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@ARTICLE{Torre2003, |
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 |
} |
41 |
|
42 |
@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 |
} |
90 |
|
91 |
@BOOK{Allen1987, |
92 |
title = {Computer Simulations of Liquids}, |
93 |
publisher = {Oxford University Press}, |
94 |
year = {1987}, |
95 |
author = {M.~P. Allen and D.~J. Tildesley}, |
96 |
address = {New York}, |
97 |
} |
98 |
|
99 |
@ARTICLE{Allison1991, |
100 |
author = {S. A. Allison}, |
101 |
title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application |
102 |
to Polarized Dynamic Light-Scattering}, |
103 |
journal = {Macromolecules}, |
104 |
year = {1991}, |
105 |
volume = {24}, |
106 |
pages = {530-536}, |
107 |
number = {2}, |
108 |
month = {Jan 21}, |
109 |
abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments |
110 |
of rigid macromolecules. It is applied to polarized dynamic light |
111 |
scattering from rodlike sturctures and from a model of a DNA fragment |
112 |
(762 base pairs). A number of rod cases are examined in which the |
113 |
translational anisotropy is increased form zero to a large value. |
114 |
Simulated first cumulants as well as amplitudes and lifetimes of |
115 |
the dynamic form factor are compared with predictions of analytic |
116 |
theories and found to be in very good agreement with them. For DNA |
117 |
fragments 762 base pairs in length or longer, translational anisotropy |
118 |
does not contribute significantly to dynamic light scattering. In |
119 |
a comparison of rigid and flexible simulations on semistiff models |
120 |
of this fragment, it is shown directly that flexing contributes |
121 |
to the faster decay processes probed by light scattering and that |
122 |
the flexible model studies are in good agreement with experiment.}, |
123 |
annote = {Eu814 Times Cited:8 Cited References Count:32}, |
124 |
issn = {0024-9297}, |
125 |
uri = {<Go to ISI>://A1991EU81400029}, |
126 |
} |
127 |
|
128 |
@ARTICLE{Andersen1983, |
129 |
author = {H. C. Andersen}, |
130 |
title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics |
131 |
Calculations}, |
132 |
journal = {Journal of Computational Physics}, |
133 |
year = {1983}, |
134 |
volume = {52}, |
135 |
pages = {24-34}, |
136 |
number = {1}, |
137 |
annote = {Rq238 Times Cited:559 Cited References Count:14}, |
138 |
issn = {0021-9991}, |
139 |
uri = {<Go to ISI>://A1983RQ23800002}, |
140 |
} |
141 |
|
142 |
@ARTICLE{Auerbach2005, |
143 |
author = {A. Auerbach}, |
144 |
title = {Gating of acetylcholine receptor channels: Brownian motion across |
145 |
a broad transition state}, |
146 |
journal = {Proceedings of the National Academy of Sciences of the United States |
147 |
of America}, |
148 |
year = {2005}, |
149 |
volume = {102}, |
150 |
pages = {1408-1412}, |
151 |
number = {5}, |
152 |
month = {Feb 1}, |
153 |
abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between |
154 |
stable #closed# and #open# conformations. In patch clamp recordings, |
155 |
diliganded AChR gating appears to be a simple, two-state reaction. |
156 |
However, mutagenesis studies indicate that during gating dozens |
157 |
of residues across the protein move asynchronously and are organized |
158 |
into rigid body gating domains (#blocks#). Moreover, there is an |
159 |
upper limit to the apparent channel opening rate constant. These |
160 |
observations suggest that the gating reaction has a broad, corrugated |
161 |
transition state region, with the maximum opening rate reflecting, |
162 |
in part, the mean first-passage time across this ensemble. Simulations |
163 |
reveal that a flat, isotropic energy profile for the transition |
164 |
state can account for many of the essential features of AChR gating. |
165 |
With this mechanism, concerted, local structural transitions that |
166 |
occur on the broad transition state ensemble give rise to fractional |
167 |
measures of reaction progress (Phi values) determined by rate-equilibrium |
168 |
free energy relationship analysis. The results suggest that the |
169 |
coarse-grained AChR gating conformational change propagates through |
170 |
the protein with dynamics that are governed by the Brownian motion |
171 |
of individual gating blocks.}, |
172 |
annote = {895QF Times Cited:9 Cited References Count:33}, |
173 |
issn = {0027-8424}, |
174 |
uri = {<Go to ISI>://000226877300030}, |
175 |
} |
176 |
|
177 |
@ARTICLE{Baber1995, |
178 |
author = {J. Baber and J. F. Ellena and D. S. Cafiso}, |
179 |
title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined |
180 |
Using H-2 Nmr and H-1-H-1 Noe Spectroscopy}, |
181 |
journal = {Biochemistry}, |
182 |
year = {1995}, |
183 |
volume = {34}, |
184 |
pages = {6533-6539}, |
185 |
number = {19}, |
186 |
month = {May 16}, |
187 |
abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane |
188 |
on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine |
189 |
membranes in the liquid crystalline phase was investigated using |
190 |
H-2 NMR. Upon the addition of the anesthetics, the first five methylene |
191 |
units near the interface generally show a very small increase in |
192 |
segmental order, while segments deeper within the bilayer show a |
193 |
small decrease in segmental order. From the H-2 NMR results, the |
194 |
chain length for the perdeuterated palmitoyl chain in the absence |
195 |
of anesthetic was found to be 12.35 Angstrom. Upon the addition |
196 |
of halothane enflurane, or isoflurane, the acyl chain undergoes |
197 |
slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively, |
198 |
at 50 mol % anesthetic. A simple model was used to estimate the |
199 |
relative amounts of anesthetic located near the interface and deeper |
200 |
in the bilayer hydrocarbon region, and only a slight preference |
201 |
for an interfacial location was observed. Intermolecular H-1-H-1 |
202 |
nuclear Overhauser effects (NOEs) were measured between phospholipid |
203 |
and halothane protons. These NOEs are consistent with the intramembrane |
204 |
location of the anesthetics suggested by the H-2 NMR data. In addition, |
205 |
the NOE data indicate that anesthetics prefer the interfacial and |
206 |
hydrocarbon regions of the membrane and are not found in high concentrations |
207 |
in the phospholipid headgroup.}, |
208 |
annote = {Qz716 Times Cited:38 Cited References Count:37}, |
209 |
issn = {0006-2960}, |
210 |
uri = {<Go to ISI>://A1995QZ71600035}, |
211 |
} |
212 |
|
213 |
@ARTICLE{Banerjee2004, |
214 |
author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray}, |
215 |
title = {Solution of quantum Langevin equation: Approximations, theoretical |
216 |
and numerical aspects}, |
217 |
journal = {Journal of Chemical Physics}, |
218 |
year = {2004}, |
219 |
volume = {120}, |
220 |
pages = {8960-8972}, |
221 |
number = {19}, |
222 |
month = {May 15}, |
223 |
abstract = {Based on a coherent state representation of noise operator and an |
224 |
ensemble averaging procedure using Wigner canonical thermal distribution |
225 |
for harmonic oscillators, a generalized quantum Langevin equation |
226 |
has been recently developed [Phys. Rev. E 65, 021109 (2002); 66, |
227 |
051106 (2002)] to derive the equations of motion for probability |
228 |
distribution functions in c-number phase-space. We extend the treatment |
229 |
to explore several systematic approximation schemes for the solutions |
230 |
of the Langevin equation for nonlinear potentials for a wide range |
231 |
of noise correlation, strength and temperature down to the vacuum |
232 |
limit. The method is exemplified by an analytic application to harmonic |
233 |
oscillator for arbitrary memory kernel and with the help of a numerical |
234 |
calculation of barrier crossing, in a cubic potential to demonstrate |
235 |
the quantum Kramers' turnover and the quantum Arrhenius plot. (C) |
236 |
2004 American Institute of Physics.}, |
237 |
annote = {816YY Times Cited:8 Cited References Count:35}, |
238 |
issn = {0021-9606}, |
239 |
uri = {<Go to ISI>://000221146400009}, |
240 |
} |
241 |
|
242 |
@ARTICLE{Barojas1973, |
243 |
author = {J. Barojas and D. Levesque}, |
244 |
title = {Simulation of Diatomic Homonuclear Liquids}, |
245 |
journal = {Phys. Rev. A}, |
246 |
year = {1973}, |
247 |
volume = {7}, |
248 |
pages = {1092-1105}, |
249 |
} |
250 |
|
251 |
@ARTICLE{Barth1998, |
252 |
author = {E. Barth and T. Schlick}, |
253 |
title = {Overcoming stability limitations in biomolecular dynamics. I. Combining |
254 |
force splitting via extrapolation with Langevin dynamics in LN}, |
255 |
journal = {Journal of Chemical Physics}, |
256 |
year = {1998}, |
257 |
volume = {109}, |
258 |
pages = {1617-1632}, |
259 |
number = {5}, |
260 |
month = {Aug 1}, |
261 |
abstract = {We present an efficient new method termed LN for propagating biomolecular |
262 |
dynamics according to the Langevin equation that arose fortuitously |
263 |
upon analysis of the range of harmonic validity of our normal-mode |
264 |
scheme LIN. LN combines force linearization with force splitting |
265 |
techniques and disposes of LIN'S computationally intensive minimization |
266 |
(anharmonic correction) component. Unlike the competitive multiple-timestepping |
267 |
(MTS) schemes today-formulated to be symplectic and time-reversible-LN |
268 |
merges the slow and fast forces via extrapolation rather than impulses; |
269 |
the Langevin heat bath prevents systematic energy drifts. This combination |
270 |
succeeds in achieving more significant speedups than these MTS methods |
271 |
which are Limited by resonance artifacts to an outer timestep less |
272 |
than some integer multiple of half the period of the fastest motion |
273 |
(around 4-5 fs for biomolecules). We show that LN achieves very |
274 |
good agreement with small-timestep solutions of the Langevin equation |
275 |
in terms of thermodynamics (energy means and variances), geometry, |
276 |
and dynamics (spectral densities) for two proteins in vacuum and |
277 |
a large water system. Significantly, the frequency of updating the |
278 |
slow forces extends to 48 fs or more, resulting in speedup factors |
279 |
exceeding 10. The implementation of LN in any program that employs |
280 |
force-splitting computations is straightforward, with only partial |
281 |
second-derivative information required, as well as sparse Hessian/vector |
282 |
multiplication routines. The linearization part of LN could even |
283 |
be replaced by direct evaluation of the fast components. The application |
284 |
of LN to biomolecular dynamics is well suited for configurational |
285 |
sampling, thermodynamic, and structural questions. (C) 1998 American |
286 |
Institute of Physics.}, |
287 |
annote = {105HH Times Cited:29 Cited References Count:49}, |
288 |
issn = {0021-9606}, |
289 |
uri = {<Go to ISI>://000075066300006}, |
290 |
} |
291 |
|
292 |
@ARTICLE{Batcho2001, |
293 |
author = {P. F. Batcho and T. Schlick}, |
294 |
title = {Special stability advantages of position-Verlet over velocity-Verlet |
295 |
in multiple-time step integration}, |
296 |
journal = {Journal of Chemical Physics}, |
297 |
year = {2001}, |
298 |
volume = {115}, |
299 |
pages = {4019-4029}, |
300 |
number = {9}, |
301 |
month = {Sep 1}, |
302 |
abstract = {We present an analysis for a simple two-component harmonic oscillator |
303 |
that compares the use of position-Verlet to velocity-Verlet for |
304 |
multiple-time step integration. The numerical stability analysis |
305 |
based on the impulse-Verlet splitting shows that position-Verlet |
306 |
has enhanced stability, in terms of the largest allowable time step, |
307 |
for cases where an ample separation of time scales exists. Numerical |
308 |
investigations confirm the advantages of the position-Verlet scheme |
309 |
when used for the fastest time scales of the system. Applications |
310 |
to a biomolecule. a solvated protein, for both Newtonian and Langevin |
311 |
dynamics echo these trends over large outer time-step regimes. (C) |
312 |
2001 American Institute of Physics.}, |
313 |
annote = {469KV Times Cited:6 Cited References Count:30}, |
314 |
issn = {0021-9606}, |
315 |
uri = {<Go to ISI>://000170813800005}, |
316 |
} |
317 |
|
318 |
@ARTICLE{Bates2005, |
319 |
author = {M. A. Bates and G. R. Luckhurst}, |
320 |
title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation |
321 |
study}, |
322 |
journal = {Physical Review E}, |
323 |
year = {2005}, |
324 |
volume = {72}, |
325 |
pages = {-}, |
326 |
number = {5}, |
327 |
month = {Nov}, |
328 |
abstract = {Inspired by recent claims that compounds composed of V-shaped molecules |
329 |
can exhibit the elusive biaxial nematic phase, we have developed |
330 |
a generic simulation model for such systems. This contains the features |
331 |
of the molecule that are essential to its liquid crystal behavior, |
332 |
namely the anisotropies of the two arms and the angle between them. |
333 |
The behavior of the model has been investigated using Monte Carlo |
334 |
simulations for a wide range of these structural parameters. This |
335 |
allows us to establish the relationship between the V-shaped molecule |
336 |
and its ability to form a biaxial nematic phase. Of particular importance |
337 |
are the criteria of geometry and the relative anisotropy necessary |
338 |
for the system to exhibit a Landau point, at which the biaxial nematic |
339 |
is formed directly from the isotropic phase. The simulations have |
340 |
also been used to determine the orientational order parameters for |
341 |
a selection of molecular axes. These are especially important because |
342 |
they reveal the phase symmetry and are connected to the experimental |
343 |
determination of this. The simulation results show that, whereas |
344 |
some positions are extremely sensitive to the phase biaxiality, |
345 |
others are totally blind to this.}, |
346 |
annote = {Part 1 988LQ Times Cited:0 Cited References Count:38}, |
347 |
issn = {1539-3755}, |
348 |
uri = {<Go to ISI>://000233603100030}, |
349 |
} |
350 |
|
351 |
@ARTICLE{Beard2003, |
352 |
author = {D. A. Beard and T. Schlick}, |
353 |
title = {Unbiased rotational moves for rigid-body dynamics}, |
354 |
journal = {Biophysical Journal}, |
355 |
year = {2003}, |
356 |
volume = {85}, |
357 |
pages = {2973-2976}, |
358 |
number = {5}, |
359 |
month = {Nov 1}, |
360 |
abstract = {We introduce an unbiased protocol for performing rotational moves |
361 |
in rigid-body dynamics simulations. This approach - based on the |
362 |
analytic solution for the rotational equations of motion for an |
363 |
orthogonal coordinate system at constant angular velocity - removes |
364 |
deficiencies that have been largely ignored in Brownian dynamics |
365 |
simulations, namely errors for finite rotations that result from |
366 |
applying the noncommuting rotational matrices in an arbitrary order. |
367 |
Our algorithm should thus replace standard approaches to rotate |
368 |
local coordinate frames in Langevin and Brownian dynamics simulations.}, |
369 |
annote = {736UA Times Cited:0 Cited References Count:11}, |
370 |
issn = {0006-3495}, |
371 |
uri = {<Go to ISI>://000186190500018}, |
372 |
} |
373 |
|
374 |
@ARTICLE{Beloborodov1998, |
375 |
author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev}, |
376 |
title = {Effect of coupling between rotational and translational Brownian |
377 |
motions on NMR spin relaxation: Consideration using green function |
378 |
of rigid body diffusion}, |
379 |
journal = {Journal of Magnetic Resonance}, |
380 |
year = {1998}, |
381 |
volume = {132}, |
382 |
pages = {328-329}, |
383 |
number = {2}, |
384 |
month = {Jun}, |
385 |
abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein, |
386 |
Biopolymers 33, 409-436, 1993), it was analytically shown that coupling |
387 |
between translation and rotation diffusion degrees of freedom does |
388 |
not affect the correlation functions relevant to the NMR intramolecular |
389 |
relaxation. It follows that spectral densities usually used for |
390 |
the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37, |
391 |
647-654, 1962) can be regarded as exact in respect to the rotation-translation |
392 |
coupling for the spin system connected with a rigid body. (C) 1998 |
393 |
Academic Press.}, |
394 |
annote = {Zu605 Times Cited:2 Cited References Count:6}, |
395 |
issn = {1090-7807}, |
396 |
uri = {<Go to ISI>://000074214800017}, |
397 |
} |
398 |
|
399 |
@ARTICLE{Berardi1996, |
400 |
author = {R. Berardi and S. Orlandi and C. Zannoni}, |
401 |
title = {Antiphase structures in polar smectic liquid crystals and their molecular |
402 |
origin}, |
403 |
journal = {Chemical Physics Letters}, |
404 |
year = {1996}, |
405 |
volume = {261}, |
406 |
pages = {357-362}, |
407 |
number = {3}, |
408 |
month = {Oct 18}, |
409 |
abstract = {We demonstrate that the overall molecular dipole organization in a |
410 |
smectic liquid crystal formed of polar molecules can be strongly |
411 |
influenced by the position of the dipole in the molecule. We study |
412 |
by large scale Monte Carlo simulations systems of attractive-repulsive |
413 |
''Gay-Berne'' elongated ellipsoids with an axial dipole at the center |
414 |
or near the end of the molecule and we show that monolayer smectic |
415 |
liquid crystals and modulated antiferroelectric bilayer stripe domains |
416 |
similar to the experimentally observed ''antiphase'' structures |
417 |
are obtained in the two cases.}, |
418 |
annote = {Vn637 Times Cited:49 Cited References Count:26}, |
419 |
issn = {0009-2614}, |
420 |
uri = {<Go to ISI>://A1996VN63700023}, |
421 |
} |
422 |
|
423 |
@ARTICLE{Berkov2005, |
424 |
author = {D. V. Berkov and N. L. Gorn}, |
425 |
title = {Magnetization precession due to a spin-polarized current in a thin |
426 |
nanoelement: Numerical simulation study}, |
427 |
journal = {Physical Review B}, |
428 |
year = {2005}, |
429 |
volume = {72}, |
430 |
pages = {-}, |
431 |
number = {9}, |
432 |
month = {Sep}, |
433 |
abstract = {In this paper a detailed numerical study (in frames of the Slonczewski |
434 |
formalism) of magnetization oscillations driven by a spin-polarized |
435 |
current through a thin elliptical nanoelement is presented. We show |
436 |
that a sophisticated micromagnetic model, where a polycrystalline |
437 |
structure of a nanoelement is taken into account, can explain qualitatively |
438 |
all most important features of the magnetization oscillation spectra |
439 |
recently observed experimentally [S. I. Kiselev , Nature 425, 380 |
440 |
(2003)], namely, existence of several equidistant spectral bands, |
441 |
sharp onset and abrupt disappearance of magnetization oscillations |
442 |
with increasing current, absence of the out-of-plane regime predicted |
443 |
by a macrospin model, and the relation between frequencies of so-called |
444 |
small-angle and quasichaotic oscillations. However, a quantitative |
445 |
agreement with experimental results (especially concerning the frequency |
