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#	Line 3 | Line 3 | Encoding: GBK
3
4		@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},
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},
8	>	methods and applications},
9		journal = {European Biophysics Journal with Biophysics Letters},
10		year = {2003},
11		volume = {32},
#	Line 13 | Line 13 | Encoding: GBK
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.},
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},
#	Line 42 | Line 42 | Encoding: GBK
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},
45	>	by time series analysis. II. Investigation of explicit solvent effects},
46		journal = {Journal of Chemical Physics},
47		year = {2005},
48		volume = {123},
#	Line 50 | Line 50 | Encoding: GBK
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.},
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{Alexander1987,
92	+	title = {A Pattern Language: Towns, Buildings, Construction},
93	+	publisher = {Oxford University Press},
94	+	year = {1987},
95	+	author = {C. Alexander},
96	+	address = {New York},
97	+	}
98	+
99		@BOOK{Allen1987,
100		title = {Computer Simulations of Liquids},
101		publisher = {Oxford University Press},
#	Line 99 | Line 107 | Encoding: GBK
107		@ARTICLE{Allison1991,
108		author = {S. A. Allison},
109		title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application
110	<	to Polarized Dynamic Light-Scattering},
110	>	to Polarized Dynamic Light-Scattering},
111		journal = {Macromolecules},
112		year = {1991},
113		volume = {24},
#	Line 107 | Line 115 | Encoding: GBK
115		number = {2},
116		month = {Jan 21},
117		abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
118	<	of rigid macromolecules. It is applied to polarized dynamic light
119	<	scattering from rodlike sturctures and from a model of a DNA fragment
120	<	(762 base pairs). A number of rod cases are examined in which the
121	<	translational anisotropy is increased form zero to a large value.
122	<	Simulated first cumulants as well as amplitudes and lifetimes of
123	<	the dynamic form factor are compared with predictions of analytic
124	<	theories and found to be in very good agreement with them. For DNA
125	<	fragments 762 base pairs in length or longer, translational anisotropy
126	<	does not contribute significantly to dynamic light scattering. In
127	<	a comparison of rigid and flexible simulations on semistiff models
128	<	of this fragment, it is shown directly that flexing contributes
129	<	to the faster decay processes probed by light scattering and that
130	<	the flexible model studies are in good agreement with experiment.},
118	>	of rigid macromolecules. It is applied to polarized dynamic light
119	>	scattering from rodlike sturctures and from a model of a DNA fragment
120	>	(762 base pairs). A number of rod cases are examined in which the
121	>	translational anisotropy is increased form zero to a large value.
122	>	Simulated first cumulants as well as amplitudes and lifetimes of
123	>	the dynamic form factor are compared with predictions of analytic
124	>	theories and found to be in very good agreement with them. For DNA
125	>	fragments 762 base pairs in length or longer, translational anisotropy
126	>	does not contribute significantly to dynamic light scattering. In
127	>	a comparison of rigid and flexible simulations on semistiff models
128	>	of this fragment, it is shown directly that flexing contributes
129	>	to the faster decay processes probed by light scattering and that
130	>	the flexible model studies are in good agreement with experiment.},
131		annote = {Eu814 Times Cited:8 Cited References Count:32},
132		issn = {0024-9297},
133		uri = {<Go to ISI>://A1991EU81400029},
134		}
135
136	+	@ARTICLE{Andersen1983,
137	+	author = {H. C. Andersen},
138	+	title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics
139	+	Calculations},
140	+	journal = {Journal of Computational Physics},
141	+	year = {1983},
142	+	volume = {52},
143	+	pages = {24-34},
144	+	number = {1},
145	+	annote = {Rq238 Times Cited:559 Cited References Count:14},
146	+	issn = {0021-9991},
147	+	uri = {<Go to ISI>://A1983RQ23800002},
148	+	}
149	+
150		@ARTICLE{Auerbach2005,
151		author = {A. Auerbach},
152		title = {Gating of acetylcholine receptor channels: Brownian motion across
153	<	a broad transition state},
153	>	a broad transition state},
154		journal = {Proceedings of the National Academy of Sciences of the United States
155	<	of America},
155	>	of America},
156		year = {2005},
157		volume = {102},
158		pages = {1408-1412},
159		number = {5},
160		month = {Feb 1},
161		abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
162	<	stable #closed# and #open# conformations. In patch clamp recordings,
163	<	diliganded AChR gating appears to be a simple, two-state reaction.
164	<	However, mutagenesis studies indicate that during gating dozens
165	<	of residues across the protein move asynchronously and are organized
166	<	into rigid body gating domains (#blocks#). Moreover, there is an
167	<	upper limit to the apparent channel opening rate constant. These
168	<	observations suggest that the gating reaction has a broad, corrugated
169	<	transition state region, with the maximum opening rate reflecting,
170	<	in part, the mean first-passage time across this ensemble. Simulations
171	<	reveal that a flat, isotropic energy profile for the transition
172	<	state can account for many of the essential features of AChR gating.
173	<	With this mechanism, concerted, local structural transitions that
174	<	occur on the broad transition state ensemble give rise to fractional
175	<	measures of reaction progress (Phi values) determined by rate-equilibrium
176	<	free energy relationship analysis. The results suggest that the
177	<	coarse-grained AChR gating conformational change propagates through
178	<	the protein with dynamics that are governed by the Brownian motion
179	<	of individual gating blocks.},
162	>	stable #closed# and #open# conformations. In patch clamp recordings,
163	>	diliganded AChR gating appears to be a simple, two-state reaction.
164	>	However, mutagenesis studies indicate that during gating dozens
165	>	of residues across the protein move asynchronously and are organized
166	>	into rigid body gating domains (#blocks#). Moreover, there is an
167	>	upper limit to the apparent channel opening rate constant. These
168	>	observations suggest that the gating reaction has a broad, corrugated
169	>	transition state region, with the maximum opening rate reflecting,
170	>	in part, the mean first-passage time across this ensemble. Simulations
171	>	reveal that a flat, isotropic energy profile for the transition
172	>	state can account for many of the essential features of AChR gating.
173	>	With this mechanism, concerted, local structural transitions that
174	>	occur on the broad transition state ensemble give rise to fractional
175	>	measures of reaction progress (Phi values) determined by rate-equilibrium
176	>	free energy relationship analysis. The results suggest that the
177	>	coarse-grained AChR gating conformational change propagates through
178	>	the protein with dynamics that are governed by the Brownian motion
179	>	of individual gating blocks.},
180		annote = {895QF Times Cited:9 Cited References Count:33},
181		issn = {0027-8424},
182		uri = {<Go to ISI>://000226877300030},
#	Line 163 | Line 185 | Encoding: GBK
185		@ARTICLE{Baber1995,
186		author = {J. Baber and J. F. Ellena and D. S. Cafiso},
187		title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined
188	<	Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
188	>	Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
189		journal = {Biochemistry},
190		year = {1995},
191		volume = {34},
#	Line 171 | Line 193 | Encoding: GBK
193		number = {19},
194		month = {May 16},
195		abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
196	<	on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine
197	<	membranes in the liquid crystalline phase was investigated using
198	<	H-2 NMR. Upon the addition of the anesthetics, the first five methylene
199	<	units near the interface generally show a very small increase in
200	<	segmental order, while segments deeper within the bilayer show a
201	<	small decrease in segmental order. From the H-2 NMR results, the
202	<	chain length for the perdeuterated palmitoyl chain in the absence
203	<	of anesthetic was found to be 12.35 Angstrom. Upon the addition
204	<	of halothane enflurane, or isoflurane, the acyl chain undergoes
205	<	slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively,
206	<	at 50 mol % anesthetic. A simple model was used to estimate the
207	<	relative amounts of anesthetic located near the interface and deeper
208	<	in the bilayer hydrocarbon region, and only a slight preference
209	<	for an interfacial location was observed. Intermolecular H-1-H-1
210	<	nuclear Overhauser effects (NOEs) were measured between phospholipid
211	<	and halothane protons. These NOEs are consistent with the intramembrane
212	<	location of the anesthetics suggested by the H-2 NMR data. In addition,
213	<	the NOE data indicate that anesthetics prefer the interfacial and
214	<	hydrocarbon regions of the membrane and are not found in high concentrations
215	<	in the phospholipid headgroup.},
196	>	on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine
197	>	membranes in the liquid crystalline phase was investigated using
198	>	H-2 NMR. Upon the addition of the anesthetics, the first five methylene
199	>	units near the interface generally show a very small increase in
200	>	segmental order, while segments deeper within the bilayer show a
201	>	small decrease in segmental order. From the H-2 NMR results, the
202	>	chain length for the perdeuterated palmitoyl chain in the absence
203	>	of anesthetic was found to be 12.35 Angstrom. Upon the addition
204	>	of halothane enflurane, or isoflurane, the acyl chain undergoes
205	>	slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively,
206	>	at 50 mol % anesthetic. A simple model was used to estimate the
207	>	relative amounts of anesthetic located near the interface and deeper
208	>	in the bilayer hydrocarbon region, and only a slight preference
209	>	for an interfacial location was observed. Intermolecular H-1-H-1
210	>	nuclear Overhauser effects (NOEs) were measured between phospholipid
211	>	and halothane protons. These NOEs are consistent with the intramembrane
212	>	location of the anesthetics suggested by the H-2 NMR data. In addition,
213	>	the NOE data indicate that anesthetics prefer the interfacial and
214	>	hydrocarbon regions of the membrane and are not found in high concentrations
215	>	in the phospholipid headgroup.},
216		annote = {Qz716 Times Cited:38 Cited References Count:37},
217		issn = {0006-2960},
218		uri = {<Go to ISI>://A1995QZ71600035},
#	Line 199 | Line 221 | Encoding: GBK
221		@ARTICLE{Banerjee2004,
222		author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
223		title = {Solution of quantum Langevin equation: Approximations, theoretical
224	<	and numerical aspects},
224	>	and numerical aspects},
225		journal = {Journal of Chemical Physics},
226		year = {2004},
227		volume = {120},
#	Line 207 | Line 229 | Encoding: GBK
229		number = {19},
230		month = {May 15},
231		abstract = {Based on a coherent state representation of noise operator and an
232	<	ensemble averaging procedure using Wigner canonical thermal distribution
233	<	for harmonic oscillators, a generalized quantum Langevin equation
234	<	has been recently developed [Phys. Rev. E 65, 021109 (2002); 66,
235	<	051106 (2002)] to derive the equations of motion for probability
236	<	distribution functions in c-number phase-space. We extend the treatment
237	<	to explore several systematic approximation schemes for the solutions
238	<	of the Langevin equation for nonlinear potentials for a wide range
239	<	of noise correlation, strength and temperature down to the vacuum
240	<	limit. The method is exemplified by an analytic application to harmonic
241	<	oscillator for arbitrary memory kernel and with the help of a numerical
242	<	calculation of barrier crossing, in a cubic potential to demonstrate
243	<	the quantum Kramers' turnover and the quantum Arrhenius plot. (C)
244	<	2004 American Institute of Physics.},
232	>	ensemble averaging procedure using Wigner canonical thermal distribution
233	>	for harmonic oscillators, a generalized quantum Langevin equation
234	>	has been recently developed [Phys. Rev. E 65, 021109 (2002); 66,
235	>	051106 (2002)] to derive the equations of motion for probability
236	>	distribution functions in c-number phase-space. We extend the treatment
237	>	to explore several systematic approximation schemes for the solutions
238	>	of the Langevin equation for nonlinear potentials for a wide range
239	>	of noise correlation, strength and temperature down to the vacuum
240	>	limit. The method is exemplified by an analytic application to harmonic
241	>	oscillator for arbitrary memory kernel and with the help of a numerical
242	>	calculation of barrier crossing, in a cubic potential to demonstrate
243	>	the quantum Kramers' turnover and the quantum Arrhenius plot. (C)
244	>	2004 American Institute of Physics.},
245		annote = {816YY Times Cited:8 Cited References Count:35},
246		issn = {0021-9606},
247		uri = {<Go to ISI>://000221146400009},
248		}
249
250	+	@ARTICLE{Barojas1973,
251	+	author = {J. Barojas and D. Levesque},
252	+	title = {Simulation of Diatomic Homonuclear Liquids},
253	+	journal = {Phys. Rev. A},
254	+	year = {1973},
255	+	volume = {7},
256	+	pages = {1092-1105},
257	+	}
258	+
259		@ARTICLE{Barth1998,
260		author = {E. Barth and T. Schlick},
261		title = {Overcoming stability limitations in biomolecular dynamics. I. Combining
262	<	force splitting via extrapolation with Langevin dynamics in LN},
262	>	force splitting via extrapolation with Langevin dynamics in LN},
263		journal = {Journal of Chemical Physics},
264		year = {1998},
265		volume = {109},
#	Line 236 | Line 267 | Encoding: GBK
267		number = {5},
268		month = {Aug 1},
269		abstract = {We present an efficient new method termed LN for propagating biomolecular
270	<	dynamics according to the Langevin equation that arose fortuitously
271	<	upon analysis of the range of harmonic validity of our normal-mode
272	<	scheme LIN. LN combines force linearization with force splitting
273	<	techniques and disposes of LIN'S computationally intensive minimization
274	<	(anharmonic correction) component. Unlike the competitive multiple-timestepping
275	<	(MTS) schemes today-formulated to be symplectic and time-reversible-LN
276	<	merges the slow and fast forces via extrapolation rather than impulses;
277	<	the Langevin heat bath prevents systematic energy drifts. This combination
278	<	succeeds in achieving more significant speedups than these MTS methods
279	<	which are Limited by resonance artifacts to an outer timestep less
280	<	than some integer multiple of half the period of the fastest motion
281	<	(around 4-5 fs for biomolecules). We show that LN achieves very
282	<	good agreement with small-timestep solutions of the Langevin equation
283	<	in terms of thermodynamics (energy means and variances), geometry,
284	<	and dynamics (spectral densities) for two proteins in vacuum and
285	<	a large water system. Significantly, the frequency of updating the
286	<	slow forces extends to 48 fs or more, resulting in speedup factors
287	<	exceeding 10. The implementation of LN in any program that employs
288	<	force-splitting computations is straightforward, with only partial
289	<	second-derivative information required, as well as sparse Hessian/vector
290	<	multiplication routines. The linearization part of LN could even
291	<	be replaced by direct evaluation of the fast components. The application
292	<	of LN to biomolecular dynamics is well suited for configurational
293	<	sampling, thermodynamic, and structural questions. (C) 1998 American
294	<	Institute of Physics.},
270	>	dynamics according to the Langevin equation that arose fortuitously
271	>	upon analysis of the range of harmonic validity of our normal-mode
272	>	scheme LIN. LN combines force linearization with force splitting
273	>	techniques and disposes of LIN'S computationally intensive minimization
274	>	(anharmonic correction) component. Unlike the competitive multiple-timestepping
275	>	(MTS) schemes today-formulated to be symplectic and time-reversible-LN
276	>	merges the slow and fast forces via extrapolation rather than impulses;
277	>	the Langevin heat bath prevents systematic energy drifts. This combination
278	>	succeeds in achieving more significant speedups than these MTS methods
279	>	which are Limited by resonance artifacts to an outer timestep less
280	>	than some integer multiple of half the period of the fastest motion
281	>	(around 4-5 fs for biomolecules). We show that LN achieves very
282	>	good agreement with small-timestep solutions of the Langevin equation
283	>	in terms of thermodynamics (energy means and variances), geometry,
284	>	and dynamics (spectral densities) for two proteins in vacuum and
285	>	a large water system. Significantly, the frequency of updating the
286	>	slow forces extends to 48 fs or more, resulting in speedup factors
287	>	exceeding 10. The implementation of LN in any program that employs
288	>	force-splitting computations is straightforward, with only partial
289	>	second-derivative information required, as well as sparse Hessian/vector
290	>	multiplication routines. The linearization part of LN could even
291	>	be replaced by direct evaluation of the fast components. The application
292	>	of LN to biomolecular dynamics is well suited for configurational
293	>	sampling, thermodynamic, and structural questions. (C) 1998 American
294	>	Institute of Physics.},
295		annote = {105HH Times Cited:29 Cited References Count:49},
296		issn = {0021-9606},
297		uri = {<Go to ISI>://000075066300006},
#	Line 269 | Line 300 | Encoding: GBK
300		@ARTICLE{Batcho2001,
301		author = {P. F. Batcho and T. Schlick},
302		title = {Special stability advantages of position-Verlet over velocity-Verlet
303	<	in multiple-time step integration},
303	>	in multiple-time step integration},
304		journal = {Journal of Chemical Physics},
305		year = {2001},
306		volume = {115},
#	Line 277 | Line 308 | Encoding: GBK
308		number = {9},
309		month = {Sep 1},
310		abstract = {We present an analysis for a simple two-component harmonic oscillator
311	<	that compares the use of position-Verlet to velocity-Verlet for
312	<	multiple-time step integration. The numerical stability analysis
313	<	based on the impulse-Verlet splitting shows that position-Verlet
314	<	has enhanced stability, in terms of the largest allowable time step,
315	<	for cases where an ample separation of time scales exists. Numerical
316	<	investigations confirm the advantages of the position-Verlet scheme
317	<	when used for the fastest time scales of the system. Applications
318	<	to a biomolecule. a solvated protein, for both Newtonian and Langevin
319	<	dynamics echo these trends over large outer time-step regimes. (C)
320	<	2001 American Institute of Physics.},
311	>	that compares the use of position-Verlet to velocity-Verlet for
312	>	multiple-time step integration. The numerical stability analysis
313	>	based on the impulse-Verlet splitting shows that position-Verlet
314	>	has enhanced stability, in terms of the largest allowable time step,
315	>	for cases where an ample separation of time scales exists. Numerical
316	>	investigations confirm the advantages of the position-Verlet scheme
317	>	when used for the fastest time scales of the system. Applications
318	>	to a biomolecule. a solvated protein, for both Newtonian and Langevin
319	>	dynamics echo these trends over large outer time-step regimes. (C)
320	>	2001 American Institute of Physics.},
321		annote = {469KV Times Cited:6 Cited References Count:30},
322		issn = {0021-9606},
323		uri = {<Go to ISI>://000170813800005},
#	Line 295 | Line 326 | Encoding: GBK
326		@ARTICLE{Bates2005,
327		author = {M. A. Bates and G. R. Luckhurst},
328		title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation
329	<	study},
329	>	study},
330		journal = {Physical Review E},
331		year = {2005},
332		volume = {72},
#	Line 303 | Line 334 | Encoding: GBK
334		number = {5},
335		month = {Nov},
336		abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
337	<	can exhibit the elusive biaxial nematic phase, we have developed
338	<	a generic simulation model for such systems. This contains the features
339	<	of the molecule that are essential to its liquid crystal behavior,
340	<	namely the anisotropies of the two arms and the angle between them.
341	<	The behavior of the model has been investigated using Monte Carlo
342	<	simulations for a wide range of these structural parameters. This
343	<	allows us to establish the relationship between the V-shaped molecule
344	<	and its ability to form a biaxial nematic phase. Of particular importance
345	<	are the criteria of geometry and the relative anisotropy necessary
346	<	for the system to exhibit a Landau point, at which the biaxial nematic
347	<	is formed directly from the isotropic phase. The simulations have
348	<	also been used to determine the orientational order parameters for
349	<	a selection of molecular axes. These are especially important because
350	<	they reveal the phase symmetry and are connected to the experimental
351	<	determination of this. The simulation results show that, whereas
352	<	some positions are extremely sensitive to the phase biaxiality,
353	<	others are totally blind to this.},
337	>	can exhibit the elusive biaxial nematic phase, we have developed
338	>	a generic simulation model for such systems. This contains the features
339	>	of the molecule that are essential to its liquid crystal behavior,
340	>	namely the anisotropies of the two arms and the angle between them.
341	>	The behavior of the model has been investigated using Monte Carlo
342	>	simulations for a wide range of these structural parameters. This
343	>	allows us to establish the relationship between the V-shaped molecule
344	>	and its ability to form a biaxial nematic phase. Of particular importance
345	>	are the criteria of geometry and the relative anisotropy necessary
346	>	for the system to exhibit a Landau point, at which the biaxial nematic
347	>	is formed directly from the isotropic phase. The simulations have
348	>	also been used to determine the orientational order parameters for
349	>	a selection of molecular axes. These are especially important because
350	>	they reveal the phase symmetry and are connected to the experimental
351	>	determination of this. The simulation results show that, whereas
352	>	some positions are extremely sensitive to the phase biaxiality,
353	>	others are totally blind to this.},
354		annote = {Part 1 988LQ Times Cited:0 Cited References Count:38},
355		issn = {1539-3755},
356		uri = {<Go to ISI>://000233603100030},
#	Line 335 | Line 366 | Encoding: GBK
366		number = {5},
367		month = {Nov 1},
368		abstract = {We introduce an unbiased protocol for performing rotational moves
369	<	in rigid-body dynamics simulations. This approach - based on the
370	<	analytic solution for the rotational equations of motion for an
371	<	orthogonal coordinate system at constant angular velocity - removes
372	<	deficiencies that have been largely ignored in Brownian dynamics
373	<	simulations, namely errors for finite rotations that result from
374	<	applying the noncommuting rotational matrices in an arbitrary order.
375	<	Our algorithm should thus replace standard approaches to rotate
376	<	local coordinate frames in Langevin and Brownian dynamics simulations.},
369	>	in rigid-body dynamics simulations. This approach - based on the
370	>	analytic solution for the rotational equations of motion for an
371	>	orthogonal coordinate system at constant angular velocity - removes
372	>	deficiencies that have been largely ignored in Brownian dynamics
373	>	simulations, namely errors for finite rotations that result from
374	>	applying the noncommuting rotational matrices in an arbitrary order.
