	>	Year = 1999}
6138	>
6139	>	@article{Shen2002,
6140	>	Abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
6141	>	structure and receptor docking mechanism are still not well understood.
6142	>	The conformational dynamics of this neuron peptide in liquid water
6143	>	are studied here by using all-atom molecular dynamics (MID) and
6144	>	implicit water Langevin dynamics (LD) simulations with AMBER potential
6145	>	functions and the three-site transferable intermolecular potential
6146	>	(TIP3P) model for water. To achieve the same simulation length in
6147	>	physical time, the full MID simulations require 200 times as much
6148	>	CPU time as the implicit water LID simulations. The solvent hydrophobicity
6149	>	and dielectric behavior are treated in the implicit solvent LD simulations
6150	>	by using a macroscopic solvation potential, a single dielectric
6151	>	constant, and atomic friction coefficients computed using the accessible
6152	>	surface area method with the TIP3P model water viscosity as determined
6153	>	here from MID simulations for pure TIP3P water. Both the local and
6154	>	the global dynamics obtained from the implicit solvent LD simulations
6155	>	agree very well with those from the explicit solvent MD simulations.
6156	>	The simulations provide insights into the conformational restrictions
6157	>	that are associated with the bioactivity of the opiate peptide dermorphin
6158	>	for the delta-receptor.},
6159	>	Annote = {540MH Times Cited:36 Cited References Count:45},
6160	>	Author = {M. Y. Shen and K. F. Freed},
6161	>	Issn = {0006-3495},
6162	>	Journal = {Biophysical Journal},
6163	>	Month = {Apr},
6164	>	Number = 4,
6165	>	Pages = {1791-1808},
6166	>	Title = {Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models},
6167	>	Uri = {<Go to ISI>://000174932400010},
6168	>	Volume = 82,
6169	>	Year = 2002}
6170	>
6171	>	@article{Shillcock2005,
6172	>	Annote = {901QJ Times Cited:9 Cited References Count:23},
6173	>	Author = {J. C. Shillcock and R. Lipowsky},
6174	>	Issn = {1476-1122},
6175	>	Journal = {Nature Materials},
6176	>	Month = {Mar},
6177	>	Number = 3,
6178	>	Pages = {225-228},
6179	>	Title = {Tension-induced fusion of bilayer membranes and vesicles},
6180	>	Uri = {<Go to ISI>://000227296700019},
6181	>	Volume = 4,
6182	>	Year = 2005}
6183	>
6184	>	@article{Shimada1993,
6185	>	Abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
6186	>	simulations, two possibilities are considered. The first is the
6187	>	famous particle-particle and particle-mesh (PPPM) method developed
6188	>	by Hockney and Eastwood, and the second is a new one developed here
6189	>	in their spirit but by the use of the multipole expansion technique
6190	>	suggested by Ladd. It is then numerically found that the new PPPM
6191	>	method gives more accurate results for a two-particle system at
6192	>	small separation of particles. Preliminary numerical examination
6193	>	of the various computational methods for a single configuration
6194	>	of a model BPTI-water system containing about 24,000 particles indicates
6195	>	that both of the PPPM methods give far more accurate values with
6196	>	reasonable computational cost than do the conventional truncation
6197	>	methods. It is concluded the two PPPM methods are nearly comparable
6198	>	in overall performance for the many-particle systems, although the
6199	>	first method has the drawback that the accuracy in the total electrostatic
6200	>	energy is not high for configurations of charged particles randomly
6201	>	generated.},
6202	>	Annote = {Lh164 Times Cited:27 Cited References Count:47},
6203	>	Author = {J. Shimada and H. Kaneko and T. Takada},
6204	>	Issn = {0192-8651},
6205	>	Journal = {Journal of Computational Chemistry},