446 |
of quasichaotic oscillations) could not be achieved in the region |
447 |
of reasonable parameter values, indicating that further model refinement |
448 |
is necessary for a complete understanding of the spin-driven magnetization |
449 |
precession even in this relatively simple experimental situation.}, |
450 |
annote = {969IT Times Cited:2 Cited References Count:55}, |
451 |
issn = {1098-0121}, |
452 |
uri = {<Go to ISI>://000232228500058}, |
453 |
} |
454 |
|
455 |
@ARTICLE{Berkov2005a, |
456 |
author = {D. V. Berkov and N. L. Gorn}, |
457 |
title = {Stochastic dynamic simulations of fast remagnetization processes: |
458 |
recent advances and applications}, |
459 |
journal = {Journal of Magnetism and Magnetic Materials}, |
460 |
year = {2005}, |
461 |
volume = {290}, |
462 |
pages = {442-448}, |
463 |
month = {Apr}, |
464 |
abstract = {Numerical simulations of fast remagnetization processes using stochastic |
465 |
dynamics are widely used to study various magnetic systems. In this |
466 |
paper, we first address several crucial methodological problems |
467 |
of such simulations: (i) the influence of finite-element discretization |
468 |
on simulated dynamics, (ii) choice between Ito and Stratonovich |
469 |
stochastic calculi by the solution of micromagnetic stochastic equations |
470 |
of motion and (iii) non-trivial correlation properties of the random |
471 |
(thermal) field. Next, we discuss several examples to demonstrate |
472 |
the great potential of the Langevin dynamics for studying fast remagnetization |
473 |
processes in technically relevant applications: we present numerical |
474 |
analysis of equilibrium magnon spectra in patterned structures, |
475 |
study thermal noise effects on the magnetization dynamics of nanoelements |
476 |
in pulsed fields and show some results for a remagnetization dynamics |
477 |
induced by a spin-polarized current. (c) 2004 Elsevier B.V. All |
478 |
rights reserved.}, |
479 |
annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25}, |
480 |
issn = {0304-8853}, |
481 |
uri = {<Go to ISI>://000228837600109}, |
482 |
} |
483 |
|
484 |
@ARTICLE{Berkov2002, |
485 |
author = {D. V. Berkov and N. L. Gorn and P. Gornert}, |
486 |
title = {Magnetization dynamics in nanoparticle systems: Numerical simulation |
487 |
using Langevin dynamics}, |
488 |
journal = {Physica Status Solidi a-Applied Research}, |
489 |
year = {2002}, |
490 |
volume = {189}, |
491 |
pages = {409-421}, |
492 |
number = {2}, |
493 |
month = {Feb 16}, |
494 |
abstract = {We report on recent progress achieved by the development of numerical |
495 |
methods based on the stochastic (Langevin) dynamics applied to systems |
496 |
of interacting magnetic nanoparticles. The method enables direct |
497 |
simulations of the trajectories of magnetic moments taking into |
498 |
account (i) all relevant interactions, (ii) precession dynamics, |
499 |
and (iii) temperature fluctuations included via the random (thermal) |
500 |
field. We present several novel results obtained using new methods |
501 |
developed for the solution of the Langevin equations. In particular, |
502 |
we have investigated magnetic nanodots and disordered granular systems |
503 |
of single-domain magnetic particles. For the first case we have |
504 |
calculated the spectrum and the spatial distribution of spin excitations. |
505 |
For the second system the complex ac susceptibility chi(omega, T) |
506 |
for various particle concentrations and particle anisotropies were |
507 |
computed and compared with numerous experimental results.}, |
508 |
annote = {526TF Times Cited:4 Cited References Count:37}, |
509 |
issn = {0031-8965}, |
510 |
uri = {<Go to ISI>://000174145200026}, |
511 |
} |
512 |
|
513 |
@ARTICLE{Bernal1980, |
514 |
author = {J.M. Bernal and J. G. {de la Torre}}, |
515 |
title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules |
516 |
with Arbitrary Shape}, |
517 |
journal = {Biopolymers}, |
518 |
year = {1980}, |
519 |
volume = {19}, |
520 |
pages = {751-766}, |
521 |
} |
522 |
|
523 |
@ARTICLE{Brunger1984, |
524 |
author = {A. Brunger and C. L. Brooks and M. Karplus}, |
525 |
title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations |
526 |
of St2 Water}, |
527 |
journal = {Chemical Physics Letters}, |
528 |
year = {1984}, |
529 |
volume = {105}, |
530 |
pages = {495-500}, |
531 |
number = {5}, |
532 |
annote = {Sm173 Times Cited:143 Cited References Count:22}, |
533 |
issn = {0009-2614}, |
534 |
uri = {<Go to ISI>://A1984SM17300007}, |
535 |
} |
536 |
|
537 |
@ARTICLE{Budd1999, |
538 |
author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell}, |
539 |
title = {Self-similar numerical solutions of the porous-medium equation using |
540 |
moving mesh methods}, |
541 |
journal = {Philosophical Transactions of the Royal Society of London Series |
542 |
a-Mathematical Physical and Engineering Sciences}, |
543 |
year = {1999}, |
544 |
volume = {357}, |
545 |
pages = {1047-1077}, |
546 |
number = {1754}, |
547 |
month = {Apr 15}, |
548 |
abstract = {This paper examines a synthesis of adaptive mesh methods with the |
549 |
use of symmetry to study a partial differential equation. In particular, |
550 |
it considers methods which admit discrete self-similar solutions, |
551 |
examining the convergence of these to the true self-similar solution |
552 |
as well as their stability. Special attention is given to the nonlinear |
553 |
diffusion equation describing flow in a porous medium.}, |
554 |
annote = {199EE Times Cited:4 Cited References Count:14}, |
555 |
issn = {1364-503X}, |
556 |
uri = {<Go to ISI>://000080466800005}, |
557 |
} |
558 |
|
559 |
@ARTICLE{Camp1999, |
560 |
author = {P. J. Camp and M. P. Allen and A. J. Masters}, |
561 |
title = {Theory and computer simulation of bent-core molecules}, |
562 |
journal = {Journal of Chemical Physics}, |
563 |
year = {1999}, |
564 |
volume = {111}, |
565 |
pages = {9871-9881}, |
566 |
number = {21}, |
567 |
month = {Dec 1}, |
568 |
abstract = {Fluids of hard bent-core molecules have been studied using theory |
569 |
and computer simulation. The molecules are composed of two hard |
570 |
spherocylinders, with length-to-breadth ratio L/D, joined by their |
571 |
ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20 |
572 |
degrees, the simulations show isotropic, nematic, smectic, and solid |
573 |
phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic, |
574 |
and solid phases are in evidence, which suggests that there is a |
575 |
nematic-smectic-solid triple point at an angle in the range 20 degrees |
576 |
< gamma < 30 degrees. In all of the orientationally ordered fluid |
577 |
phases the order is purely uniaxial. For gamma = 10 degrees and |
578 |
20 degrees, at the studied densities, the solid is also uniaxially |
579 |
ordered, whilst for gamma = 30 degrees the solid layers are biaxially |
580 |
ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find |
581 |
no spontaneous orientational ordering. This is shown to be due to |
582 |
the interlocking of dimer pairs which precludes alignment. We find |
583 |
similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial |
584 |
nematic transition is predicted by Onsager theory. Simulations in |
585 |
the biaxial nematic phase show it to be at least mechanically stable |
586 |
with respect to the isotropic phase, however. We have compared the |
587 |
quasi-exact simulation results in the isotropic phase with the predicted |
588 |
equations of state from three theories: the virial expansion containing |
589 |
the second and third virial coefficients; the Parsons-Lee equation |
590 |
of state; an application of Wertheim's theory of associating fluids |
591 |
in the limit of infinite attractive association energy. For all |
592 |
of the molecule elongations and geometries we have simulated, the |
593 |
Wertheim theory proved to be the most accurate. Interestingly, the |
594 |
isotropic equation of state is virtually independent of the dimer |
595 |
bond angle-a feature that is also reflected in the lack of variation |
596 |
with angle of the calculated second and third virial coefficients. |
597 |
(C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].}, |
598 |
annote = {255TC Times Cited:24 Cited References Count:38}, |
599 |
issn = {0021-9606}, |
600 |
uri = {<Go to ISI>://000083685400056}, |
601 |
} |
602 |
|
603 |
@ARTICLE{Care2005, |
604 |
author = {C. M. Care and D. J. Cleaver}, |
605 |
title = {Computer simulation of liquid crystals}, |
606 |
journal = {Reports on Progress in Physics}, |
607 |
year = {2005}, |
608 |
volume = {68}, |
609 |
pages = {2665-2700}, |
610 |
number = {11}, |
611 |
month = {Nov}, |
612 |
abstract = {A review is presented of molecular and mesoscopic computer simulations |
613 |
of liquid crystalline systems. Molecular simulation approaches applied |
614 |
to such systems are described, and the key findings for bulk phase |
615 |
behaviour are reported. Following this, recently developed lattice |
616 |
Boltzmann approaches to the mesoscale modelling of nemato-dynanics |
617 |
are reviewed. This paper concludes with a discussion of possible |
618 |
areas for future development in this field.}, |
619 |
annote = {989TU Times Cited:2 Cited References Count:258}, |
620 |
issn = {0034-4885}, |
621 |
uri = {<Go to ISI>://000233697600004}, |
622 |
} |
623 |
|
624 |
@ARTICLE{Carrasco1999, |
625 |
author = {B. Carrasco and J. G. {de la Torre}}, |
626 |
title = {Hydrodynamic properties of rigid particles: Comparison of different |
627 |
modeling and computational procedures}, |
628 |
journal = {Biophysical Journal}, |
629 |
year = {1999}, |
630 |
volume = {76}, |
631 |
pages = {3044-3057}, |
632 |
number = {6}, |
633 |
month = {Jun}, |
634 |
abstract = {The hydrodynamic properties of rigid particles are calculated from |
635 |
models composed of spherical elements (beads) using theories developed |
636 |
by Kirkwood, Bloomfield, and their coworkers. Bead models have usually |
637 |
been built in such a way that the beads fill the volume occupied |
638 |
by the particles. Sometimes the beads are few and of varying sizes |
639 |
(bead models in the strict sense), and other times there are many |
640 |
small beads (filling models). Because hydrodynamic friction takes |
641 |
place at the molecular surface, another possibility is to use shell |
642 |
models, as originally proposed by Bloomfield. In this work, we have |
643 |
developed procedures to build models of the various kinds, and we |
644 |
describe the theory and methods for calculating their hydrodynamic |
645 |
properties, including approximate methods that may be needed to |
646 |
treat models with a very large number of elements. By combining |
647 |
the various possibilities of model building and hydrodynamic calculation, |
648 |
several strategies can be designed. We have made a quantitative |
649 |
comparison of the performance of the various strategies by applying |
650 |
them to some test cases, for which the properties are known a priori. |
651 |
We provide guidelines and computational tools for bead modeling.}, |
652 |
annote = {200TT Times Cited:46 Cited References Count:57}, |
653 |
issn = {0006-3495}, |
654 |
uri = {<Go to ISI>://000080556700016}, |
655 |
} |
656 |
|
657 |
@ARTICLE{Chandra1999, |
658 |
author = {A. Chandra and T. Ichiye}, |
659 |
title = {Dynamical properties of the soft sticky dipole model of water: Molecular |
660 |
dynamics simulations}, |
661 |
journal = {Journal of Chemical Physics}, |
662 |
year = {1999}, |
663 |
volume = {111}, |
664 |
pages = {2701-2709}, |
665 |
number = {6}, |
666 |
month = {Aug 8}, |
667 |
abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water |
668 |
are calculated by means of molecular dynamics simulations. Since |
669 |
this is not a simple point model, the forces and torques arising |
670 |
from the SSD potential are derived here. Simulations are carried |
671 |
out in the microcanonical ensemble employing the Ewald method for |
672 |
the electrostatic interactions. Various time correlation functions |
673 |
and dynamical quantities associated with the translational and rotational |
674 |
motion of water molecules are evaluated and compared with those |
675 |
of two other commonly used models of liquid water, namely the transferable |
676 |
intermolecular potential-three points (TIP3P) and simple point charge/extended |
677 |
(SPC/E) models, and also with experiments. The dynamical properties |
678 |
of the SSD water model are found to be in good agreement with the |
679 |
experimental results and appear to be better than the TIP3P and |
680 |
SPC/E models in most cases, as has been previously shown for its |
681 |
thermodynamic, structural, and dielectric properties. Also, molecular |
682 |
dynamics simulations of the SSD model are found to run much faster |
683 |
than TIP3P, SPC/E, and other multisite models. (C) 1999 American |
684 |
Institute of Physics. [S0021-9606(99)51430-X].}, |
685 |
annote = {221EN Times Cited:14 Cited References Count:66}, |
686 |
issn = {0021-9606}, |
687 |
uri = {<Go to ISI>://000081711200038}, |
688 |
} |
689 |
|
690 |
@ARTICLE{Channell1990, |
691 |
author = {P. J. Channell and C. Scovel}, |
692 |
title = {Symplectic Integration of Hamiltonian-Systems}, |
693 |
journal = {Nonlinearity}, |
694 |
year = {1990}, |
695 |
volume = {3}, |
696 |
pages = {231-259}, |
697 |
number = {2}, |
698 |
month = {may}, |
699 |
annote = {Dk631 Times Cited:152 Cited References Count:34}, |
700 |
issn = {0951-7715}, |
701 |
uri = {<Go to ISI>://A1990DK63100001}, |
702 |
} |
703 |
|
704 |
@ARTICLE{Chen2003, |
705 |
author = {B. Chen and F. Solis}, |
706 |
title = {Explicit mixed finite order Runge-Kutta methods}, |
707 |
journal = {Applied Numerical Mathematics}, |
708 |
year = {2003}, |
709 |
volume = {44}, |
710 |
pages = {21-30}, |
711 |
number = {1-2}, |
712 |
month = {Jan}, |
713 |
abstract = {We investigate the asymptotic behavior of systems of nonlinear differential |
714 |
equations and introduce a family of mixed methods from combinations |
715 |
of explicit Runge-Kutta methods. These methods have better stability |
716 |
behavior than traditional Runge-Kutta methods and generally extend |
717 |
the range of validity of the calculated solutions. These methods |
718 |
also give a way of determining if the numerical solutions are real |
719 |
or spurious. Emphasis is put on examples coming from mathematical |
720 |
models in ecology. (C) 2002 IMACS. Published by Elsevier Science |
721 |
B.V. All rights reserved.}, |
722 |
annote = {633ZD Times Cited:0 Cited References Count:9}, |
723 |
issn = {0168-9274}, |
724 |
uri = {<Go to ISI>://000180314200002}, |
725 |
} |
726 |
|
727 |
@ARTICLE{Cheung2004, |
728 |
author = {D. L. Cheung and S. J. Clark and M. R. Wilson}, |
729 |
title = {Calculation of flexoelectric coefficients for a nematic liquid crystal |
730 |
by atomistic simulation}, |
731 |
journal = {Journal of Chemical Physics}, |
732 |
year = {2004}, |
733 |
volume = {121}, |
734 |
pages = {9131-9139}, |
735 |
number = {18}, |
736 |
month = {Nov 8}, |
737 |
abstract = {Equilibrium molecular dynamics calculations have been performed for |
738 |
the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile |
739 |
(PCH5) using a fully atomistic model. Simulation data have been |
740 |
obtained for a series of temperatures in the nematic phase. The |
741 |
simulation data have been used to calculate the flexoelectric coefficients |
742 |
e(s) and e(b) using the linear response formalism of Osipov and |
743 |
Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr. |
744 |
31, 125 (1986)]. The temperature and order parameter dependence |
745 |
of e(s) and e(b) are examined, as are separate contributions from |
746 |
different intermolecular interactions. Values of e(s) and e(b) calculated |
747 |
from simulation are consistent with those found from experiment. |
748 |
(C) 2004 American Institute of Physics.}, |
749 |
annote = {866UM Times Cited:4 Cited References Count:61}, |
750 |
issn = {0021-9606}, |
751 |
uri = {<Go to ISI>://000224798900053}, |
752 |
} |
753 |
|
754 |
@ARTICLE{Cheung2002, |
755 |
author = {D. L. Cheung and S. J. Clark and M. R. Wilson}, |
756 |
title = {Calculation of the rotational viscosity of a nematic liquid crystal}, |
757 |
journal = {Chemical Physics Letters}, |
758 |
year = {2002}, |
759 |
volume = {356}, |
760 |
pages = {140-146}, |
761 |
number = {1-2}, |
762 |
month = {Apr 15}, |
763 |
abstract = {Equilibrium molecular dynamics calculations have been performed for |
764 |
the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile |
765 |
(PCH5) using a fully atomistic model. Simulation data has been obtained |
766 |
for a series of temperatures in the nematic phase. The rotational |
767 |
viscosity co-efficient gamma(1), has been calculated using the angular |
768 |
velocity correlation function of the nematic director, n, the mean |
769 |
squared diffusion of n and statistical mechanical methods based |
770 |
on the rotational diffusion co-efficient. We find good agreement |
771 |
between the first two methods and experimental values. (C) 2002 |
772 |
Published by Elsevier Science B.V.}, |
773 |
annote = {547KF Times Cited:8 Cited References Count:31}, |
774 |
issn = {0009-2614}, |
775 |
uri = {<Go to ISI>://000175331000020}, |
776 |
} |
777 |
|
778 |
@ARTICLE{Chin2004, |
779 |
author = {S. A. Chin}, |
780 |
title = {Dynamical multiple-time stepping methods for overcoming resonance |
781 |
instabilities}, |
782 |
journal = {Journal of Chemical Physics}, |
783 |
year = {2004}, |
784 |
volume = {120}, |
785 |
pages = {8-13}, |
786 |
number = {1}, |
787 |
month = {Jan 1}, |
788 |
abstract = {Current molecular dynamics simulations of biomolecules using multiple |
789 |
time steps to update the slowly changing force are hampered by instabilities |
790 |
beginning at time steps near the half period of the fastest vibrating |
791 |
mode. These #resonance# instabilities have became a critical barrier |
792 |
preventing the long time simulation of biomolecular dynamics. Attempts |
793 |
to tame these instabilities by altering the slowly changing force |
794 |
and efforts to damp them out by Langevin dynamics do not address |
795 |
the fundamental cause of these instabilities. In this work, we trace |
796 |
the instability to the nonanalytic character of the underlying spectrum |
797 |
and show that a correct splitting of the Hamiltonian, which renders |
798 |
the spectrum analytic, restores stability. The resulting Hamiltonian |
799 |
dictates that in addition to updating the momentum due to the slowly |
800 |
changing force, one must also update the position with a modified |
801 |
mass. Thus multiple-time stepping must be done dynamically. (C) |
802 |
2004 American Institute of Physics.}, |
803 |
annote = {757TK Times Cited:1 Cited References Count:22}, |
804 |
issn = {0021-9606}, |
805 |
uri = {<Go to ISI>://000187577400003}, |