375	>	Our algorithm should thus replace standard approaches to rotate
376	>	local coordinate frames in Langevin and Brownian dynamics simulations.},
377		annote = {736UA Times Cited:0 Cited References Count:11},
378		issn = {0006-3495},
379		uri = {<Go to ISI>://000186190500018},
#	Line 351 | Line 382 | Encoding: GBK
382		@ARTICLE{Beloborodov1998,
383		author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev},
384		title = {Effect of coupling between rotational and translational Brownian
385	<	motions on NMR spin relaxation: Consideration using green function
386	<	of rigid body diffusion},
385	>	motions on NMR spin relaxation: Consideration using green function
386	>	of rigid body diffusion},
387		journal = {Journal of Magnetic Resonance},
388		year = {1998},
389		volume = {132},
#	Line 360 | Line 391 | Encoding: GBK
391		number = {2},
392		month = {Jun},
393		abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
394	<	Biopolymers 33, 409-436, 1993), it was analytically shown that coupling
395	<	between translation and rotation diffusion degrees of freedom does
396	<	not affect the correlation functions relevant to the NMR intramolecular
397	<	relaxation. It follows that spectral densities usually used for
398	<	the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37,
399	<	647-654, 1962) can be regarded as exact in respect to the rotation-translation
400	<	coupling for the spin system connected with a rigid body. (C) 1998
401	<	Academic Press.},
394	>	Biopolymers 33, 409-436, 1993), it was analytically shown that coupling
395	>	between translation and rotation diffusion degrees of freedom does
396	>	not affect the correlation functions relevant to the NMR intramolecular
397	>	relaxation. It follows that spectral densities usually used for
398	>	the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37,
399	>	647-654, 1962) can be regarded as exact in respect to the rotation-translation
400	>	coupling for the spin system connected with a rigid body. (C) 1998
401	>	Academic Press.},
402		annote = {Zu605 Times Cited:2 Cited References Count:6},
403		issn = {1090-7807},
404		uri = {<Go to ISI>://000074214800017},
#	Line 376 | Line 407 | Encoding: GBK
407		@ARTICLE{Berardi1996,
408		author = {R. Berardi and S. Orlandi and C. Zannoni},
409		title = {Antiphase structures in polar smectic liquid crystals and their molecular
410	<	origin},
410	>	origin},
411		journal = {Chemical Physics Letters},
412		year = {1996},
413		volume = {261},
#	Line 384 | Line 415 | Encoding: GBK
415		number = {3},
416		month = {Oct 18},
417		abstract = {We demonstrate that the overall molecular dipole organization in a
418	<	smectic liquid crystal formed of polar molecules can be strongly
419	<	influenced by the position of the dipole in the molecule. We study
420	<	by large scale Monte Carlo simulations systems of attractive-repulsive
421	<	''Gay-Berne'' elongated ellipsoids with an axial dipole at the center
422	<	or near the end of the molecule and we show that monolayer smectic
423	<	liquid crystals and modulated antiferroelectric bilayer stripe domains
424	<	similar to the experimentally observed ''antiphase'' structures
425	<	are obtained in the two cases.},
418	>	smectic liquid crystal formed of polar molecules can be strongly
419	>	influenced by the position of the dipole in the molecule. We study
420	>	by large scale Monte Carlo simulations systems of attractive-repulsive
421	>	''Gay-Berne'' elongated ellipsoids with an axial dipole at the center
422	>	or near the end of the molecule and we show that monolayer smectic
423	>	liquid crystals and modulated antiferroelectric bilayer stripe domains
424	>	similar to the experimentally observed ''antiphase'' structures
425	>	are obtained in the two cases.},
426		annote = {Vn637 Times Cited:49 Cited References Count:26},
427		issn = {0009-2614},
428		uri = {<Go to ISI>://A1996VN63700023},
#	Line 399 | Line 430 | Encoding: GBK
430
431		@ARTICLE{Berkov2005,
432		author = {D. V. Berkov and N. L. Gorn},
402	–	title = {Stochastic dynamic simulations of fast remagnetization processes:
403	–	recent advances and applications},
404	–	journal = {Journal of Magnetism and Magnetic Materials},
405	–	year = {2005},
406	–	volume = {290},
407	–	pages = {442-448},
408	–	month = {Apr},
409	–	abstract = {Numerical simulations of fast remagnetization processes using stochastic
410	–	dynamics are widely used to study various magnetic systems. In this
411	–	paper, we first address several crucial methodological problems
412	–	of such simulations: (i) the influence of finite-element discretization
413	–	on simulated dynamics, (ii) choice between Ito and Stratonovich
414	–	stochastic calculi by the solution of micromagnetic stochastic equations
415	–	of motion and (iii) non-trivial correlation properties of the random
416	–	(thermal) field. Next, we discuss several examples to demonstrate
417	–	the great potential of the Langevin dynamics for studying fast remagnetization
418	–	processes in technically relevant applications: we present numerical
419	–	analysis of equilibrium magnon spectra in patterned structures,
420	–	study thermal noise effects on the magnetization dynamics of nanoelements
421	–	in pulsed fields and show some results for a remagnetization dynamics
422	–	induced by a spin-polarized current. (c) 2004 Elsevier B.V. All
423	–	rights reserved.},
424	–	annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
425	–	issn = {0304-8853},
426	–	uri = {<Go to ISI>://000228837600109},
427	–	}
428	–
429	–	@ARTICLE{Berkov2005a,
430	–	author = {D. V. Berkov and N. L. Gorn},
433		title = {Magnetization precession due to a spin-polarized current in a thin
434	<	nanoelement: Numerical simulation study},
434	>	nanoelement: Numerical simulation study},
435		journal = {Physical Review B},
436		year = {2005},
437		volume = {72},
#	Line 437 | Line 439 | Encoding: GBK
439		number = {9},
440		month = {Sep},
441		abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
442	<	formalism) of magnetization oscillations driven by a spin-polarized
443	<	current through a thin elliptical nanoelement is presented. We show
444	<	that a sophisticated micromagnetic model, where a polycrystalline
445	<	structure of a nanoelement is taken into account, can explain qualitatively
446	<	all most important features of the magnetization oscillation spectra
447	<	recently observed experimentally [S. I. Kiselev , Nature 425, 380
448	<	(2003)], namely, existence of several equidistant spectral bands,
449	<	sharp onset and abrupt disappearance of magnetization oscillations
450	<	with increasing current, absence of the out-of-plane regime predicted
451	<	by a macrospin model, and the relation between frequencies of so-called
452	<	small-angle and quasichaotic oscillations. However, a quantitative
453	<	agreement with experimental results (especially concerning the frequency
454	<	of quasichaotic oscillations) could not be achieved in the region
455	<	of reasonable parameter values, indicating that further model refinement
456	<	is necessary for a complete understanding of the spin-driven magnetization
457	<	precession even in this relatively simple experimental situation.},
442	>	formalism) of magnetization oscillations driven by a spin-polarized
443	>	current through a thin elliptical nanoelement is presented. We show
444	>	that a sophisticated micromagnetic model, where a polycrystalline
445	>	structure of a nanoelement is taken into account, can explain qualitatively
446	>	all most important features of the magnetization oscillation spectra
447	>	recently observed experimentally [S. I. Kiselev , Nature 425, 380
448	>	(2003)], namely, existence of several equidistant spectral bands,
449	>	sharp onset and abrupt disappearance of magnetization oscillations
450	>	with increasing current, absence of the out-of-plane regime predicted
451	>	by a macrospin model, and the relation between frequencies of so-called
452	>	small-angle and quasichaotic oscillations. However, a quantitative
453	>	agreement with experimental results (especially concerning the frequency
454	>	of quasichaotic oscillations) could not be achieved in the region
455	>	of reasonable parameter values, indicating that further model refinement
456	>	is necessary for a complete understanding of the spin-driven magnetization
457	>	precession even in this relatively simple experimental situation.},
458		annote = {969IT Times Cited:2 Cited References Count:55},
459		issn = {1098-0121},
460		uri = {<Go to ISI>://000232228500058},
461		}
462
463	+	@ARTICLE{Berkov2005a,
464	+	author = {D. V. Berkov and N. L. Gorn},
465	+	title = {Stochastic dynamic simulations of fast remagnetization processes:
466	+	recent advances and applications},
467	+	journal = {Journal of Magnetism and Magnetic Materials},
468	+	year = {2005},
469	+	volume = {290},
470	+	pages = {442-448},
471	+	month = {Apr},
472	+	abstract = {Numerical simulations of fast remagnetization processes using stochastic
473	+	dynamics are widely used to study various magnetic systems. In this
474	+	paper, we first address several crucial methodological problems
475	+	of such simulations: (i) the influence of finite-element discretization
476	+	on simulated dynamics, (ii) choice between Ito and Stratonovich
477	+	stochastic calculi by the solution of micromagnetic stochastic equations
478	+	of motion and (iii) non-trivial correlation properties of the random
479	+	(thermal) field. Next, we discuss several examples to demonstrate
480	+	the great potential of the Langevin dynamics for studying fast remagnetization
481	+	processes in technically relevant applications: we present numerical
482	+	analysis of equilibrium magnon spectra in patterned structures,
483	+	study thermal noise effects on the magnetization dynamics of nanoelements
484	+	in pulsed fields and show some results for a remagnetization dynamics
485	+	induced by a spin-polarized current. (c) 2004 Elsevier B.V. All
486	+	rights reserved.},
487	+	annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
488	+	issn = {0304-8853},
489	+	uri = {<Go to ISI>://000228837600109},
490	+	}
491	+
492		@ARTICLE{Berkov2002,
493		author = {D. V. Berkov and N. L. Gorn and P. Gornert},
494		title = {Magnetization dynamics in nanoparticle systems: Numerical simulation
495	<	using Langevin dynamics},
495	>	using Langevin dynamics},
496		journal = {Physica Status Solidi a-Applied Research},
497		year = {2002},
498		volume = {189},
#	Line 469 | Line 500 | Encoding: GBK
500		number = {2},
501		month = {Feb 16},
502		abstract = {We report on recent progress achieved by the development of numerical
503	<	methods based on the stochastic (Langevin) dynamics applied to systems
504	<	of interacting magnetic nanoparticles. The method enables direct
505	<	simulations of the trajectories of magnetic moments taking into
506	<	account (i) all relevant interactions, (ii) precession dynamics,
507	<	and (iii) temperature fluctuations included via the random (thermal)
508	<	field. We present several novel results obtained using new methods
509	<	developed for the solution of the Langevin equations. In particular,
510	<	we have investigated magnetic nanodots and disordered granular systems
511	<	of single-domain magnetic particles. For the first case we have
512	<	calculated the spectrum and the spatial distribution of spin excitations.
513	<	For the second system the complex ac susceptibility chi(omega, T)
514	<	for various particle concentrations and particle anisotropies were
515	<	computed and compared with numerous experimental results.},
503	>	methods based on the stochastic (Langevin) dynamics applied to systems
504	>	of interacting magnetic nanoparticles. The method enables direct
505	>	simulations of the trajectories of magnetic moments taking into
506	>	account (i) all relevant interactions, (ii) precession dynamics,
507	>	and (iii) temperature fluctuations included via the random (thermal)
508	>	field. We present several novel results obtained using new methods
509	>	developed for the solution of the Langevin equations. In particular,
510	>	we have investigated magnetic nanodots and disordered granular systems
511	>	of single-domain magnetic particles. For the first case we have
512	>	calculated the spectrum and the spatial distribution of spin excitations.
513	>	For the second system the complex ac susceptibility chi(omega, T)
514	>	for various particle concentrations and particle anisotropies were
515	>	computed and compared with numerous experimental results.},
516		annote = {526TF Times Cited:4 Cited References Count:37},
517		issn = {0031-8965},
518		uri = {<Go to ISI>://000174145200026},
#	Line 490 | Line 521 | Encoding: GBK
521		@ARTICLE{Bernal1980,
522		author = {J.M. Bernal and J. G. {de la Torre}},
523		title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules
524	<	with Arbitrary Shape},
524	>	with Arbitrary Shape},
525		journal = {Biopolymers},
526		year = {1980},
527		volume = {19},
528		pages = {751-766},
529		}
530
531	+	@ARTICLE{Brenner1967,
532	+	author = {H. Brenner },
533	+	title = {Coupling between the Translational and Rotational Brownian Motions
534	+	of Rigid Particles of Arbitrary shape},
535	+	journal = {J. Collid. Int. Sci.},
536	+	year = {1967},
537	+	volume = {23},
538	+	pages = {407-436},
539	+	}
540	+
541	+	@ARTICLE{Brooks1983,
542	+	author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States
543	+	and S. Swaminathan and M. Karplus},
544	+	title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics
545	+	Calculations},
546	+	journal = {Journal of Computational Chemistry},
547	+	year = {1983},
548	+	volume = {4},
549	+	pages = {187-217},
550	+	number = {2},
551	+	annote = {Qp423 Times Cited:6414 Cited References Count:96},
552	+	issn = {0192-8651},
553	+	uri = {<Go to ISI>://A1983QP42300010},
554	+	}
555	+
556		@ARTICLE{Brunger1984,
557		author = {A. Brunger and C. L. Brooks and M. Karplus},
558		title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations
559	<	of St2 Water},
559	>	of St2 Water},
560		journal = {Chemical Physics Letters},
561		year = {1984},
562		volume = {105},
#	Line 511 | Line 567 | Encoding: GBK
567		uri = {<Go to ISI>://A1984SM17300007},
568		}
569
570	+	@ARTICLE{Budd1999,
571	+	author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell},
572	+	title = {Self-similar numerical solutions of the porous-medium equation using
573	+	moving mesh methods},
574	+	journal = {Philosophical Transactions of the Royal Society of London Series
575	+	a-Mathematical Physical and Engineering Sciences},
576	+	year = {1999},
577	+	volume = {357},
578	+	pages = {1047-1077},
579	+	number = {1754},
580	+	month = {Apr 15},
581	+	abstract = {This paper examines a synthesis of adaptive mesh methods with the
582	+	use of symmetry to study a partial differential equation. In particular,
583	+	it considers methods which admit discrete self-similar solutions,
584	+	examining the convergence of these to the true self-similar solution
585	+	as well as their stability. Special attention is given to the nonlinear
586	+	diffusion equation describing flow in a porous medium.},
587	+	annote = {199EE Times Cited:4 Cited References Count:14},
588	+	issn = {1364-503X},
589	+	uri = {<Go to ISI>://000080466800005},
590	+	}
591	+
592		@ARTICLE{Camp1999,
593		author = {P. J. Camp and M. P. Allen and A. J. Masters},
594		title = {Theory and computer simulation of bent-core molecules},
#	Line 521 | Line 599 | Encoding: GBK
599		number = {21},
600		month = {Dec 1},
601		abstract = {Fluids of hard bent-core molecules have been studied using theory
602	<	and computer simulation. The molecules are composed of two hard
603	<	spherocylinders, with length-to-breadth ratio L/D, joined by their
604	<	ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20
605	<	degrees, the simulations show isotropic, nematic, smectic, and solid
606	<	phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic,
607	<	and solid phases are in evidence, which suggests that there is a
608	<	nematic-smectic-solid triple point at an angle in the range 20 degrees
609	<	< gamma < 30 degrees. In all of the orientationally ordered fluid
610	<	phases the order is purely uniaxial. For gamma = 10 degrees and
611	<	20 degrees, at the studied densities, the solid is also uniaxially
612	<	ordered, whilst for gamma = 30 degrees the solid layers are biaxially
613	<	ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find
614	<	no spontaneous orientational ordering. This is shown to be due to
615	<	the interlocking of dimer pairs which precludes alignment. We find
616	<	similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial
617	<	nematic transition is predicted by Onsager theory. Simulations in
618	<	the biaxial nematic phase show it to be at least mechanically stable
619	<	with respect to the isotropic phase, however. We have compared the
620	<	quasi-exact simulation results in the isotropic phase with the predicted
621	<	equations of state from three theories: the virial expansion containing
622	<	the second and third virial coefficients; the Parsons-Lee equation
623	<	of state; an application of Wertheim's theory of associating fluids
624	<	in the limit of infinite attractive association energy. For all
625	<	of the molecule elongations and geometries we have simulated, the
626	<	Wertheim theory proved to be the most accurate. Interestingly, the
627	<	isotropic equation of state is virtually independent of the dimer
628	<	bond angle-a feature that is also reflected in the lack of variation
629	<	with angle of the calculated second and third virial coefficients.
630	<	(C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].},
602	>	and computer simulation. The molecules are composed of two hard
603	>	spherocylinders, with length-to-breadth ratio L/D, joined by their
604	>	ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20
605	>	degrees, the simulations show isotropic, nematic, smectic, and solid
606	>	phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic,
607	>	and solid phases are in evidence, which suggests that there is a
608	>	nematic-smectic-solid triple point at an angle in the range 20 degrees
609	>	< gamma < 30 degrees. In all of the orientationally ordered fluid
610	>	phases the order is purely uniaxial. For gamma = 10 degrees and
611	>	20 degrees, at the studied densities, the solid is also uniaxially
612	>	ordered, whilst for gamma = 30 degrees the solid layers are biaxially
613	>	ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find
614	>	no spontaneous orientational ordering. This is shown to be due to
615	>	the interlocking of dimer pairs which precludes alignment. We find
616	>	similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial
617	>	nematic transition is predicted by Onsager theory. Simulations in
618	>	the biaxial nematic phase show it to be at least mechanically stable
619	>	with respect to the isotropic phase, however. We have compared the
620	>	quasi-exact simulation results in the isotropic phase with the predicted
621	>	equations of state from three theories: the virial expansion containing
622	>	the second and third virial coefficients; the Parsons-Lee equation
623	>	of state; an application of Wertheim's theory of associating fluids
624	>	in the limit of infinite attractive association energy. For all
625	>	of the molecule elongations and geometries we have simulated, the
626	>	Wertheim theory proved to be the most accurate. Interestingly, the
627	>	isotropic equation of state is virtually independent of the dimer
628	>	bond angle-a feature that is also reflected in the lack of variation
629	>	with angle of the calculated second and third virial coefficients.
630	>	(C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].},
631		annote = {255TC Times Cited:24 Cited References Count:38},
632		issn = {0021-9606},
633		uri = {<Go to ISI>://000083685400056},
#	Line 565 | Line 643 | Encoding: GBK
643		number = {11},
644		month = {Nov},
645		abstract = {A review is presented of molecular and mesoscopic computer simulations
646	<	of liquid crystalline systems. Molecular simulation approaches applied
647	<	to such systems are described, and the key findings for bulk phase
648	<	behaviour are reported. Following this, recently developed lattice
649	<	Boltzmann approaches to the mesoscale modelling of nemato-dynanics
650	<	are reviewed. This paper concludes with a discussion of possible
651	<	areas for future development in this field.},
646	>	of liquid crystalline systems. Molecular simulation approaches applied
647	>	to such systems are described, and the key findings for bulk phase
648	>	behaviour are reported. Following this, recently developed lattice
649	>	Boltzmann approaches to the mesoscale modelling of nemato-dynanics
650	>	are reviewed. This paper concludes with a discussion of possible
651	>	areas for future development in this field.},
652		annote = {989TU Times Cited:2 Cited References Count:258},
653		issn = {0034-4885},
654		uri = {<Go to ISI>://000233697600004},
#	Line 579 | Line 657 | Encoding: GBK
657		@ARTICLE{Carrasco1999,
658		author = {B. Carrasco and J. G. {de la Torre}},
659		title = {Hydrodynamic properties of rigid particles: Comparison of different
660	<	modeling and computational procedures},
660	>	modeling and computational procedures},
661		journal = {Biophysical Journal},
662		year = {1999},
663		volume = {76},
#	Line 587 | Line 665 | Encoding: GBK
665		number = {6},
666		month = {Jun},
667		abstract = {The hydrodynamic properties of rigid particles are calculated from
668	<	models composed of spherical elements (beads) using theories developed
669	<	by Kirkwood, Bloomfield, and their coworkers. Bead models have usually
670	<	been built in such a way that the beads fill the volume occupied
671	<	by the particles. Sometimes the beads are few and of varying sizes
672	<	(bead models in the strict sense), and other times there are many
673	<	small beads (filling models). Because hydrodynamic friction takes
674	<	place at the molecular surface, another possibility is to use shell
675	<	models, as originally proposed by Bloomfield. In this work, we have
676	<	developed procedures to build models of the various kinds, and we
677	<	describe the theory and methods for calculating their hydrodynamic
678	<	properties, including approximate methods that may be needed to
679	<	treat models with a very large number of elements. By combining
680	<	the various possibilities of model building and hydrodynamic calculation,
681	<	several strategies can be designed. We have made a quantitative
682	<	comparison of the performance of the various strategies by applying
683	<	them to some test cases, for which the properties are known a priori.
684	<	We provide guidelines and computational tools for bead modeling.},
668	>	models composed of spherical elements (beads) using theories developed
669	>	by Kirkwood, Bloomfield, and their coworkers. Bead models have usually
670	>	been built in such a way that the beads fill the volume occupied
671	>	by the particles. Sometimes the beads are few and of varying sizes
672	>	(bead models in the strict sense), and other times there are many
673	>	small beads (filling models). Because hydrodynamic friction takes
674	>	place at the molecular surface, another possibility is to use shell
675	>	models, as originally proposed by Bloomfield. In this work, we have
676	>	developed procedures to build models of the various kinds, and we
677	>	describe the theory and methods for calculating their hydrodynamic
678	>	properties, including approximate methods that may be needed to
679	>	treat models with a very large number of elements. By combining
680	>	the various possibilities of model building and hydrodynamic calculation,
681	>	several strategies can be designed. We have made a quantitative
682	>	comparison of the performance of the various strategies by applying
683	>	them to some test cases, for which the properties are known a priori.