6206	>	Month = {Jul},
6207	>	Number = 7,
6208	>	Pages = {867-878},
6209	>	Title = {Efficient Calculations of Coulombic Interactions in Biomolecular Simulations with Periodic Boundary-Conditions},
6210	>	Uri = {<Go to ISI>://A1993LH16400011},
6211	>	Volume = 14,
6212	>	Year = 1993}
6213	>
6214	>	@article{Skeel2002,
6215	>	Abstract = {The best simple method for Newtonian molecular dynamics is indisputably
6216	>	the leapfrog Stormer-Verlet method. The appropriate generalization
6217	>	to simple Langevin dynamics is unclear. An analysis is presented
6218	>	comparing an 'impulse method' (kick; fluctuate; kick), the 1982
6219	>	method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus
6220	>	(BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen
6221	>	methods can be implemented as efficiently as the BBK method. Other
6222	>	considerations suggest that the impulse method is the best basic
6223	>	method for simple Langevin dynamics, with the van Gunsteren-Berendsen
6224	>	method a close contender.},
6225	>	Annote = {633RX Times Cited:8 Cited References Count:22},
6226	>	Author = {R. D. Skeel and J. A. Izaguirre},
6227	>	Issn = {0026-8976},
6228	>	Journal = {Molecular Physics},
6229	>	Month = {Dec 20},
6230	>	Number = 24,
6231	>	Pages = {3885-3891},
6232	>	Title = {An impulse integrator for Langevin dynamics},
6233	>	Uri = {<Go to ISI>://000180297200014},
6234	>	Volume = 100,
6235	>	Year = 2002}
6236	>
6237	>	@article{Skeel1997,
6238	>	Abstract = {The following integration methods for special second-order ordinary
6239	>	differential equations are studied: leapfrog, implicit midpoint,
6240	>	trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all
6241	>	are members, or equivalent to members, of a one-parameter family
6242	>	of schemes. Some methods have more than one common form, and we
6243	>	discuss a systematic enumeration of these forms. We also present
6244	>	a stability and accuracy analysis based on the idea of ''modified
6245	>	equations'' and a proof of symplecticness. It follows that Cowell-Numerov
6246	>	and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic.
6247	>	A different interpretation of the values used by these integrators
6248	>	leads to higher accuracy and better energy conservation. Hence,
6249	>	we suggest that the straightforward analysis of energy conservation
6250	>	is misleading.},
6251	>	Annote = {We981 Times Cited:30 Cited References Count:35},
6252	>	Author = {R. D. Skeel and G. H. Zhang and T. Schlick},
6253	>	Issn = {1064-8275},
6254	>	Journal = {Siam Journal on Scientific Computing},
6255	>	Month = {Jan},
6256	>	Number = 1,
6257	>	Pages = {203-222},
6258	>	Title = {A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications},
6259	>	Uri = {<Go to ISI>://A1997WE98100012},
6260	>	Volume = 18,
6261	>	Year = 1997}
6262	>
6263	>	@article{Tao2005,
6264	>	Abstract = {Recently a microscopic theory for the dynamics of suspensions of long
6265	>	thin rigid rods was presented, confirming and expanding the well-known
6266	>	theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon,
6267	>	Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here
6268	>	this theory is put to the test by comparing it against computer
6269	>	simulations. A Brownian dynamics simulation program was developed
6270	>	to follow the dynamics of the rods, with a length over a diameter
6271	>	ratio of 60, on the Smoluchowski time scale. The model accounts
6272	>	for excluded volume interactions between rods, but neglects hydrodynamic
6273	>	interactions. The self-rotational diffusion coefficients D-r(phi)
6274	>	of the rods were calculated by standard methods and by a new, more
6275	>	efficient method based on calculating average restoring torques.