806 |
} |
807 |
|
808 |
@ARTICLE{Cook2000, |
809 |
author = {M. J. Cook and M. R. Wilson}, |
810 |
title = {Simulation studies of dipole correlation in the isotropic liquid |
811 |
phase}, |
812 |
journal = {Liquid Crystals}, |
813 |
year = {2000}, |
814 |
volume = {27}, |
815 |
pages = {1573-1583}, |
816 |
number = {12}, |
817 |
month = {Dec}, |
818 |
abstract = {The Kirkwood correlation factor g(1) determines the preference for |
819 |
local parallel or antiparallel dipole association in the isotropic |
820 |
phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood |
821 |
factors greater than 1 have an enhanced effective dipole moment |
822 |
along the molecular long axis. This leads to higher values of Delta |
823 |
epsilon in the nematic phase. This paper describes state-of-the-art |
824 |
molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile |
825 |
(PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl) |
826 |
in the isotropic liquid phase using an all-atom force field and |
827 |
taking long range electrostatics into account using an Ewald summation. |
828 |
Using this methodology, PCH5 is seen to prefer antiparallel dipole |
829 |
alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel |
830 |
dipole alignment with a positive g(1); this is in accordance with |
831 |
experimental dielectric measurements. Analysis of the molecular |
832 |
dynamics trajectories allows an assessment of why these molecules |
833 |
behave differently.}, |
834 |
annote = {376BF Times Cited:10 Cited References Count:16}, |
835 |
issn = {0267-8292}, |
836 |
uri = {<Go to ISI>://000165437800002}, |
837 |
} |
838 |
|
839 |
@ARTICLE{Cui2003, |
840 |
author = {B. X. Cui and M. Y. Shen and K. F. Freed}, |
841 |
title = {Folding and misfolding of the papillomavirus E6 interacting peptide |
842 |
E6ap}, |
843 |
journal = {Proceedings of the National Academy of Sciences of the United States |
844 |
of America}, |
845 |
year = {2003}, |
846 |
volume = {100}, |
847 |
pages = {7087-7092}, |
848 |
number = {12}, |
849 |
month = {Jun 10}, |
850 |
abstract = {All-atom Langevin dynamics simulations have been performed to study |
851 |
the folding pathways of the 18-residue binding domain fragment E6ap |
852 |
of the human papillomavirus E6 interacting peptide. Six independent |
853 |
folding trajectories, with a total duration of nearly 2 mus, all |
854 |
lead to the same native state in which the E6ap adopts a fluctuating |
855 |
a-helix structure in the central portion (Ser-4-Leu-13) but with |
856 |
very flexible N and C termini. Simulations starting from different |
857 |
core configurations exhibit the E6ap folding dynamics as either |
858 |
a two- or three-state folder with an intermediate misfolded state. |
859 |
The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13) |
860 |
is well conserved in the native-state structure but absent in the |
861 |
intermediate structure, suggesting that the leucine core is not |
862 |
only essential for the binding activity of E6ap but also important |
863 |
for the stability of the native structure. The free energy landscape |
864 |
reveals a significant barrier between the basins separating the |
865 |
native and misfolded states. We also discuss the various underlying |
866 |
forces that drive the peptide into its native state.}, |
867 |
annote = {689LC Times Cited:3 Cited References Count:48}, |
868 |
issn = {0027-8424}, |
869 |
uri = {<Go to ISI>://000183493500037}, |
870 |
} |
871 |
|
872 |
@ARTICLE{Denisov2003, |
873 |
author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou}, |
874 |
title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles}, |
875 |
journal = {Physical Review B}, |
876 |
year = {2003}, |
877 |
volume = {67}, |
878 |
pages = {-}, |
879 |
number = {1}, |
880 |
month = {Jan 1}, |
881 |
abstract = {We study the slow phase of thermally activated magnetic relaxation |
882 |
in finite two-dimensional ensembles of dipolar interacting ferromagnetic |
883 |
nanoparticles whose easy axes of magnetization are perpendicular |
884 |
to the distribution plane. We develop a method to numerically simulate |
885 |
the magnetic relaxation for the case that the smallest heights of |
886 |
the potential barriers between the equilibrium directions of the |
887 |
nanoparticle magnetic moments are much larger than the thermal energy. |
888 |
Within this framework, we analyze in detail the role that the correlations |
889 |
of the nanoparticle magnetic moments and the finite size of the |
890 |
nanoparticle ensemble play in magnetic relaxation.}, |
891 |
annote = {642XH Times Cited:11 Cited References Count:31}, |
892 |
issn = {1098-0121}, |
893 |
uri = {<Go to ISI>://000180830400056}, |
894 |
} |
895 |
|
896 |
@ARTICLE{Derreumaux1998, |
897 |
author = {P. Derreumaux and T. Schlick}, |
898 |
title = {The loop opening/closing motion of the enzyme triosephosphate isomerase}, |
899 |
journal = {Biophysical Journal}, |
900 |
year = {1998}, |
901 |
volume = {74}, |
902 |
pages = {72-81}, |
903 |
number = {1}, |
904 |
month = {Jan}, |
905 |
abstract = {To explore the origin of the large-scale motion of triosephosphate |
906 |
isomerase's flexible loop (residues 166 to 176) at the active site, |
907 |
several simulation protocols are employed both for the free enzyme |
908 |
in vacuo and for the free enzyme with some solvent modeling: high-temperature |
909 |
Langevin dynamics simulations, sampling by a #dynamics##driver# |
910 |
approach, and potential-energy surface calculations. Our focus is |
911 |
on obtaining the energy barrier to the enzyme's motion and establishing |
912 |
the nature of the loop movement. Previous calculations did not determine |
913 |
this energy barrier and the effect of solvent on the barrier. High-temperature |
914 |
molecular dynamics simulations and crystallographic studies have |
915 |
suggested a rigid-body motion with two hinges located at both ends |
916 |
of the loop; Brownian dynamics simulations at room temperature pointed |
917 |
to a very flexible behavior. The present simulations and analyses |
918 |
reveal that although solute/solvent hydrogen bonds play a crucial |
919 |
role in lowering the energy along the pathway, there still remains |
920 |
a high activation barrier, This finding clearly indicates that, |
921 |
if the loop opens and closes in the absence of a substrate at standard |
922 |
conditions (e.g., room temperature, appropriate concentration of |
923 |
isomerase), the time scale for transition is not in the nanosecond |
924 |
but rather the microsecond range. Our results also indicate that |
925 |
in the context of spontaneous opening in the free enzyme, the motion |
926 |
is of rigid-body type and that the specific interaction between |
927 |
residues Ala(176) and Tyr(208) plays a crucial role in the loop |
928 |
opening/closing mechanism.}, |
929 |
annote = {Zl046 Times Cited:30 Cited References Count:29}, |
930 |
issn = {0006-3495}, |
931 |
uri = {<Go to ISI>://000073393400009}, |
932 |
} |
933 |
|
934 |
@ARTICLE{Dullweber1997, |
935 |
author = {A. Dullweber and B. Leimkuhler and R. McLachlan}, |
936 |
title = {Symplectic splitting methods for rigid body molecular dynamics}, |
937 |
journal = {Journal of Chemical Physics}, |
938 |
year = {1997}, |
939 |
volume = {107}, |
940 |
pages = {5840-5851}, |
941 |
number = {15}, |
942 |
month = {Oct 15}, |
943 |
abstract = {Rigid body molecular models possess symplectic structure and time-reversal |
944 |
symmetry. Standard numerical integration methods destroy both properties, |
945 |
introducing nonphysical dynamical behavior such as numerically induced |
946 |
dissipative states and drift in the energy during long term simulations. |
947 |
This article describes the construction, implementation, and practical |
948 |
application of fast explicit symplectic-reversible integrators for |
949 |
multiple rigid body molecular simulations, These methods use a reduction |
950 |
to Euler equations for the free rigid body, together with a symplectic |
951 |
splitting technique. In every time step, the orientational dynamics |
952 |
of each rigid body is integrated by a sequence of planar rotations. |
953 |
Besides preserving the symplectic and reversible structures of the |
954 |
flow, this scheme accurately conserves the total angular momentum |
955 |
of a system of interacting rigid bodies. Excellent energy conservation |
956 |
fan be obtained relative to traditional methods, especially in long-time |
957 |
simulations. The method is implemented in a research code, ORIENT |
958 |
and compared with a quaternion/extrapolation scheme for the TIP4P |
959 |
model of water. Our experiments show that the symplectic-reversible |
960 |
scheme is far superior to the more traditional quaternion method. |
961 |
(C) 1997 American Institute of Physics.}, |
962 |
annote = {Ya587 Times Cited:35 Cited References Count:32}, |
963 |
issn = {0021-9606}, |
964 |
uri = {<Go to ISI>://A1997YA58700024}, |
965 |
} |
966 |
|
967 |
@ARTICLE{Edwards2005, |
968 |
author = {S. A. Edwards and D. R. M. Williams}, |
969 |
title = {Stretching a single diblock copolymer in a selective solvent: Langevin |
970 |
dynamics simulations}, |
971 |
journal = {Macromolecules}, |
972 |
year = {2005}, |
973 |
volume = {38}, |
974 |
pages = {10590-10595}, |
975 |
number = {25}, |
976 |
month = {Dec 13}, |
977 |
abstract = {Using the Langevin dynamics technique, we have carried out simulations |
978 |
of a single-chain flexible diblock copolymer. The polymer consists |
979 |
of two blocks of equal length, one very poorly solvated and the |
980 |
other close to theta-conditions. We study what happens when such |
981 |
a polymer is stretched, for a range of different stretching speeds, |
982 |
and correlate our observations with features in the plot of force |
983 |
vs extension. We find that at slow speeds this force profile does |
984 |
not increase monotonically, in disagreement with earlier predictions, |
985 |
and that at high speeds there is a strong dependence on which end |
986 |
of the polymer is pulled, as well as a high level of hysteresis.}, |
987 |
annote = {992EC Times Cited:0 Cited References Count:13}, |
988 |
issn = {0024-9297}, |
989 |
uri = {<Go to ISI>://000233866200035}, |
990 |
} |
991 |
|
992 |
@ARTICLE{Egberts1988, |
993 |
author = {E. Egberts and H. J. C. Berendsen}, |
994 |
title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic |
995 |
Detail}, |
996 |
journal = {Journal of Chemical Physics}, |
997 |
year = {1988}, |
998 |
volume = {89}, |
999 |
pages = {3718-3732}, |
1000 |
number = {6}, |
1001 |
month = {Sep 15}, |
1002 |
annote = {Q0188 Times Cited:219 Cited References Count:43}, |
1003 |
issn = {0021-9606}, |
1004 |
uri = {<Go to ISI>://A1988Q018800036}, |
1005 |
} |
1006 |
|
1007 |
@ARTICLE{Ermak1978, |
1008 |
author = {D. L. Ermak and J. A. Mccammon}, |
1009 |
title = {Brownian Dynamics with Hydrodynamic Interactions}, |
1010 |
journal = {Journal of Chemical Physics}, |
1011 |
year = {1978}, |
1012 |
volume = {69}, |
1013 |
pages = {1352-1360}, |
1014 |
number = {4}, |
1015 |
annote = {Fp216 Times Cited:785 Cited References Count:42}, |
1016 |
issn = {0021-9606}, |
1017 |
uri = {<Go to ISI>://A1978FP21600004}, |
1018 |
} |
1019 |
|
1020 |
@ARTICLE{Fennell2004, |
1021 |
author = {C. J. Fennell and J. D. Gezelter}, |
1022 |
title = {On the structural and transport properties of the soft sticky dipole |
1023 |
and related single-point water models}, |
1024 |
journal = {Journal of Chemical Physics}, |
1025 |
year = {2004}, |
1026 |
volume = {120}, |
1027 |
pages = {9175-9184}, |
1028 |
number = {19}, |
1029 |
month = {May 15}, |
1030 |
abstract = {The density maximum and temperature dependence of the self-diffusion |
1031 |
constant were investigated for the soft sticky dipole (SSD) water |
1032 |
model and two related reparametrizations of this single-point model. |
1033 |
A combination of microcanonical and isobaric-isothermal molecular |
1034 |
dynamics simulations was used to calculate these properties, both |
1035 |
with and without the use of reaction field to handle long-range |
1036 |
electrostatics. The isobaric-isothermal simulations of the melting |
1037 |
of both ice-I-h and ice-I-c showed a density maximum near 260 K. |
1038 |
In most cases, the use of the reaction field resulted in calculated |
1039 |
densities which were significantly lower than experimental densities. |
1040 |
Analysis of self-diffusion constants shows that the original SSD |
1041 |
model captures the transport properties of experimental water very |
1042 |
well in both the normal and supercooled liquid regimes. We also |
1043 |
present our reparametrized versions of SSD for use both with the |
1044 |
reaction field or without any long-range electrostatic corrections. |
1045 |
These are called the SSD/RF and SSD/E models, respectively. These |
1046 |
modified models were shown to maintain or improve upon the experimental |
1047 |
agreement with the structural and transport properties that can |
1048 |
be obtained with either the original SSD or the density-corrected |
1049 |
version of the original model (SSD1). Additionally, a novel low-density |
1050 |
ice structure is presented which appears to be the most stable ice |
1051 |
structure for the entire SSD family. (C) 2004 American Institute |
1052 |
of Physics.}, |
1053 |
annote = {816YY Times Cited:5 Cited References Count:39}, |
1054 |
issn = {0021-9606}, |
1055 |
uri = {<Go to ISI>://000221146400032}, |
1056 |
} |
1057 |
|
1058 |
@ARTICLE{Fernandes2002, |
1059 |
author = {M. X. Fernandes and J. G. {de la Torre}}, |
1060 |
title = {Brownian dynamics simulation of rigid particles of arbitrary shape |
1061 |
in external fields}, |
1062 |
journal = {Biophysical Journal}, |
1063 |
year = {2002}, |
1064 |
volume = {83}, |
1065 |
pages = {3039-3048}, |
1066 |
number = {6}, |
1067 |
month = {Dec}, |
1068 |
abstract = {We have developed a Brownian dynamics simulation algorithm to generate |
1069 |
Brownian trajectories of an isolated, rigid particle of arbitrary |
1070 |
shape in the presence of electric fields or any other external agents. |
1071 |
Starting from the generalized diffusion tensor, which can be calculated |
1072 |
with the existing HYDRO software, the new program BROWNRIG (including |
1073 |
a case-specific subprogram for the external agent) carries out a |
1074 |
simulation that is analyzed later to extract the observable dynamic |
1075 |
properties. We provide a variety of examples of utilization of this |
1076 |
method, which serve as tests of its performance, and also illustrate |
1077 |
its applicability. Examples include free diffusion, transport in |
1078 |
an electric field, and diffusion in a restricting environment.}, |
1079 |
annote = {633AD Times Cited:2 Cited References Count:43}, |
1080 |
issn = {0006-3495}, |
1081 |
uri = {<Go to ISI>://000180256300012}, |
1082 |
} |
1083 |
|
1084 |
@ARTICLE{Gay1981, |
1085 |
author = {J. G. Gay and B. J. Berne}, |
1086 |
title = {Modification of the Overlap Potential to Mimic a Linear Site-Site |
1087 |
Potential}, |
1088 |
journal = {Journal of Chemical Physics}, |
1089 |
year = {1981}, |
1090 |
volume = {74}, |
1091 |
pages = {3316-3319}, |
1092 |
number = {6}, |
1093 |
annote = {Lj347 Times Cited:482 Cited References Count:13}, |
1094 |
issn = {0021-9606}, |
1095 |
uri = {<Go to ISI>://A1981LJ34700029}, |
1096 |
} |
1097 |
|
1098 |
@ARTICLE{Gelin1999, |
1099 |
author = {M. F. Gelin}, |
1100 |
title = {Inertial effects in the Brownian dynamics with rigid constraints}, |
1101 |
journal = {Macromolecular Theory and Simulations}, |
1102 |
year = {1999}, |
1103 |
volume = {8}, |
1104 |
pages = {529-543}, |
1105 |
number = {6}, |
1106 |
month = {Nov}, |
1107 |
abstract = {To investigate the influence of inertial effects on the dynamics of |
1108 |
an assembly of beads subjected to rigid constraints and placed in |
1109 |
a buffer medium, a convenient method to introduce suitable generalized |
1110 |
coordinates is presented. Without any restriction on the nature |
1111 |
of the soft forces involved (both stochastic and deterministic), |
1112 |
pertinent Langevin equations are derived. Provided that the Brownian |
1113 |
forces are Gaussian and Markovian, the corresponding Fokker-Planck |
1114 |
equation (FPE) is obtained in the complete phase space of generalized |
1115 |
coordinates and momenta. The correct short time behavior for correlation |
1116 |
functions (CFs) of generalized coordinates is established, and the |
1117 |
diffusion equation with memory (DEM) is deduced from the FPE in |
1118 |
the high friction Limit. The DEM is invoked to perform illustrative |
1119 |
calculations in two dimensions of the orientational CFs for once |
1120 |
broken nonrigid rods immobilized on a surface. These calculations |
1121 |
reveal that the CFs under certain conditions exhibit an oscillatory |
1122 |
behavior, which is irreproducible within the standard diffusion |
1123 |
equation. Several methods are considered for the approximate solution |
1124 |
of the DEM, and their application to three dimensional DEMs is discussed.}, |
1125 |
annote = {257MM Times Cited:2 Cited References Count:82}, |
1126 |
issn = {1022-1344}, |
1127 |
uri = {<Go to ISI>://000083785700002}, |
1128 |
} |
1129 |
|
1130 |
@BOOK{Goldstein2001, |
1131 |
title = {Classical Mechanics}, |
1132 |
publisher = {Addison Wesley}, |
1133 |
year = {2001}, |
1134 |
author = {H. Goldstein and C. Poole and J. Safko}, |
1135 |
address = {San Francisco}, |
1136 |
edition = {3rd}, |
1137 |
} |
1138 |
|
1139 |
@ARTICLE{Gray2003, |
1140 |
author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and |
1141 |
B. Kuhlman and C. A. Rohl and D. Baker}, |
1142 |
title = {Protein-protein docking with simultaneous optimization of rigid-body |
1143 |
displacement and side-chain conformations}, |
1144 |
journal = {Journal of Molecular Biology}, |
1145 |
year = {2003}, |
1146 |
volume = {331}, |
1147 |
pages = {281-299}, |
1148 |
number = {1}, |
1149 |
month = {Aug 1}, |
1150 |
abstract = {Protein-protein docking algorithms provide a means to elucidate structural |
1151 |
details for presently unknown complexes. Here, we present and evaluate |
1152 |
a new method to predict protein-protein complexes from the coordinates |
1153 |
of the unbound monomer components. The method employs a low-resolution, |
1154 |
rigid-body, Monte Carlo search followed by simultaneous optimization |
1155 |
of backbone displacement and side-chain conformations using Monte |
1156 |
Carlo minimization. Up to 10(5) independent simulations are carried |
1157 |
out, and the resulting #decoys# are ranked using an energy function |
1158 |
dominated by van der Waals interactions, an implicit solvation model, |
1159 |
and an orientation-dependent hydrogen bonding potential. Top-ranking |
1160 |
decoys are clustered to select the final predictions. Small-perturbation |
1161 |
studies reveal the formation of binding funnels in 42 of 54 cases |