684	>	We provide guidelines and computational tools for bead modeling.},
685		annote = {200TT Times Cited:46 Cited References Count:57},
686		issn = {0006-3495},
687		uri = {<Go to ISI>://000080556700016},
#	Line 612 | Line 690 | Encoding: GBK
690		@ARTICLE{Chandra1999,
691		author = {A. Chandra and T. Ichiye},
692		title = {Dynamical properties of the soft sticky dipole model of water: Molecular
693	<	dynamics simulations},
693	>	dynamics simulations},
694		journal = {Journal of Chemical Physics},
695		year = {1999},
696		volume = {111},
#	Line 620 | Line 698 | Encoding: GBK
698		number = {6},
699		month = {Aug 8},
700		abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
701	<	are calculated by means of molecular dynamics simulations. Since
702	<	this is not a simple point model, the forces and torques arising
703	<	from the SSD potential are derived here. Simulations are carried
704	<	out in the microcanonical ensemble employing the Ewald method for
705	<	the electrostatic interactions. Various time correlation functions
706	<	and dynamical quantities associated with the translational and rotational
707	<	motion of water molecules are evaluated and compared with those
708	<	of two other commonly used models of liquid water, namely the transferable
709	<	intermolecular potential-three points (TIP3P) and simple point charge/extended
710	<	(SPC/E) models, and also with experiments. The dynamical properties
711	<	of the SSD water model are found to be in good agreement with the
712	<	experimental results and appear to be better than the TIP3P and
713	<	SPC/E models in most cases, as has been previously shown for its
714	<	thermodynamic, structural, and dielectric properties. Also, molecular
715	<	dynamics simulations of the SSD model are found to run much faster
716	<	than TIP3P, SPC/E, and other multisite models. (C) 1999 American
717	<	Institute of Physics. [S0021-9606(99)51430-X].},
701	>	are calculated by means of molecular dynamics simulations. Since
702	>	this is not a simple point model, the forces and torques arising
703	>	from the SSD potential are derived here. Simulations are carried
704	>	out in the microcanonical ensemble employing the Ewald method for
705	>	the electrostatic interactions. Various time correlation functions
706	>	and dynamical quantities associated with the translational and rotational
707	>	motion of water molecules are evaluated and compared with those
708	>	of two other commonly used models of liquid water, namely the transferable
709	>	intermolecular potential-three points (TIP3P) and simple point charge/extended
710	>	(SPC/E) models, and also with experiments. The dynamical properties
711	>	of the SSD water model are found to be in good agreement with the
712	>	experimental results and appear to be better than the TIP3P and
713	>	SPC/E models in most cases, as has been previously shown for its
714	>	thermodynamic, structural, and dielectric properties. Also, molecular
715	>	dynamics simulations of the SSD model are found to run much faster
716	>	than TIP3P, SPC/E, and other multisite models. (C) 1999 American
717	>	Institute of Physics. [S0021-9606(99)51430-X].},
718		annote = {221EN Times Cited:14 Cited References Count:66},
719		issn = {0021-9606},
720		uri = {<Go to ISI>://000081711200038},
721		}
722
723	+	@ARTICLE{Channell1990,
724	+	author = {P. J. Channell and C. Scovel},
725	+	title = {Symplectic Integration of Hamiltonian-Systems},
726	+	journal = {Nonlinearity},
727	+	year = {1990},
728	+	volume = {3},
729	+	pages = {231-259},
730	+	number = {2},
731	+	month = {may},
732	+	annote = {Dk631 Times Cited:152 Cited References Count:34},
733	+	issn = {0951-7715},
734	+	uri = {<Go to ISI>://A1990DK63100001},
735	+	}
736	+
737	+	@ARTICLE{Chen2003,
738	+	author = {B. Chen and F. Solis},
739	+	title = {Explicit mixed finite order Runge-Kutta methods},
740	+	journal = {Applied Numerical Mathematics},
741	+	year = {2003},
742	+	volume = {44},
743	+	pages = {21-30},
744	+	number = {1-2},
745	+	month = {Jan},
746	+	abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
747	+	equations and introduce a family of mixed methods from combinations
748	+	of explicit Runge-Kutta methods. These methods have better stability
749	+	behavior than traditional Runge-Kutta methods and generally extend
750	+	the range of validity of the calculated solutions. These methods
751	+	also give a way of determining if the numerical solutions are real
752	+	or spurious. Emphasis is put on examples coming from mathematical
753	+	models in ecology. (C) 2002 IMACS. Published by Elsevier Science
754	+	B.V. All rights reserved.},
755	+	annote = {633ZD Times Cited:0 Cited References Count:9},
756	+	issn = {0168-9274},
757	+	uri = {<Go to ISI>://000180314200002},
758	+	}
759	+
760		@ARTICLE{Cheung2004,
761		author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
762		title = {Calculation of flexoelectric coefficients for a nematic liquid crystal
763	<	by atomistic simulation},
763	>	by atomistic simulation},
764		journal = {Journal of Chemical Physics},
765		year = {2004},
766		volume = {121},
#	Line 653 | Line 768 | Encoding: GBK
768		number = {18},
769		month = {Nov 8},
770		abstract = {Equilibrium molecular dynamics calculations have been performed for
771	<	the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile
772	<	(PCH5) using a fully atomistic model. Simulation data have been
773	<	obtained for a series of temperatures in the nematic phase. The
774	<	simulation data have been used to calculate the flexoelectric coefficients
775	<	e(s) and e(b) using the linear response formalism of Osipov and
776	<	Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr.
777	<	31, 125 (1986)]. The temperature and order parameter dependence
778	<	of e(s) and e(b) are examined, as are separate contributions from
779	<	different intermolecular interactions. Values of e(s) and e(b) calculated
780	<	from simulation are consistent with those found from experiment.
781	<	(C) 2004 American Institute of Physics.},
771	>	the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile
772	>	(PCH5) using a fully atomistic model. Simulation data have been
773	>	obtained for a series of temperatures in the nematic phase. The
774	>	simulation data have been used to calculate the flexoelectric coefficients
775	>	e(s) and e(b) using the linear response formalism of Osipov and
776	>	Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr.
777	>	31, 125 (1986)]. The temperature and order parameter dependence
778	>	of e(s) and e(b) are examined, as are separate contributions from
779	>	different intermolecular interactions. Values of e(s) and e(b) calculated
780	>	from simulation are consistent with those found from experiment.
781	>	(C) 2004 American Institute of Physics.},
782		annote = {866UM Times Cited:4 Cited References Count:61},
783		issn = {0021-9606},
784		uri = {<Go to ISI>://000224798900053},
#	Line 679 | Line 794 | Encoding: GBK
794		number = {1-2},
795		month = {Apr 15},
796		abstract = {Equilibrium molecular dynamics calculations have been performed for
797	<	the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile
798	<	(PCH5) using a fully atomistic model. Simulation data has been obtained
799	<	for a series of temperatures in the nematic phase. The rotational
800	<	viscosity co-efficient gamma(1), has been calculated using the angular
801	<	velocity correlation function of the nematic director, n, the mean
802	<	squared diffusion of n and statistical mechanical methods based
803	<	on the rotational diffusion co-efficient. We find good agreement
804	<	between the first two methods and experimental values. (C) 2002
805	<	Published by Elsevier Science B.V.},
797	>	the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile
798	>	(PCH5) using a fully atomistic model. Simulation data has been obtained
799	>	for a series of temperatures in the nematic phase. The rotational
800	>	viscosity co-efficient gamma(1), has been calculated using the angular
801	>	velocity correlation function of the nematic director, n, the mean
802	>	squared diffusion of n and statistical mechanical methods based
803	>	on the rotational diffusion co-efficient. We find good agreement
804	>	between the first two methods and experimental values. (C) 2002
805	>	Published by Elsevier Science B.V.},
806		annote = {547KF Times Cited:8 Cited References Count:31},
807		issn = {0009-2614},
808		uri = {<Go to ISI>://000175331000020},
#	Line 696 | Line 811 | Encoding: GBK
811		@ARTICLE{Chin2004,
812		author = {S. A. Chin},
813		title = {Dynamical multiple-time stepping methods for overcoming resonance
814	<	instabilities},
814	>	instabilities},
815		journal = {Journal of Chemical Physics},
816		year = {2004},
817		volume = {120},
#	Line 704 | Line 819 | Encoding: GBK
819		number = {1},
820		month = {Jan 1},
821		abstract = {Current molecular dynamics simulations of biomolecules using multiple
822	<	time steps to update the slowly changing force are hampered by instabilities
823	<	beginning at time steps near the half period of the fastest vibrating
824	<	mode. These #resonance# instabilities have became a critical barrier
825	<	preventing the long time simulation of biomolecular dynamics. Attempts
826	<	to tame these instabilities by altering the slowly changing force
827	<	and efforts to damp them out by Langevin dynamics do not address
828	<	the fundamental cause of these instabilities. In this work, we trace
829	<	the instability to the nonanalytic character of the underlying spectrum
830	<	and show that a correct splitting of the Hamiltonian, which renders
831	<	the spectrum analytic, restores stability. The resulting Hamiltonian
832	<	dictates that in addition to updating the momentum due to the slowly
833	<	changing force, one must also update the position with a modified
834	<	mass. Thus multiple-time stepping must be done dynamically. (C)
835	<	2004 American Institute of Physics.},
822	>	time steps to update the slowly changing force are hampered by instabilities
823	>	beginning at time steps near the half period of the fastest vibrating
824	>	mode. These #resonance# instabilities have became a critical barrier
825	>	preventing the long time simulation of biomolecular dynamics. Attempts
826	>	to tame these instabilities by altering the slowly changing force
827	>	and efforts to damp them out by Langevin dynamics do not address
828	>	the fundamental cause of these instabilities. In this work, we trace
829	>	the instability to the nonanalytic character of the underlying spectrum
830	>	and show that a correct splitting of the Hamiltonian, which renders
831	>	the spectrum analytic, restores stability. The resulting Hamiltonian
832	>	dictates that in addition to updating the momentum due to the slowly
833	>	changing force, one must also update the position with a modified
834	>	mass. Thus multiple-time stepping must be done dynamically. (C)
835	>	2004 American Institute of Physics.},
836		annote = {757TK Times Cited:1 Cited References Count:22},
837		issn = {0021-9606},
838		uri = {<Go to ISI>://000187577400003},
#	Line 726 | Line 841 | Encoding: GBK
841		@ARTICLE{Cook2000,
842		author = {M. J. Cook and M. R. Wilson},
843		title = {Simulation studies of dipole correlation in the isotropic liquid
844	<	phase},
844	>	phase},
845		journal = {Liquid Crystals},
846		year = {2000},
847		volume = {27},
#	Line 734 | Line 849 | Encoding: GBK
849		number = {12},
850		month = {Dec},
851		abstract = {The Kirkwood correlation factor g(1) determines the preference for
852	<	local parallel or antiparallel dipole association in the isotropic
853	<	phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood
854	<	factors greater than 1 have an enhanced effective dipole moment
855	<	along the molecular long axis. This leads to higher values of Delta
856	<	epsilon in the nematic phase. This paper describes state-of-the-art
857	<	molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile
858	<	(PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl)
859	<	in the isotropic liquid phase using an all-atom force field and
860	<	taking long range electrostatics into account using an Ewald summation.
861	<	Using this methodology, PCH5 is seen to prefer antiparallel dipole
862	<	alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel
863	<	dipole alignment with a positive g(1); this is in accordance with
864	<	experimental dielectric measurements. Analysis of the molecular
865	<	dynamics trajectories allows an assessment of why these molecules
866	<	behave differently.},
852	>	local parallel or antiparallel dipole association in the isotropic
853	>	phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood
854	>	factors greater than 1 have an enhanced effective dipole moment
855	>	along the molecular long axis. This leads to higher values of Delta
856	>	epsilon in the nematic phase. This paper describes state-of-the-art
857	>	molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile
858	>	(PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl)
859	>	in the isotropic liquid phase using an all-atom force field and
860	>	taking long range electrostatics into account using an Ewald summation.
861	>	Using this methodology, PCH5 is seen to prefer antiparallel dipole
862	>	alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel
863	>	dipole alignment with a positive g(1); this is in accordance with
864	>	experimental dielectric measurements. Analysis of the molecular
865	>	dynamics trajectories allows an assessment of why these molecules
866	>	behave differently.},
867		annote = {376BF Times Cited:10 Cited References Count:16},
868		issn = {0267-8292},
869		uri = {<Go to ISI>://000165437800002},
#	Line 757 | Line 872 | Encoding: GBK
872		@ARTICLE{Cui2003,
873		author = {B. X. Cui and M. Y. Shen and K. F. Freed},
874		title = {Folding and misfolding of the papillomavirus E6 interacting peptide
875	<	E6ap},
875	>	E6ap},
876		journal = {Proceedings of the National Academy of Sciences of the United States
877	<	of America},
877	>	of America},
878		year = {2003},
879		volume = {100},
880		pages = {7087-7092},
881		number = {12},
882		month = {Jun 10},
883		abstract = {All-atom Langevin dynamics simulations have been performed to study
884	<	the folding pathways of the 18-residue binding domain fragment E6ap
885	<	of the human papillomavirus E6 interacting peptide. Six independent
886	<	folding trajectories, with a total duration of nearly 2 mus, all
887	<	lead to the same native state in which the E6ap adopts a fluctuating
888	<	a-helix structure in the central portion (Ser-4-Leu-13) but with
889	<	very flexible N and C termini. Simulations starting from different
890	<	core configurations exhibit the E6ap folding dynamics as either
891	<	a two- or three-state folder with an intermediate misfolded state.
892	<	The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13)
893	<	is well conserved in the native-state structure but absent in the
894	<	intermediate structure, suggesting that the leucine core is not
895	<	only essential for the binding activity of E6ap but also important
896	<	for the stability of the native structure. The free energy landscape
897	<	reveals a significant barrier between the basins separating the
898	<	native and misfolded states. We also discuss the various underlying
899	<	forces that drive the peptide into its native state.},
884	>	the folding pathways of the 18-residue binding domain fragment E6ap
885	>	of the human papillomavirus E6 interacting peptide. Six independent
886	>	folding trajectories, with a total duration of nearly 2 mus, all
887	>	lead to the same native state in which the E6ap adopts a fluctuating
888	>	a-helix structure in the central portion (Ser-4-Leu-13) but with
889	>	very flexible N and C termini. Simulations starting from different
890	>	core configurations exhibit the E6ap folding dynamics as either
891	>	a two- or three-state folder with an intermediate misfolded state.
892	>	The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13)
893	>	is well conserved in the native-state structure but absent in the
894	>	intermediate structure, suggesting that the leucine core is not
895	>	only essential for the binding activity of E6ap but also important
896	>	for the stability of the native structure. The free energy landscape
897	>	reveals a significant barrier between the basins separating the
898	>	native and misfolded states. We also discuss the various underlying
899	>	forces that drive the peptide into its native state.},
900		annote = {689LC Times Cited:3 Cited References Count:48},
901		issn = {0027-8424},
902		uri = {<Go to ISI>://000183493500037},
#	Line 797 | Line 912 | Encoding: GBK
912		number = {1},
913		month = {Jan 1},
914		abstract = {We study the slow phase of thermally activated magnetic relaxation
915	<	in finite two-dimensional ensembles of dipolar interacting ferromagnetic
916	<	nanoparticles whose easy axes of magnetization are perpendicular
917	<	to the distribution plane. We develop a method to numerically simulate
918	<	the magnetic relaxation for the case that the smallest heights of
919	<	the potential barriers between the equilibrium directions of the
920	<	nanoparticle magnetic moments are much larger than the thermal energy.
921	<	Within this framework, we analyze in detail the role that the correlations
922	<	of the nanoparticle magnetic moments and the finite size of the
923	<	nanoparticle ensemble play in magnetic relaxation.},
915	>	in finite two-dimensional ensembles of dipolar interacting ferromagnetic
916	>	nanoparticles whose easy axes of magnetization are perpendicular
917	>	to the distribution plane. We develop a method to numerically simulate
918	>	the magnetic relaxation for the case that the smallest heights of
919	>	the potential barriers between the equilibrium directions of the
920	>	nanoparticle magnetic moments are much larger than the thermal energy.
921	>	Within this framework, we analyze in detail the role that the correlations
922	>	of the nanoparticle magnetic moments and the finite size of the
923	>	nanoparticle ensemble play in magnetic relaxation.},
924		annote = {642XH Times Cited:11 Cited References Count:31},
925		issn = {1098-0121},
926		uri = {<Go to ISI>://000180830400056},
#	Line 821 | Line 936 | Encoding: GBK
936		number = {1},
937		month = {Jan},
938		abstract = {To explore the origin of the large-scale motion of triosephosphate
939	<	isomerase's flexible loop (residues 166 to 176) at the active site,
940	<	several simulation protocols are employed both for the free enzyme
941	<	in vacuo and for the free enzyme with some solvent modeling: high-temperature
942	<	Langevin dynamics simulations, sampling by a #dynamics##driver#
943	<	approach, and potential-energy surface calculations. Our focus is
944	<	on obtaining the energy barrier to the enzyme's motion and establishing
945	<	the nature of the loop movement. Previous calculations did not determine
946	<	this energy barrier and the effect of solvent on the barrier. High-temperature
947	<	molecular dynamics simulations and crystallographic studies have
948	<	suggested a rigid-body motion with two hinges located at both ends
949	<	of the loop; Brownian dynamics simulations at room temperature pointed
950	<	to a very flexible behavior. The present simulations and analyses
951	<	reveal that although solute/solvent hydrogen bonds play a crucial
952	<	role in lowering the energy along the pathway, there still remains
953	<	a high activation barrier, This finding clearly indicates that,
954	<	if the loop opens and closes in the absence of a substrate at standard
955	<	conditions (e.g., room temperature, appropriate concentration of
956	<	isomerase), the time scale for transition is not in the nanosecond
957	<	but rather the microsecond range. Our results also indicate that
958	<	in the context of spontaneous opening in the free enzyme, the motion
959	<	is of rigid-body type and that the specific interaction between
960	<	residues Ala(176) and Tyr(208) plays a crucial role in the loop
961	<	opening/closing mechanism.},
939	>	isomerase's flexible loop (residues 166 to 176) at the active site,
940	>	several simulation protocols are employed both for the free enzyme
941	>	in vacuo and for the free enzyme with some solvent modeling: high-temperature
942	>	Langevin dynamics simulations, sampling by a #dynamics##driver#
943	>	approach, and potential-energy surface calculations. Our focus is
944	>	on obtaining the energy barrier to the enzyme's motion and establishing
945	>	the nature of the loop movement. Previous calculations did not determine
946	>	this energy barrier and the effect of solvent on the barrier. High-temperature
947	>	molecular dynamics simulations and crystallographic studies have
948	>	suggested a rigid-body motion with two hinges located at both ends
949	>	of the loop; Brownian dynamics simulations at room temperature pointed
950	>	to a very flexible behavior. The present simulations and analyses
951	>	reveal that although solute/solvent hydrogen bonds play a crucial
952	>	role in lowering the energy along the pathway, there still remains
953	>	a high activation barrier, This finding clearly indicates that,
954	>	if the loop opens and closes in the absence of a substrate at standard
955	>	conditions (e.g., room temperature, appropriate concentration of
956	>	isomerase), the time scale for transition is not in the nanosecond
957	>	but rather the microsecond range. Our results also indicate that
958	>	in the context of spontaneous opening in the free enzyme, the motion
959	>	is of rigid-body type and that the specific interaction between
960	>	residues Ala(176) and Tyr(208) plays a crucial role in the loop
961	>	opening/closing mechanism.},
962		annote = {Zl046 Times Cited:30 Cited References Count:29},
963		issn = {0006-3495},
964		uri = {<Go to ISI>://000073393400009},
#	Line 859 | Line 974 | Encoding: GBK
974		number = {15},
975		month = {Oct 15},
976		abstract = {Rigid body molecular models possess symplectic structure and time-reversal
977	<	symmetry. Standard numerical integration methods destroy both properties,
978	<	introducing nonphysical dynamical behavior such as numerically induced
979	<	dissipative states and drift in the energy during long term simulations.
980	<	This article describes the construction, implementation, and practical
981	<	application of fast explicit symplectic-reversible integrators for
982	<	multiple rigid body molecular simulations, These methods use a reduction
983	<	to Euler equations for the free rigid body, together with a symplectic
984	<	splitting technique. In every time step, the orientational dynamics
985	<	of each rigid body is integrated by a sequence of planar rotations.
986	<	Besides preserving the symplectic and reversible structures of the
987	<	flow, this scheme accurately conserves the total angular momentum
988	<	of a system of interacting rigid bodies. Excellent energy conservation
989	<	fan be obtained relative to traditional methods, especially in long-time
990	<	simulations. The method is implemented in a research code, ORIENT
991	<	and compared with a quaternion/extrapolation scheme for the TIP4P
992	<	model of water. Our experiments show that the symplectic-reversible
993	<	scheme is far superior to the more traditional quaternion method.
994	<	(C) 1997 American Institute of Physics.},
995	<	annote = {Ya587 Times Cited:35 Cited References Count:32},
996	<	issn = {0021-9606},
997	<	uri = {<Go to ISI>://A1997YA58700024},
998	<	}
999	<
1000	<	@ARTICLE{Edwards2005,
977	>	symmetry. Standard numerical integration methods destroy both properties,
978	>	introducing nonphysical dynamical behavior such as numerically induced
979	>	dissipative states and drift in the energy during long term simulations.
980	>	This article describes the construction, implementation, and practical
981	>	application of fast explicit symplectic-reversible integrators for
982	>	multiple rigid body molecular simulations, These methods use a reduction
983	>	to Euler equations for the free rigid body, together with a symplectic
984	>	splitting technique. In every time step, the orientational dynamics
985	>	of each rigid body is integrated by a sequence of planar rotations.
986	>	Besides preserving the symplectic and reversible structures of the
987	>	flow, this scheme accurately conserves the total angular momentum
988	>	of a system of interacting rigid bodies. Excellent energy conservation
989	>	fan be obtained relative to traditional methods, especially in long-time
990	>	simulations. The method is implemented in a research code, ORIENT
991	>	and compared with a quaternion/extrapolation scheme for the TIP4P
992	>	model of water. Our experiments show that the symplectic-reversible
993	>	scheme is far superior to the more traditional quaternion method.