6276	>	Collective decay of orientational order was calculated by means
6277	>	of equilibrium and nonequilibrium simulations. Our results show
6278	>	that, for the currently accessible volume fractions, the decay times
6279	>	in both cases are virtually identical. Moreover, the observed decay
6280	>	of diffusion coefficients with volume fraction is much quicker than
6281	>	predicted by the theory, which is attributed to an oversimplification
6282	>	of dynamic correlations in the theory. (c) 2005 American Institute
6283	>	of Physics.},
6284	>	Annote = {943DN Times Cited:3 Cited References Count:26},
6285	>	Author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont and W. J. Briels},
6286	>	Issn = {0021-9606},
6287	>	Journal = {Journal of Chemical Physics},
6288	>	Month = {Jun 22},
6289	>	Number = 24,
6290	>	Pages = {-},
6291	>	Title = {Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods},
6292	>	Uri = {<Go to ISI>://000230332400077},
6293	>	Volume = 122,
6294	>	Year = 2005}
6295	>
6296	>	@book{Tolman1979,
6297	>	Address = {New York},
6298	>	Author = {R.~C. Tolman},
6299	>	Chapter = 2,
6300	>	Pages = {19-22},
6301	>	Publisher = {Dover Publications, Inc.},
6302	>	Title = {The Principles of Statistical Mechanics},
6303	>	Year = 1979}
6304	>
6305	>	@article{Tu1995,
6306	>	Abstract = {We report a constant pressure and temperature molecular dynamics simulation
6307	>	of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine
6308	>	at 50 degrees C and 28 water molecules/lipid. We have shown that
6309	>	the bilayer is stable throughout the 1550-ps simulation and have
6310	>	demonstrated convergence of the system dimensions. Several important
6311	>	aspects of the bilayer structure have been investigated and compared
6312	>	favorably with experimental results. For example, the average positions
6313	>	of specific carbon atoms along the bilayer normal agree well with
6314	>	neutron diffraction data, and the electron density profile is in
6315	>	accord with x-ray diffraction results. The hydrocarbon chain deuterium
6316	>	order parameters agree reasonably well with NMR results for the
6317	>	middles of the chains, but the simulation predicts too much order
6318	>	at the chain ends. In spite of the deviations in the order parameters,
6319	>	the hydrocarbon chain packing density appears to be essentially
6320	>	correct, inasmuch as the area/lipid and bilayer thickness are in
6321	>	agreement with the most refined experimental estimates. The deuterium
6322	>	order parameters for the glycerol and choline groups, as well as
6323	>	the phosphorus chemical shift anisotropy, are in qualitative agreement
6324	>	with those extracted from NMR measurements.},
6325	>	Annote = {Tv018 Times Cited:108 Cited References Count:34},
6326	>	Author = {K. Tu and D. J. Tobias and M. L. Klein},
6327	>	Issn = {0006-3495},
6328	>	Journal = {Biophysical Journal},
6329	>	Month = {Dec},
6330	>	Number = 6,
6331	>	Pages = {2558-2562},
6332	>	Title = {Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer},
6333	>	Uri = {<Go to ISI>://A1995TV01800037},
6334	>	Volume = 69,
6335	>	Year = 1995}
6336	>
6337	>	@article{Tuckerman1992,
6338	>	Abstract = {The Trotter factorization of the Liouville propagator is used to generate
6339	>	new reversible molecular dynamics integrators. This strategy is
6340	>	applied to derive reversible reference system propagator algorithms
6341	>	(RESPA) that greatly accelerate simulations of systems with a separation
6342	>	of time scales or with long range forces. The new algorithms have
6343	>	all of the advantages of previous RESPA integrators but are reversible,
6344	>	and more stable than those methods. These methods are applied to
6345	>	a set of paradigmatic systems and are shown to be superior to earlier
6346	>	methods. It is shown how the new RESPA methods are related to predictor-corrector
6347	>	integrators. Finally, we show how these methods can be used to accelerate
6348	>	the integration of the equations of motion of systems with Nose
6349	>	thermostats.},
6350	>	Annote = {Je891 Times Cited:680 Cited References Count:19},
6351	>	Author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
6352	>	Issn = {0021-9606},
6353	>	Journal = {Journal of Chemical Physics},
6354	>	Month = {Aug 1},
6355	>	Number = 3,
6356	>	Pages = {1990-2001},
6357	>	Title = {Reversible Multiple Time Scale Molecular-Dynamics},
6358	>	Uri = {<Go to ISI>://A1992JE89100044},
6359	>	Volume = 97,
6360	>	Year = 1992}
6361	>
6362	>	@book{Varadarajan1974,
6363	>	Address = {New York},
6364	>	Author = {V.S. Varadarajan},
6365	>	Publisher = {Prentice-Hall},
6366	>	Title = {Lie groups, Lie algebras, and their representations},
6367	>	Year = 1974}
6368	>
6369	>	@article{Vincent1995,
6370	>	Abstract = {We have implemented a portable parallel version of the macromolecular
6371	>	modeling package AMBER4. The message passing paradigm was used.
6372	>	All message passing constructs are compliant with the Message Passing
6373	>	Interface (MPI) standard. The molecular dynamics/minimization module
6374	>	MINMD and the free-energy perturbation module Gibbs have been implemented
6375	>	in parallel on a number of machines, including a Gray T3D, an IBM
6376	>	SP1/SP2, and a collection of networked workstations. In addition,
6377	>	the code has been tested with an MPI implementation from Argonne
6378	>	National Laboratories/Mississippi State University which runs on
6379	>	many parallel machines. The goal of this work is to decrease the
6380	>	amount of time required to perform molecular dynamics simulations.