1162 |
using coordinates derived from the bound complexes and in 32 of |
1163 |
54 cases using independently determined coordinates of one or both |
1164 |
monomers. Experimental binding affinities correlate with the calculated |
1165 |
score function and explain the predictive success or failure of |
1166 |
many targets. Global searches using one or both unbound components |
1167 |
predict at least 25% of the native residue-residue contacts in 28 |
1168 |
of the 32 cases where binding funnels exist. The results suggest |
1169 |
that the method may soon be useful for generating models of biologically |
1170 |
important complexes from the structures of the isolated components, |
1171 |
but they also highlight the challenges that must be met to achieve |
1172 |
consistent and accurate prediction of protein-protein interactions. |
1173 |
(C) 2003 Elsevier Ltd. All rights reserved.}, |
1174 |
annote = {704QL Times Cited:48 Cited References Count:60}, |
1175 |
issn = {0022-2836}, |
1176 |
uri = {<Go to ISI>://000184351300022}, |
1177 |
} |
1178 |
|
1179 |
@ARTICLE{Greengard1994, |
1180 |
author = {L. Greengard}, |
1181 |
title = {Fast Algorithms for Classical Physics}, |
1182 |
journal = {Science}, |
1183 |
year = {1994}, |
1184 |
volume = {265}, |
1185 |
pages = {909-914}, |
1186 |
number = {5174}, |
1187 |
month = {Aug 12}, |
1188 |
abstract = {Some of the recently developed fast summation methods that have arisen |
1189 |
in scientific computing are described. These methods require an |
1190 |
amount of work proportional to N or N log N to evaluate all pairwise |
1191 |
interactions in an ensemble of N particles. Traditional methods, |
1192 |
by contrast, require an amount of work proportional to N-2. AS a |
1193 |
result, large-scale simulations can be carried out using only modest |
1194 |
computer resources. In combination with supercomputers, it is possible |
1195 |
to address questions that were previously out of reach. Problems |
1196 |
from diffusion, gravitation, and wave propagation are considered.}, |
1197 |
annote = {Pb499 Times Cited:99 Cited References Count:44}, |
1198 |
issn = {0036-8075}, |
1199 |
uri = {<Go to ISI>://A1994PB49900031}, |
1200 |
} |
1201 |
|
1202 |
@ARTICLE{Greengard1987, |
1203 |
author = {L. Greengard and V. Rokhlin}, |
1204 |
title = {A Fast Algorithm for Particle Simulations}, |
1205 |
journal = {Journal of Computational Physics}, |
1206 |
year = {1987}, |
1207 |
volume = {73}, |
1208 |
pages = {325-348}, |
1209 |
number = {2}, |
1210 |
month = {Dec}, |
1211 |
annote = {L0498 Times Cited:899 Cited References Count:7}, |
1212 |
issn = {0021-9991}, |
1213 |
uri = {<Go to ISI>://A1987L049800006}, |
1214 |
} |
1215 |
|
1216 |
@ARTICLE{Hairer1997, |
1217 |
author = {E. Hairer and C. Lubich}, |
1218 |
title = {The life-span of backward error analysis for numerical integrators}, |
1219 |
journal = {Numerische Mathematik}, |
1220 |
year = {1997}, |
1221 |
volume = {76}, |
1222 |
pages = {441-462}, |
1223 |
number = {4}, |
1224 |
month = {Jun}, |
1225 |
abstract = {Backward error analysis is a useful tool for the study of numerical |
1226 |
approximations to ordinary differential equations. The numerical |
1227 |
solution is formally interpreted as the exact solution of a perturbed |
1228 |
differential equation, given as a formal and usually divergent series |
1229 |
in powers of the step size. For a rigorous analysis, this series |
1230 |
has to be truncated. In this article we study the influence of this |
1231 |
truncation to the difference between the numerical solution and |
1232 |
the exact solution of the perturbed differential equation. Results |
1233 |
on the long-time behaviour of numerical solutions are obtained in |
1234 |
this way. We present applications to the numerical phase portrait |
1235 |
near hyperbolic equilibrium points, to asymptotically stable periodic |
1236 |
orbits and Hopf bifurcation, and to energy conservation and approximation |
1237 |
of invariant tori in Hamiltonian systems.}, |
1238 |
annote = {Xj488 Times Cited:50 Cited References Count:19}, |
1239 |
issn = {0029-599X}, |
1240 |
uri = {<Go to ISI>://A1997XJ48800002}, |
1241 |
} |
1242 |
|
1243 |
@ARTICLE{Hao1993, |
1244 |
author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga}, |
1245 |
title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic |
1246 |
Trypsin-Inhibitor Studied by Computer-Simulations}, |
1247 |
journal = {Biochemistry}, |
1248 |
year = {1993}, |
1249 |
volume = {32}, |
1250 |
pages = {9614-9631}, |
1251 |
number = {37}, |
1252 |
month = {Sep 21}, |
1253 |
abstract = {A new procedure for studying the folding and unfolding of proteins, |
1254 |
with an application to bovine pancreatic trypsin inhibitor (BPTI), |
1255 |
is reported. The unfolding and refolding of the native structure |
1256 |
of the protein are characterized by the dimensions of the protein, |
1257 |
expressed in terms of the three principal radii of the structure |
1258 |
considered as an ellipsoid. A dynamic equation, describing the variations |
1259 |
of the principal radii on the unfolding path, and a numerical procedure |
1260 |
to solve this equation are proposed. Expanded and distorted conformations |
1261 |
are refolded to the native structure by a dimensional-constraint |
1262 |
energy minimization procedure. A unique and reproducible unfolding |
1263 |
pathway for an intermediate of BPTI lacking the [30,51] disulfide |
1264 |
bond is obtained. The resulting unfolded conformations are extended; |
1265 |
they contain near-native local structure, but their longest principal |
1266 |
radii are more than 2.5 times greater than that of the native structure. |
1267 |
The most interesting finding is that the majority of expanded conformations, |
1268 |
generated under various conditions, can be refolded closely to the |
1269 |
native structure, as measured by the correct overall chain fold, |
1270 |
by the rms deviations from the native structure of only 1.9-3.1 |
1271 |
angstrom, and by the energy differences of about 10 kcal/mol from |
1272 |
the native structure. Introduction of the [30,51] disulfide bond |
1273 |
at this stage, followed by minimization, improves the closeness |
1274 |
of the refolded structures to the native structure, reducing the |
1275 |
rms deviations to 0.9-2.0 angstrom. The unique refolding of these |
1276 |
expanded structures over such a large conformational space implies |
1277 |
that the folding is strongly dictated by the interactions in the |
1278 |
amino acid sequence of BPTI. The simulations indicate that, under |
1279 |
conditions that favor a compact structure as mimicked by the volume |
1280 |
constraints in our algorithm; the expanded conformations have a |
1281 |
strong tendency to move toward the native structure; therefore, |
1282 |
they probably would be favorable folding intermediates. The results |
1283 |
presented here support a general model for protein folding, i.e., |
1284 |
progressive formation of partially folded structural units, followed |
1285 |
by collapse to the compact native structure. The general applicability |
1286 |
of the procedure is also discussed.}, |
1287 |
annote = {Ly294 Times Cited:27 Cited References Count:57}, |
1288 |
issn = {0006-2960}, |
1289 |
uri = {<Go to ISI>://A1993LY29400014}, |
1290 |
} |
1291 |
|
1292 |
@ARTICLE{Hinsen2000, |
1293 |
author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel |
1294 |
and G. R. Kneller}, |
1295 |
title = {Harmonicity in slow protein dynamics}, |
1296 |
journal = {Chemical Physics}, |
1297 |
year = {2000}, |
1298 |
volume = {261}, |
1299 |
pages = {25-37}, |
1300 |
number = {1-2}, |
1301 |
month = {Nov 1}, |
1302 |
abstract = {The slow dynamics of proteins around its native folded state is usually |
1303 |
described by diffusion in a strongly anharmonic potential. In this |
1304 |
paper, we try to understand the form and origin of the anharmonicities, |
1305 |
with the principal aim of gaining a better understanding of the |
1306 |
principal motion types, but also in order to develop more efficient |
1307 |
numerical methods for simulating neutron scattering spectra of large |
1308 |
proteins. First, we decompose a molecular dynamics (MD) trajectory |
1309 |
of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water |
1310 |
into three contributions that we expect to be independent: the global |
1311 |
motion of the residues, the rigid-body motion of the sidechains |
1312 |
relative to the backbone, and the internal deformations of the sidechains. |
1313 |
We show that they are indeed almost independent by verifying the |
1314 |
factorization of the incoherent intermediate scattering function. |
1315 |
Then, we show that the global residue motions, which include all |
1316 |
large-scale backbone motions, can be reproduced by a simple harmonic |
1317 |
model which contains two contributions: a short-time vibrational |
1318 |
term, described by a standard normal mode calculation in a local |
1319 |
minimum, and a long-time diffusive term, described by Brownian motion |
1320 |
in an effective harmonic potential. The potential and the friction |
1321 |
constants were fitted to the MD data. The major anharmonic contribution |
1322 |
to the incoherent intermediate scattering function comes from the |
1323 |
rigid-body diffusion of the sidechains. This model can be used to |
1324 |
calculate scattering functions for large proteins and for long-time |
1325 |
scales very efficiently, and thus provides a useful complement to |
1326 |
MD simulations, which are best suited for detailed studies on smaller |
1327 |
systems or for shorter time scales. (C) 2000 Elsevier Science B.V. |
1328 |
All rights reserved.}, |
1329 |
annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31}, |
1330 |
issn = {0301-0104}, |
1331 |
uri = {<Go to ISI>://000090121700003}, |
1332 |
} |
1333 |
|
1334 |
@ARTICLE{Ho1992, |
1335 |
author = {C. Ho and C. D. Stubbs}, |
1336 |
title = {Hydration at the Membrane Protein-Lipid Interface}, |
1337 |
journal = {Biophysical Journal}, |
1338 |
year = {1992}, |
1339 |
volume = {63}, |
1340 |
pages = {897-902}, |
1341 |
number = {4}, |
1342 |
month = {Oct}, |
1343 |
abstract = {Evidence has been found for the existence water at the protein-lipid |
1344 |
hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome |
1345 |
C, using two related fluorescence spectroscopic approaches. The |
1346 |
first approach exploited the fact that the presence of water in |
1347 |
the excited state solvent cage of a fluorophore increases the rate |
1348 |
of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl) |
1349 |
phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores |
1350 |
are located in the hydrophobic core of the lipid bilayer, the introduction |
1351 |
of gramicidin reduced the fluorescence lifetime, indicative of an |
1352 |
increased presence of water in the bilayer. Since a high protein:lipid |
1353 |
ratio was used, the fluorophores were forced to be adjacent to the |
1354 |
protein hydrophobic surface, hence the presence of water in this |
1355 |
region could be inferred. Cholesterol is known to reduce the water |
1356 |
content of lipid bilayers and this effect was maintained at the |
1357 |
protein-lipid interface with both gramicidin and apocytochrome C, |
1358 |
again suggesting hydration in this region. The second approach was |
1359 |
to use the fluorescence enhancement induced by exchanging deuterium |
1360 |
oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH, |
1361 |
located in the lipid head group region, and of the gramicidin intrinsic |
1362 |
tryptophans were greater in a D2O buffer compared with H2O, showing |
1363 |
that the fluorophores were exposed to water in the bilayer at the |
1364 |
protein-lipid interface. In the presence of cholesterol the fluorescence |
1365 |
intensity ratio of D2O to H2O decreased, indicating a removal of |
1366 |
water by the cholesterol, in keeping with the lifetime data. Altered |
1367 |
hydration at the protein-lipid interface could affect conformation, |
1368 |
thereby offering a new route by which membrane protein functioning |
1369 |
may be modified.}, |
1370 |
annote = {Ju251 Times Cited:55 Cited References Count:44}, |
1371 |
issn = {0006-3495}, |
1372 |
uri = {<Go to ISI>://A1992JU25100002}, |
1373 |
} |
1374 |
|
1375 |
@BOOK{Hockney1981, |
1376 |
title = {Computer Simulation Using Particles}, |
1377 |
publisher = {McGraw-Hill}, |
1378 |
year = {1981}, |
1379 |
author = {R.W. Hockney and J.W. Eastwood}, |
1380 |
address = {New York}, |
1381 |
} |
1382 |
|
1383 |
@ARTICLE{Huh2004, |
1384 |
author = {Y. Huh and N. M. Cann}, |
1385 |
title = {Discrimination in isotropic, nematic, and smectic phases of chiral |
1386 |
calamitic molecules: A computer simulation study}, |
1387 |
journal = {Journal of Chemical Physics}, |
1388 |
year = {2004}, |
1389 |
volume = {121}, |
1390 |
pages = {10299-10308}, |
1391 |
number = {20}, |
1392 |
month = {Nov 22}, |
1393 |
abstract = {Racemic fluids of chiral calamitic molecules are investigated with |
1394 |
molecular dynamics simulations. In particular, the phase behavior |
1395 |
as a function of density is examined for eight racemates. The relationship |
1396 |
between chiral discrimination and orientational order in the phase |
1397 |
is explored. We find that the transition from the isotropic phase |
1398 |
to a liquid crystal phase is accompanied by an increase in chiral |
1399 |
discrimination, as measured by differences in radial distributions. |
1400 |
Among ordered phases, discrimination is largest for smectic phases |
1401 |
with a significant preference for heterochiral contact within the |
1402 |
layers. (C) 2004 American Institute of Physics.}, |
1403 |
annote = {870FJ Times Cited:0 Cited References Count:63}, |
1404 |
issn = {0021-9606}, |
1405 |
uri = {<Go to ISI>://000225042700059}, |
1406 |
} |
1407 |
|
1408 |
@ARTICLE{Izaguirre2001, |
1409 |
author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel}, |
1410 |
title = {Langevin stabilization of molecular dynamics}, |
1411 |
journal = {Journal of Chemical Physics}, |
1412 |
year = {2001}, |
1413 |
volume = {114}, |
1414 |
pages = {2090-2098}, |
1415 |
number = {5}, |
1416 |
month = {Feb 1}, |
1417 |
abstract = {In this paper we show the possibility of using very mild stochastic |
1418 |
damping to stabilize long time step integrators for Newtonian molecular |
1419 |
dynamics. More specifically, stable and accurate integrations are |
1420 |
obtained for damping coefficients that are only a few percent of |
1421 |
the natural decay rate of processes of interest, such as the velocity |
1422 |
autocorrelation function. Two new multiple time stepping integrators, |
1423 |
Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are |
1424 |
introduced in this paper. Both use the mollified impulse method |
1425 |
for the Newtonian term. LM uses a discretization of the Langevin |
1426 |
equation that is exact for the constant force, and BBK-M uses the |
1427 |
popular Brunger-Brooks-Karplus integrator (BBK). These integrators, |
1428 |
along with an extrapolative method called LN, are evaluated across |
1429 |
a wide range of damping coefficient values. When large damping coefficients |
1430 |
are used, as one would for the implicit modeling of solvent molecules, |
1431 |
the method LN is superior, with LM closely following. However, with |
1432 |
mild damping of 0.2 ps(-1), LM produces the best results, allowing |
1433 |
long time steps of 14 fs in simulations containing explicitly modeled |
1434 |
flexible water. With BBK-M and the same damping coefficient, time |
1435 |
steps of 12 fs are possible for the same system. Similar results |
1436 |
are obtained for a solvated protein-DNA simulation of estrogen receptor |
1437 |
ER with estrogen response element ERE. A parallel version of BBK-M |
1438 |
runs nearly three times faster than the Verlet-I/r-RESPA (reversible |
1439 |
reference system propagator algorithm) when using the largest stable |
1440 |
time step on each one, and it also parallelizes well. The computation |
1441 |
of diffusion coefficients for flexible water and ER/ERE shows that |
1442 |
when mild damping of up to 0.2 ps-1 is used the dynamics are not |
1443 |
significantly distorted. (C) 2001 American Institute of Physics.}, |
1444 |
annote = {397CQ Times Cited:14 Cited References Count:36}, |
1445 |
issn = {0021-9606}, |
1446 |
uri = {<Go to ISI>://000166676100020}, |
1447 |
} |
1448 |
|
1449 |
@ARTICLE{Torre1977, |
1450 |
author = {Jose Garcia De La Torre, V.A. Bloomfield}, |
1451 |
title = {Hydrodynamic properties of macromolecular complexes. I. Translation}, |
1452 |
journal = {Biopolymers}, |
1453 |
year = {1977}, |
1454 |
volume = {16}, |
1455 |
pages = {1747-1763}, |
1456 |
} |
1457 |
|
1458 |
@ARTICLE{Kane2000, |
1459 |
author = {C. Kane and J. E. Marsden and M. Ortiz and M. West}, |
1460 |
title = {Variational integrators and the Newmark algorithm for conservative |
1461 |
and dissipative mechanical systems}, |
1462 |
journal = {International Journal for Numerical Methods in Engineering}, |
1463 |
year = {2000}, |
1464 |
volume = {49}, |
1465 |
pages = {1295-1325}, |
1466 |
number = {10}, |
1467 |
month = {Dec 10}, |
1468 |
abstract = {The purpose of this work is twofold. First, we demonstrate analytically |
1469 |
that the classical Newmark family as well as related integration |
1470 |
algorithms are variational in the sense of the Veselov formulation |
1471 |
of discrete mechanics. Such variational algorithms are well known |
1472 |
to be symplectic and momentum preserving and to often have excellent |
1473 |
global energy behaviour. This analytical result is verified through |
1474 |
numerical examples and is believed to be one of the primary reasons |
1475 |
that this class of algorithms performs so well. Second, we develop |
1476 |
algorithms for mechanical systems with forcing, and in particular, |
1477 |
for dissipative systems. In this case, we develop integrators that |
1478 |
are based on a discretization of the Lagrange d'Alembert principle |
1479 |
as well as on a variational formulation of dissipation. It is demonstrated |
1480 |
that these types of structured integrators have good numerical behaviour |
1481 |
in terms of obtaining the correct amounts by which the energy changes |
1482 |
over the integration run. Copyright (C) 2000 John Wiley & Sons, |
1483 |
Ltd.}, |
1484 |
annote = {373CJ Times Cited:30 Cited References Count:41}, |
1485 |
issn = {0029-5981}, |
1486 |
uri = {<Go to ISI>://000165270600004}, |
1487 |
} |
1488 |
|
1489 |
@ARTICLE{Klimov1997, |
1490 |
author = {D. K. Klimov and D. Thirumalai}, |
1491 |
title = {Viscosity dependence of the folding rates of proteins}, |
1492 |
journal = {Physical Review Letters}, |
1493 |
year = {1997}, |
1494 |
volume = {79}, |
1495 |
pages = {317-320}, |
1496 |
number = {2}, |
1497 |
month = {Jul 14}, |
1498 |
abstract = {The viscosity (eta) dependence of the folding rates for four sequences |