994	>	(C) 1997 American Institute of Physics.},
995	>	annote = {Ya587 Times Cited:35 Cited References Count:32},
996	>	issn = {0021-9606},
997	>	uri = {<Go to ISI>://A1997YA58700024},
998	>	}
999	>
1000	>	@BOOK{Gamma1994,
1001	>	title = {Design Patterns: Elements of Reusable Object-Oriented Software},
1002	>	publisher = {Perason Education},
1003	>	year = {1994},
1004	>	author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
1005	>	address = {London},
1006	>	chapter = {7},
1007	>	}
1008	>
1009	>	@ARTICLE{Edwards2005,
1010		author = {S. A. Edwards and D. R. M. Williams},
1011		title = {Stretching a single diblock copolymer in a selective solvent: Langevin
1012	<	dynamics simulations},
1012	>	dynamics simulations},
1013		journal = {Macromolecules},
1014		year = {2005},
1015		volume = {38},
#	Line 893 | Line 1017 | Encoding: GBK
1017		number = {25},
1018		month = {Dec 13},
1019		abstract = {Using the Langevin dynamics technique, we have carried out simulations
1020	<	of a single-chain flexible diblock copolymer. The polymer consists
1021	<	of two blocks of equal length, one very poorly solvated and the
1022	<	other close to theta-conditions. We study what happens when such
1023	<	a polymer is stretched, for a range of different stretching speeds,
1024	<	and correlate our observations with features in the plot of force
1025	<	vs extension. We find that at slow speeds this force profile does
1026	<	not increase monotonically, in disagreement with earlier predictions,
1027	<	and that at high speeds there is a strong dependence on which end
1028	<	of the polymer is pulled, as well as a high level of hysteresis.},
1020	>	of a single-chain flexible diblock copolymer. The polymer consists
1021	>	of two blocks of equal length, one very poorly solvated and the
1022	>	other close to theta-conditions. We study what happens when such
1023	>	a polymer is stretched, for a range of different stretching speeds,
1024	>	and correlate our observations with features in the plot of force
1025	>	vs extension. We find that at slow speeds this force profile does
1026	>	not increase monotonically, in disagreement with earlier predictions,
1027	>	and that at high speeds there is a strong dependence on which end
1028	>	of the polymer is pulled, as well as a high level of hysteresis.},
1029		annote = {992EC Times Cited:0 Cited References Count:13},
1030		issn = {0024-9297},
1031		uri = {<Go to ISI>://000233866200035},
#	Line 910 | Line 1034 | Encoding: GBK
1034		@ARTICLE{Egberts1988,
1035		author = {E. Egberts and H. J. C. Berendsen},
1036		title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic
1037	<	Detail},
1037	>	Detail},
1038		journal = {Journal of Chemical Physics},
1039		year = {1988},
1040		volume = {89},
#	Line 935 | Line 1059 | Encoding: GBK
1059		uri = {<Go to ISI>://A1978FP21600004},
1060		}
1061
1062	+	@ARTICLE{Evans1977,
1063	+	author = {D. J. Evans},
1064	+	title = {Representation of Orientation Space},
1065	+	journal = {Molecular Physics},
1066	+	year = {1977},
1067	+	volume = {34},
1068	+	pages = {317-325},
1069	+	number = {2},
1070	+	annote = {Ds757 Times Cited:271 Cited References Count:18},
1071	+	issn = {0026-8976},
1072	+	uri = {<Go to ISI>://A1977DS75700002},
1073	+	}
1074	+
1075		@ARTICLE{Fennell2004,
1076		author = {C. J. Fennell and J. D. Gezelter},
1077		title = {On the structural and transport properties of the soft sticky dipole
1078	<	and related single-point water models},
1078	>	and related single-point water models},
1079		journal = {Journal of Chemical Physics},
1080		year = {2004},
1081		volume = {120},
#	Line 946 | Line 1083 | Encoding: GBK
1083		number = {19},
1084		month = {May 15},
1085		abstract = {The density maximum and temperature dependence of the self-diffusion
1086	<	constant were investigated for the soft sticky dipole (SSD) water
1087	<	model and two related reparametrizations of this single-point model.
1088	<	A combination of microcanonical and isobaric-isothermal molecular
1089	<	dynamics simulations was used to calculate these properties, both
1090	<	with and without the use of reaction field to handle long-range
1091	<	electrostatics. The isobaric-isothermal simulations of the melting
1092	<	of both ice-I-h and ice-I-c showed a density maximum near 260 K.
1093	<	In most cases, the use of the reaction field resulted in calculated
1094	<	densities which were significantly lower than experimental densities.
1095	<	Analysis of self-diffusion constants shows that the original SSD
1096	<	model captures the transport properties of experimental water very
1097	<	well in both the normal and supercooled liquid regimes. We also
1098	<	present our reparametrized versions of SSD for use both with the
1099	<	reaction field or without any long-range electrostatic corrections.
1100	<	These are called the SSD/RF and SSD/E models, respectively. These
1101	<	modified models were shown to maintain or improve upon the experimental
1102	<	agreement with the structural and transport properties that can
1103	<	be obtained with either the original SSD or the density-corrected
1104	<	version of the original model (SSD1). Additionally, a novel low-density
1105	<	ice structure is presented which appears to be the most stable ice
1106	<	structure for the entire SSD family. (C) 2004 American Institute
1107	<	of Physics.},
1086	>	constant were investigated for the soft sticky dipole (SSD) water
1087	>	model and two related reparametrizations of this single-point model.
1088	>	A combination of microcanonical and isobaric-isothermal molecular
1089	>	dynamics simulations was used to calculate these properties, both
1090	>	with and without the use of reaction field to handle long-range
1091	>	electrostatics. The isobaric-isothermal simulations of the melting
1092	>	of both ice-I-h and ice-I-c showed a density maximum near 260 K.
1093	>	In most cases, the use of the reaction field resulted in calculated
1094	>	densities which were significantly lower than experimental densities.
1095	>	Analysis of self-diffusion constants shows that the original SSD
1096	>	model captures the transport properties of experimental water very
1097	>	well in both the normal and supercooled liquid regimes. We also
1098	>	present our reparametrized versions of SSD for use both with the
1099	>	reaction field or without any long-range electrostatic corrections.
1100	>	These are called the SSD/RF and SSD/E models, respectively. These
1101	>	modified models were shown to maintain or improve upon the experimental
1102	>	agreement with the structural and transport properties that can
1103	>	be obtained with either the original SSD or the density-corrected
1104	>	version of the original model (SSD1). Additionally, a novel low-density
1105	>	ice structure is presented which appears to be the most stable ice
1106	>	structure for the entire SSD family. (C) 2004 American Institute
1107	>	of Physics.},
1108		annote = {816YY Times Cited:5 Cited References Count:39},
1109		issn = {0021-9606},
1110		uri = {<Go to ISI>://000221146400032},
#	Line 976 | Line 1113 | Encoding: GBK
1113		@ARTICLE{Fernandes2002,
1114		author = {M. X. Fernandes and J. G. {de la Torre}},
1115		title = {Brownian dynamics simulation of rigid particles of arbitrary shape
1116	<	in external fields},
1116	>	in external fields},
1117		journal = {Biophysical Journal},
1118		year = {2002},
1119		volume = {83},
#	Line 984 | Line 1121 | Encoding: GBK
1121		number = {6},
1122		month = {Dec},
1123		abstract = {We have developed a Brownian dynamics simulation algorithm to generate
1124	<	Brownian trajectories of an isolated, rigid particle of arbitrary
1125	<	shape in the presence of electric fields or any other external agents.
1126	<	Starting from the generalized diffusion tensor, which can be calculated
1127	<	with the existing HYDRO software, the new program BROWNRIG (including
1128	<	a case-specific subprogram for the external agent) carries out a
1129	<	simulation that is analyzed later to extract the observable dynamic
1130	<	properties. We provide a variety of examples of utilization of this
1131	<	method, which serve as tests of its performance, and also illustrate
1132	<	its applicability. Examples include free diffusion, transport in
1133	<	an electric field, and diffusion in a restricting environment.},
1124	>	Brownian trajectories of an isolated, rigid particle of arbitrary
1125	>	shape in the presence of electric fields or any other external agents.
1126	>	Starting from the generalized diffusion tensor, which can be calculated
1127	>	with the existing HYDRO software, the new program BROWNRIG (including
1128	>	a case-specific subprogram for the external agent) carries out a
1129	>	simulation that is analyzed later to extract the observable dynamic
1130	>	properties. We provide a variety of examples of utilization of this
1131	>	method, which serve as tests of its performance, and also illustrate
1132	>	its applicability. Examples include free diffusion, transport in
1133	>	an electric field, and diffusion in a restricting environment.},
1134		annote = {633AD Times Cited:2 Cited References Count:43},
1135		issn = {0006-3495},
1136		uri = {<Go to ISI>://000180256300012},
1137		}
1138
1139	+	@BOOK{Frenkel1996,
1140	+	title = {Understanding Molecular Simulation : From Algorithms to Applications},
1141	+	publisher = {Academic Press},
1142	+	year = {1996},
1143	+	author = {D. Frenkel and B. Smit},
1144	+	address = {New York},
1145	+	}
1146	+
1147		@ARTICLE{Gay1981,
1148		author = {J. G. Gay and B. J. Berne},
1149		title = {Modification of the Overlap Potential to Mimic a Linear Site-Site
1150	<	Potential},
1150	>	Potential},
1151		journal = {Journal of Chemical Physics},
1152		year = {1981},
1153		volume = {74},
#	Line 1023 | Line 1168 | Encoding: GBK
1168		number = {6},
1169		month = {Nov},
1170		abstract = {To investigate the influence of inertial effects on the dynamics of
1171	<	an assembly of beads subjected to rigid constraints and placed in
1172	<	a buffer medium, a convenient method to introduce suitable generalized
1173	<	coordinates is presented. Without any restriction on the nature
1174	<	of the soft forces involved (both stochastic and deterministic),
1175	<	pertinent Langevin equations are derived. Provided that the Brownian
1176	<	forces are Gaussian and Markovian, the corresponding Fokker-Planck
1177	<	equation (FPE) is obtained in the complete phase space of generalized
1178	<	coordinates and momenta. The correct short time behavior for correlation
1179	<	functions (CFs) of generalized coordinates is established, and the
1180	<	diffusion equation with memory (DEM) is deduced from the FPE in
1181	<	the high friction Limit. The DEM is invoked to perform illustrative
1182	<	calculations in two dimensions of the orientational CFs for once
1183	<	broken nonrigid rods immobilized on a surface. These calculations
1184	<	reveal that the CFs under certain conditions exhibit an oscillatory
1185	<	behavior, which is irreproducible within the standard diffusion
1186	<	equation. Several methods are considered for the approximate solution
1187	<	of the DEM, and their application to three dimensional DEMs is discussed.},
1171	>	an assembly of beads subjected to rigid constraints and placed in
1172	>	a buffer medium, a convenient method to introduce suitable generalized
1173	>	coordinates is presented. Without any restriction on the nature
1174	>	of the soft forces involved (both stochastic and deterministic),
1175	>	pertinent Langevin equations are derived. Provided that the Brownian
1176	>	forces are Gaussian and Markovian, the corresponding Fokker-Planck
1177	>	equation (FPE) is obtained in the complete phase space of generalized
1178	>	coordinates and momenta. The correct short time behavior for correlation
1179	>	functions (CFs) of generalized coordinates is established, and the
1180	>	diffusion equation with memory (DEM) is deduced from the FPE in
1181	>	the high friction Limit. The DEM is invoked to perform illustrative
1182	>	calculations in two dimensions of the orientational CFs for once
1183	>	broken nonrigid rods immobilized on a surface. These calculations
1184	>	reveal that the CFs under certain conditions exhibit an oscillatory
1185	>	behavior, which is irreproducible within the standard diffusion
1186	>	equation. Several methods are considered for the approximate solution
1187	>	of the DEM, and their application to three dimensional DEMs is discussed.},
1188		annote = {257MM Times Cited:2 Cited References Count:82},
1189		issn = {1022-1344},
1190		uri = {<Go to ISI>://000083785700002},
1191		}
1192
1193	+	@ARTICLE{Goetz1998,
1194	+	author = {R. Goetz and R. Lipowsky},
1195	+	title = {Computer simulations of bilayer membranes: Self-assembly and interfacial
1196	+	tension},
1197	+	journal = {Journal of Chemical Physics},
1198	+	year = {1998},
1199	+	volume = {108},
1200	+	pages = {7397},
1201	+	number = {17},
1202	+	}
1203	+
1204		@BOOK{Goldstein2001,
1205		title = {Classical Mechanics},
1206		publisher = {Addison Wesley},
#	Line 1056 | Line 1212 | Encoding: GBK
1212
1213		@ARTICLE{Gray2003,
1214		author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and
1215	<	B. Kuhlman and C. A. Rohl and D. Baker},
1215	>	B. Kuhlman and C. A. Rohl and D. Baker},
1216		title = {Protein-protein docking with simultaneous optimization of rigid-body
1217	<	displacement and side-chain conformations},
1217	>	displacement and side-chain conformations},
1218		journal = {Journal of Molecular Biology},
1219		year = {2003},
1220		volume = {331},
#	Line 1066 | Line 1222 | Encoding: GBK
1222		number = {1},
1223		month = {Aug 1},
1224		abstract = {Protein-protein docking algorithms provide a means to elucidate structural
1225	<	details for presently unknown complexes. Here, we present and evaluate
1226	<	a new method to predict protein-protein complexes from the coordinates
1227	<	of the unbound monomer components. The method employs a low-resolution,
1228	<	rigid-body, Monte Carlo search followed by simultaneous optimization
1229	<	of backbone displacement and side-chain conformations using Monte
1230	<	Carlo minimization. Up to 10(5) independent simulations are carried
1231	<	out, and the resulting #decoys# are ranked using an energy function
1232	<	dominated by van der Waals interactions, an implicit solvation model,
1233	<	and an orientation-dependent hydrogen bonding potential. Top-ranking
1234	<	decoys are clustered to select the final predictions. Small-perturbation
1235	<	studies reveal the formation of binding funnels in 42 of 54 cases
1236	<	using coordinates derived from the bound complexes and in 32 of
1237	<	54 cases using independently determined coordinates of one or both
1238	<	monomers. Experimental binding affinities correlate with the calculated
1239	<	score function and explain the predictive success or failure of
1240	<	many targets. Global searches using one or both unbound components
1241	<	predict at least 25% of the native residue-residue contacts in 28
1242	<	of the 32 cases where binding funnels exist. The results suggest
1243	<	that the method may soon be useful for generating models of biologically
1244	<	important complexes from the structures of the isolated components,
1245	<	but they also highlight the challenges that must be met to achieve
1246	<	consistent and accurate prediction of protein-protein interactions.
1247	<	(C) 2003 Elsevier Ltd. All rights reserved.},
1225	>	details for presently unknown complexes. Here, we present and evaluate
1226	>	a new method to predict protein-protein complexes from the coordinates
1227	>	of the unbound monomer components. The method employs a low-resolution,
1228	>	rigid-body, Monte Carlo search followed by simultaneous optimization
1229	>	of backbone displacement and side-chain conformations using Monte
1230	>	Carlo minimization. Up to 10(5) independent simulations are carried
1231	>	out, and the resulting #decoys# are ranked using an energy function
1232	>	dominated by van der Waals interactions, an implicit solvation model,
1233	>	and an orientation-dependent hydrogen bonding potential. Top-ranking
1234	>	decoys are clustered to select the final predictions. Small-perturbation
1235	>	studies reveal the formation of binding funnels in 42 of 54 cases
1236	>	using coordinates derived from the bound complexes and in 32 of
1237	>	54 cases using independently determined coordinates of one or both
1238	>	monomers. Experimental binding affinities correlate with the calculated
1239	>	score function and explain the predictive success or failure of
1240	>	many targets. Global searches using one or both unbound components
1241	>	predict at least 25% of the native residue-residue contacts in 28
1242	>	of the 32 cases where binding funnels exist. The results suggest
1243	>	that the method may soon be useful for generating models of biologically
1244	>	important complexes from the structures of the isolated components,
1245	>	but they also highlight the challenges that must be met to achieve
1246	>	consistent and accurate prediction of protein-protein interactions.
1247	>	(C) 2003 Elsevier Ltd. All rights reserved.},
1248		annote = {704QL Times Cited:48 Cited References Count:60},
1249		issn = {0022-2836},
1250		uri = {<Go to ISI>://000184351300022},
1251		}
1252
1253	+	@ARTICLE{Greengard1994,
1254	+	author = {L. Greengard},
1255	+	title = {Fast Algorithms for Classical Physics},
1256	+	journal = {Science},
1257	+	year = {1994},
1258	+	volume = {265},
1259	+	pages = {909-914},
1260	+	number = {5174},
1261	+	month = {Aug 12},
1262	+	abstract = {Some of the recently developed fast summation methods that have arisen
1263	+	in scientific computing are described. These methods require an
1264	+	amount of work proportional to N or N log N to evaluate all pairwise
1265	+	interactions in an ensemble of N particles. Traditional methods,
1266	+	by contrast, require an amount of work proportional to N-2. AS a
1267	+	result, large-scale simulations can be carried out using only modest
1268	+	computer resources. In combination with supercomputers, it is possible
1269	+	to address questions that were previously out of reach. Problems
1270	+	from diffusion, gravitation, and wave propagation are considered.},
1271	+	annote = {Pb499 Times Cited:99 Cited References Count:44},
1272	+	issn = {0036-8075},
1273	+	uri = {<Go to ISI>://A1994PB49900031},
1274	+	}
1275	+
1276	+	@ARTICLE{Greengard1987,
1277	+	author = {L. Greengard and V. Rokhlin},
1278	+	title = {A Fast Algorithm for Particle Simulations},
1279	+	journal = {Journal of Computational Physics},
1280	+	year = {1987},
1281	+	volume = {73},
1282	+	pages = {325-348},
1283	+	number = {2},
1284	+	month = {Dec},
1285	+	annote = {L0498 Times Cited:899 Cited References Count:7},
1286	+	issn = {0021-9991},
1287	+	uri = {<Go to ISI>://A1987L049800006},
1288	+	}
1289	+
1290	+	@ARTICLE{Hairer1997,
1291	+	author = {E. Hairer and C. Lubich},
1292	+	title = {The life-span of backward error analysis for numerical integrators},
1293	+	journal = {Numerische Mathematik},
1294	+	year = {1997},
1295	+	volume = {76},
1296	+	pages = {441-462},
1297	+	number = {4},
1298	+	month = {Jun},
1299	+	abstract = {Backward error analysis is a useful tool for the study of numerical
1300	+	approximations to ordinary differential equations. The numerical
1301	+	solution is formally interpreted as the exact solution of a perturbed
1302	+	differential equation, given as a formal and usually divergent series
1303	+	in powers of the step size. For a rigorous analysis, this series
1304	+	has to be truncated. In this article we study the influence of this
1305	+	truncation to the difference between the numerical solution and
1306	+	the exact solution of the perturbed differential equation. Results
1307	+	on the long-time behaviour of numerical solutions are obtained in
1308	+	this way. We present applications to the numerical phase portrait
1309	+	near hyperbolic equilibrium points, to asymptotically stable periodic
1310	+	orbits and Hopf bifurcation, and to energy conservation and approximation
1311	+	of invariant tori in Hamiltonian systems.},
1312	+	annote = {Xj488 Times Cited:50 Cited References Count:19},
1313	+	issn = {0029-599X},
1314	+	uri = {<Go to ISI>://A1997XJ48800002},
1315	+	}
1316	+
1317		@ARTICLE{Hao1993,
1318		author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga},
1319		title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic
1320	<	Trypsin-Inhibitor Studied by Computer-Simulations},
1320	>	Trypsin-Inhibitor Studied by Computer-Simulations},
1321		journal = {Biochemistry},
1322		year = {1993},
1323		volume = {32},
#	Line 1105 | Line 1325 | Encoding: GBK
1325		number = {37},
1326		month = {Sep 21},
1327		abstract = {A new procedure for studying the folding and unfolding of proteins,
1328	<	with an application to bovine pancreatic trypsin inhibitor (BPTI),
1329	<	is reported. The unfolding and refolding of the native structure
1330	<	of the protein are characterized by the dimensions of the protein,
1331	<	expressed in terms of the three principal radii of the structure
1332	<	considered as an ellipsoid. A dynamic equation, describing the variations
1333	<	of the principal radii on the unfolding path, and a numerical procedure
1334	<	to solve this equation are proposed. Expanded and distorted conformations
1335	<	are refolded to the native structure by a dimensional-constraint
1336	<	energy minimization procedure. A unique and reproducible unfolding
1337	<	pathway for an intermediate of BPTI lacking the [30,51] disulfide
1338	<	bond is obtained. The resulting unfolded conformations are extended;
1339	<	they contain near-native local structure, but their longest principal
1340	<	radii are more than 2.5 times greater than that of the native structure.
1341	<	The most interesting finding is that the majority of expanded conformations,
1342	<	generated under various conditions, can be refolded closely to the
1343	<	native structure, as measured by the correct overall chain fold,
1344	<	by the rms deviations from the native structure of only 1.9-3.1
1345	<	angstrom, and by the energy differences of about 10 kcal/mol from
1346	<	the native structure. Introduction of the [30,51] disulfide bond
1347	<	at this stage, followed by minimization, improves the closeness
1348	<	of the refolded structures to the native structure, reducing the
1349	<	rms deviations to 0.9-2.0 angstrom. The unique refolding of these
1350	<	expanded structures over such a large conformational space implies
1351	<	that the folding is strongly dictated by the interactions in the
1352	<	amino acid sequence of BPTI. The simulations indicate that, under
1353	<	conditions that favor a compact structure as mimicked by the volume
1354	<	constraints in our algorithm; the expanded conformations have a
1355	<	strong tendency to move toward the native structure; therefore,
1356	<	they probably would be favorable folding intermediates. The results
1357	<	presented here support a general model for protein folding, i.e.,
1358	<	progressive formation of partially folded structural units, followed
1359	<	by collapse to the compact native structure. The general applicability
1360	<	of the procedure is also discussed.},
1328	>	with an application to bovine pancreatic trypsin inhibitor (BPTI),
1329	>	is reported. The unfolding and refolding of the native structure
1330	>	of the protein are characterized by the dimensions of the protein,
1331	>	expressed in terms of the three principal radii of the structure
1332	>	considered as an ellipsoid. A dynamic equation, describing the variations
1333	>	of the principal radii on the unfolding path, and a numerical procedure
1334	>	to solve this equation are proposed. Expanded and distorted conformations
1335	>	are refolded to the native structure by a dimensional-constraint
1336	>	energy minimization procedure. A unique and reproducible unfolding
1337	>	pathway for an intermediate of BPTI lacking the [30,51] disulfide
1338	>	bond is obtained. The resulting unfolded conformations are extended;
1339	>	they contain near-native local structure, but their longest principal
1340	>	radii are more than 2.5 times greater than that of the native structure.