6381	>	Performance results for a Lipid bilayer molecular dynamics simulation
6382	>	on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995
6383	>	by John Wiley & Sons, Inc.},
6384	>	Annote = {Ta403 Times Cited:16 Cited References Count:23},
6385	>	Author = {J. J. Vincent and K. M. Merz},
6386	>	Issn = {0192-8651},
6387	>	Journal = {Journal of Computational Chemistry},
6388	>	Month = {Nov},
6389	>	Number = 11,
6390	>	Pages = {1420-1427},
6391	>	Title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing Interface Standard},
6392	>	Uri = {<Go to ISI>://A1995TA40300009},
6393	>	Volume = 16,
6394	>	Year = 1995}
6395	>
6396	>	@article{Wegener1979,
6397	>	Author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
6398	>	Journal = {Proc. Natl. Acad. Sci.},
6399	>	Number = 12,
6400	>	Pages = {6356-6360},
6401	>	Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
6402	>	Volume = 76,
6403	>	Year = 1979}
6404	>
6405	>	@article{Wilson2006,
6406	>	Author = {G.~V. Wilson},
6407	>	Journal = {American Scientist},
6408	>	Title = {Where's the Real Bottleneck in Scientific Computing?},
6409	>	Volume = 94,
6410	>	Year = 2006}
6411	>
6412	>	@article{Withers2003,
6413	>	Abstract = {The effects of longitudinal quadrupole moments on the formation of
6414	>	liquid crystalline phases are studied by means of constant NPT Monte
6415	>	Carlo simulation methods. The popular Gay-Berne model mesogen is
6416	>	used as the reference fluid, which displays the phase sequences
6417	>	isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0)
6418	>	and low (T*=1.5) temperatures, respectively. With increasing quadrupole
6419	>	magnitude the smectic phases are observed to be stabilized with
6420	>	respect to the isotropic liquid, while the smectic B is destabilized
6421	>	with respect to the smectic A. At the lower temperature, a sufficiently
6422	>	large quadrupole magnitude results in the injection of the smectic
6423	>	A phase into the phase sequence and the replacement of the smectic
6424	>	B phase by the tilted smectic J phase. The nematic phase is also
6425	>	injected into the phase sequence at both temperatures considered,
6426	>	and ultimately for sufficiently large quadrupole magnitudes no coherent
6427	>	layered structures were observed. The stabilization of the smectic
6428	>	A phase supports the commonly held belief that, while the inclusion
6429	>	of polar groups is not a prerequisite for the formation of the smectic
6430	>	A phase, quadrupolar interactions help to increase the temperature
6431	>	and pressure range for which the smectic A phase is observed. The
6432	>	quality of the layered structure is worsened with increasing quadrupole
6433	>	magnitude. This behavior, along with the injection of the nematic
6434	>	phase into the phase sequence, indicate that the general tendency
6435	>	of the quadrupolar interactions is to destabilize the layered structure.
6436	>	A pressure dependence upon the smectic layer spacing is observed.
6437	>	This behavior is in much closer agreement with experimental findings
6438	>	than has been observed previously for nonpolar Gay-Berne and hard
6439	>	spherocylinder models. (C) 2003 American Institute of Physics.},
6440	>	Annote = {738EF Times Cited:3 Cited References Count:43},
6441	>	Author = {I. M. Withers},
6442	>	Issn = {0021-9606},
6443	>	Journal = {Journal of Chemical Physics},
6444	>	Month = {Nov 15},
6445	>	Number = 19,
6446	>	Pages = {10209-10223},
6447	>	Title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne fluid},
6448	>	Uri = {<Go to ISI>://000186273200027},
6449	>	Volume = 119,
6450	>	Year = 2003}
6451	>
6452	>	@article{Wolf1999,
6453	>	Abstract = {Based on a recent result showing that the net Coulomb potential in
6454	>	condensed ionic systems is rather short ranged, an exact and physically
6455	>	transparent method permitting the evaluation of the Coulomb potential
6456	>	by direct summation over the r(-1) Coulomb pair potential is presented.