1499 |
(the native state of three sequences is a beta sheet, while the |
1500 |
fourth forms an alpha helix) is calculated for off-lattice models |
1501 |
of proteins. Assuming that the dynamics is given by the Langevin |
1502 |
equation, we show that the folding rates increase linearly at low |
1503 |
viscosities eta, decrease as 1/eta at large eta, and have a maximum |
1504 |
at intermediate values. The Kramers' theory of barrier crossing |
1505 |
provides a quantitative fit of the numerical results. By mapping |
1506 |
the simulation results to real proteins we estimate that for optimized |
1507 |
sequences the time scale for forming a four turn alpha-helix topology |
1508 |
is about 500 ns, whereas for beta sheet it is about 10 mu s.}, |
1509 |
annote = {Xk293 Times Cited:77 Cited References Count:17}, |
1510 |
issn = {0031-9007}, |
1511 |
uri = {<Go to ISI>://A1997XK29300035}, |
1512 |
} |
1513 |
|
1514 |
@ARTICLE{Kol1997, |
1515 |
author = {A. Kol and B. B. Laird and B. J. Leimkuhler}, |
1516 |
title = {A symplectic method for rigid-body molecular simulation}, |
1517 |
journal = {Journal of Chemical Physics}, |
1518 |
year = {1997}, |
1519 |
volume = {107}, |
1520 |
pages = {2580-2588}, |
1521 |
number = {7}, |
1522 |
month = {Aug 15}, |
1523 |
abstract = {Rigid-body molecular dynamics simulations typically are performed |
1524 |
in a quaternion representation. The nonseparable form of the Hamiltonian |
1525 |
in quaternions prevents the use of a standard leapfrog (Verlet) |
1526 |
integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation |
1527 |
methods are generally used, This is unfortunate since symplectic |
1528 |
methods like Verlet exhibit superior energy conservation in long-time |
1529 |
integrations. In this article, we describe an alternative method, |
1530 |
which we call RSHAKE (for rotation-SHAKE), in which the entire rotation |
1531 |
matrix is evolved (using the scheme of McLachlan and Scovel [J. |
1532 |
Nonlin. Sci, 16 233 (1995)]) in tandem with the particle positions. |
1533 |
We employ a fast approximate Newton solver to preserve the orthogonality |
1534 |
of the rotation matrix. We test our method on a system of soft-sphere |
1535 |
dipoles and compare with quaternion evolution using a 4th-order |
1536 |
predictor-corrector integrator, Although the short-time error of |
1537 |
the quaternion algorithm is smaller for fixed time step than that |
1538 |
for RSHAKE, the quaternion scheme exhibits an energy drift which |
1539 |
is not observed in simulations with RSHAKE, hence a fixed energy |
1540 |
tolerance can be achieved by using a larger time step, The superiority |
1541 |
of RSHAKE increases with system size. (C) 1997 American Institute |
1542 |
of Physics.}, |
1543 |
annote = {Xq332 Times Cited:11 Cited References Count:18}, |
1544 |
issn = {0021-9606}, |
1545 |
uri = {<Go to ISI>://A1997XQ33200046}, |
1546 |
} |
1547 |
|
1548 |
@ARTICLE{Lansac2001, |
1549 |
author = {Y. Lansac and M. A. Glaser and N. A. Clark}, |
1550 |
title = {Microscopic structure and dynamics of a partial bilayer smectic liquid |
1551 |
crystal}, |
1552 |
journal = {Physical Review E}, |
1553 |
year = {2001}, |
1554 |
volume = {6405}, |
1555 |
pages = {-}, |
1556 |
number = {5}, |
1557 |
month = {Nov}, |
1558 |
abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied |
1559 |
class of mesogens. Many of the peculiar properties of nCB's (e.g., |
1560 |
the occurence of the partial bilayer smectic-A(d) phase) are thought |
1561 |
to be a manifestation of short-range antiparallel association of |
1562 |
neighboring molecules, resulting from strong dipole-dipole interactions |
1563 |
between cyano groups. To test and extend existing models of microscopic |
1564 |
ordering in nCB's, we carry out large-scale atomistic simulation |
1565 |
studies of the microscopic structure and dynamics of the Sm-A(d) |
1566 |
phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of |
1567 |
thermodynamic, structural, and dynamical properties for this material, |
1568 |
and make a detailed comparison of our results with experimental |
1569 |
measurements in order to validate our molecular model. Semiquantitative |
1570 |
agreement with experiment is found: the smectic layer spacing and |
1571 |
mass density are well reproduced, translational diffusion constants |
1572 |
are similar to experiment, but the orientational ordering of alkyl |
1573 |
chains is overestimated. This simulation provides a detailed picture |
1574 |
of molecular conformation, smectic layer structure, and intermolecular |
1575 |
correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range |
1576 |
antiparallel association of molecules arising from dipole-dipole |
1577 |
interactions plays a dominant role in determining the molecular-scale |
1578 |
structure of 8CB.}, |
1579 |
annote = {Part 1 496QF Times Cited:10 Cited References Count:60}, |
1580 |
issn = {1063-651X}, |
1581 |
uri = {<Go to ISI>://000172406900063}, |
1582 |
} |
1583 |
|
1584 |
@ARTICLE{Lansac2003, |
1585 |
author = {Y. Lansac and P. K. Maiti and N. A. Clark and M. A. Glaser}, |
1586 |
title = {Phase behavior of bent-core molecules}, |
1587 |
journal = {Physical Review E}, |
1588 |
year = {2003}, |
1589 |
volume = {67}, |
1590 |
pages = {-}, |
1591 |
number = {1}, |
1592 |
month = {Jan}, |
1593 |
abstract = {Recently, a new class of smectic liquid crystal phases characterized |
1594 |
by the spontaneous formation of macroscopic chiral domains from |
1595 |
achiral bent-core molecules has been discovered. We have carried |
1596 |
out Monte Carlo simulations of a minimal hard spherocylinder dimer |
1597 |
model to investigate the role of excluded volume interactions in |
1598 |
determining the phase behavior of bent-core materials and to probe |
1599 |
the molecular origins of polar and chiral symmetry breaking. We |
1600 |
present the phase diagram of hard spherocylinder dimers of length-diameter |
1601 |
ratio of 5 as a function of pressure or density and dimer opening |
1602 |
angle psi. With decreasing psi, a transition from a nonpolar to |
1603 |
a polar smectic A phase is observed near psi=167degrees, and the |
1604 |
nematic phase becomes thermodynamically unstable for psi<135degrees. |
1605 |
Free energy calculations indicate that the antipolar smectic A (SmAP(A)) |
1606 |
phase is more stable than the polar smectic A phase (SmAP(F)). No |
1607 |
chiral smectic or biaxial nematic phases were found.}, |
1608 |
annote = {Part 1 646CM Times Cited:15 Cited References Count:38}, |
1609 |
issn = {1063-651X}, |
1610 |
uri = {<Go to ISI>://000181017300042}, |
1611 |
} |
1612 |
|
1613 |
@BOOK{Leach2001, |
1614 |
title = {Molecular Modeling: Principles and Applications}, |
1615 |
publisher = {Pearson Educated Limited}, |
1616 |
year = {2001}, |
1617 |
author = {A. Leach}, |
1618 |
address = {Harlow, England}, |
1619 |
edition = {2nd}, |
1620 |
} |
1621 |
|
1622 |
@ARTICLE{Leimkuhler1999, |
1623 |
author = {B. Leimkuhler}, |
1624 |
title = {Reversible adaptive regularization: perturbed Kepler motion and classical |
1625 |
atomic trajectories}, |
1626 |
journal = {Philosophical Transactions of the Royal Society of London Series |
1627 |
a-Mathematical Physical and Engineering Sciences}, |
1628 |
year = {1999}, |
1629 |
volume = {357}, |
1630 |
pages = {1101-1133}, |
1631 |
number = {1754}, |
1632 |
month = {Apr 15}, |
1633 |
abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel |
1634 |
regularization and modified Sundman transformations are applied |
1635 |
to simulate general perturbed Kepler motion and to compute classical |
1636 |
trajectories of atomic systems (e.g. Rydberg atoms). The new family |
1637 |
of reversible adaptive regularization methods also conserves angular |
1638 |
momentum and exhibits superior energy conservation and numerical |
1639 |
stability in long-time integrations. The schemes are appropriate |
1640 |
for scattering, for astronomical calculations of escape time and |
1641 |
long-term stability, and for classical and semiclassical studies |
1642 |
of atomic dynamics. The components of an algorithm for trajectory |
1643 |
calculations are described. Numerical experiments illustrate the |
1644 |
effectiveness of the reversible approach.}, |
1645 |
annote = {199EE Times Cited:11 Cited References Count:48}, |
1646 |
issn = {1364-503X}, |
1647 |
uri = {<Go to ISI>://000080466800007}, |
1648 |
} |
1649 |
|
1650 |
@BOOK{Leimkuhler2004, |
1651 |
title = {Simulating Hamiltonian Dynamics}, |
1652 |
publisher = {Cambridge University Press}, |
1653 |
year = {2004}, |
1654 |
author = {B. Leimkuhler and S. Reich}, |
1655 |
address = {Cambridge}, |
1656 |
} |
1657 |
|
1658 |
@ARTICLE{Levelut1981, |
1659 |
author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard |
1660 |
and G. Sigaud}, |
1661 |
title = {Number of Sa Phases}, |
1662 |
journal = {Physical Review A}, |
1663 |
year = {1981}, |
1664 |
volume = {24}, |
1665 |
pages = {2180-2186}, |
1666 |
number = {4}, |
1667 |
annote = {Ml751 Times Cited:96 Cited References Count:16}, |
1668 |
issn = {1050-2947}, |
1669 |
uri = {<Go to ISI>://A1981ML75100057}, |
1670 |
} |
1671 |
|
1672 |
@ARTICLE{Lieb1982, |
1673 |
author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn}, |
1674 |
title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - |
1675 |
Evidence from Raman-Scattering}, |
1676 |
journal = {Biochimica Et Biophysica Acta}, |
1677 |
year = {1982}, |
1678 |
volume = {688}, |
1679 |
pages = {388-398}, |
1680 |
number = {2}, |
1681 |
annote = {Nu461 Times Cited:40 Cited References Count:28}, |
1682 |
issn = {0006-3002}, |
1683 |
uri = {<Go to ISI>://A1982NU46100012}, |
1684 |
} |
1685 |
|
1686 |
@ARTICLE{Link1997, |
1687 |
author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A. |
1688 |
Clark and E. Korblova and D. M. Walba}, |
1689 |
title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic |
1690 |
phase of achiral molecules}, |
1691 |
journal = {Science}, |
1692 |
year = {1997}, |
1693 |
volume = {278}, |
1694 |
pages = {1924-1927}, |
1695 |
number = {5345}, |
1696 |
month = {Dec 12}, |
1697 |
abstract = {A smectic liquid-crystal phase made from achiral molecules with bent |
1698 |
cores was found to have fluid layers that exhibit two spontaneous |
1699 |
symmetry-breaking instabilities: polar molecular orientational ordering |
1700 |
about the layer normal and molecular tilt. These instabilities combine |
1701 |
to form a chiral layer structure with a handedness that depends |
1702 |
on the sign of the tilt. The bulk states are either antiferroelectric-racemic, |
1703 |
with the layer polar direction and handedness alternating in sign |
1704 |
from layer to layer, or antiferroelectric-chiral, which is of uniform |
1705 |
layer handedness. Both states exhibit an electric field-induced |
1706 |
transition from antiferroelectric to ferroelectric.}, |
1707 |
annote = {Yl002 Times Cited:407 Cited References Count:25}, |
1708 |
issn = {0036-8075}, |
1709 |
uri = {<Go to ISI>://A1997YL00200028}, |
1710 |
} |
1711 |
|
1712 |
@ARTICLE{Liwo2005, |
1713 |
author = {A. Liwo and M. Khalili and H. A. Scheraga}, |
1714 |
title = {Ab initio simulations of protein folding pathways by molecular dynamics |
1715 |
with the united-residue (UNRES) model of polypeptide chains}, |
1716 |
journal = {Febs Journal}, |
1717 |
year = {2005}, |
1718 |
volume = {272}, |
1719 |
pages = {359-360}, |
1720 |
month = {Jul}, |
1721 |
annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0}, |
1722 |
issn = {1742-464X}, |
1723 |
uri = {<Go to ISI>://000234826102043}, |
1724 |
} |
1725 |
|
1726 |
@ARTICLE{Luty1994, |
1727 |
author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren}, |
1728 |
title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods |
1729 |
for Calculating Electrostatic Interactions in Periodic Molecular-Systems}, |
1730 |
journal = {Molecular Simulation}, |
1731 |
year = {1994}, |
1732 |
volume = {14}, |
1733 |
pages = {11-20}, |
1734 |
number = {1}, |
1735 |
abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods |
1736 |
for calculating electrostatic interactions in periodic molecular |
1737 |
systems. A brief comparison of the theories shows that the methods |
1738 |
are very similar differing mainly in the technique which is used |
1739 |
to perform the ''k-space'' or mesh calculation. Because the PPPM |
1740 |
utilizes the highly efficient numerical Fast Fourier Transform (FFT) |
1741 |
method it requires significantly less computational effort than |
1742 |
the Ewald method and scale's almost linearly with system size.}, |
1743 |
annote = {Qf464 Times Cited:50 Cited References Count:20}, |
1744 |
issn = {0892-7022}, |
1745 |
uri = {<Go to ISI>://A1994QF46400002}, |
1746 |
} |
1747 |
|
1748 |
@BOOK{Marion1990, |
1749 |
title = {Classical Dynamics of Particles and Systems}, |
1750 |
publisher = {Academic Press}, |
1751 |
year = {1990}, |
1752 |
author = {J.~B. Marion}, |
1753 |
address = {New York}, |
1754 |
edition = {2rd}, |
1755 |
} |
1756 |
|
1757 |
@ARTICLE{Marsden1998, |
1758 |
author = {J. E. Marsden and G. W. Patrick and S. Shkoller}, |
1759 |
title = {Multisymplectic geometry, variational integrators, and nonlinear |
1760 |
PDEs}, |
1761 |
journal = {Communications in Mathematical Physics}, |
1762 |
year = {1998}, |
1763 |
volume = {199}, |
1764 |
pages = {351-395}, |
1765 |
number = {2}, |
1766 |
month = {Dec}, |
1767 |
abstract = {This paper presents a geometric-variational approach to continuous |
1768 |
and discrete mechanics and field theories. Using multisymplectic |
1769 |
geometry, we show that the existence of the fundamental geometric |
1770 |
structures as well as their preservation along solutions can be |
1771 |
obtained directly from the variational principle. In particular, |
1772 |
we prove that a unique multisymplectic structure is obtained by |
1773 |
taking the derivative of an action function, and use this structure |
1774 |
to prove covariant generalizations of conservation of symplecticity |
1775 |
and Noether's theorem. Natural discretization schemes for PDEs, |
1776 |
which have these important preservation properties, then follow |
1777 |
by choosing a discrete action functional. In the case of mechanics, |
1778 |
we recover the variational symplectic integrators of Veselov type, |
1779 |
while for PDEs we obtain covariant spacetime integrators which conserve |
1780 |
the corresponding discrete multisymplectic form as well as the discrete |
1781 |
momentum mappings corresponding to symmetries. We show that the |
1782 |
usual notion of symplecticity along an infinite-dimensional space |
1783 |
of fields can be naturally obtained by making a spacetime split. |
1784 |
All of the aspects of our method are demonstrated with a nonlinear |
1785 |
sine-Gordon equation, including computational results and a comparison |
1786 |
with other discretization schemes.}, |
1787 |
annote = {154RH Times Cited:88 Cited References Count:36}, |
1788 |
issn = {0010-3616}, |
1789 |
uri = {<Go to ISI>://000077902200006}, |
1790 |
} |
1791 |
|
1792 |
@ARTICLE{McLachlan1993, |
1793 |
author = {R.~I McLachlan}, |
1794 |
title = {Explicit Lie-Poisson integration and the Euler equations}, |
1795 |
journal = {prl}, |
1796 |
year = {1993}, |
1797 |
volume = {71}, |
1798 |
pages = {3043-3046}, |
1799 |
} |
1800 |
|
1801 |
@ARTICLE{McLachlan1998a, |
1802 |
author = {R. I. McLachlan and G. R. W. Quispel}, |
1803 |
title = {Generating functions for dynamical systems with symmetries, integrals, |
1804 |
and differential invariants}, |
1805 |
journal = {Physica D}, |
1806 |
year = {1998}, |
1807 |
volume = {112}, |
1808 |
pages = {298-309}, |
1809 |
number = {1-2}, |
1810 |
month = {Jan 15}, |
1811 |
abstract = {We give a survey and some new examples of generating functions for |
1812 |
systems with symplectic structure, systems with a first integral, |
1813 |
systems that preserve volume, and systems with symmetries and/or |
1814 |
time-reversing symmetries. Both ODEs and maps are treated, and we |
1815 |
discuss how generating functions may be used in the structure-preserving |
1816 |
numerical integration of ODEs with the above properties.}, |
1817 |
annote = {Yt049 Times Cited:7 Cited References Count:26}, |
1818 |
issn = {0167-2789}, |
1819 |
uri = {<Go to ISI>://000071558900021}, |
1820 |
} |
1821 |
|
1822 |
@ARTICLE{McLachlan1998, |
1823 |
author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner}, |
1824 |
title = {Numerical integrators that preserve symmetries and reversing symmetries}, |
1825 |
journal = {Siam Journal on Numerical Analysis}, |
1826 |
year = {1998}, |
1827 |
volume = {35}, |
1828 |
pages = {586-599}, |
1829 |
number = {2}, |
1830 |
month = {Apr}, |
1831 |
abstract = {We consider properties of flows, the relationships between them, and |
1832 |
whether numerical integrators can be made to preserve these properties. |
1833 |
This is done in the context of automorphisms and antiautomorphisms |
1834 |
of a certain group generated by maps associated to vector fields. |
1835 |
This new framework unifies several known constructions. We also |
1836 |
use the concept of #covariance# of a numerical method with respect |
1837 |
to a group of coordinate transformations. The main application is |
1838 |
to explore the relationship between spatial symmetries, reversing |
1839 |
symmetries, and time symmetry of flows and numerical integrators.}, |
1840 |
annote = {Zc449 Times Cited:14 Cited References Count:33}, |
1841 |
issn = {0036-1429}, |
1842 |
uri = {<Go to ISI>://000072580500010}, |
1843 |
} |
1844 |
|
1845 |
@ARTICLE{McLachlan2005, |
1846 |
author = {R. I. McLachlan and A. Zanna}, |
1847 |
title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited}, |
1848 |
journal = {Foundations of Computational Mathematics}, |
1849 |
year = {2005}, |
1850 |
volume = {5}, |
1851 |
pages = {87-123}, |
1852 |
number = {1}, |
1853 |
month = {Feb}, |
1854 |
abstract = {In this paper we revisit the Moser-Veselov description of the free |
1855 |
rigid body in body coordinates, which, in the 3 x 3 case, can be |
1856 |
implemented as an explicit, second-order, integrable approximation |
1857 |
of the continuous solution. By backward error analysis, we study |
1858 |
the modified vector field which is integrated exactly by the discrete |
1859 |
algorithm. We deduce that the discrete Moser-Veselov (DMV) is well |
1860 |
approximated to higher order by time reparametrizations of the continuous |
1861 |
equations (modified vector field). We use the modified vector field |
1862 |
to scale the initial data of the DMV to improve the order of the |
1863 |
approximation and show the equivalence of the DMV and the RATTLE |
1864 |
algorithm. Numerical integration with these preprocessed initial |
1865 |
data is several orders of magnitude more accurate than the original |
1866 |
DMV and RATTLE approach.}, |
1867 |
annote = {911NS Times Cited:0 Cited References Count:14}, |
1868 |
issn = {1615-3375}, |
1869 |