1341	>	The most interesting finding is that the majority of expanded conformations,
1342	>	generated under various conditions, can be refolded closely to the
1343	>	native structure, as measured by the correct overall chain fold,
1344	>	by the rms deviations from the native structure of only 1.9-3.1
1345	>	angstrom, and by the energy differences of about 10 kcal/mol from
1346	>	the native structure. Introduction of the [30,51] disulfide bond
1347	>	at this stage, followed by minimization, improves the closeness
1348	>	of the refolded structures to the native structure, reducing the
1349	>	rms deviations to 0.9-2.0 angstrom. The unique refolding of these
1350	>	expanded structures over such a large conformational space implies
1351	>	that the folding is strongly dictated by the interactions in the
1352	>	amino acid sequence of BPTI. The simulations indicate that, under
1353	>	conditions that favor a compact structure as mimicked by the volume
1354	>	constraints in our algorithm; the expanded conformations have a
1355	>	strong tendency to move toward the native structure; therefore,
1356	>	they probably would be favorable folding intermediates. The results
1357	>	presented here support a general model for protein folding, i.e.,
1358	>	progressive formation of partially folded structural units, followed
1359	>	by collapse to the compact native structure. The general applicability
1360	>	of the procedure is also discussed.},
1361		annote = {Ly294 Times Cited:27 Cited References Count:57},
1362		issn = {0006-2960},
1363		uri = {<Go to ISI>://A1993LY29400014},
#	Line 1145 | Line 1365 | Encoding: GBK
1365
1366		@ARTICLE{Hinsen2000,
1367		author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel
1368	<	and G. R. Kneller},
1368	>	and G. R. Kneller},
1369		title = {Harmonicity in slow protein dynamics},
1370		journal = {Chemical Physics},
1371		year = {2000},
#	Line 1154 | Line 1374 | Encoding: GBK
1374		number = {1-2},
1375		month = {Nov 1},
1376		abstract = {The slow dynamics of proteins around its native folded state is usually
1377	<	described by diffusion in a strongly anharmonic potential. In this
1378	<	paper, we try to understand the form and origin of the anharmonicities,
1379	<	with the principal aim of gaining a better understanding of the
1380	<	principal motion types, but also in order to develop more efficient
1381	<	numerical methods for simulating neutron scattering spectra of large
1382	<	proteins. First, we decompose a molecular dynamics (MD) trajectory
1383	<	of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water
1384	<	into three contributions that we expect to be independent: the global
1385	<	motion of the residues, the rigid-body motion of the sidechains
1386	<	relative to the backbone, and the internal deformations of the sidechains.
1387	<	We show that they are indeed almost independent by verifying the
1388	<	factorization of the incoherent intermediate scattering function.
1389	<	Then, we show that the global residue motions, which include all
1390	<	large-scale backbone motions, can be reproduced by a simple harmonic
1391	<	model which contains two contributions: a short-time vibrational
1392	<	term, described by a standard normal mode calculation in a local
1393	<	minimum, and a long-time diffusive term, described by Brownian motion
1394	<	in an effective harmonic potential. The potential and the friction
1395	<	constants were fitted to the MD data. The major anharmonic contribution
1396	<	to the incoherent intermediate scattering function comes from the
1397	<	rigid-body diffusion of the sidechains. This model can be used to
1398	<	calculate scattering functions for large proteins and for long-time
1399	<	scales very efficiently, and thus provides a useful complement to
1400	<	MD simulations, which are best suited for detailed studies on smaller
1401	<	systems or for shorter time scales. (C) 2000 Elsevier Science B.V.
1402	<	All rights reserved.},
1377	>	described by diffusion in a strongly anharmonic potential. In this
1378	>	paper, we try to understand the form and origin of the anharmonicities,
1379	>	with the principal aim of gaining a better understanding of the
1380	>	principal motion types, but also in order to develop more efficient
1381	>	numerical methods for simulating neutron scattering spectra of large
1382	>	proteins. First, we decompose a molecular dynamics (MD) trajectory
1383	>	of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water
1384	>	into three contributions that we expect to be independent: the global
1385	>	motion of the residues, the rigid-body motion of the sidechains
1386	>	relative to the backbone, and the internal deformations of the sidechains.
1387	>	We show that they are indeed almost independent by verifying the
1388	>	factorization of the incoherent intermediate scattering function.
1389	>	Then, we show that the global residue motions, which include all
1390	>	large-scale backbone motions, can be reproduced by a simple harmonic
1391	>	model which contains two contributions: a short-time vibrational
1392	>	term, described by a standard normal mode calculation in a local
1393	>	minimum, and a long-time diffusive term, described by Brownian motion
1394	>	in an effective harmonic potential. The potential and the friction
1395	>	constants were fitted to the MD data. The major anharmonic contribution
1396	>	to the incoherent intermediate scattering function comes from the
1397	>	rigid-body diffusion of the sidechains. This model can be used to
1398	>	calculate scattering functions for large proteins and for long-time
1399	>	scales very efficiently, and thus provides a useful complement to
1400	>	MD simulations, which are best suited for detailed studies on smaller
1401	>	systems or for shorter time scales. (C) 2000 Elsevier Science B.V.
1402	>	All rights reserved.},
1403		annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31},
1404		issn = {0301-0104},
1405		uri = {<Go to ISI>://000090121700003},
#	Line 1195 | Line 1415 | Encoding: GBK
1415		number = {4},
1416		month = {Oct},
1417		abstract = {Evidence has been found for the existence water at the protein-lipid
1418	<	hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome
1419	<	C, using two related fluorescence spectroscopic approaches. The
1420	<	first approach exploited the fact that the presence of water in
1421	<	the excited state solvent cage of a fluorophore increases the rate
1422	<	of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl)
1423	<	phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores
1424	<	are located in the hydrophobic core of the lipid bilayer, the introduction
1425	<	of gramicidin reduced the fluorescence lifetime, indicative of an
1426	<	increased presence of water in the bilayer. Since a high protein:lipid
1427	<	ratio was used, the fluorophores were forced to be adjacent to the
1428	<	protein hydrophobic surface, hence the presence of water in this
1429	<	region could be inferred. Cholesterol is known to reduce the water
1430	<	content of lipid bilayers and this effect was maintained at the
1431	<	protein-lipid interface with both gramicidin and apocytochrome C,
1432	<	again suggesting hydration in this region. The second approach was
1433	<	to use the fluorescence enhancement induced by exchanging deuterium
1434	<	oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH,
1435	<	located in the lipid head group region, and of the gramicidin intrinsic
1436	<	tryptophans were greater in a D2O buffer compared with H2O, showing
1437	<	that the fluorophores were exposed to water in the bilayer at the
1438	<	protein-lipid interface. In the presence of cholesterol the fluorescence
1439	<	intensity ratio of D2O to H2O decreased, indicating a removal of
1440	<	water by the cholesterol, in keeping with the lifetime data. Altered
1441	<	hydration at the protein-lipid interface could affect conformation,
1442	<	thereby offering a new route by which membrane protein functioning
1443	<	may be modified.},
1418	>	hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome
1419	>	C, using two related fluorescence spectroscopic approaches. The
1420	>	first approach exploited the fact that the presence of water in
1421	>	the excited state solvent cage of a fluorophore increases the rate
1422	>	of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl)
1423	>	phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores
1424	>	are located in the hydrophobic core of the lipid bilayer, the introduction
1425	>	of gramicidin reduced the fluorescence lifetime, indicative of an
1426	>	increased presence of water in the bilayer. Since a high protein:lipid
1427	>	ratio was used, the fluorophores were forced to be adjacent to the
1428	>	protein hydrophobic surface, hence the presence of water in this
1429	>	region could be inferred. Cholesterol is known to reduce the water
1430	>	content of lipid bilayers and this effect was maintained at the
1431	>	protein-lipid interface with both gramicidin and apocytochrome C,
1432	>	again suggesting hydration in this region. The second approach was
1433	>	to use the fluorescence enhancement induced by exchanging deuterium
1434	>	oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH,
1435	>	located in the lipid head group region, and of the gramicidin intrinsic
1436	>	tryptophans were greater in a D2O buffer compared with H2O, showing
1437	>	that the fluorophores were exposed to water in the bilayer at the
1438	>	protein-lipid interface. In the presence of cholesterol the fluorescence
1439	>	intensity ratio of D2O to H2O decreased, indicating a removal of
1440	>	water by the cholesterol, in keeping with the lifetime data. Altered
1441	>	hydration at the protein-lipid interface could affect conformation,
1442	>	thereby offering a new route by which membrane protein functioning
1443	>	may be modified.},
1444		annote = {Ju251 Times Cited:55 Cited References Count:44},
1445		issn = {0006-3495},
1446		uri = {<Go to ISI>://A1992JU25100002},
1447		}
1448
1449	+	@BOOK{Hockney1981,
1450	+	title = {Computer Simulation Using Particles},
1451	+	publisher = {McGraw-Hill},
1452	+	year = {1981},
1453	+	author = {R.W. Hockney and J.W. Eastwood},
1454	+	address = {New York},
1455	+	}
1456	+
1457	+	@ARTICLE{Hoover1985,
1458	+	author = {W. G. Hoover},
1459	+	title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
1460	+	journal = {Physical Review A},
1461	+	year = {1985},
1462	+	volume = {31},
1463	+	pages = {1695-1697},
1464	+	number = {3},
1465	+	annote = {Acr30 Times Cited:1809 Cited References Count:11},
1466	+	issn = {1050-2947},
1467	+	uri = {<Go to ISI>://A1985ACR3000056},
1468	+	}
1469	+
1470		@ARTICLE{Huh2004,
1471		author = {Y. Huh and N. M. Cann},
1472		title = {Discrimination in isotropic, nematic, and smectic phases of chiral
1473	<	calamitic molecules: A computer simulation study},
1473	>	calamitic molecules: A computer simulation study},
1474		journal = {Journal of Chemical Physics},
1475		year = {2004},
1476		volume = {121},
#	Line 1237 | Line 1478 | Encoding: GBK
1478		number = {20},
1479		month = {Nov 22},
1480		abstract = {Racemic fluids of chiral calamitic molecules are investigated with
1481	<	molecular dynamics simulations. In particular, the phase behavior
1482	<	as a function of density is examined for eight racemates. The relationship
1483	<	between chiral discrimination and orientational order in the phase
1484	<	is explored. We find that the transition from the isotropic phase
1485	<	to a liquid crystal phase is accompanied by an increase in chiral
1486	<	discrimination, as measured by differences in radial distributions.
1487	<	Among ordered phases, discrimination is largest for smectic phases
1488	<	with a significant preference for heterochiral contact within the
1489	<	layers. (C) 2004 American Institute of Physics.},
1481	>	molecular dynamics simulations. In particular, the phase behavior
1482	>	as a function of density is examined for eight racemates. The relationship
1483	>	between chiral discrimination and orientational order in the phase
1484	>	is explored. We find that the transition from the isotropic phase
1485	>	to a liquid crystal phase is accompanied by an increase in chiral
1486	>	discrimination, as measured by differences in radial distributions.
1487	>	Among ordered phases, discrimination is largest for smectic phases
1488	>	with a significant preference for heterochiral contact within the
1489	>	layers. (C) 2004 American Institute of Physics.},
1490		annote = {870FJ Times Cited:0 Cited References Count:63},
1491		issn = {0021-9606},
1492		uri = {<Go to ISI>://000225042700059},
1493		}
1494
1495	+	@ARTICLE{Humphrey1996,
1496	+	author = {W. Humphrey and A. Dalke and K. Schulten},
1497	+	title = {VMD: Visual molecular dynamics},
1498	+	journal = {Journal of Molecular Graphics},
1499	+	year = {1996},
1500	+	volume = {14},
1501	+	pages = {33-\&},
1502	+	number = {1},
1503	+	month = {Feb},
1504	+	abstract = {VMD is a molecular graphics program designed for the display and analysis
1505	+	of molecular assemblies, in particular biopolymers such as proteins
1506	+	and nucleic acids. VMD can simultaneously display any number of
1507	+	structures using a wide variety of rendering styles and coloring
1508	+	methods. Molecules are displayed as one or more ''representations,''
1509	+	in which each representation embodies a particular rendering method
1510	+	and coloring scheme for a selected subset of atoms. The atoms displayed
1511	+	in each representation are chosen using an extensive atom selection
1512	+	syntax, which includes Boolean operators and regular expressions.
1513	+	VMD provides a complete graphical user interface for program control,
1514	+	as well as a text interface using the Tcl embeddable parser to allow
1515	+	for complex scripts with variable substitution, control loops, and
1516	+	function calls. Full session logging is supported, which produces
1517	+	a VMD command script for later playback. High-resolution raster
1518	+	images of displayed molecules may be produced by generating input
1519	+	scripts for use by a number of photorealistic image-rendering applications.
1520	+	VMD has also been expressly designed with the ability to animate
1521	+	molecular dynamics (MD) simulation trajectories, imported either
1522	+	from files or from a direct connection to a running MD simulation.
1523	+	VMD is the visualization component of MDScope, a set of tools for
1524	+	interactive problem solving in structural biology, which also includes
1525	+	the parallel MD program NAMD, and the MDCOMM software used to connect
1526	+	the visualization and simulation programs. VMD is written in C++,
1527	+	using an object-oriented design; the program, including source code
1528	+	and extensive documentation, is freely available via anonymous ftp
1529	+	and through the World Wide Web.},
1530	+	annote = {Uh515 Times Cited:1418 Cited References Count:19},
1531	+	issn = {0263-7855},
1532	+	uri = {<Go to ISI>://A1996UH51500005},
1533	+	}
1534	+
1535		@ARTICLE{Izaguirre2001,
1536		author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
1537		title = {Langevin stabilization of molecular dynamics},
#	Line 1261 | Line 1542 | Encoding: GBK
1542		number = {5},
1543		month = {Feb 1},
1544		abstract = {In this paper we show the possibility of using very mild stochastic
1545	<	damping to stabilize long time step integrators for Newtonian molecular
1546	<	dynamics. More specifically, stable and accurate integrations are
1547	<	obtained for damping coefficients that are only a few percent of
1548	<	the natural decay rate of processes of interest, such as the velocity
1549	<	autocorrelation function. Two new multiple time stepping integrators,
1550	<	Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are
1551	<	introduced in this paper. Both use the mollified impulse method
1552	<	for the Newtonian term. LM uses a discretization of the Langevin
1553	<	equation that is exact for the constant force, and BBK-M uses the
1554	<	popular Brunger-Brooks-Karplus integrator (BBK). These integrators,
1555	<	along with an extrapolative method called LN, are evaluated across
1556	<	a wide range of damping coefficient values. When large damping coefficients
1557	<	are used, as one would for the implicit modeling of solvent molecules,
1558	<	the method LN is superior, with LM closely following. However, with
1559	<	mild damping of 0.2 ps(-1), LM produces the best results, allowing
1560	<	long time steps of 14 fs in simulations containing explicitly modeled
1561	<	flexible water. With BBK-M and the same damping coefficient, time
1562	<	steps of 12 fs are possible for the same system. Similar results
1563	<	are obtained for a solvated protein-DNA simulation of estrogen receptor
1564	<	ER with estrogen response element ERE. A parallel version of BBK-M
1565	<	runs nearly three times faster than the Verlet-I/r-RESPA (reversible
1566	<	reference system propagator algorithm) when using the largest stable
1567	<	time step on each one, and it also parallelizes well. The computation
1568	<	of diffusion coefficients for flexible water and ER/ERE shows that
1569	<	when mild damping of up to 0.2 ps-1 is used the dynamics are not
1570	<	significantly distorted. (C) 2001 American Institute of Physics.},
1545	>	damping to stabilize long time step integrators for Newtonian molecular
1546	>	dynamics. More specifically, stable and accurate integrations are
1547	>	obtained for damping coefficients that are only a few percent of
1548	>	the natural decay rate of processes of interest, such as the velocity
1549	>	autocorrelation function. Two new multiple time stepping integrators,
1550	>	Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are
1551	>	introduced in this paper. Both use the mollified impulse method
1552	>	for the Newtonian term. LM uses a discretization of the Langevin
1553	>	equation that is exact for the constant force, and BBK-M uses the
1554	>	popular Brunger-Brooks-Karplus integrator (BBK). These integrators,
1555	>	along with an extrapolative method called LN, are evaluated across
1556	>	a wide range of damping coefficient values. When large damping coefficients
1557	>	are used, as one would for the implicit modeling of solvent molecules,
1558	>	the method LN is superior, with LM closely following. However, with
1559	>	mild damping of 0.2 ps(-1), LM produces the best results, allowing
1560	>	long time steps of 14 fs in simulations containing explicitly modeled
1561	>	flexible water. With BBK-M and the same damping coefficient, time
1562	>	steps of 12 fs are possible for the same system. Similar results
1563	>	are obtained for a solvated protein-DNA simulation of estrogen receptor
1564	>	ER with estrogen response element ERE. A parallel version of BBK-M
1565	>	runs nearly three times faster than the Verlet-I/r-RESPA (reversible
1566	>	reference system propagator algorithm) when using the largest stable
1567	>	time step on each one, and it also parallelizes well. The computation
1568	>	of diffusion coefficients for flexible water and ER/ERE shows that
1569	>	when mild damping of up to 0.2 ps-1 is used the dynamics are not
1570	>	significantly distorted. (C) 2001 American Institute of Physics.},
1571		annote = {397CQ Times Cited:14 Cited References Count:36},
1572		issn = {0021-9606},
1573		uri = {<Go to ISI>://000166676100020},
1574		}
1575
1576	<	@ARTICLE{Gray2003,
1577	<	author = {J.~J Gray,S. Moughon, C. Wang },
1578	<	title = {Protein-protein docking with simultaneous optimization of rigid-body
1579	<	displacement and side-chain conformations},
1580	<	journal = {jmb},
1581	<	year = {2003},
1582	<	volume = {331},
1302	<	pages = {281-299},
1576	>	@ARTICLE{Torre1977,
1577	>	author = {Jose Garcia De La Torre, V.A. Bloomfield},
1578	>	title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
1579	>	journal = {Biopolymers},
1580	>	year = {1977},
1581	>	volume = {16},
1582	>	pages = {1747-1763},
1583		}
1584
1585	+	@ARTICLE{Kale1999,
1586	+	author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy
1587	+	and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan
1588	+	and K. Schulten},
1589	+	title = {NAMD2: Greater scalability for parallel molecular dynamics},
1590	+	journal = {Journal of Computational Physics},
1591	+	year = {1999},
1592	+	volume = {151},
1593	+	pages = {283-312},
1594	+	number = {1},
1595	+	month = {May 1},
1596	+	abstract = {Molecular dynamics programs simulate the behavior of biomolecular
1597	+	systems, leading to understanding of their functions. However, the
1598	+	computational complexity of such simulations is enormous. Parallel
1599	+	machines provide the potential to meet this computational challenge.
1600	+	To harness this potential, it is necessary to develop a scalable
1601	+	program. It is also necessary that the program be easily modified
1602	+	by application-domain programmers. The NAMD2 program presented in
1603	+	this paper seeks to provide these desirable features. It uses spatial
1604	+	decomposition combined with force decomposition to enhance scalability.
1605	+	It uses intelligent periodic load balancing, so as to maximally
1606	+	utilize the available compute power. It is modularly organized,
1607	+	and implemented using Charm++, a parallel C++ dialect, so as to
1608	+	enhance its modifiability. It uses a combination of numerical techniques
1609	+	and algorithms to ensure that energy drifts are minimized, ensuring
1610	+	accuracy in long running calculations. NAMD2 uses a portable run-time
1611	+	framework called Converse that also supports interoperability among
1612	+	multiple parallel paradigms. As a result, different components of
1613	+	applications can be written in the most appropriate parallel paradigms.
1614	+	NAMD2 runs on most parallel machines including workstation clusters
1615	+	and has yielded speedups in excess of 180 on 220 processors. This
1616	+	paper also describes the performance obtained on some benchmark
1617	+	applications. (C) 1999 Academic Press.},
1618	+	annote = {194FM Times Cited:373 Cited References Count:51},
1619	+	issn = {0021-9991},
1620	+	uri = {<Go to ISI>://000080181500013},
1621	+	}
1622	+
1623	+	@ARTICLE{Kane2000,
1624	+	author = {C. Kane and J. E. Marsden and M. Ortiz and M. West},
1625	+	title = {Variational integrators and the Newmark algorithm for conservative
1626	+	and dissipative mechanical systems},
1627	+	journal = {International Journal for Numerical Methods in Engineering},
1628	+	year = {2000},
1629	+	volume = {49},
1630	+	pages = {1295-1325},
1631	+	number = {10},
1632	+	month = {Dec 10},
1633	+	abstract = {The purpose of this work is twofold. First, we demonstrate analytically
1634	+	that the classical Newmark family as well as related integration
1635	+	algorithms are variational in the sense of the Veselov formulation
1636	+	of discrete mechanics. Such variational algorithms are well known
1637	+	to be symplectic and momentum preserving and to often have excellent
1638	+	global energy behaviour. This analytical result is verified through
1639	+	numerical examples and is believed to be one of the primary reasons
1640	+	that this class of algorithms performs so well. Second, we develop
1641	+	algorithms for mechanical systems with forcing, and in particular,
1642	+	for dissipative systems. In this case, we develop integrators that
1643	+	are based on a discretization of the Lagrange d'Alembert principle
1644	+	as well as on a variational formulation of dissipation. It is demonstrated
1645	+	that these types of structured integrators have good numerical behaviour
1646	+	in terms of obtaining the correct amounts by which the energy changes
1647	+	over the integration run. Copyright (C) 2000 John Wiley & Sons,
1648	+	Ltd.},
1649	+	annote = {373CJ Times Cited:30 Cited References Count:41},
1650	+	issn = {0029-5981},
1651	+	uri = {<Go to ISI>://000165270600004},
1652	+	}
1653	+
1654		@ARTICLE{Klimov1997,
1655		author = {D. K. Klimov and D. Thirumalai},
1656		title = {Viscosity dependence of the folding rates of proteins},
#	Line 1312 | Line 1661 | Encoding: GBK
1661		number = {2},
1662		month = {Jul 14},
1663		abstract = {The viscosity (eta) dependence of the folding rates for four sequences
1664	<	(the native state of three sequences is a beta sheet, while the
1665	<	fourth forms an alpha helix) is calculated for off-lattice models
1666	<	of proteins. Assuming that the dynamics is given by the Langevin
1667	<	equation, we show that the folding rates increase linearly at low
1668	<	viscosities eta, decrease as 1/eta at large eta, and have a maximum
1669	<	at intermediate values. The Kramers' theory of barrier crossing
1670	<	provides a quantitative fit of the numerical results. By mapping
1671	<	the simulation results to real proteins we estimate that for optimized
1672	<	sequences the time scale for forming a four turn alpha-helix topology
1673	<	is about 500 ns, whereas for beta sheet it is about 10 mu s.},
1664	>	(the native state of three sequences is a beta sheet, while the
1665	>	fourth forms an alpha helix) is calculated for off-lattice models
1666	>	of proteins. Assuming that the dynamics is given by the Langevin
1667	>	equation, we show that the folding rates increase linearly at low
1668	>	viscosities eta, decrease as 1/eta at large eta, and have a maximum
1669	>	at intermediate values. The Kramers' theory of barrier crossing
1670	>	provides a quantitative fit of the numerical results. By mapping
1671	>	the simulation results to real proteins we estimate that for optimized
1672	>	sequences the time scale for forming a four turn alpha-helix topology
1673	>	is about 500 ns, whereas for beta sheet it is about 10 mu s.},
1674		annote = {Xk293 Times Cited:77 Cited References Count:17},
1675		issn = {0031-9007},
1676		uri = {<Go to ISI>://A1997XK29300035},
1677		}
1678
1679	+	@ARTICLE{Kol1997,
1680	+	author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
1681	+	title = {A symplectic method for rigid-body molecular simulation},
1682	+	journal = {Journal of Chemical Physics},
1683	+	year = {1997},
1684	+	volume = {107},
1685	+	pages = {2580-2588},
1686	+	number = {7},
1687	+	month = {Aug 15},
1688	+	abstract = {Rigid-body molecular dynamics simulations typically are performed
1689	+	in a quaternion representation. The nonseparable form of the Hamiltonian
1690	+	in quaternions prevents the use of a standard leapfrog (Verlet)
1691	+	integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation
1692	+	methods are generally used, This is unfortunate since symplectic
1693	+	methods like Verlet exhibit superior energy conservation in long-time
1694	+	integrations. In this article, we describe an alternative method,
1695	+	which we call RSHAKE (for rotation-SHAKE), in which the entire rotation
1696	+	matrix is evolved (using the scheme of McLachlan and Scovel [J.