6457	>	The key observation is that the problems encountered in determining
6458	>	the Coulomb energy by pairwise, spherically truncated r(-1) summation
6459	>	are a direct consequence of the fact that the system summed over
6460	>	is practically never neutral. A simple method is developed that
6461	>	achieves charge neutralization wherever the r(-1) pair potential
6462	>	is truncated. This enables the extraction of the Coulomb energy,
6463	>	forces, and stresses from a spherically truncated, usually charged
6464	>	environment in a manner that is independent of the grouping of the
6465	>	pair terms. The close connection of our approach with the Ewald
6466	>	method is demonstrated and exploited, providing an efficient method
6467	>	for the simulation of even highly disordered ionic systems by direct,
6468	>	pairwise r(-1) summation with spherical truncation at rather short
6469	>	range, i.e., a method which fully exploits the short-ranged nature
6470	>	of the interactions in ionic systems. The method is validated by
6471	>	simulations of crystals, liquids, and interfacial systems, such
6472	>	as free surfaces and grain boundaries. (C) 1999 American Institute
6473	>	of Physics. [S0021-9606(99)51517-1].},
6474	>	Annote = {189PD Times Cited:70 Cited References Count:34},
6475	>	Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
6476	>	Issn = {0021-9606},
6477	>	Journal = {Journal of Chemical Physics},
6478	>	Month = {May 1},
6479	>	Number = 17,
6480	>	Pages = {8254-8282},
6481	>	Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r(-1) summation},
6482	>	Uri = {<Go to ISI>://000079913000008},
6483	>	Volume = 110,
6484	>	Year = 1999}
6485	>
6486	>	@article{Yoshida1990,
6487	>	Annote = {Ej798 Times Cited:492 Cited References Count:9},
6488	>	Author = {H. Yoshida},
6489	>	Issn = {0375-9601},
6490	>	Journal = {Physics Letters A},
6491	>	Month = {Nov 12},
6492	>	Number = {5-7},
6493	>	Pages = {262-268},
6494	>	Title = {Construction of Higher-Order Symplectic Integrators},
6495	>	Uri = {<Go to ISI>://A1990EJ79800009},
6496	>	Volume = 150,
6497	>	Year = 1990}
6498	>
6499	>	@article{Blum1972,
6500	>	Author = {L. Blum and A.~J. Torruella},
6501	>	Journal = {Journal of Chemical Physics},
6502	>	Number = 1,
6503	>	Pages = {303-309},
6504	>	Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
6505	>	Volume = 56,
6506	>	Year = 1972}
6507	>
6508	>	@article{Stone1978,
6509	>	Author = {A.~J. Stone},
6510	>	Journal = {Molecular Physics},
6511	>	Number = 1,
6512	>	Pages = {241-256},
6513	>	Title = {The description of bimolecular potentials, forces and torques: the S and V function expansions},
6514	>	Volume = 36,
6515	>	Year = 1978}
6516	>
6517	>	@article{Berardi2003,
6518	>	Author = {R. Berardi, M. Cecchini and C. Zannoni},
6519	>	Journal = {Journal of Chemical Physics},
6520	>	Number = 18,
6521	>	Pages = {9933-9946},
6522	>	Title = {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
6523	>	Volume = 119,
6524	>	Year = 2003}
6525	>
6526	>	@article{Beard2000,
6527	>	Author = {D. A. Beard and T. Schlick},
6528	>	Journal = {Journal of Chemical Physics},
6529	>	Number = 17,
6530	>	Pages = {7313-7322},
6531	>	Title = {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
6532	>	Volume = 112,
6533	>	Year = 2000}
6534	>
6535	>	@book{Hirsch1997,
6536	>	Address = {New York},
6537	>	Author = {M.W. Hirsch},
6538	>	Publisher = {Springer},
6539	>	Title = {Differential Topology},
6540	>	Year = 1997}
6541	>
6542	>	@book{Jost2002,
6543	>	Address = {Berlin},
6544	>	Author = {J. Jost},
6545	>	Publisher = {Springer-Verlag},
6546	>	Title = {Riemannian Geometry and Geometric Analysis},
6547	>	Year = 2002}
6548	>
6549	>	@book{McDuff1998,
6550	>	Address = {Oxford},
6551	>	Author = {D. McDuff and D. Salamon},
6552	>	Publisher = {Oxford Mathematical Monographs},
6553	>	Title = {Introduction to Symplectic Topology},
6554	>	Year = 1998}
6555	>
6556	>	@article{Matubayasi1999,
6557	>	Author = {N. Matubayasi and M. Nakahara},
6558	>	Journal = {Journal of Chemical Physics},
6559	>	Number = 7,
6560	>	Pages = {3291-3301},
6561	>	Title = {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
6562	>	Volume = 110,