uri = {<Go to ISI>://000228011900003}, |
1870 |
} |
1871 |
|
1872 |
@ARTICLE{Memmer2002, |
1873 |
author = {R. Memmer}, |
1874 |
title = {Liquid crystal phases of achiral banana-shaped molecules: a computer |
1875 |
simulation study}, |
1876 |
journal = {Liquid Crystals}, |
1877 |
year = {2002}, |
1878 |
volume = {29}, |
1879 |
pages = {483-496}, |
1880 |
number = {4}, |
1881 |
month = {Apr}, |
1882 |
abstract = {The phase behaviour of achiral banana-shaped molecules was studied |
1883 |
by computer simulation. The banana-shaped molecules were described |
1884 |
by model intermolecular interactions based on the Gay-Berne potential. |
1885 |
The characteristic molecular structure was considered by joining |
1886 |
two calamitic Gay-Berne particles through a bond to form a biaxial |
1887 |
molecule of point symmetry group C-2v with a suitable bending angle. |
1888 |
The dependence on temperature of systems of N=1024 rigid banana-shaped |
1889 |
molecules with bending angle phi=140degrees has been studied by |
1890 |
means of Monte Carlo simulations in the isobaric-isothermal ensemble |
1891 |
(NpT). On cooling an isotropic system, two phase transitions characterized |
1892 |
by phase transition enthalpy, entropy and relative volume change |
1893 |
have been observed. For the first time by computer simulation of |
1894 |
a many-particle system of banana-shaped molecules, at low temperature |
1895 |
an untilted smectic phase showing a global phase biaxiality and |
1896 |
a spontaneous local polarization in the layers, i.e. a local polar |
1897 |
arrangement of the steric dipoles, with an antiferroelectric-like |
1898 |
superstructure could be proven, a phase structure which recently |
1899 |
has been discovered experimentally. Additionally, at intermediate |
1900 |
temperature a nematic-like phase has been proved, whereas close |
1901 |
to the transition to the smectic phase hints of a spontaneous achiral |
1902 |
symmetry breaking have been determined. Here, in the absence of |
1903 |
a layered structure a helical superstructure has been formed. All |
1904 |
phases have been characterized by visual representations of selected |
1905 |
configurations, scalar and pseudoscalar correlation functions, and |
1906 |
order parameters.}, |
1907 |
annote = {531HT Times Cited:12 Cited References Count:37}, |
1908 |
issn = {0267-8292}, |
1909 |
uri = {<Go to ISI>://000174410500001}, |
1910 |
} |
1911 |
|
1912 |
@ARTICLE{Metropolis1949, |
1913 |
author = {N. Metropolis and S. Ulam}, |
1914 |
title = {The $\mbox{Monte Carlo}$ Method}, |
1915 |
journal = {J. Am. Stat. Ass.}, |
1916 |
year = {1949}, |
1917 |
volume = {44}, |
1918 |
pages = {335-341}, |
1919 |
} |
1920 |
|
1921 |
@ARTICLE{Mielke2004, |
1922 |
author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen |
1923 |
and C. J. Benham}, |
1924 |
title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian |
1925 |
dynamics study}, |
1926 |
journal = {Journal of Chemical Physics}, |
1927 |
year = {2004}, |
1928 |
volume = {121}, |
1929 |
pages = {8104-8112}, |
1930 |
number = {16}, |
1931 |
month = {Oct 22}, |
1932 |
abstract = {The torque generated by RNA polymerase as it tracks along double-stranded |
1933 |
DNA can potentially induce long-range structural deformations integral |
1934 |
to mechanisms of biological significance in both prokaryotes and |
1935 |
eukaryotes. In this paper, we introduce a dynamic computer model |
1936 |
for investigating this phenomenon. Duplex DNA is represented as |
1937 |
a chain of hydrodynamic beads interacting through potentials of |
1938 |
linearly elastic stretching, bending, and twisting, as well as excluded |
1939 |
volume. The chain, linear when relaxed, is looped to form two open |
1940 |
but topologically constrained subdomains. This permits the dynamic |
1941 |
introduction of torsional stress via a centrally applied torque. |
1942 |
We simulate by Brownian dynamics the 100 mus response of a 477-base |
1943 |
pair B-DNA template to the localized torque generated by the prokaryotic |
1944 |
transcription ensemble. Following a sharp rise at early times, the |
1945 |
distributed twist assumes a nearly constant value in both subdomains, |
1946 |
and a succession of supercoiling deformations occurs as superhelical |
1947 |
stress is increasingly partitioned to writhe. The magnitude of writhe |
1948 |
surpasses that of twist before also leveling off when the structure |
1949 |
reaches mechanical equilibrium with the torsional load. Superhelicity |
1950 |
is simultaneously right handed in one subdomain and left handed |
1951 |
in the other, as predicted by the #transcription-induced##twin-supercoiled-domain# |
1952 |
model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, |
1953 |
7024 (1987)]. The properties of the chain at the onset of writhing |
1954 |
agree well with predictions from theory, and the generated stress |
1955 |
is ample for driving secondary structural transitions in physiological |
1956 |
DNA. (C) 2004 American Institute of Physics.}, |
1957 |
annote = {861ZF Times Cited:3 Cited References Count:34}, |
1958 |
issn = {0021-9606}, |
1959 |
uri = {<Go to ISI>://000224456500064}, |
1960 |
} |
1961 |
|
1962 |
@ARTICLE{Naess2001, |
1963 |
author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter}, |
1964 |
title = {Brownian dynamics simulation of rigid bodies and segmented polymer |
1965 |
chains. Use of Cartesian rotation vectors as the generalized coordinates |
1966 |
describing angular orientations}, |
1967 |
journal = {Physica A}, |
1968 |
year = {2001}, |
1969 |
volume = {294}, |
1970 |
pages = {323-339}, |
1971 |
number = {3-4}, |
1972 |
month = {May 15}, |
1973 |
abstract = {The three Eulerian angles constitute the classical choice of generalized |
1974 |
coordinates used to describe the three degrees of rotational freedom |
1975 |
of a rigid body, but it has long been known that this choice yields |
1976 |
singular equations of motion. The latter is also true when Eulerian |
1977 |
angles are used in Brownian dynamics analyses of the angular orientation |
1978 |
of single rigid bodies and segmented polymer chains. Starting from |
1979 |
kinetic theory we here show that by instead employing the three |
1980 |
components of Cartesian rotation vectors as the generalized coordinates |
1981 |
describing angular orientation, no singularity appears in the configuration |
1982 |
space diffusion equation and the associated Brownian dynamics algorithm. |
1983 |
The suitability of Cartesian rotation vectors in Brownian dynamics |
1984 |
simulations of segmented polymer chains with spring-like or ball-socket |
1985 |
joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.}, |
1986 |
annote = {433TA Times Cited:7 Cited References Count:19}, |
1987 |
issn = {0378-4371}, |
1988 |
uri = {<Go to ISI>://000168774800005}, |
1989 |
} |
1990 |
|
1991 |
@ARTICLE{Niori1996, |
1992 |
author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe}, |
1993 |
title = {Distinct ferroelectric smectic liquid crystals consisting of banana |
1994 |
shaped achiral molecules}, |
1995 |
journal = {Journal of Materials Chemistry}, |
1996 |
year = {1996}, |
1997 |
volume = {6}, |
1998 |
pages = {1231-1233}, |
1999 |
number = {7}, |
2000 |
month = {Jul}, |
2001 |
abstract = {The synthesis of a banana-shaped molecule is reported and it is found |
2002 |
that the smectic phase which it forms is biaxial with the molecules |
2003 |
packed in the best,direction into a layer. Because of this characteristic |
2004 |
packing, spontaneous polarization appears parallel to the layer |
2005 |
and switches on reversal of an applied electric field. This is the |
2006 |
first obvious example of ferroelectricity in an achiral smectic |
2007 |
phase and is ascribed to the C-2v symmetry of the molecular packing.}, |
2008 |
annote = {Ux855 Times Cited:447 Cited References Count:18}, |
2009 |
issn = {0959-9428}, |
2010 |
uri = {<Go to ISI>://A1996UX85500025}, |
2011 |
} |
2012 |
|
2013 |
@ARTICLE{Noguchi2002, |
2014 |
author = {H. Noguchi and M. Takasu}, |
2015 |
title = {Structural changes of pulled vesicles: A Brownian dynamics simulation}, |
2016 |
journal = {Physical Review E}, |
2017 |
year = {2002}, |
2018 |
volume = {65}, |
2019 |
pages = {-}, |
2020 |
number = {5}, |
2021 |
month = {may}, |
2022 |
abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical |
2023 |
forces using a Brownian dynamics simulation. Two nanoparticles, |
2024 |
which interact repulsively with amphiphilic molecules, are put inside |
2025 |
a vesicle. The position of one nanoparticle is fixed, and the other |
2026 |
is moved by a constant force as in optical-trapping experiments. |
2027 |
First, the pulled vesicle stretches into a pear or tube shape. Then |
2028 |
the inner monolayer in the tube-shaped region is deformed, and a |
2029 |
cylindrical structure is formed between two vesicles. After stretching |
2030 |
the cylindrical region, fission occurs near the moved vesicle. Soon |
2031 |
after this the cylindrical region shrinks. The trapping force similar |
2032 |
to 100 pN is needed to induce the formation of the cylindrical structure |
2033 |
and fission.}, |
2034 |
annote = {Part 1 568PX Times Cited:5 Cited References Count:39}, |
2035 |
issn = {1063-651X}, |
2036 |
uri = {<Go to ISI>://000176552300084}, |
2037 |
} |
2038 |
|
2039 |
@ARTICLE{Noguchi2001, |
2040 |
author = {H. Noguchi and M. Takasu}, |
2041 |
title = {Fusion pathways of vesicles: A Brownian dynamics simulation}, |
2042 |
journal = {Journal of Chemical Physics}, |
2043 |
year = {2001}, |
2044 |
volume = {115}, |
2045 |
pages = {9547-9551}, |
2046 |
number = {20}, |
2047 |
month = {Nov 22}, |
2048 |
abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics |
2049 |
simulation. Amphiphilic molecules spontaneously form vesicles with |
2050 |
a bilayer structure. Two vesicles come into contact and form a stalk |
2051 |
intermediate, in which a necklike structure only connects the outer |
2052 |
monolayers, as predicted by the stalk hypothesis. We have found |
2053 |
a new pathway of pore opening from stalks at high temperature: the |
2054 |
elliptic stalk bends and contact between the ends of the arc-shaped |
2055 |
stalk leads to pore opening. On the other hand, we have clarified |
2056 |
that the pore-opening process at low temperature agrees with the |
2057 |
modified stalk model: a pore is induced by contact between the inner |
2058 |
monolayers inside the stalk. (C) 2001 American Institute of Physics.}, |
2059 |
annote = {491UW Times Cited:48 Cited References Count:25}, |
2060 |
issn = {0021-9606}, |
2061 |
uri = {<Go to ISI>://000172129300049}, |
2062 |
} |
2063 |
|
2064 |
@BOOK{Olver1986, |
2065 |
title = {Applications of Lie groups to differential equatitons}, |
2066 |
publisher = {Springer}, |
2067 |
year = {1986}, |
2068 |
author = {P.J. Olver}, |
2069 |
address = {New York}, |
2070 |
} |
2071 |
|
2072 |
@ARTICLE{Omelyan1998, |
2073 |
author = {I. P. Omelyan}, |
2074 |
title = {On the numerical integration of motion for rigid polyatomics: The |
2075 |
modified quaternion approach}, |
2076 |
journal = {Computers in Physics}, |
2077 |
year = {1998}, |
2078 |
volume = {12}, |
2079 |
pages = {97-103}, |
2080 |
number = {1}, |
2081 |
month = {Jan-Feb}, |
2082 |
abstract = {A revised version of the quaternion approach for numerical integration |
2083 |
of the equations of motion for rigid polyatomic molecules is proposed. |
2084 |
The modified approach is based on a formulation of the quaternion |
2085 |
dynamics with constraints. This allows one to resolve the rigidity |
2086 |
problem rigorously using constraint forces. It is shown that the |
2087 |
procedure for preservation of molecular rigidity can be realized |
2088 |
particularly simply within the Verlet algorithm in velocity form. |
2089 |
We demonstrate that the method presented leads to an improved numerical |
2090 |
stability with respect to the usual quaternion rescaling scheme |
2091 |
and it is roughly as good as the cumbersome atomic-constraint technique. |
2092 |
(C) 1998 American Institute of Physics.}, |
2093 |
annote = {Yx279 Times Cited:12 Cited References Count:28}, |
2094 |
issn = {0894-1866}, |
2095 |
uri = {<Go to ISI>://000072024300025}, |
2096 |
} |
2097 |
|
2098 |
@ARTICLE{Omelyan1998a, |
2099 |
author = {I. P. Omelyan}, |
2100 |
title = {Algorithm for numerical integration of the rigid-body equations of |
2101 |
motion}, |
2102 |
journal = {Physical Review E}, |
2103 |
year = {1998}, |
2104 |
volume = {58}, |
2105 |
pages = {1169-1172}, |
2106 |
number = {1}, |
2107 |
month = {Jul}, |
2108 |
abstract = {An algorithm for numerical integration of the rigid-body equations |
2109 |
of motion is proposed. The algorithm uses the leapfrog scheme and |
2110 |
the quantities involved are angular velocities and orientational |
2111 |
variables that can be expressed in terms of either principal axes |
2112 |
or quaternions. Due to specific features of the algorithm, orthonormality |
2113 |
and unit norms of the orientational variables are integrals of motion, |
2114 |
despite an approximate character of the produced trajectories. It |
2115 |
is shown that the method presented appears to be the most efficient |
2116 |
among all such algorithms known.}, |
2117 |
annote = {101XL Times Cited:8 Cited References Count:22}, |
2118 |
issn = {1063-651X}, |
2119 |
uri = {<Go to ISI>://000074893400151}, |
2120 |
} |
2121 |
|
2122 |
@ARTICLE{Orlandi2006, |
2123 |
author = {S. Orlandi and R. Berardi and J. Steltzer and C. Zannoni}, |
2124 |
title = {A Monte Carlo study of the mesophases formed by polar bent-shaped |
2125 |
molecules}, |
2126 |
journal = {Journal of Chemical Physics}, |
2127 |
year = {2006}, |
2128 |
volume = {124}, |
2129 |
pages = {-}, |
2130 |
number = {12}, |
2131 |
month = {Mar 28}, |
2132 |
abstract = {Liquid crystal phases formed by bent-shaped (or #banana#) molecules |
2133 |
are currently of great interest. Here we investigate by Monte Carlo |
2134 |
computer simulations the phases formed by rigid banana molecules |
2135 |
modeled combining three Gay-Berne sites and containing either one |
2136 |
central or two lateral and transversal dipoles. We show that changing |
2137 |
the dipole position and orientation has a profound effect on the |
2138 |
mesophase stability and molecular organization. In particular, we |
2139 |
find a uniaxial nematic phase only for off-center dipolar models |
2140 |
and tilted phases only for the one with terminal dipoles. (c) 2006 |
2141 |
American Institute of Physics.}, |
2142 |
annote = {028CP Times Cited:0 Cited References Count:42}, |
2143 |
issn = {0021-9606}, |
2144 |
uri = {<Go to ISI>://000236464000072}, |
2145 |
} |
2146 |
|
2147 |
@ARTICLE{Owren1992, |
2148 |
author = {B. Owren and M. Zennaro}, |
2149 |
title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods}, |
2150 |
journal = {Siam Journal on Scientific and Statistical Computing}, |
2151 |
year = {1992}, |
2152 |
volume = {13}, |
2153 |
pages = {1488-1501}, |
2154 |
number = {6}, |
2155 |
month = {Nov}, |
2156 |
abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of |
2157 |
stages are considered. These methods are continuously differentiable |
2158 |
if and only if one of the stages is the FSAL evaluation. A characterization |
2159 |
of a subclass of these methods is developed for orders 3, 4, and |
2160 |
5. It is shown how the free parameters of these methods can be used |
2161 |
either to minimize the continuous truncation error coefficients |
2162 |
or to maximize the stability region. As a representative for these |
2163 |
methods the fifth-order method with minimized error coefficients |
2164 |
is chosen, supplied with an error estimation method, and analysed |
2165 |
by using the DETEST software. The results are compared with a similar |
2166 |
implementation of the Dormand-Prince 5(4) pair with interpolant, |
2167 |
showing a significant advantage in the new method for the chosen |
2168 |
problems.}, |
2169 |
annote = {Ju936 Times Cited:25 Cited References Count:20}, |
2170 |
issn = {0196-5204}, |
2171 |
uri = {<Go to ISI>://A1992JU93600013}, |
2172 |
} |
2173 |
|
2174 |
@ARTICLE{Palacios1998, |
2175 |
author = {J. L. Garcia-Palacios and F. J. Lazaro}, |
2176 |
title = {Langevin-dynamics study of the dynamical properties of small magnetic |
2177 |
particles}, |
2178 |
journal = {Physical Review B}, |
2179 |
year = {1998}, |
2180 |
volume = {58}, |
2181 |
pages = {14937-14958}, |
2182 |
number = {22}, |
2183 |
month = {Dec 1}, |
2184 |
abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical |
2185 |
magnetic moment is numerically solved (properly observing the customary |
2186 |
interpretation of it as a Stratonovich stochastic differential equation), |
2187 |
in order to study the dynamics of magnetic nanoparticles. The corresponding |
2188 |
Langevin-dynamics approach allows for the study of the fluctuating |
2189 |
trajectories of individual magnetic moments, where we have encountered |
2190 |
remarkable phenomena in the overbarrier rotation process, such as |
2191 |
crossing-back or multiple crossing of the potential barrier, rooted |
2192 |
in the gyromagnetic nature of the system. Concerning averaged quantities, |
2193 |
we study the linear dynamic response of the archetypal ensemble |
2194 |
of noninteracting classical magnetic moments with axially symmetric |
2195 |
magnetic anisotropy. The results are compared with different analytical |
2196 |
expressions used to model the relaxation of nanoparticle ensembles, |
2197 |
assessing their accuracy. It has been found that, among a number |
2198 |
of heuristic expressions for the linear dynamic susceptibility, |
2199 |
only the simple formula proposed by Shliomis and Stepanov matches |
2200 |
the coarse features of the susceptibility reasonably. By comparing |
2201 |
the numerical results with the asymptotic formula of Storonkin {Sov. |
2202 |
Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]}, |
2203 |
the effects of the intra-potential-well relaxation modes on the |
2204 |
low-temperature longitudinal dynamic response have been assessed, |
2205 |
showing their relatively small reflection in the susceptibility |
2206 |
curves but their dramatic influence on the phase shifts. Comparison |
2207 |
of the numerical results with the exact zero-damping expression |
2208 |
for the transverse susceptibility by Garanin, Ishchenko, and Panina |
2209 |
{Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242 |
2210 |
(1990)]}, reveals a sizable contribution of the spread of the precession |
2211 |
frequencies of the magnetic moment in the anisotropy field to the |
2212 |
dynamic response at intermediate-to-high temperatures. [S0163-1829 |
2213 |
(98)00446-9].}, |
2214 |
annote = {146XW Times Cited:66 Cited References Count:45}, |
2215 |
issn = {0163-1829}, |
2216 |
uri = {<Go to ISI>://000077460000052}, |
2217 |
} |
2218 |
|
2219 |
@ARTICLE{Pastor1988, |
2220 |
author = {R. W. Pastor and B. R. Brooks and A. Szabo}, |
2221 |