1697	+	Nonlin. Sci, 16 233 (1995)]) in tandem with the particle positions.
1698	+	We employ a fast approximate Newton solver to preserve the orthogonality
1699	+	of the rotation matrix. We test our method on a system of soft-sphere
1700	+	dipoles and compare with quaternion evolution using a 4th-order
1701	+	predictor-corrector integrator, Although the short-time error of
1702	+	the quaternion algorithm is smaller for fixed time step than that
1703	+	for RSHAKE, the quaternion scheme exhibits an energy drift which
1704	+	is not observed in simulations with RSHAKE, hence a fixed energy
1705	+	tolerance can be achieved by using a larger time step, The superiority
1706	+	of RSHAKE increases with system size. (C) 1997 American Institute
1707	+	of Physics.},
1708	+	annote = {Xq332 Times Cited:11 Cited References Count:18},
1709	+	issn = {0021-9606},
1710	+	uri = {<Go to ISI>://A1997XQ33200046},
1711	+	}
1712	+
1713		@ARTICLE{Lansac2001,
1714		author = {Y. Lansac and M. A. Glaser and N. A. Clark},
1715		title = {Microscopic structure and dynamics of a partial bilayer smectic liquid
1716	<	crystal},
1716	>	crystal},
1717		journal = {Physical Review E},
1718		year = {2001},
1719		volume = {6405},
#	Line 1338 | Line 1721 | Encoding: GBK
1721		number = {5},
1722		month = {Nov},
1723		abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
1724	<	class of mesogens. Many of the peculiar properties of nCB's (e.g.,
1725	<	the occurence of the partial bilayer smectic-A(d) phase) are thought
1726	<	to be a manifestation of short-range antiparallel association of
1727	<	neighboring molecules, resulting from strong dipole-dipole interactions
1728	<	between cyano groups. To test and extend existing models of microscopic
1729	<	ordering in nCB's, we carry out large-scale atomistic simulation
1730	<	studies of the microscopic structure and dynamics of the Sm-A(d)
1731	<	phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of
1732	<	thermodynamic, structural, and dynamical properties for this material,
1733	<	and make a detailed comparison of our results with experimental
1734	<	measurements in order to validate our molecular model. Semiquantitative
1735	<	agreement with experiment is found: the smectic layer spacing and
1736	<	mass density are well reproduced, translational diffusion constants
1737	<	are similar to experiment, but the orientational ordering of alkyl
1738	<	chains is overestimated. This simulation provides a detailed picture
1739	<	of molecular conformation, smectic layer structure, and intermolecular
1740	<	correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range
1741	<	antiparallel association of molecules arising from dipole-dipole
1742	<	interactions plays a dominant role in determining the molecular-scale
1743	<	structure of 8CB.},
1724	>	class of mesogens. Many of the peculiar properties of nCB's (e.g.,
1725	>	the occurence of the partial bilayer smectic-A(d) phase) are thought
1726	>	to be a manifestation of short-range antiparallel association of
1727	>	neighboring molecules, resulting from strong dipole-dipole interactions
1728	>	between cyano groups. To test and extend existing models of microscopic
1729	>	ordering in nCB's, we carry out large-scale atomistic simulation
1730	>	studies of the microscopic structure and dynamics of the Sm-A(d)
1731	>	phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of
1732	>	thermodynamic, structural, and dynamical properties for this material,
1733	>	and make a detailed comparison of our results with experimental
1734	>	measurements in order to validate our molecular model. Semiquantitative
1735	>	agreement with experiment is found: the smectic layer spacing and
1736	>	mass density are well reproduced, translational diffusion constants
1737	>	are similar to experiment, but the orientational ordering of alkyl
1738	>	chains is overestimated. This simulation provides a detailed picture
1739	>	of molecular conformation, smectic layer structure, and intermolecular
1740	>	correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range
1741	>	antiparallel association of molecules arising from dipole-dipole
1742	>	interactions plays a dominant role in determining the molecular-scale
1743	>	structure of 8CB.},
1744		annote = {Part 1 496QF Times Cited:10 Cited References Count:60},
1745		issn = {1063-651X},
1746		uri = {<Go to ISI>://000172406900063},
#	Line 1373 | Line 1756 | Encoding: GBK
1756		number = {1},
1757		month = {Jan},
1758		abstract = {Recently, a new class of smectic liquid crystal phases characterized
1759	<	by the spontaneous formation of macroscopic chiral domains from
1760	<	achiral bent-core molecules has been discovered. We have carried
1761	<	out Monte Carlo simulations of a minimal hard spherocylinder dimer
1762	<	model to investigate the role of excluded volume interactions in
1763	<	determining the phase behavior of bent-core materials and to probe
1764	<	the molecular origins of polar and chiral symmetry breaking. We
1765	<	present the phase diagram of hard spherocylinder dimers of length-diameter
1766	<	ratio of 5 as a function of pressure or density and dimer opening
1767	<	angle psi. With decreasing psi, a transition from a nonpolar to
1768	<	a polar smectic A phase is observed near psi=167degrees, and the
1769	<	nematic phase becomes thermodynamically unstable for psi<135degrees.
1770	<	Free energy calculations indicate that the antipolar smectic A (SmAP(A))
1771	<	phase is more stable than the polar smectic A phase (SmAP(F)). No
1772	<	chiral smectic or biaxial nematic phases were found.},
1759	>	by the spontaneous formation of macroscopic chiral domains from
1760	>	achiral bent-core molecules has been discovered. We have carried
1761	>	out Monte Carlo simulations of a minimal hard spherocylinder dimer
1762	>	model to investigate the role of excluded volume interactions in
1763	>	determining the phase behavior of bent-core materials and to probe
1764	>	the molecular origins of polar and chiral symmetry breaking. We
1765	>	present the phase diagram of hard spherocylinder dimers of length-diameter
1766	>	ratio of 5 as a function of pressure or density and dimer opening
1767	>	angle psi. With decreasing psi, a transition from a nonpolar to
1768	>	a polar smectic A phase is observed near psi=167degrees, and the
1769	>	nematic phase becomes thermodynamically unstable for psi<135degrees.
1770	>	Free energy calculations indicate that the antipolar smectic A (SmAP(A))
1771	>	phase is more stable than the polar smectic A phase (SmAP(F)). No
1772	>	chiral smectic or biaxial nematic phases were found.},
1773		annote = {Part 1 646CM Times Cited:15 Cited References Count:38},
1774		issn = {1063-651X},
1775		uri = {<Go to ISI>://000181017300042},
#	Line 1401 | Line 1784 | Encoding: GBK
1784		edition = {2nd},
1785		}
1786
1787	+	@ARTICLE{Leimkuhler1999,
1788	+	author = {B. Leimkuhler},
1789	+	title = {Reversible adaptive regularization: perturbed Kepler motion and classical
1790	+	atomic trajectories},
1791	+	journal = {Philosophical Transactions of the Royal Society of London Series
1792	+	a-Mathematical Physical and Engineering Sciences},
1793	+	year = {1999},
1794	+	volume = {357},
1795	+	pages = {1101-1133},
1796	+	number = {1754},
1797	+	month = {Apr 15},
1798	+	abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
1799	+	regularization and modified Sundman transformations are applied
1800	+	to simulate general perturbed Kepler motion and to compute classical
1801	+	trajectories of atomic systems (e.g. Rydberg atoms). The new family
1802	+	of reversible adaptive regularization methods also conserves angular
1803	+	momentum and exhibits superior energy conservation and numerical
1804	+	stability in long-time integrations. The schemes are appropriate
1805	+	for scattering, for astronomical calculations of escape time and
1806	+	long-term stability, and for classical and semiclassical studies
1807	+	of atomic dynamics. The components of an algorithm for trajectory
1808	+	calculations are described. Numerical experiments illustrate the
1809	+	effectiveness of the reversible approach.},
1810	+	annote = {199EE Times Cited:11 Cited References Count:48},
1811	+	issn = {1364-503X},
1812	+	uri = {<Go to ISI>://000080466800007},
1813	+	}
1814	+
1815		@BOOK{Leimkuhler2004,
1816		title = {Simulating Hamiltonian Dynamics},
1817		publisher = {Cambridge University Press},
#	Line 1411 | Line 1822 | Encoding: GBK
1822
1823		@ARTICLE{Levelut1981,
1824		author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard
1825	<	and G. Sigaud},
1825	>	and G. Sigaud},
1826		title = {Number of Sa Phases},
1827		journal = {Physical Review A},
1828		year = {1981},
#	Line 1426 | Line 1837 | Encoding: GBK
1837		@ARTICLE{Lieb1982,
1838		author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
1839		title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers -
1840	<	Evidence from Raman-Scattering},
1840	>	Evidence from Raman-Scattering},
1841		journal = {Biochimica Et Biophysica Acta},
1842		year = {1982},
1843		volume = {688},
#	Line 1439 | Line 1850 | Encoding: GBK
1850
1851		@ARTICLE{Link1997,
1852		author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A.
1853	<	Clark and E. Korblova and D. M. Walba},
1853	>	Clark and E. Korblova and D. M. Walba},
1854		title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic
1855	<	phase of achiral molecules},
1855	>	phase of achiral molecules},
1856		journal = {Science},
1857		year = {1997},
1858		volume = {278},
#	Line 1449 | Line 1860 | Encoding: GBK
1860		number = {5345},
1861		month = {Dec 12},
1862		abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
1863	<	cores was found to have fluid layers that exhibit two spontaneous
1864	<	symmetry-breaking instabilities: polar molecular orientational ordering
1865	<	about the layer normal and molecular tilt. These instabilities combine
1866	<	to form a chiral layer structure with a handedness that depends
1867	<	on the sign of the tilt. The bulk states are either antiferroelectric-racemic,
1868	<	with the layer polar direction and handedness alternating in sign
1869	<	from layer to layer, or antiferroelectric-chiral, which is of uniform
1870	<	layer handedness. Both states exhibit an electric field-induced
1871	<	transition from antiferroelectric to ferroelectric.},
1863	>	cores was found to have fluid layers that exhibit two spontaneous
1864	>	symmetry-breaking instabilities: polar molecular orientational ordering
1865	>	about the layer normal and molecular tilt. These instabilities combine
1866	>	to form a chiral layer structure with a handedness that depends
1867	>	on the sign of the tilt. The bulk states are either antiferroelectric-racemic,
1868	>	with the layer polar direction and handedness alternating in sign
1869	>	from layer to layer, or antiferroelectric-chiral, which is of uniform
1870	>	layer handedness. Both states exhibit an electric field-induced
1871	>	transition from antiferroelectric to ferroelectric.},
1872		annote = {Yl002 Times Cited:407 Cited References Count:25},
1873		issn = {0036-8075},
1874		uri = {<Go to ISI>://A1997YL00200028},
#	Line 1466 | Line 1877 | Encoding: GBK
1877		@ARTICLE{Liwo2005,
1878		author = {A. Liwo and M. Khalili and H. A. Scheraga},
1879		title = {Ab initio simulations of protein folding pathways by molecular dynamics
1880	<	with the united-residue (UNRES) model of polypeptide chains},
1880	>	with the united-residue (UNRES) model of polypeptide chains},
1881		journal = {Febs Journal},
1882		year = {2005},
1883		volume = {272},
#	Line 1477 | Line 1888 | Encoding: GBK
1888		uri = {<Go to ISI>://000234826102043},
1889		}
1890
1891	+	@ARTICLE{Luty1994,
1892	+	author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
1893	+	title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods
1894	+	for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
1895	+	journal = {Molecular Simulation},
1896	+	year = {1994},
1897	+	volume = {14},
1898	+	pages = {11-20},
1899	+	number = {1},
1900	+	abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
1901	+	for calculating electrostatic interactions in periodic molecular
1902	+	systems. A brief comparison of the theories shows that the methods
1903	+	are very similar differing mainly in the technique which is used
1904	+	to perform the ''k-space'' or mesh calculation. Because the PPPM
1905	+	utilizes the highly efficient numerical Fast Fourier Transform (FFT)
1906	+	method it requires significantly less computational effort than
1907	+	the Ewald method and scale's almost linearly with system size.},
1908	+	annote = {Qf464 Times Cited:50 Cited References Count:20},
1909	+	issn = {0892-7022},
1910	+	uri = {<Go to ISI>://A1994QF46400002},
1911	+	}
1912	+
1913		@BOOK{Marion1990,
1914		title = {Classical Dynamics of Particles and Systems},
1915		publisher = {Academic Press},
#	Line 1486 | Line 1919 | Encoding: GBK
1919		edition = {2rd},
1920		}
1921
1922	+	@ARTICLE{Marrink1994,
1923	+	author = {S. J. Marrink and H. J. C. Berendsen},
1924	+	title = {Simulation of Water Transport through a Lipid-Membrane},
1925	+	journal = {Journal of Physical Chemistry},
1926	+	year = {1994},
1927	+	volume = {98},
1928	+	pages = {4155-4168},
1929	+	number = {15},
1930	+	month = {Apr 14},
1931	+	abstract = {To obtain insight in the process of water permeation through a lipid
1932	+	membrane, we performed molecular dynamics simulations on a phospholipid
1933	+	(DPPC)/water system with atomic detail. Since the actual process
1934	+	of permeation is too slow to be studied directly, we deduced the
1935	+	permeation rate indirectly via computation of the free energy and
1936	+	diffusion rate profiles of a water molecule across the bilayer.
1937	+	We conclude that the permeation of water through a lipid membrane
1938	+	cannot be described adequately by a simple homogeneous solubility-diffusion
1939	+	model. Both the excess free energy and the diffusion rate strongly
1940	+	depend on the position in the membrane, as a result from the inhomogeneous
1941	+	nature of the membrane. The calculated excess free energy profile
1942	+	has a shallow slope and a maximum height of 26 kJ/mol. The diffusion
1943	+	rate is highest in the middle of the membrane where the lipid density
1944	+	is low. In the interfacial region almost all water molecules are
1945	+	bound by the lipid headgroups, and the diffusion turns out to be
1946	+	1 order of magnitude smaller. The total transport process is essentially
1947	+	determined by the free energy barrier. The rate-limiting step is
1948	+	the permeation through the dense part of the lipid tails, where
1949	+	the resistance is highest. We found a permeation rate of 7(+/-3)
1950	+	x 10(-2) cm/s at 350 K, comparable to experimental values for DPPC
1951	+	membranes, if corrected for the temperature of the simulation. Taking
1952	+	the inhomogeneity of the membrane into account, we define a new
1953	+	''four-region'' model which seems to be more realistic than the
1954	+	''two-phase'' solubility-diffusion model.},
1955	+	annote = {Ng219 Times Cited:187 Cited References Count:25},
1956	+	issn = {0022-3654},
1957	+	uri = {<Go to ISI>://A1994NG21900040},
1958	+	}
1959	+
1960	+	@ARTICLE{Marrink2004,
1961	+	author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
1962	+	title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
1963	+	journal = {J. Phys. Chem. B},
1964	+	year = {2004},
1965	+	volume = {108},
1966	+	pages = {750-760},
1967	+	}
1968	+
1969	+	@ARTICLE{Marsden1998,
1970	+	author = {J. E. Marsden and G. W. Patrick and S. Shkoller},
1971	+	title = {Multisymplectic geometry, variational integrators, and nonlinear
1972	+	PDEs},
1973	+	journal = {Communications in Mathematical Physics},
1974	+	year = {1998},
1975	+	volume = {199},
1976	+	pages = {351-395},
1977	+	number = {2},
1978	+	month = {Dec},
1979	+	abstract = {This paper presents a geometric-variational approach to continuous
1980	+	and discrete mechanics and field theories. Using multisymplectic
1981	+	geometry, we show that the existence of the fundamental geometric
1982	+	structures as well as their preservation along solutions can be
1983	+	obtained directly from the variational principle. In particular,
1984	+	we prove that a unique multisymplectic structure is obtained by
1985	+	taking the derivative of an action function, and use this structure
1986	+	to prove covariant generalizations of conservation of symplecticity
1987	+	and Noether's theorem. Natural discretization schemes for PDEs,
1988	+	which have these important preservation properties, then follow
1989	+	by choosing a discrete action functional. In the case of mechanics,
1990	+	we recover the variational symplectic integrators of Veselov type,
1991	+	while for PDEs we obtain covariant spacetime integrators which conserve
1992	+	the corresponding discrete multisymplectic form as well as the discrete
1993	+	momentum mappings corresponding to symmetries. We show that the
1994	+	usual notion of symplecticity along an infinite-dimensional space
1995	+	of fields can be naturally obtained by making a spacetime split.
1996	+	All of the aspects of our method are demonstrated with a nonlinear
1997	+	sine-Gordon equation, including computational results and a comparison
1998	+	with other discretization schemes.},
1999	+	annote = {154RH Times Cited:88 Cited References Count:36},
2000	+	issn = {0010-3616},
2001	+	uri = {<Go to ISI>://000077902200006},
2002	+	}
2003	+
2004	+	@ARTICLE{Matthey2004,
2005	+	author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and
2006	+	M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre},
2007	+	title = {ProtoMol, an object-oriented framework for prototyping novel algorithms
2008	+	for molecular dynamics},
2009	+	journal = {Acm Transactions on Mathematical Software},
2010	+	year = {2004},
2011	+	volume = {30},
2012	+	pages = {237-265},
2013	+	number = {3},
2014	+	month = {Sep},
2015	+	abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
2016	+	of novel algorithms for molecular dynamics and related applications.
2017	+	Its flexibility is achieved primarily through the use of inheritance
2018	+	and design patterns (object-oriented programming): Performance is
2019	+	obtained by using templates that enable generation of efficient
2020	+	code for sections critical to performance (generic programming).
2021	+	The framework encapsulates important optimizations that can be used
2022	+	by developers, such as parallelism in the force computation. Its
2023	+	design is based on domain analysis of numerical integrators for
2024	+	molecular dynamics (MD) and of fast solvers for the force computation,
2025	+	particularly due to electrostatic interactions. Several new and
2026	+	efficient algorithms are implemented in PROTOMOL. Finally, it is
2027	+	shown that PROTOMOL'S sequential performance is excellent when compared
2028	+	to a leading MD program, and that it scales well for moderate number
2029	+	of processors. Binaries and source codes for Windows, Linux, Solaris,
2030	+	IRIX, HP-UX, and AIX platforms are available under open source license
2031	+	at http://protomol.sourceforge.net.},
2032	+	annote = {860EP Times Cited:2 Cited References Count:52},
2033	+	issn = {0098-3500},
2034	+	uri = {<Go to ISI>://000224325600001},
2035	+	}
2036	+
2037		@ARTICLE{McLachlan1993,
2038		author = {R.~I McLachlan},
2039		title = {Explicit Lie-Poisson integration and the Euler equations},
#	Line 1495 | Line 2043 | Encoding: GBK
2043		pages = {3043-3046},
2044		}
2045
2046	<	@ARTICLE{McLachlan2005,
2047	<	author = {R. I. McLachlan and A. Zanna},
2048	<	title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
2049	<	journal = {Foundations of Computational Mathematics},
2050	<	year = {2005},
2051	<	volume = {5},
2052	<	pages = {87-123},
2053	<	number = {1},
2054	<	month = {Feb},
2055	<	abstract = {In this paper we revisit the Moser-Veselov description of the free
2056	<	rigid body in body coordinates, which, in the 3 x 3 case, can be
2057	<	implemented as an explicit, second-order, integrable approximation
2058	<	of the continuous solution. By backward error analysis, we study
2059	<	the modified vector field which is integrated exactly by the discrete
2060	<	algorithm. We deduce that the discrete Moser-Veselov (DMV) is well
2061	<	approximated to higher order by time reparametrizations of the continuous
2062	<	equations (modified vector field). We use the modified vector field
2063	<	to scale the initial data of the DMV to improve the order of the
2064	<	approximation and show the equivalence of the DMV and the RATTLE
2065	<	algorithm. Numerical integration with these preprocessed initial
2066	<	data is several orders of magnitude more accurate than the original
2067	<	DMV and RATTLE approach.},
2046	>	@ARTICLE{McLachlan1998,
2047	>	author = {R. I. McLachlan and G. R. W. Quispel},
2048	>	title = {Generating functions for dynamical systems with symmetries, integrals,
2049	>	and differential invariants},
2050	>	journal = {Physica D},
2051	>	year = {1998},
2052	>	volume = {112},
2053	>	pages = {298-309},
2054	>	number = {1-2},
2055	>	month = {Jan 15},
2056	>	abstract = {We give a survey and some new examples of generating functions for
2057	>	systems with symplectic structure, systems with a first integral,
2058	>	systems that preserve volume, and systems with symmetries and/or
2059	>	time-reversing symmetries. Both ODEs and maps are treated, and we
2060	>	discuss how generating functions may be used in the structure-preserving
2061	>	numerical integration of ODEs with the above properties.},
2062	>	annote = {Yt049 Times Cited:7 Cited References Count:26},
2063	>	issn = {0167-2789},
2064	>	uri = {<Go to ISI>://000071558900021},
2065	>	}
2066	>
2067	>	@ARTICLE{McLachlan1998a,
2068	>	author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner},
2069	>	title = {Numerical integrators that preserve symmetries and reversing symmetries},
2070	>	journal = {Siam Journal on Numerical Analysis},
2071	>	year = {1998},
2072	>	volume = {35},
2073	>	pages = {586-599},
2074	>	number = {2},
2075	>	month = {Apr},
2076	>	abstract = {We consider properties of flows, the relationships between them, and
2077	>	whether numerical integrators can be made to preserve these properties.