6563	>	Year = 1999}
6564	>
6565	>	@article{Miller2002,
6566	>	Author = {T.F. Miller III, M. Eleftheriou},
6567	>	Journal = {Journal of Chemical Physics},
6568	>	Number = 20,
6569	>	Pages = {8649-8659},
6570	>	Title = {Symplectic quaternion scheme for biophysical molecular dynamics},
6571	>	Volume = 116,
6572	>	Year = 1999}
6573	>
6574	>	@article{McMillan1971,
6575	>	Author = {W.L. McMillan},
6576	>	Journal = {Journal of Chemical Physics},
6577	>	Number = 3,
6578	>	Pages = {1238-1246},
6579	>	Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},
6580	>	Volume = 4,
6581	>	Year = 1971}
6582	>
6583	>	@article{Gilmore1974,
6584	>	Author = {R. Gilmore},
6585	>	Journal = {Journal of Mathematical Physics},
6586	>	Number = 12,
6587	>	Pages = {2090-2092},
6588	>	Title = {Baker-Campbell-Hausdorff Formulas},
6589	>	Volume = 15,
6590	>	Year = 1974}
6591	>
6592	>	@article{Strang1968,
6593	>	Author = {G. Strang},
6594	>	Journal = {SIAM Journal on Numerical Analysis},
6595	>	Number = 3,
6596	>	Pages = {506-517},
6597	>	Title = {On the construction and comparision of difference schemes},
6598	>	Volume = 5,
6599	>	Year = 1968}
6600	>
6601	>	@article{Trotter1959,
6602	>	Author = {H.F. Trotter},
6603	>	Journal = {SIAM Journal on Numerical Analysis},
6604	>	Number = 14,
6605	>	Pages = {545-551},
6606	>	Title = {On the product of semi-groups of operators},
6607	>	Volume = 10,
6608	>	Year = 1959}
6609	>
6610	>	@article{Cartwright1992,
6611	>	Author = {J.H.E. Cartwright and O. Piro},
6612	>	Journal = {International Journal of Bifurcation and Chaos},
6613	>	Number = 3,
6614	>	Pages = {427-449},
6615	>	Title = {The Dynamics of Runge-Kutta Methods},
6616	>	Volume = 2,
6617	>	Year = 1992}
6618	>
6619	>	@article{HuseyinKaya07012005,
6620	>	Abstract = {It has been demonstrated that a "near-Levinthal" cooperative mechanism, whereby the common G[o] interaction scheme is augmented by an extra favorability for the native state as a whole, can lead to apparent two-state folding/unfolding kinetics over a broad range of native stabilities in lattice models of proteins. Here such a mechanism is shown to be generalizable to a simplified continuum (off-lattice) Langevin dynamics model with a C{alpha} protein chain representation, with the resulting chevron plots exhibiting an extended quasilinear regime reminiscent of that of apparent two-state real proteins. Similarly high degrees of cooperativity are possible in G[o]-like continuum models with rudimentary pairwise desolvation barriers as well. In these models, cooperativity increases with increasing desolvation barrier height, suggesting strongly that two-state-like folding/unfolding kinetics would be achievable when the pairwise desolvation barrier becomes sufficiently high. Besides cooperativity, another generic folding property of interest that has emerged from published experiments on several apparent two-state proteins is that their folding relaxation under constant native stability (isostability) conditions is essentially Arrhenius, entailing high intrinsic enthalpic folding barriers of [~]17-30 kcal/mol. Based on a new analysis of published data on barnase, here we propose that a similar property should also apply to a certain class of non-two-state proteins that fold with chevron rollovers. However, several continuum G[o]-like constructs considered here fail to predict any significant intrinsic enthalpic folding barrier under isostability conditions; thus the physical origin of such barriers in real proteins remains to be elucidated.
6621	>	},
6622	>	Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun},
6623	>	Doi = {10.1529/biophysj.104.057471},
6624	>	Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf},
6625	>	Journal = {Biophys. J.},
6626	>	Number = 1,
6627	>	Pages = {520-535},
6628	>	Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}},
6629	>	Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6630	>	Volume = 89,
6631	>	Year = 2005,
6632	>	Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
6633	>	Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}}

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