title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms}, |
2222 |
journal = {Molecular Physics}, |
2223 |
year = {1988}, |
2224 |
volume = {65}, |
2225 |
pages = {1409-1419}, |
2226 |
number = {6}, |
2227 |
month = {Dec 20}, |
2228 |
annote = {T1302 Times Cited:61 Cited References Count:26}, |
2229 |
issn = {0026-8976}, |
2230 |
uri = {<Go to ISI>://A1988T130200011}, |
2231 |
} |
2232 |
|
2233 |
@ARTICLE{Pelzl1999, |
2234 |
author = {G. Pelzl and S. Diele and W. Weissflog}, |
2235 |
title = {Banana-shaped compounds - A new field of liquid crystals}, |
2236 |
journal = {Advanced Materials}, |
2237 |
year = {1999}, |
2238 |
volume = {11}, |
2239 |
pages = {707-724}, |
2240 |
number = {9}, |
2241 |
month = {Jul 5}, |
2242 |
annote = {220RC Times Cited:313 Cited References Count:49}, |
2243 |
issn = {0935-9648}, |
2244 |
uri = {<Go to ISI>://000081680400007}, |
2245 |
} |
2246 |
|
2247 |
@ARTICLE{Perram1985, |
2248 |
author = {J. W. Perram and M. S. Wertheim}, |
2249 |
title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and |
2250 |
the Contact Function}, |
2251 |
journal = {Journal of Computational Physics}, |
2252 |
year = {1985}, |
2253 |
volume = {58}, |
2254 |
pages = {409-416}, |
2255 |
number = {3}, |
2256 |
annote = {Akb93 Times Cited:71 Cited References Count:12}, |
2257 |
issn = {0021-9991}, |
2258 |
uri = {<Go to ISI>://A1985AKB9300008}, |
2259 |
} |
2260 |
|
2261 |
@ARTICLE{Rotne1969, |
2262 |
author = {F. Perrin}, |
2263 |
title = {Variational treatment of hydrodynamic interaction in polymers}, |
2264 |
journal = {J. Chem. Phys.}, |
2265 |
year = {1969}, |
2266 |
volume = {50}, |
2267 |
pages = {4831¨C4837}, |
2268 |
} |
2269 |
|
2270 |
@ARTICLE{Perrin1936, |
2271 |
author = {F. Perrin}, |
2272 |
title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation |
2273 |
des fluorescences. Translation et diffusion de moleculese ellipsoidales}, |
2274 |
journal = {J. Phys. Radium}, |
2275 |
year = {1936}, |
2276 |
volume = {7}, |
2277 |
pages = {1-11}, |
2278 |
} |
2279 |
|
2280 |
@ARTICLE{Perrin1934, |
2281 |
author = {F. Perrin}, |
2282 |
title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour |
2283 |
des molecules ellipsoidales}, |
2284 |
journal = {J. Phys. Radium}, |
2285 |
year = {1934}, |
2286 |
volume = {5}, |
2287 |
pages = {497-511}, |
2288 |
} |
2289 |
|
2290 |
@ARTICLE{Petrache1998, |
2291 |
author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle}, |
2292 |
title = {Fluid phase structure of EPC and DMPC bilayers}, |
2293 |
journal = {Chemistry and Physics of Lipids}, |
2294 |
year = {1998}, |
2295 |
volume = {95}, |
2296 |
pages = {83-94}, |
2297 |
number = {1}, |
2298 |
month = {Sep}, |
2299 |
abstract = {X-ray diffraction data taken at high instrumental resolution were |
2300 |
obtained for EPC and DMPC under various osmotic pressures, primarily |
2301 |
at T = 30 degrees C. The headgroup thickness D-HH was obtained from |
2302 |
relative electron density profiles. By using volumetric results |
2303 |
and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4 |
2304 |
+/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The |
2305 |
analysis also gives estimates for the areal compressibility K-A. |
2306 |
The A(F) results lead to other structural results regarding membrane |
2307 |
thickness and associated waters. Using the recently determined absolute |
2308 |
electrons density profile of DPPC, the AF results also lead to absolute |
2309 |
electron density profiles and absolute continuous transforms \F(q)\ |
2310 |
for EPC and DMPC, Limited measurements of temperature dependence |
2311 |
show directly that fluctuations increase with increasing temperature |
2312 |
and that a small decrease in bending modulus K-c accounts for the |
2313 |
increased water spacing reported by Simon et al. (1995) Biophys. |
2314 |
J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights |
2315 |
reserved.}, |
2316 |
annote = {130AT Times Cited:98 Cited References Count:39}, |
2317 |
issn = {0009-3084}, |
2318 |
uri = {<Go to ISI>://000076497600007}, |
2319 |
} |
2320 |
|
2321 |
@ARTICLE{Powles1973, |
2322 |
author = {J.~G. Powles}, |
2323 |
title = {A general ellipsoid can not always serve as a modle for the rotational |
2324 |
diffusion properties of arbitrary shaped rigid molecules}, |
2325 |
journal = {Advan. Phys.}, |
2326 |
year = {1973}, |
2327 |
volume = {22}, |
2328 |
pages = {1-56}, |
2329 |
} |
2330 |
|
2331 |
@ARTICLE{Recio2004, |
2332 |
author = {J. Fernandez-Recio and M. Totrov and R. Abagyan}, |
2333 |
title = {Identification of protein-protein interaction sites from docking |
2334 |
energy landscapes}, |
2335 |
journal = {Journal of Molecular Biology}, |
2336 |
year = {2004}, |
2337 |
volume = {335}, |
2338 |
pages = {843-865}, |
2339 |
number = {3}, |
2340 |
month = {Jan 16}, |
2341 |
abstract = {Protein recognition is one of the most challenging and intriguing |
2342 |
problems in structural biology. Despite all the available structural, |
2343 |
sequence and biophysical information about protein-protein complexes, |
2344 |
the physico-chemical patterns, if any, that make a protein surface |
2345 |
likely to be involved in protein-protein interactions, remain elusive. |
2346 |
Here, we apply protein docking simulations and analysis of the interaction |
2347 |
energy landscapes to identify protein-protein interaction sites. |
2348 |
The new protocol for global docking based on multi-start global |
2349 |
energy optimization of an allatom model of the ligand, with detailed |
2350 |
receptor potentials and atomic solvation parameters optimized in |
2351 |
a training set of 24 complexes, explores the conformational space |
2352 |
around the whole receptor without restrictions. The ensembles of |
2353 |
the rigid-body docking solutions generated by the simulations were |
2354 |
subsequently used to project the docking energy landscapes onto |
2355 |
the protein surfaces. We found that highly populated low-energy |
2356 |
regions consistently corresponded to actual binding sites. The procedure |
2357 |
was validated on a test set of 21 known protein-protein complexes |
2358 |
not used in the training set. As much as 81% of the predicted high-propensity |
2359 |
patch residues were located correctly in the native interfaces. |
2360 |
This approach can guide the design of mutations on the surfaces |
2361 |
of proteins, provide geometrical details of a possible interaction, |
2362 |
and help to annotate protein surfaces in structural proteomics. |
2363 |
(C) 2003 Elsevier Ltd. All rights reserved.}, |
2364 |
annote = {763GQ Times Cited:21 Cited References Count:59}, |
2365 |
issn = {0022-2836}, |
2366 |
uri = {<Go to ISI>://000188066900016}, |
2367 |
} |
2368 |
|
2369 |
@ARTICLE{Reddy2006, |
2370 |
author = {R. A. Reddy and C. Tschierske}, |
2371 |
title = {Bent-core liquid crystals: polar order, superstructural chirality |
2372 |
and spontaneous desymmetrisation in soft matter systems}, |
2373 |
journal = {Journal of Materials Chemistry}, |
2374 |
year = {2006}, |
2375 |
volume = {16}, |
2376 |
pages = {907-961}, |
2377 |
number = {10}, |
2378 |
abstract = {An overview on the recent developments in the field of liquid crystalline |
2379 |
bent-core molecules (so-called banana liquid crystals) is given. |
2380 |
After some basic issues, dealing with general aspects of the systematisation |
2381 |
of the mesophases, development of polar order and chirality in this |
2382 |
class of LC systems and explaining some general structure-property |
2383 |
relationships, we focus on fascinating new developments in this |
2384 |
field, such as modulated, undulated and columnar phases, so-called |
2385 |
B7 phases, phase biaxiality, ferroelectric and antiferroelectric |
2386 |
polar order in smectic and columnar phases, amplification and switching |
2387 |
of chirality and the spontaneous formation of superstructural and |
2388 |
supramolecular chirality.}, |
2389 |
annote = {021NS Times Cited:2 Cited References Count:316}, |
2390 |
issn = {0959-9428}, |
2391 |
uri = {<Go to ISI>://000235990500001}, |
2392 |
} |
2393 |
|
2394 |
@ARTICLE{Reich1999, |
2395 |
author = {S. Reich}, |
2396 |
title = {Backward error analysis for numerical integrators}, |
2397 |
journal = {Siam Journal on Numerical Analysis}, |
2398 |
year = {1999}, |
2399 |
volume = {36}, |
2400 |
pages = {1549-1570}, |
2401 |
number = {5}, |
2402 |
month = {Sep 8}, |
2403 |
abstract = {Backward error analysis has become an important tool for understanding |
2404 |
the long time behavior of numerical integration methods. This is |
2405 |
true in particular for the integration of Hamiltonian systems where |
2406 |
backward error analysis can be used to show that a symplectic method |
2407 |
will conserve energy over exponentially long periods of time. Such |
2408 |
results are typically based on two aspects of backward error analysis: |
2409 |
(i) It can be shown that the modified vector fields have some qualitative |
2410 |
properties which they share with the given problem and (ii) an estimate |
2411 |
is given for the difference between the best interpolating vector |
2412 |
field and the numerical method. These aspects have been investigated |
2413 |
recently, for example, by Benettin and Giorgilli in [J. Statist. |
2414 |
Phys., 74 (1994), pp. 1117-1143], by Hairer in [Ann. Numer. Math., |
2415 |
1 (1994), pp. 107-132], and by Hairer and Lubich in [Numer. Math., |
2416 |
76 (1997), pp. 441-462]. In this paper we aim at providing a unifying |
2417 |
framework and a simplification of the existing results and corresponding |
2418 |
proofs. Our approach to backward error analysis is based on a simple |
2419 |
recursive definition of the modified vector fields that does not |
2420 |
require explicit Taylor series expansion of the numerical method |
2421 |
and the corresponding flow maps as in the above-cited works. As |
2422 |
an application we discuss the long time integration of chaotic Hamiltonian |
2423 |
systems and the approximation of time averages along numerically |
2424 |
computed trajectories.}, |
2425 |
annote = {237HV Times Cited:43 Cited References Count:41}, |
2426 |
issn = {0036-1429}, |
2427 |
uri = {<Go to ISI>://000082650600010}, |
2428 |
} |
2429 |
|
2430 |
@ARTICLE{Ros2005, |
2431 |
author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia}, |
2432 |
title = {Banana-shaped liquid crystals: a new field to explore}, |
2433 |
journal = {Journal of Materials Chemistry}, |
2434 |
year = {2005}, |
2435 |
volume = {15}, |
2436 |
pages = {5093-5098}, |
2437 |
number = {48}, |
2438 |
abstract = {The recent literature in the field of liquid crystals shows that banana-shaped |
2439 |
mesogenic materials represent a bewitching and stimulating field |
2440 |
of research that is interesting both academically and in terms of |
2441 |
applications. Numerous topics are open to investigation in this |
2442 |
area because of the rich phenomenology and new possibilities that |
2443 |
these materials offer. The principal concepts in this area are reviewed |
2444 |
along with recent results. In addition, new directions to stimulate |
2445 |
further research activities are highlighted.}, |
2446 |
annote = {990XA Times Cited:3 Cited References Count:72}, |
2447 |
issn = {0959-9428}, |
2448 |
uri = {<Go to ISI>://000233775500001}, |
2449 |
} |
2450 |
|
2451 |
@ARTICLE{Roy2005, |
2452 |
author = {A. Roy and N. V. Madhusudana}, |
2453 |
title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases |
2454 |
in banana shaped molecules}, |
2455 |
journal = {European Physical Journal E}, |
2456 |
year = {2005}, |
2457 |
volume = {18}, |
2458 |
pages = {253-258}, |
2459 |
number = {3}, |
2460 |
month = {Nov}, |
2461 |
abstract = {A vast majority of compounds with bent core or banana shaped molecules |
2462 |
exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased |
2463 |
in a homologous series. The B-6 phase has an intercalated fluid |
2464 |
lamellar structure with a layer spacing of half the molecular length. |
2465 |
The B-1 phase has a two dimensionally periodic rectangular columnar |
2466 |
structure. The B-2 phase has a monolayer fluid lamellar structure |
2467 |
with molecules tilted with respect to the layer normal. Neglecting |
2468 |
the tilt order of the molecules in the B-2 phase, we have developed |
2469 |
a frustrated packing model to describe this phase sequence qualitatively. |
2470 |
The model has some analogy with that of the frustrated smectics |
2471 |
exhibited by highly polar rod like molecules.}, |
2472 |
annote = {985FW Times Cited:0 Cited References Count:30}, |
2473 |
issn = {1292-8941}, |
2474 |
uri = {<Go to ISI>://000233363300002}, |
2475 |
} |
2476 |
|
2477 |
@ARTICLE{Ryckaert1977, |
2478 |
author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen}, |
2479 |
title = {Numerical-Integration of Cartesian Equations of Motion of a System |
2480 |
with Constraints - Molecular-Dynamics of N-Alkanes}, |
2481 |
journal = {Journal of Computational Physics}, |
2482 |
year = {1977}, |
2483 |
volume = {23}, |
2484 |
pages = {327-341}, |
2485 |
number = {3}, |
2486 |
annote = {Cz253 Times Cited:3680 Cited References Count:7}, |
2487 |
issn = {0021-9991}, |
2488 |
uri = {<Go to ISI>://A1977CZ25300007}, |
2489 |
} |
2490 |
|
2491 |
@ARTICLE{Sagui1999, |
2492 |
author = {C. Sagui and T. A. Darden}, |
2493 |
title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic |
2494 |
effects}, |
2495 |
journal = {Annual Review of Biophysics and Biomolecular Structure}, |
2496 |
year = {1999}, |
2497 |
volume = {28}, |
2498 |
pages = {155-179}, |
2499 |
abstract = {Current computer simulations of biomolecules typically make use of |
2500 |
classical molecular dynamics methods, as a very large number (tens |
2501 |
to hundreds of thousands) of atoms are involved over timescales |
2502 |
of many nanoseconds. The methodology for treating short-range bonded |
2503 |
and van der Waals interactions has matured. However, long-range |
2504 |
electrostatic interactions still represent a bottleneck in simulations. |
2505 |
In this article, we introduce the basic issues for an accurate representation |
2506 |
of the relevant electrostatic interactions. In spite of the huge |
2507 |
computational time demanded by most biomolecular systems, it is |
2508 |
no longer necessary to resort to uncontrolled approximations such |
2509 |
as the use of cutoffs. In particular, we discuss the Ewald summation |
2510 |
methods, the fast particle mesh methods, and the fast multipole |
2511 |
methods. We also review recent efforts to understand the role of |
2512 |
boundary conditions in systems with long-range interactions, and |
2513 |
conclude with a short perspective on future trends.}, |
2514 |
annote = {213KJ Times Cited:126 Cited References Count:73}, |
2515 |
issn = {1056-8700}, |
2516 |
uri = {<Go to ISI>://000081271400008}, |
2517 |
} |
2518 |
|
2519 |
@ARTICLE{Sandu1999, |
2520 |
author = {A. Sandu and T. Schlick}, |
2521 |
title = {Masking resonance artifacts in force-splitting methods for biomolecular |
2522 |
simulations by extrapolative Langevin dynamics}, |
2523 |
journal = {Journal of Computational Physics}, |
2524 |
year = {1999}, |
2525 |
volume = {151}, |
2526 |
pages = {74-113}, |
2527 |
number = {1}, |
2528 |
month = {May 1}, |
2529 |
abstract = {Numerical resonance artifacts have become recognized recently as a |
2530 |
limiting factor to increasing the timestep in multiple-timestep |
2531 |
(MTS) biomolecular dynamics simulations. At certain timesteps correlated |
2532 |
to internal motions (e.g., 5 fs, around half the period of the fastest |
2533 |
bond stretch, T-min), visible inaccuracies or instabilities can |
2534 |
occur. Impulse-MTS schemes are vulnerable to these resonance errors |
2535 |
since large energy pulses are introduced to the governing dynamics |
2536 |
equations when the slow forces are evaluated. We recently showed |
2537 |
that such resonance artifacts can be masked significantly by applying |
2538 |
extrapolative splitting to stochastic dynamics. Theoretical and |
2539 |
numerical analyses of force-splitting integrators based on the Verlet |
2540 |
discretization are reported here for linear models to explain these |
2541 |
observations and to suggest how to construct effective integrators |
2542 |
for biomolecular dynamics that balance stability with accuracy. |
2543 |
Analyses for Newtonian dynamics demonstrate the severe resonance |
2544 |
patterns of the Impulse splitting, with this severity worsening |
2545 |
with the outer timestep. Delta t: Constant Extrapolation is generally |
2546 |
unstable, but the disturbances do not grow with Delta t. Thus. the |
2547 |
stochastic extrapolative combination can counteract generic instabilities |
2548 |
and largely alleviate resonances with a sufficiently strong Langevin |
2549 |
heat-bath coupling (gamma), estimates for which are derived here |
2550 |
based on the fastest and slowest motion periods. These resonance |
2551 |
results generally hold for nonlinear test systems: a water tetramer |
2552 |
and solvated protein. Proposed related approaches such as Extrapolation/Correction |
2553 |
and Midpoint Extrapolation work better than Constant Extrapolation |
2554 |
only for timesteps less than T-min/2. An effective extrapolative |
2555 |
stochastic approach for biomolecules that balances long-timestep |
2556 |
stability with good accuracy for the fast subsystem is then applied |
2557 |
to a biomolecule using a three-class partitioning: the medium forces |
2558 |
are treated by Midpoint Extrapolation via position Verlet, and the |
2559 |
slow forces are incorporated by Constant Extrapolation. The resulting |
2560 |
algorithm (LN) performs well on a solvated protein system in terms |
2561 |
of thermodynamic properties and yields an order of magnitude speedup |
2562 |
with respect to single-timestep Langevin trajectories. Computed |
2563 |
spectral density functions also show how the Newtonian modes can |
2564 |
be approximated by using a small gamma in the range Of 5-20 ps(-1). |
2565 |
(C) 1999 Academic Press.}, |
2566 |
annote = {194FM Times Cited:14 Cited References Count:32}, |
2567 |
issn = {0021-9991}, |
2568 |
uri = {<Go to ISI>://000080181500004}, |
2569 |
} |
2570 |
|
2571 |
@ARTICLE{Satoh1996, |
2572 |
author = {K. Satoh and S. Mita and S. Kondo}, |
2573 |
title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect |
2574 |
of terminal dipole moment on mesophase formation}, |
2575 |
journal = {Chemical Physics Letters}, |
2576 |
year = {1996}, |
2577 |
volume = {255}, |
2578 |
pages = {99-104}, |
2579 |
number = {1-3}, |
2580 |
month = {Jun 7}, |
2581 |
abstract = {The effects of dipole-dipole interaction on mesophase formation are |
2582 |
investigated with a Monte Carlo simulation using the dipolar Gay-Berne |
2583 |
potential. It is shown that the dipole moment at the end of a molecule |
2584 |
causes a shift in the nematic-isotropic transition toward higher |
2585 |