2078	>	This is done in the context of automorphisms and antiautomorphisms
2079	>	of a certain group generated by maps associated to vector fields.
2080	>	This new framework unifies several known constructions. We also
2081	>	use the concept of #covariance# of a numerical method with respect
2082	>	to a group of coordinate transformations. The main application is
2083	>	to explore the relationship between spatial symmetries, reversing
2084	>	symmetries, and time symmetry of flows and numerical integrators.},
2085	>	annote = {Zc449 Times Cited:14 Cited References Count:33},
2086	>	issn = {0036-1429},
2087	>	uri = {<Go to ISI>://000072580500010},
2088	>	}
2089	>
2090	>	@ARTICLE{McLachlan2005,
2091	>	author = {R. I. McLachlan and A. Zanna},
2092	>	title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
2093	>	journal = {Foundations of Computational Mathematics},
2094	>	year = {2005},
2095	>	volume = {5},
2096	>	pages = {87-123},
2097	>	number = {1},
2098	>	month = {Feb},
2099	>	abstract = {In this paper we revisit the Moser-Veselov description of the free
2100	>	rigid body in body coordinates, which, in the 3 x 3 case, can be
2101	>	implemented as an explicit, second-order, integrable approximation
2102	>	of the continuous solution. By backward error analysis, we study
2103	>	the modified vector field which is integrated exactly by the discrete
2104	>	algorithm. We deduce that the discrete Moser-Veselov (DMV) is well
2105	>	approximated to higher order by time reparametrizations of the continuous
2106	>	equations (modified vector field). We use the modified vector field
2107	>	to scale the initial data of the DMV to improve the order of the
2108	>	approximation and show the equivalence of the DMV and the RATTLE
2109	>	algorithm. Numerical integration with these preprocessed initial
2110	>	data is several orders of magnitude more accurate than the original
2111	>	DMV and RATTLE approach.},
2112		annote = {911NS Times Cited:0 Cited References Count:14},
2113		issn = {1615-3375},
2114		uri = {<Go to ISI>://000228011900003},
2115		}
2116
2117	+	@ARTICLE{Meineke2005,
2118	+	author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and
2119	+	J. D. Gezelter},
2120	+	title = {OOPSE: An object-oriented parallel simulation engine for molecular
2121	+	dynamics},
2122	+	journal = {Journal of Computational Chemistry},
2123	+	year = {2005},
2124	+	volume = {26},
2125	+	pages = {252-271},
2126	+	number = {3},
2127	+	month = {Feb},
2128	+	abstract = {OOPSE is a new molecular dynamics simulation program that is capable
2129	+	of efficiently integrating equations of motion for atom types with
2130	+	orientational degrees of freedom (e.g. #sticky# atoms and point
2131	+	dipoles). Transition metals can also be simulated using the embedded
2132	+	atom method (EAM) potential included in the code. Parallel simulations
2133	+	are carried out using the force-based decomposition method. Simulations
2134	+	are specified using a very simple C-based meta-data language. A
2135	+	number of advanced integrators are included, and the basic integrator
2136	+	for orientational dynamics provides substantial improvements over
2137	+	older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.},
2138	+	annote = {891CF Times Cited:1 Cited References Count:56},
2139	+	issn = {0192-8651},
2140	+	uri = {<Go to ISI>://000226558200006},
2141	+	}
2142	+
2143	+	@ARTICLE{Melchionna1993,
2144	+	author = {S. Melchionna and G. Ciccotti and B. L. Holian},
2145	+	title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
2146	+	journal = {Molecular Physics},
2147	+	year = {1993},
2148	+	volume = {78},
2149	+	pages = {533-544},
2150	+	number = {3},
2151	+	month = {Feb 20},
2152	+	abstract = {In this paper we write down equations of motion (following the approach
2153	+	pioneered by Hoover) for an exact isothermal-isobaric molecular
2154	+	dynamics simulation, and we extend them to multiple thermostating
2155	+	rates, to a shape-varying cell and to molecular systems, coherently
2156	+	with the previous 'extended system method'. An integration scheme
2157	+	is proposed together with a numerical illustration of the method.},
2158	+	annote = {Kq355 Times Cited:172 Cited References Count:17},
2159	+	issn = {0026-8976},
2160	+	uri = {<Go to ISI>://A1993KQ35500002},
2161	+	}
2162	+
2163		@ARTICLE{Memmer2002,
2164		author = {R. Memmer},
2165		title = {Liquid crystal phases of achiral banana-shaped molecules: a computer
2166	<	simulation study},
2166	>	simulation study},
2167		journal = {Liquid Crystals},
2168		year = {2002},
2169		volume = {29},
#	Line 1533 | Line 2171 | Encoding: GBK
2171		number = {4},
2172		month = {Apr},
2173		abstract = {The phase behaviour of achiral banana-shaped molecules was studied
2174	<	by computer simulation. The banana-shaped molecules were described
2175	<	by model intermolecular interactions based on the Gay-Berne potential.
2176	<	The characteristic molecular structure was considered by joining
2177	<	two calamitic Gay-Berne particles through a bond to form a biaxial
2178	<	molecule of point symmetry group C-2v with a suitable bending angle.
2179	<	The dependence on temperature of systems of N=1024 rigid banana-shaped
2180	<	molecules with bending angle phi=140degrees has been studied by
2181	<	means of Monte Carlo simulations in the isobaric-isothermal ensemble
2182	<	(NpT). On cooling an isotropic system, two phase transitions characterized
2183	<	by phase transition enthalpy, entropy and relative volume change
2184	<	have been observed. For the first time by computer simulation of
2185	<	a many-particle system of banana-shaped molecules, at low temperature
2186	<	an untilted smectic phase showing a global phase biaxiality and
2187	<	a spontaneous local polarization in the layers, i.e. a local polar
2188	<	arrangement of the steric dipoles, with an antiferroelectric-like
2189	<	superstructure could be proven, a phase structure which recently
2190	<	has been discovered experimentally. Additionally, at intermediate
2191	<	temperature a nematic-like phase has been proved, whereas close
2192	<	to the transition to the smectic phase hints of a spontaneous achiral
2193	<	symmetry breaking have been determined. Here, in the absence of
2194	<	a layered structure a helical superstructure has been formed. All
2195	<	phases have been characterized by visual representations of selected
2196	<	configurations, scalar and pseudoscalar correlation functions, and
2197	<	order parameters.},
2174	>	by computer simulation. The banana-shaped molecules were described
2175	>	by model intermolecular interactions based on the Gay-Berne potential.
2176	>	The characteristic molecular structure was considered by joining
2177	>	two calamitic Gay-Berne particles through a bond to form a biaxial
2178	>	molecule of point symmetry group C-2v with a suitable bending angle.
2179	>	The dependence on temperature of systems of N=1024 rigid banana-shaped
2180	>	molecules with bending angle phi=140degrees has been studied by
2181	>	means of Monte Carlo simulations in the isobaric-isothermal ensemble
2182	>	(NpT). On cooling an isotropic system, two phase transitions characterized
2183	>	by phase transition enthalpy, entropy and relative volume change
2184	>	have been observed. For the first time by computer simulation of
2185	>	a many-particle system of banana-shaped molecules, at low temperature
2186	>	an untilted smectic phase showing a global phase biaxiality and
2187	>	a spontaneous local polarization in the layers, i.e. a local polar
2188	>	arrangement of the steric dipoles, with an antiferroelectric-like
2189	>	superstructure could be proven, a phase structure which recently
2190	>	has been discovered experimentally. Additionally, at intermediate
2191	>	temperature a nematic-like phase has been proved, whereas close
2192	>	to the transition to the smectic phase hints of a spontaneous achiral
2193	>	symmetry breaking have been determined. Here, in the absence of
2194	>	a layered structure a helical superstructure has been formed. All
2195	>	phases have been characterized by visual representations of selected
2196	>	configurations, scalar and pseudoscalar correlation functions, and
2197	>	order parameters.},
2198		annote = {531HT Times Cited:12 Cited References Count:37},
2199		issn = {0267-8292},
2200		uri = {<Go to ISI>://000174410500001},
#	Line 1573 | Line 2211 | Encoding: GBK
2211
2212		@ARTICLE{Mielke2004,
2213		author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen
2214	<	and C. J. Benham},
2214	>	and C. J. Benham},
2215		title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian
2216	<	dynamics study},
2216	>	dynamics study},
2217		journal = {Journal of Chemical Physics},
2218		year = {2004},
2219		volume = {121},
#	Line 1583 | Line 2221 | Encoding: GBK
2221		number = {16},
2222		month = {Oct 22},
2223		abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
2224	<	DNA can potentially induce long-range structural deformations integral
2225	<	to mechanisms of biological significance in both prokaryotes and
2226	<	eukaryotes. In this paper, we introduce a dynamic computer model
2227	<	for investigating this phenomenon. Duplex DNA is represented as
2228	<	a chain of hydrodynamic beads interacting through potentials of
2229	<	linearly elastic stretching, bending, and twisting, as well as excluded
2230	<	volume. The chain, linear when relaxed, is looped to form two open
2231	<	but topologically constrained subdomains. This permits the dynamic
2232	<	introduction of torsional stress via a centrally applied torque.
2233	<	We simulate by Brownian dynamics the 100 mus response of a 477-base
2234	<	pair B-DNA template to the localized torque generated by the prokaryotic
2235	<	transcription ensemble. Following a sharp rise at early times, the
2236	<	distributed twist assumes a nearly constant value in both subdomains,
2237	<	and a succession of supercoiling deformations occurs as superhelical
2238	<	stress is increasingly partitioned to writhe. The magnitude of writhe
2239	<	surpasses that of twist before also leveling off when the structure
2240	<	reaches mechanical equilibrium with the torsional load. Superhelicity
2241	<	is simultaneously right handed in one subdomain and left handed
2242	<	in the other, as predicted by the #transcription-induced##twin-supercoiled-domain#
2243	<	model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84,
2244	<	7024 (1987)]. The properties of the chain at the onset of writhing
2245	<	agree well with predictions from theory, and the generated stress
2246	<	is ample for driving secondary structural transitions in physiological
2247	<	DNA. (C) 2004 American Institute of Physics.},
2224	>	DNA can potentially induce long-range structural deformations integral
2225	>	to mechanisms of biological significance in both prokaryotes and
2226	>	eukaryotes. In this paper, we introduce a dynamic computer model
2227	>	for investigating this phenomenon. Duplex DNA is represented as
2228	>	a chain of hydrodynamic beads interacting through potentials of
2229	>	linearly elastic stretching, bending, and twisting, as well as excluded
2230	>	volume. The chain, linear when relaxed, is looped to form two open
2231	>	but topologically constrained subdomains. This permits the dynamic
2232	>	introduction of torsional stress via a centrally applied torque.
2233	>	We simulate by Brownian dynamics the 100 mus response of a 477-base
2234	>	pair B-DNA template to the localized torque generated by the prokaryotic
2235	>	transcription ensemble. Following a sharp rise at early times, the
2236	>	distributed twist assumes a nearly constant value in both subdomains,
2237	>	and a succession of supercoiling deformations occurs as superhelical
2238	>	stress is increasingly partitioned to writhe. The magnitude of writhe
2239	>	surpasses that of twist before also leveling off when the structure
2240	>	reaches mechanical equilibrium with the torsional load. Superhelicity
2241	>	is simultaneously right handed in one subdomain and left handed
2242	>	in the other, as predicted by the #transcription-induced##twin-supercoiled-domain#
2243	>	model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84,
2244	>	7024 (1987)]. The properties of the chain at the onset of writhing
2245	>	agree well with predictions from theory, and the generated stress
2246	>	is ample for driving secondary structural transitions in physiological
2247	>	DNA. (C) 2004 American Institute of Physics.},
2248		annote = {861ZF Times Cited:3 Cited References Count:34},
2249		issn = {0021-9606},
2250		uri = {<Go to ISI>://000224456500064},
#	Line 1615 | Line 2253 | Encoding: GBK
2253		@ARTICLE{Naess2001,
2254		author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter},
2255		title = {Brownian dynamics simulation of rigid bodies and segmented polymer
2256	<	chains. Use of Cartesian rotation vectors as the generalized coordinates
2257	<	describing angular orientations},
2256	>	chains. Use of Cartesian rotation vectors as the generalized coordinates
2257	>	describing angular orientations},
2258		journal = {Physica A},
2259		year = {2001},
2260		volume = {294},
#	Line 1624 | Line 2262 | Encoding: GBK
2262		number = {3-4},
2263		month = {May 15},
2264		abstract = {The three Eulerian angles constitute the classical choice of generalized
2265	<	coordinates used to describe the three degrees of rotational freedom
2266	<	of a rigid body, but it has long been known that this choice yields
2267	<	singular equations of motion. The latter is also true when Eulerian
2268	<	angles are used in Brownian dynamics analyses of the angular orientation
2269	<	of single rigid bodies and segmented polymer chains. Starting from
2270	<	kinetic theory we here show that by instead employing the three
2271	<	components of Cartesian rotation vectors as the generalized coordinates
2272	<	describing angular orientation, no singularity appears in the configuration
2273	<	space diffusion equation and the associated Brownian dynamics algorithm.
2274	<	The suitability of Cartesian rotation vectors in Brownian dynamics
2275	<	simulations of segmented polymer chains with spring-like or ball-socket
2276	<	joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.},
2265	>	coordinates used to describe the three degrees of rotational freedom
2266	>	of a rigid body, but it has long been known that this choice yields
2267	>	singular equations of motion. The latter is also true when Eulerian
2268	>	angles are used in Brownian dynamics analyses of the angular orientation
2269	>	of single rigid bodies and segmented polymer chains. Starting from
2270	>	kinetic theory we here show that by instead employing the three
2271	>	components of Cartesian rotation vectors as the generalized coordinates
2272	>	describing angular orientation, no singularity appears in the configuration
2273	>	space diffusion equation and the associated Brownian dynamics algorithm.
2274	>	The suitability of Cartesian rotation vectors in Brownian dynamics
2275	>	simulations of segmented polymer chains with spring-like or ball-socket
2276	>	joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.},
2277		annote = {433TA Times Cited:7 Cited References Count:19},
2278		issn = {0378-4371},
2279		uri = {<Go to ISI>://000168774800005},
#	Line 1644 | Line 2282 | Encoding: GBK
2282		@ARTICLE{Niori1996,
2283		author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe},
2284		title = {Distinct ferroelectric smectic liquid crystals consisting of banana
2285	<	shaped achiral molecules},
2285	>	shaped achiral molecules},
2286		journal = {Journal of Materials Chemistry},
2287		year = {1996},
2288		volume = {6},
#	Line 1652 | Line 2290 | Encoding: GBK
2290		number = {7},
2291		month = {Jul},
2292		abstract = {The synthesis of a banana-shaped molecule is reported and it is found
2293	<	that the smectic phase which it forms is biaxial with the molecules
2294	<	packed in the best,direction into a layer. Because of this characteristic
2295	<	packing, spontaneous polarization appears parallel to the layer
2296	<	and switches on reversal of an applied electric field. This is the
2297	<	first obvious example of ferroelectricity in an achiral smectic
2298	<	phase and is ascribed to the C-2v symmetry of the molecular packing.},
2293	>	that the smectic phase which it forms is biaxial with the molecules
2294	>	packed in the best,direction into a layer. Because of this characteristic
2295	>	packing, spontaneous polarization appears parallel to the layer
2296	>	and switches on reversal of an applied electric field. This is the
2297	>	first obvious example of ferroelectricity in an achiral smectic
2298	>	phase and is ascribed to the C-2v symmetry of the molecular packing.},
2299		annote = {Ux855 Times Cited:447 Cited References Count:18},
2300		issn = {0959-9428},
2301		uri = {<Go to ISI>://A1996UX85500025},
#	Line 1673 | Line 2311 | Encoding: GBK
2311		number = {5},
2312		month = {may},
2313		abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
2314	<	forces using a Brownian dynamics simulation. Two nanoparticles,
2315	<	which interact repulsively with amphiphilic molecules, are put inside
2316	<	a vesicle. The position of one nanoparticle is fixed, and the other
2317	<	is moved by a constant force as in optical-trapping experiments.
2318	<	First, the pulled vesicle stretches into a pear or tube shape. Then
2319	<	the inner monolayer in the tube-shaped region is deformed, and a
2320	<	cylindrical structure is formed between two vesicles. After stretching
2321	<	the cylindrical region, fission occurs near the moved vesicle. Soon
2322	<	after this the cylindrical region shrinks. The trapping force similar
2323	<	to 100 pN is needed to induce the formation of the cylindrical structure
2324	<	and fission.},
2314	>	forces using a Brownian dynamics simulation. Two nanoparticles,
2315	>	which interact repulsively with amphiphilic molecules, are put inside
2316	>	a vesicle. The position of one nanoparticle is fixed, and the other
2317	>	is moved by a constant force as in optical-trapping experiments.
2318	>	First, the pulled vesicle stretches into a pear or tube shape. Then
2319	>	the inner monolayer in the tube-shaped region is deformed, and a
2320	>	cylindrical structure is formed between two vesicles. After stretching
2321	>	the cylindrical region, fission occurs near the moved vesicle. Soon
2322	>	after this the cylindrical region shrinks. The trapping force similar
2323	>	to 100 pN is needed to induce the formation of the cylindrical structure
2324	>	and fission.},
2325		annote = {Part 1 568PX Times Cited:5 Cited References Count:39},
2326		issn = {1063-651X},
2327		uri = {<Go to ISI>://000176552300084},
#	Line 1699 | Line 2337 | Encoding: GBK
2337		number = {20},
2338		month = {Nov 22},
2339		abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
2340	<	simulation. Amphiphilic molecules spontaneously form vesicles with
2341	<	a bilayer structure. Two vesicles come into contact and form a stalk
2342	<	intermediate, in which a necklike structure only connects the outer
2343	<	monolayers, as predicted by the stalk hypothesis. We have found
2344	<	a new pathway of pore opening from stalks at high temperature: the
2345	<	elliptic stalk bends and contact between the ends of the arc-shaped
2346	<	stalk leads to pore opening. On the other hand, we have clarified
2347	<	that the pore-opening process at low temperature agrees with the
2348	<	modified stalk model: a pore is induced by contact between the inner
2349	<	monolayers inside the stalk. (C) 2001 American Institute of Physics.},
2340	>	simulation. Amphiphilic molecules spontaneously form vesicles with
2341	>	a bilayer structure. Two vesicles come into contact and form a stalk
2342	>	intermediate, in which a necklike structure only connects the outer
2343	>	monolayers, as predicted by the stalk hypothesis. We have found
2344	>	a new pathway of pore opening from stalks at high temperature: the
2345	>	elliptic stalk bends and contact between the ends of the arc-shaped
2346	>	stalk leads to pore opening. On the other hand, we have clarified
2347	>	that the pore-opening process at low temperature agrees with the
2348	>	modified stalk model: a pore is induced by contact between the inner
2349	>	monolayers inside the stalk. (C) 2001 American Institute of Physics.},
2350		annote = {491UW Times Cited:48 Cited References Count:25},
2351		issn = {0021-9606},
2352		uri = {<Go to ISI>://000172129300049},
2353	+	}
2354	+
2355	+	@BOOK{Olver1986,
2356	+	title = {Applications of Lie groups to differential equatitons},
2357	+	publisher = {Springer},
2358	+	year = {1986},
2359	+	author = {P.J. Olver},
2360	+	address = {New York},
2361	+	}
2362	+
2363	+	@ARTICLE{Omelyan1998,
2364	+	author = {I. P. Omelyan},
2365	+	title = {On the numerical integration of motion for rigid polyatomics: The
2366	+	modified quaternion approach},
2367	+	journal = {Computers in Physics},
2368	+	year = {1998},
2369	+	volume = {12},
2370	+	pages = {97-103},
2371	+	number = {1},
2372	+	month = {Jan-Feb},
2373	+	abstract = {A revised version of the quaternion approach for numerical integration
2374	+	of the equations of motion for rigid polyatomic molecules is proposed.
2375	+	The modified approach is based on a formulation of the quaternion
2376	+	dynamics with constraints. This allows one to resolve the rigidity
2377	+	problem rigorously using constraint forces. It is shown that the
2378	+	procedure for preservation of molecular rigidity can be realized
2379	+	particularly simply within the Verlet algorithm in velocity form.
2380	+	We demonstrate that the method presented leads to an improved numerical
2381	+	stability with respect to the usual quaternion rescaling scheme
2382	+	and it is roughly as good as the cumbersome atomic-constraint technique.