temperature and a spread of the temperature range of the nematic |
2586 |
phase and that layer structures with various interdigitations are |
2587 |
formed in the smectic phase.}, |
2588 |
annote = {Uq975 Times Cited:32 Cited References Count:33}, |
2589 |
issn = {0009-2614}, |
2590 |
uri = {<Go to ISI>://A1996UQ97500017}, |
2591 |
} |
2592 |
|
2593 |
@ARTICLE{Shen2002, |
2594 |
author = {M. Y. Shen and K. F. Freed}, |
2595 |
title = {Long time dynamics of met-enkephalin: Comparison of explicit and |
2596 |
implicit solvent models}, |
2597 |
journal = {Biophysical Journal}, |
2598 |
year = {2002}, |
2599 |
volume = {82}, |
2600 |
pages = {1791-1808}, |
2601 |
number = {4}, |
2602 |
month = {Apr}, |
2603 |
abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical |
2604 |
structure and receptor docking mechanism are still not well understood. |
2605 |
The conformational dynamics of this neuron peptide in liquid water |
2606 |
are studied here by using all-atom molecular dynamics (MID) and |
2607 |
implicit water Langevin dynamics (LD) simulations with AMBER potential |
2608 |
functions and the three-site transferable intermolecular potential |
2609 |
(TIP3P) model for water. To achieve the same simulation length in |
2610 |
physical time, the full MID simulations require 200 times as much |
2611 |
CPU time as the implicit water LID simulations. The solvent hydrophobicity |
2612 |
and dielectric behavior are treated in the implicit solvent LD simulations |
2613 |
by using a macroscopic solvation potential, a single dielectric |
2614 |
constant, and atomic friction coefficients computed using the accessible |
2615 |
surface area method with the TIP3P model water viscosity as determined |
2616 |
here from MID simulations for pure TIP3P water. Both the local and |
2617 |
the global dynamics obtained from the implicit solvent LD simulations |
2618 |
agree very well with those from the explicit solvent MD simulations. |
2619 |
The simulations provide insights into the conformational restrictions |
2620 |
that are associated with the bioactivity of the opiate peptide dermorphin |
2621 |
for the delta-receptor.}, |
2622 |
annote = {540MH Times Cited:36 Cited References Count:45}, |
2623 |
issn = {0006-3495}, |
2624 |
uri = {<Go to ISI>://000174932400010}, |
2625 |
} |
2626 |
|
2627 |
@ARTICLE{Shillcock2005, |
2628 |
author = {J. C. Shillcock and R. Lipowsky}, |
2629 |
title = {Tension-induced fusion of bilayer membranes and vesicles}, |
2630 |
journal = {Nature Materials}, |
2631 |
year = {2005}, |
2632 |
volume = {4}, |
2633 |
pages = {225-228}, |
2634 |
number = {3}, |
2635 |
month = {Mar}, |
2636 |
annote = {901QJ Times Cited:9 Cited References Count:23}, |
2637 |
issn = {1476-1122}, |
2638 |
uri = {<Go to ISI>://000227296700019}, |
2639 |
} |
2640 |
|
2641 |
@ARTICLE{Shimada1993, |
2642 |
author = {J. Shimada and H. Kaneko and T. Takada}, |
2643 |
title = {Efficient Calculations of Coulombic Interactions in Biomolecular |
2644 |
Simulations with Periodic Boundary-Conditions}, |
2645 |
journal = {Journal of Computational Chemistry}, |
2646 |
year = {1993}, |
2647 |
volume = {14}, |
2648 |
pages = {867-878}, |
2649 |
number = {7}, |
2650 |
month = {Jul}, |
2651 |
abstract = {To make improved treatments of electrostatic interactions in biomacromolecular |
2652 |
simulations, two possibilities are considered. The first is the |
2653 |
famous particle-particle and particle-mesh (PPPM) method developed |
2654 |
by Hockney and Eastwood, and the second is a new one developed here |
2655 |
in their spirit but by the use of the multipole expansion technique |
2656 |
suggested by Ladd. It is then numerically found that the new PPPM |
2657 |
method gives more accurate results for a two-particle system at |
2658 |
small separation of particles. Preliminary numerical examination |
2659 |
of the various computational methods for a single configuration |
2660 |
of a model BPTI-water system containing about 24,000 particles indicates |
2661 |
that both of the PPPM methods give far more accurate values with |
2662 |
reasonable computational cost than do the conventional truncation |
2663 |
methods. It is concluded the two PPPM methods are nearly comparable |
2664 |
in overall performance for the many-particle systems, although the |
2665 |
first method has the drawback that the accuracy in the total electrostatic |
2666 |
energy is not high for configurations of charged particles randomly |
2667 |
generated.}, |
2668 |
annote = {Lh164 Times Cited:27 Cited References Count:47}, |
2669 |
issn = {0192-8651}, |
2670 |
uri = {<Go to ISI>://A1993LH16400011}, |
2671 |
} |
2672 |
|
2673 |
@ARTICLE{Skeel2002, |
2674 |
author = {R. D. Skeel and J. A. Izaguirre}, |
2675 |
title = {An impulse integrator for Langevin dynamics}, |
2676 |
journal = {Molecular Physics}, |
2677 |
year = {2002}, |
2678 |
volume = {100}, |
2679 |
pages = {3885-3891}, |
2680 |
number = {24}, |
2681 |
month = {Dec 20}, |
2682 |
abstract = {The best simple method for Newtonian molecular dynamics is indisputably |
2683 |
the leapfrog Stormer-Verlet method. The appropriate generalization |
2684 |
to simple Langevin dynamics is unclear. An analysis is presented |
2685 |
comparing an 'impulse method' (kick; fluctuate; kick), the 1982 |
2686 |
method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus |
2687 |
(BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen |
2688 |
methods can be implemented as efficiently as the BBK method. Other |
2689 |
considerations suggest that the impulse method is the best basic |
2690 |
method for simple Langevin dynamics, with the van Gunsteren-Berendsen |
2691 |
method a close contender.}, |
2692 |
annote = {633RX Times Cited:8 Cited References Count:22}, |
2693 |
issn = {0026-8976}, |
2694 |
uri = {<Go to ISI>://000180297200014}, |
2695 |
} |
2696 |
|
2697 |
@ARTICLE{Skeel1997, |
2698 |
author = {R. D. Skeel and G. H. Zhang and T. Schlick}, |
2699 |
title = {A family of symplectic integrators: Stability, accuracy, and molecular |
2700 |
dynamics applications}, |
2701 |
journal = {Siam Journal on Scientific Computing}, |
2702 |
year = {1997}, |
2703 |
volume = {18}, |
2704 |
pages = {203-222}, |
2705 |
number = {1}, |
2706 |
month = {Jan}, |
2707 |
abstract = {The following integration methods for special second-order ordinary |
2708 |
differential equations are studied: leapfrog, implicit midpoint, |
2709 |
trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all |
2710 |
are members, or equivalent to members, of a one-parameter family |
2711 |
of schemes. Some methods have more than one common form, and we |
2712 |
discuss a systematic enumeration of these forms. We also present |
2713 |
a stability and accuracy analysis based on the idea of ''modified |
2714 |
equations'' and a proof of symplecticness. It follows that Cowell-Numerov |
2715 |
and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic. |
2716 |
A different interpretation of the values used by these integrators |
2717 |
leads to higher accuracy and better energy conservation. Hence, |
2718 |
we suggest that the straightforward analysis of energy conservation |
2719 |
is misleading.}, |
2720 |
annote = {We981 Times Cited:30 Cited References Count:35}, |
2721 |
issn = {1064-8275}, |
2722 |
uri = {<Go to ISI>://A1997WE98100012}, |
2723 |
} |
2724 |
|
2725 |
@ARTICLE{Tao2005, |
2726 |
author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont |
2727 |
and W. J. Briels}, |
2728 |
title = {Brownian dynamics simulations of the self- and collective rotational |
2729 |
diffusion coefficients of rigid long thin rods}, |
2730 |
journal = {Journal of Chemical Physics}, |
2731 |
year = {2005}, |
2732 |
volume = {122}, |
2733 |
pages = {-}, |
2734 |
number = {24}, |
2735 |
month = {Jun 22}, |
2736 |
abstract = {Recently a microscopic theory for the dynamics of suspensions of long |
2737 |
thin rigid rods was presented, confirming and expanding the well-known |
2738 |
theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, |
2739 |
Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here |
2740 |
this theory is put to the test by comparing it against computer |
2741 |
simulations. A Brownian dynamics simulation program was developed |
2742 |
to follow the dynamics of the rods, with a length over a diameter |
2743 |
ratio of 60, on the Smoluchowski time scale. The model accounts |
2744 |
for excluded volume interactions between rods, but neglects hydrodynamic |
2745 |
interactions. The self-rotational diffusion coefficients D-r(phi) |
2746 |
of the rods were calculated by standard methods and by a new, more |
2747 |
efficient method based on calculating average restoring torques. |
2748 |
Collective decay of orientational order was calculated by means |
2749 |
of equilibrium and nonequilibrium simulations. Our results show |
2750 |
that, for the currently accessible volume fractions, the decay times |
2751 |
in both cases are virtually identical. Moreover, the observed decay |
2752 |
of diffusion coefficients with volume fraction is much quicker than |
2753 |
predicted by the theory, which is attributed to an oversimplification |
2754 |
of dynamic correlations in the theory. (c) 2005 American Institute |
2755 |
of Physics.}, |
2756 |
annote = {943DN Times Cited:3 Cited References Count:26}, |
2757 |
issn = {0021-9606}, |
2758 |
uri = {<Go to ISI>://000230332400077}, |
2759 |
} |
2760 |
|
2761 |
@BOOK{Tolman1979, |
2762 |
title = {The Principles of Statistical Mechanics}, |
2763 |
publisher = {Dover Publications, Inc.}, |
2764 |
year = {1979}, |
2765 |
author = {R.~C. Tolman}, |
2766 |
address = {New York}, |
2767 |
chapter = {2}, |
2768 |
pages = {19-22}, |
2769 |
} |
2770 |
|
2771 |
@ARTICLE{Tu1995, |
2772 |
author = {K. Tu and D. J. Tobias and M. L. Klein}, |
2773 |
title = {Constant pressure and temperature molecular dynamics simulation of |
2774 |
a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine |
2775 |
bilayer}, |
2776 |
journal = {Biophysical Journal}, |
2777 |
year = {1995}, |
2778 |
volume = {69}, |
2779 |
pages = {2558-2562}, |
2780 |
number = {6}, |
2781 |
month = {Dec}, |
2782 |
abstract = {We report a constant pressure and temperature molecular dynamics simulation |
2783 |
of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine |
2784 |
at 50 degrees C and 28 water molecules/lipid. We have shown that |
2785 |
the bilayer is stable throughout the 1550-ps simulation and have |
2786 |
demonstrated convergence of the system dimensions. Several important |
2787 |
aspects of the bilayer structure have been investigated and compared |
2788 |
favorably with experimental results. For example, the average positions |
2789 |
of specific carbon atoms along the bilayer normal agree well with |
2790 |
neutron diffraction data, and the electron density profile is in |
2791 |
accord with x-ray diffraction results. The hydrocarbon chain deuterium |
2792 |
order parameters agree reasonably well with NMR results for the |
2793 |
middles of the chains, but the simulation predicts too much order |
2794 |
at the chain ends. In spite of the deviations in the order parameters, |
2795 |
the hydrocarbon chain packing density appears to be essentially |
2796 |
correct, inasmuch as the area/lipid and bilayer thickness are in |
2797 |
agreement with the most refined experimental estimates. The deuterium |
2798 |
order parameters for the glycerol and choline groups, as well as |
2799 |
the phosphorus chemical shift anisotropy, are in qualitative agreement |
2800 |
with those extracted from NMR measurements.}, |
2801 |
annote = {Tv018 Times Cited:108 Cited References Count:34}, |
2802 |
issn = {0006-3495}, |
2803 |
uri = {<Go to ISI>://A1995TV01800037}, |
2804 |
} |
2805 |
|
2806 |
@ARTICLE{Tuckerman1992, |
2807 |
author = {M. Tuckerman and B. J. Berne and G. J. Martyna}, |
2808 |
title = {Reversible Multiple Time Scale Molecular-Dynamics}, |
2809 |
journal = {Journal of Chemical Physics}, |
2810 |
year = {1992}, |
2811 |
volume = {97}, |
2812 |
pages = {1990-2001}, |
2813 |
number = {3}, |
2814 |
month = {Aug 1}, |
2815 |
abstract = {The Trotter factorization of the Liouville propagator is used to generate |
2816 |
new reversible molecular dynamics integrators. This strategy is |
2817 |
applied to derive reversible reference system propagator algorithms |
2818 |
(RESPA) that greatly accelerate simulations of systems with a separation |
2819 |
of time scales or with long range forces. The new algorithms have |
2820 |
all of the advantages of previous RESPA integrators but are reversible, |
2821 |
and more stable than those methods. These methods are applied to |
2822 |
a set of paradigmatic systems and are shown to be superior to earlier |
2823 |
methods. It is shown how the new RESPA methods are related to predictor-corrector |
2824 |
integrators. Finally, we show how these methods can be used to accelerate |
2825 |
the integration of the equations of motion of systems with Nose |
2826 |
thermostats.}, |
2827 |
annote = {Je891 Times Cited:680 Cited References Count:19}, |
2828 |
issn = {0021-9606}, |
2829 |
uri = {<Go to ISI>://A1992JE89100044}, |
2830 |
} |
2831 |
|
2832 |
@BOOK{Varadarajan1974, |
2833 |
title = {Lie groups, Lie algebras, and their representations}, |
2834 |
publisher = {Prentice-Hall}, |
2835 |
year = {1974}, |
2836 |
author = {V.S. Varadarajan}, |
2837 |
address = {New York}, |
2838 |
} |
2839 |
|
2840 |
@ARTICLE{Wegener1979, |
2841 |
author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben}, |
2842 |
title = {A general ellipsoid can not always serve as a modle for the rotational |
2843 |
diffusion properties of arbitrary shaped rigid molecules}, |
2844 |
journal = {Proc. Natl. Acad. Sci.}, |
2845 |
year = {1979}, |
2846 |
volume = {76}, |
2847 |
pages = {6356-6360}, |
2848 |
number = {12}, |
2849 |
} |
2850 |
|
2851 |
@ARTICLE{Withers2003, |
2852 |
author = {I. M. Withers}, |
2853 |
title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne |
2854 |
fluid}, |
2855 |
journal = {Journal of Chemical Physics}, |
2856 |
year = {2003}, |
2857 |
volume = {119}, |
2858 |
pages = {10209-10223}, |
2859 |
number = {19}, |
2860 |
month = {Nov 15}, |
2861 |
abstract = {The effects of longitudinal quadrupole moments on the formation of |
2862 |
liquid crystalline phases are studied by means of constant NPT Monte |
2863 |
Carlo simulation methods. The popular Gay-Berne model mesogen is |
2864 |
used as the reference fluid, which displays the phase sequences |
2865 |
isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0) |
2866 |
and low (T*=1.5) temperatures, respectively. With increasing quadrupole |
2867 |
magnitude the smectic phases are observed to be stabilized with |
2868 |
respect to the isotropic liquid, while the smectic B is destabilized |
2869 |
with respect to the smectic A. At the lower temperature, a sufficiently |
2870 |
large quadrupole magnitude results in the injection of the smectic |
2871 |
A phase into the phase sequence and the replacement of the smectic |
2872 |
B phase by the tilted smectic J phase. The nematic phase is also |
2873 |
injected into the phase sequence at both temperatures considered, |
2874 |
and ultimately for sufficiently large quadrupole magnitudes no coherent |
2875 |
layered structures were observed. The stabilization of the smectic |
2876 |
A phase supports the commonly held belief that, while the inclusion |
2877 |
of polar groups is not a prerequisite for the formation of the smectic |
2878 |
A phase, quadrupolar interactions help to increase the temperature |
2879 |
and pressure range for which the smectic A phase is observed. The |
2880 |
quality of the layered structure is worsened with increasing quadrupole |
2881 |
magnitude. This behavior, along with the injection of the nematic |
2882 |
phase into the phase sequence, indicate that the general tendency |
2883 |
of the quadrupolar interactions is to destabilize the layered structure. |
2884 |
A pressure dependence upon the smectic layer spacing is observed. |
2885 |
This behavior is in much closer agreement with experimental findings |
2886 |
than has been observed previously for nonpolar Gay-Berne and hard |
2887 |
spherocylinder models. (C) 2003 American Institute of Physics.}, |
2888 |
annote = {738EF Times Cited:3 Cited References Count:43}, |
2889 |
issn = {0021-9606}, |
2890 |
uri = {<Go to ISI>://000186273200027}, |
2891 |
} |
2892 |
|
2893 |
@ARTICLE{Wolf1999, |
2894 |
author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht}, |
2895 |
title = {Exact method for the simulation of Coulombic systems by spherically |
2896 |
truncated, pairwise r(-1) summation}, |
2897 |
journal = {Journal of Chemical Physics}, |
2898 |
year = {1999}, |
2899 |
volume = {110}, |
2900 |
pages = {8254-8282}, |
2901 |
number = {17}, |
2902 |
month = {May 1}, |
2903 |
abstract = {Based on a recent result showing that the net Coulomb potential in |
2904 |
condensed ionic systems is rather short ranged, an exact and physically |
2905 |
transparent method permitting the evaluation of the Coulomb potential |
2906 |
by direct summation over the r(-1) Coulomb pair potential is presented. |
2907 |
The key observation is that the problems encountered in determining |
2908 |
the Coulomb energy by pairwise, spherically truncated r(-1) summation |
2909 |
are a direct consequence of the fact that the system summed over |
2910 |
is practically never neutral. A simple method is developed that |
2911 |
achieves charge neutralization wherever the r(-1) pair potential |
2912 |
is truncated. This enables the extraction of the Coulomb energy, |
2913 |
forces, and stresses from a spherically truncated, usually charged |
2914 |
environment in a manner that is independent of the grouping of the |
2915 |
pair terms. The close connection of our approach with the Ewald |
2916 |
method is demonstrated and exploited, providing an efficient method |
2917 |
for the simulation of even highly disordered ionic systems by direct, |
2918 |
pairwise r(-1) summation with spherical truncation at rather short |
2919 |
range, i.e., a method which fully exploits the short-ranged nature |
2920 |
of the interactions in ionic systems. The method is validated by |
2921 |
simulations of crystals, liquids, and interfacial systems, such |
2922 |
as free surfaces and grain boundaries. (C) 1999 American Institute |
2923 |
of Physics. [S0021-9606(99)51517-1].}, |
2924 |
annote = {189PD Times Cited:70 Cited References Count:34}, |
2925 |
issn = {0021-9606}, |
2926 |
uri = {<Go to ISI>://000079913000008}, |
2927 |
} |
2928 |
|
2929 |
@ARTICLE{Yoshida1990, |
2930 |
author = {H. Yoshida}, |
2931 |
title = {Construction of Higher-Order Symplectic Integrators}, |
2932 |
journal = {Physics Letters A}, |
2933 |
year = {1990}, |
2934 |
volume = {150}, |
2935 |
pages = {262-268}, |
2936 |
number = {5-7}, |
2937 |
month = {Nov 12}, |
2938 |
annote = {Ej798 Times Cited:492 Cited References Count:9}, |
2939 |
issn = {0375-9601}, |
2940 |
uri = {<Go to ISI>://A1990EJ79800009}, |
2941 |
} |