2383	+	(C) 1998 American Institute of Physics.},
2384	+	annote = {Yx279 Times Cited:12 Cited References Count:28},
2385	+	issn = {0894-1866},
2386	+	uri = {<Go to ISI>://000072024300025},
2387	+	}
2388	+
2389	+	@ARTICLE{Omelyan1998a,
2390	+	author = {I. P. Omelyan},
2391	+	title = {Algorithm for numerical integration of the rigid-body equations of
2392	+	motion},
2393	+	journal = {Physical Review E},
2394	+	year = {1998},
2395	+	volume = {58},
2396	+	pages = {1169-1172},
2397	+	number = {1},
2398	+	month = {Jul},
2399	+	abstract = {An algorithm for numerical integration of the rigid-body equations
2400	+	of motion is proposed. The algorithm uses the leapfrog scheme and
2401	+	the quantities involved are angular velocities and orientational
2402	+	variables that can be expressed in terms of either principal axes
2403	+	or quaternions. Due to specific features of the algorithm, orthonormality
2404	+	and unit norms of the orientational variables are integrals of motion,
2405	+	despite an approximate character of the produced trajectories. It
2406	+	is shown that the method presented appears to be the most efficient
2407	+	among all such algorithms known.},
2408	+	annote = {101XL Times Cited:8 Cited References Count:22},
2409	+	issn = {1063-651X},
2410	+	uri = {<Go to ISI>://000074893400151},
2411		}
2412
2413		@ARTICLE{Orlandi2006,
2414		author = {S. Orlandi and R. Berardi and J. Steltzer and C. Zannoni},
2415		title = {A Monte Carlo study of the mesophases formed by polar bent-shaped
2416	<	molecules},
2416	>	molecules},
2417		journal = {Journal of Chemical Physics},
2418		year = {2006},
2419		volume = {124},
#	Line 1725 | Line 2421 | Encoding: GBK
2421		number = {12},
2422		month = {Mar 28},
2423		abstract = {Liquid crystal phases formed by bent-shaped (or #banana#) molecules
2424	<	are currently of great interest. Here we investigate by Monte Carlo
2425	<	computer simulations the phases formed by rigid banana molecules
2426	<	modeled combining three Gay-Berne sites and containing either one
2427	<	central or two lateral and transversal dipoles. We show that changing
2428	<	the dipole position and orientation has a profound effect on the
2429	<	mesophase stability and molecular organization. In particular, we
2430	<	find a uniaxial nematic phase only for off-center dipolar models
2431	<	and tilted phases only for the one with terminal dipoles. (c) 2006
2432	<	American Institute of Physics.},
2424	>	are currently of great interest. Here we investigate by Monte Carlo
2425	>	computer simulations the phases formed by rigid banana molecules
2426	>	modeled combining three Gay-Berne sites and containing either one
2427	>	central or two lateral and transversal dipoles. We show that changing
2428	>	the dipole position and orientation has a profound effect on the
2429	>	mesophase stability and molecular organization. In particular, we
2430	>	find a uniaxial nematic phase only for off-center dipolar models
2431	>	and tilted phases only for the one with terminal dipoles. (c) 2006
2432	>	American Institute of Physics.},
2433		annote = {028CP Times Cited:0 Cited References Count:42},
2434		issn = {0021-9606},
2435		uri = {<Go to ISI>://000236464000072},
2436		}
2437
2438	+	@ARTICLE{Owren1992,
2439	+	author = {B. Owren and M. Zennaro},
2440	+	title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
2441	+	journal = {Siam Journal on Scientific and Statistical Computing},
2442	+	year = {1992},
2443	+	volume = {13},
2444	+	pages = {1488-1501},
2445	+	number = {6},
2446	+	month = {Nov},
2447	+	abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
2448	+	stages are considered. These methods are continuously differentiable
2449	+	if and only if one of the stages is the FSAL evaluation. A characterization
2450	+	of a subclass of these methods is developed for orders 3, 4, and
2451	+	5. It is shown how the free parameters of these methods can be used
2452	+	either to minimize the continuous truncation error coefficients
2453	+	or to maximize the stability region. As a representative for these
2454	+	methods the fifth-order method with minimized error coefficients
2455	+	is chosen, supplied with an error estimation method, and analysed
2456	+	by using the DETEST software. The results are compared with a similar
2457	+	implementation of the Dormand-Prince 5(4) pair with interpolant,
2458	+	showing a significant advantage in the new method for the chosen
2459	+	problems.},
2460	+	annote = {Ju936 Times Cited:25 Cited References Count:20},
2461	+	issn = {0196-5204},
2462	+	uri = {<Go to ISI>://A1992JU93600013},
2463	+	}
2464	+
2465		@ARTICLE{Palacios1998,
2466		author = {J. L. Garcia-Palacios and F. J. Lazaro},
2467		title = {Langevin-dynamics study of the dynamical properties of small magnetic
2468	<	particles},
2468	>	particles},
2469		journal = {Physical Review B},
2470		year = {1998},
2471		volume = {58},
#	Line 1750 | Line 2473 | Encoding: GBK
2473		number = {22},
2474		month = {Dec 1},
2475		abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
2476	<	magnetic moment is numerically solved (properly observing the customary
2477	<	interpretation of it as a Stratonovich stochastic differential equation),
2478	<	in order to study the dynamics of magnetic nanoparticles. The corresponding
2479	<	Langevin-dynamics approach allows for the study of the fluctuating
2480	<	trajectories of individual magnetic moments, where we have encountered
2481	<	remarkable phenomena in the overbarrier rotation process, such as
2482	<	crossing-back or multiple crossing of the potential barrier, rooted
2483	<	in the gyromagnetic nature of the system. Concerning averaged quantities,
2484	<	we study the linear dynamic response of the archetypal ensemble
2485	<	of noninteracting classical magnetic moments with axially symmetric
2486	<	magnetic anisotropy. The results are compared with different analytical
2487	<	expressions used to model the relaxation of nanoparticle ensembles,
2488	<	assessing their accuracy. It has been found that, among a number
2489	<	of heuristic expressions for the linear dynamic susceptibility,
2490	<	only the simple formula proposed by Shliomis and Stepanov matches
2491	<	the coarse features of the susceptibility reasonably. By comparing
2492	<	the numerical results with the asymptotic formula of Storonkin {Sov.
2493	<	Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]},
2494	<	the effects of the intra-potential-well relaxation modes on the
2495	<	low-temperature longitudinal dynamic response have been assessed,
2496	<	showing their relatively small reflection in the susceptibility
2497	<	curves but their dramatic influence on the phase shifts. Comparison
2498	<	of the numerical results with the exact zero-damping expression
2499	<	for the transverse susceptibility by Garanin, Ishchenko, and Panina
2500	<	{Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242
2501	<	(1990)]}, reveals a sizable contribution of the spread of the precession
2502	<	frequencies of the magnetic moment in the anisotropy field to the
2503	<	dynamic response at intermediate-to-high temperatures. [S0163-1829
2504	<	(98)00446-9].},
2476	>	magnetic moment is numerically solved (properly observing the customary
2477	>	interpretation of it as a Stratonovich stochastic differential equation),
2478	>	in order to study the dynamics of magnetic nanoparticles. The corresponding
2479	>	Langevin-dynamics approach allows for the study of the fluctuating
2480	>	trajectories of individual magnetic moments, where we have encountered
2481	>	remarkable phenomena in the overbarrier rotation process, such as
2482	>	crossing-back or multiple crossing of the potential barrier, rooted
2483	>	in the gyromagnetic nature of the system. Concerning averaged quantities,
2484	>	we study the linear dynamic response of the archetypal ensemble
2485	>	of noninteracting classical magnetic moments with axially symmetric
2486	>	magnetic anisotropy. The results are compared with different analytical
2487	>	expressions used to model the relaxation of nanoparticle ensembles,
2488	>	assessing their accuracy. It has been found that, among a number
2489	>	of heuristic expressions for the linear dynamic susceptibility,
2490	>	only the simple formula proposed by Shliomis and Stepanov matches
2491	>	the coarse features of the susceptibility reasonably. By comparing
2492	>	the numerical results with the asymptotic formula of Storonkin {Sov.
2493	>	Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]},
2494	>	the effects of the intra-potential-well relaxation modes on the
2495	>	low-temperature longitudinal dynamic response have been assessed,
2496	>	showing their relatively small reflection in the susceptibility
2497	>	curves but their dramatic influence on the phase shifts. Comparison
2498	>	of the numerical results with the exact zero-damping expression
2499	>	for the transverse susceptibility by Garanin, Ishchenko, and Panina
2500	>	{Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242
2501	>	(1990)]}, reveals a sizable contribution of the spread of the precession
2502	>	frequencies of the magnetic moment in the anisotropy field to the
2503	>	dynamic response at intermediate-to-high temperatures. [S0163-1829
2504	>	(98)00446-9].},
2505		annote = {146XW Times Cited:66 Cited References Count:45},
2506		issn = {0163-1829},
2507		uri = {<Go to ISI>://000077460000052},
2508		}
2509
2510	+	@ARTICLE{Parr1995,
2511	+	author = {T. J. Parr and R. W. Quong},
2512	+	title = {Antlr - a Predicated-Ll(K) Parser Generator},
2513	+	journal = {Software-Practice \& Experience},
2514	+	year = {1995},
2515	+	volume = {25},
2516	+	pages = {789-810},
2517	+	number = {7},
2518	+	month = {Jul},
2519	+	abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
2520	+	often choose to write recursive-descent parsers by hand to obtain
2521	+	increased flexibility, better error handling, and ease of debugging.
2522	+	We introduce ANTLR, a public-domain parser generator that combines
2523	+	the flexibility of hand-coded parsing with the convenience of a
2524	+	parser generator, which is a component of PCCTS. ANTLR has many
2525	+	features that make it easier to use than other language tools. Most
2526	+	important, ANTLR provides predicates which let the programmer systematically
2527	+	direct the parse via arbitrary expressions using semantic and syntactic
2528	+	context; in practice, the use of predicates eliminates the need
2529	+	to hand-tweak the ANTLR output, even for difficult parsing problems.
2530	+	ANTLR also integrates the description of lexical and syntactic analysis,
2531	+	accepts LL(k) grammars for k > 1 with extended BNF notation, and
2532	+	can automatically generate abstract syntax trees. ANTLR is widely
2533	+	used, with over 1000 registered industrial and academic users in
2534	+	37 countries. It has been ported to many popular systems such as
2535	+	the PC, Macintosh, and a variety of UNIX platforms; a commercial
2536	+	C++ front-end has been developed as a result of one of our industrial
2537	+	collaborations.},
2538	+	annote = {Rk104 Times Cited:19 Cited References Count:10},
2539	+	issn = {0038-0644},
2540	+	uri = {<Go to ISI>://A1995RK10400004},
2541	+	}
2542	+
2543		@ARTICLE{Pastor1988,
2544		author = {R. W. Pastor and B. R. Brooks and A. Szabo},
2545		title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
#	Line 1815 | Line 2571 | Encoding: GBK
2571		@ARTICLE{Perram1985,
2572		author = {J. W. Perram and M. S. Wertheim},
2573		title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and
2574	<	the Contact Function},
2574	>	the Contact Function},
2575		journal = {Journal of Computational Physics},
2576		year = {1985},
2577		volume = {58},
#	Line 1824 | Line 2580 | Encoding: GBK
2580		annote = {Akb93 Times Cited:71 Cited References Count:12},
2581		issn = {0021-9991},
2582		uri = {<Go to ISI>://A1985AKB9300008},
2583	+	}
2584	+
2585	+	@ARTICLE{Rotne1969,
2586	+	author = {F. Perrin},
2587	+	title = {Variational treatment of hydrodynamic interaction in polymers},
2588	+	journal = {J. Chem. Phys.},
2589	+	year = {1969},
2590	+	volume = {50},
2591	+	pages = {4831¨C4837},
2592	+	}
2593	+
2594	+	@ARTICLE{Perrin1936,
2595	+	author = {F. Perrin},
2596	+	title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation
2597	+	des fluorescences. Translation et diffusion de moleculese ellipsoidales},
2598	+	journal = {J. Phys. Radium},
2599	+	year = {1936},
2600	+	volume = {7},
2601	+	pages = {1-11},
2602	+	}
2603	+
2604	+	@ARTICLE{Perrin1934,
2605	+	author = {F. Perrin},
2606	+	title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour
2607	+	des molecules ellipsoidales},
2608	+	journal = {J. Phys. Radium},
2609	+	year = {1934},
2610	+	volume = {5},
2611	+	pages = {497-511},
2612		}
2613
2614	+	@ARTICLE{Petrache2000,
2615	+	author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
2616	+	title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines
2617	+	Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
2618	+	journal = {Biophysical Journal},
2619	+	year = {2000},
2620	+	volume = {79},
2621	+	pages = {3172-3192},
2622	+	}
2623	+
2624		@ARTICLE{Petrache1998,
2625		author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle},
2626		title = {Fluid phase structure of EPC and DMPC bilayers},
#	Line 1836 | Line 2631 | Encoding: GBK
2631		number = {1},
2632		month = {Sep},
2633		abstract = {X-ray diffraction data taken at high instrumental resolution were
2634	<	obtained for EPC and DMPC under various osmotic pressures, primarily
2635	<	at T = 30 degrees C. The headgroup thickness D-HH was obtained from
2636	<	relative electron density profiles. By using volumetric results
2637	<	and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4
2638	<	+/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The
2639	<	analysis also gives estimates for the areal compressibility K-A.
2640	<	The A(F) results lead to other structural results regarding membrane
2641	<	thickness and associated waters. Using the recently determined absolute
2642	<	electrons density profile of DPPC, the AF results also lead to absolute
2643	<	electron density profiles and absolute continuous transforms \F(q)\
2644	<	for EPC and DMPC, Limited measurements of temperature dependence
2645	<	show directly that fluctuations increase with increasing temperature
2646	<	and that a small decrease in bending modulus K-c accounts for the
2647	<	increased water spacing reported by Simon et al. (1995) Biophys.
2648	<	J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights
2649	<	reserved.},
2634	>	obtained for EPC and DMPC under various osmotic pressures, primarily
2635	>	at T = 30 degrees C. The headgroup thickness D-HH was obtained from
2636	>	relative electron density profiles. By using volumetric results
2637	>	and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4
2638	>	+/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The
2639	>	analysis also gives estimates for the areal compressibility K-A.
2640	>	The A(F) results lead to other structural results regarding membrane
2641	>	thickness and associated waters. Using the recently determined absolute
2642	>	electrons density profile of DPPC, the AF results also lead to absolute
2643	>	electron density profiles and absolute continuous transforms \F(q)\
2644	>	for EPC and DMPC, Limited measurements of temperature dependence
2645	>	show directly that fluctuations increase with increasing temperature
2646	>	and that a small decrease in bending modulus K-c accounts for the
2647	>	increased water spacing reported by Simon et al. (1995) Biophys.
2648	>	J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights
2649	>	reserved.},
2650		annote = {130AT Times Cited:98 Cited References Count:39},
2651		issn = {0009-3084},
2652		uri = {<Go to ISI>://000076497600007},
#	Line 1860 | Line 2655 | Encoding: GBK
2655		@ARTICLE{Powles1973,
2656		author = {J.~G. Powles},
2657		title = {A general ellipsoid can not always serve as a modle for the rotational
2658	<	diffusion properties of arbitrary shaped rigid molecules},
2658	>	diffusion properties of arbitrary shaped rigid molecules},
2659		journal = {Advan. Phys.},
2660		year = {1973},
2661		volume = {22},
#	Line 1870 | Line 2665 | Encoding: GBK
2665		@ARTICLE{Recio2004,
2666		author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
2667		title = {Identification of protein-protein interaction sites from docking
2668	<	energy landscapes},
2668	>	energy landscapes},
2669		journal = {Journal of Molecular Biology},
2670		year = {2004},
2671		volume = {335},
#	Line 1878 | Line 2673 | Encoding: GBK
2673		number = {3},
2674		month = {Jan 16},
2675		abstract = {Protein recognition is one of the most challenging and intriguing
2676	<	problems in structural biology. Despite all the available structural,
2677	<	sequence and biophysical information about protein-protein complexes,
2678	<	the physico-chemical patterns, if any, that make a protein surface
2679	<	likely to be involved in protein-protein interactions, remain elusive.
2680	<	Here, we apply protein docking simulations and analysis of the interaction
2681	<	energy landscapes to identify protein-protein interaction sites.
2682	<	The new protocol for global docking based on multi-start global
2683	<	energy optimization of an allatom model of the ligand, with detailed
2684	<	receptor potentials and atomic solvation parameters optimized in
2685	<	a training set of 24 complexes, explores the conformational space
2686	<	around the whole receptor without restrictions. The ensembles of
2687	<	the rigid-body docking solutions generated by the simulations were
2688	<	subsequently used to project the docking energy landscapes onto
2689	<	the protein surfaces. We found that highly populated low-energy
2690	<	regions consistently corresponded to actual binding sites. The procedure
2691	<	was validated on a test set of 21 known protein-protein complexes
2692	<	not used in the training set. As much as 81% of the predicted high-propensity
2693	<	patch residues were located correctly in the native interfaces.
2694	<	This approach can guide the design of mutations on the surfaces
2695	<	of proteins, provide geometrical details of a possible interaction,
2696	<	and help to annotate protein surfaces in structural proteomics.
2697	<	(C) 2003 Elsevier Ltd. All rights reserved.},
2676	>	problems in structural biology. Despite all the available structural,
2677	>	sequence and biophysical information about protein-protein complexes,
2678	>	the physico-chemical patterns, if any, that make a protein surface
2679	>	likely to be involved in protein-protein interactions, remain elusive.
2680	>	Here, we apply protein docking simulations and analysis of the interaction
2681	>	energy landscapes to identify protein-protein interaction sites.
2682	>	The new protocol for global docking based on multi-start global
2683	>	energy optimization of an allatom model of the ligand, with detailed
2684	>	receptor potentials and atomic solvation parameters optimized in
2685	>	a training set of 24 complexes, explores the conformational space
2686	>	around the whole receptor without restrictions. The ensembles of
2687	>	the rigid-body docking solutions generated by the simulations were
2688	>	subsequently used to project the docking energy landscapes onto
2689	>	the protein surfaces. We found that highly populated low-energy
2690	>	regions consistently corresponded to actual binding sites. The procedure
2691	>	was validated on a test set of 21 known protein-protein complexes
2692	>	not used in the training set. As much as 81% of the predicted high-propensity
2693	>	patch residues were located correctly in the native interfaces.
2694	>	This approach can guide the design of mutations on the surfaces
2695	>	of proteins, provide geometrical details of a possible interaction,
2696	>	and help to annotate protein surfaces in structural proteomics.
2697	>	(C) 2003 Elsevier Ltd. All rights reserved.},
2698		annote = {763GQ Times Cited:21 Cited References Count:59},
2699		issn = {0022-2836},
2700		uri = {<Go to ISI>://000188066900016},
#	Line 1908 | Line 2703 | Encoding: GBK
2703		@ARTICLE{Reddy2006,
2704		author = {R. A. Reddy and C. Tschierske},
2705		title = {Bent-core liquid crystals: polar order, superstructural chirality
2706	<	and spontaneous desymmetrisation in soft matter systems},
2706	>	and spontaneous desymmetrisation in soft matter systems},
2707		journal = {Journal of Materials Chemistry},
2708		year = {2006},
2709		volume = {16},
2710		pages = {907-961},
2711		number = {10},
2712		abstract = {An overview on the recent developments in the field of liquid crystalline
2713	<	bent-core molecules (so-called banana liquid crystals) is given.
2714	<	After some basic issues, dealing with general aspects of the systematisation
2715	<	of the mesophases, development of polar order and chirality in this
2716	<	class of LC systems and explaining some general structure-property
2717	<	relationships, we focus on fascinating new developments in this
2718	<	field, such as modulated, undulated and columnar phases, so-called
2719	<	B7 phases, phase biaxiality, ferroelectric and antiferroelectric
2720	<	polar order in smectic and columnar phases, amplification and switching
2721	<	of chirality and the spontaneous formation of superstructural and
2722	<	supramolecular chirality.},
2713	>	bent-core molecules (so-called banana liquid crystals) is given.
2714	>	After some basic issues, dealing with general aspects of the systematisation
2715	>	of the mesophases, development of polar order and chirality in this
2716	>	class of LC systems and explaining some general structure-property
2717	>	relationships, we focus on fascinating new developments in this
2718	>	field, such as modulated, undulated and columnar phases, so-called
2719	>	B7 phases, phase biaxiality, ferroelectric and antiferroelectric
2720	>	polar order in smectic and columnar phases, amplification and switching
2721	>	of chirality and the spontaneous formation of superstructural and
2722	>	supramolecular chirality.},
2723		annote = {021NS Times Cited:2 Cited References Count:316},
2724		issn = {0959-9428},
2725		uri = {<Go to ISI>://000235990500001},
2726		}
2727
2728	+	@ARTICLE{Reich1999,
2729	+	author = {S. Reich},
2730	+	title = {Backward error analysis for numerical integrators},
2731	+	journal = {Siam Journal on Numerical Analysis},
2732	+	year = {1999},
2733	+	volume = {36},
2734	+	pages = {1549-1570},
2735	+	number = {5},
2736	+	month = {Sep 8},
2737	+	abstract = {Backward error analysis has become an important tool for understanding
2738	+	the long time behavior of numerical integration methods. This is
2739	+	true in particular for the integration of Hamiltonian systems where
2740	+	backward error analysis can be used to show that a symplectic method
2741	+	will conserve energy over exponentially long periods of time. Such
2742	+	results are typically based on two aspects of backward error analysis:
2743	+	(i) It can be shown that the modified vector fields have some qualitative
2744	+	properties which they share with the given problem and (ii) an estimate
2745	+	is given for the difference between the best interpolating vector
2746	+	field and the numerical method. These aspects have been investigated
2747	+	recently, for example, by Benettin and Giorgilli in [J. Statist.
2748	+	Phys., 74 (1994), pp. 1117-1143], by Hairer in [Ann. Numer. Math.,
2749	+	1 (1994), pp. 107-132], and by Hairer and Lubich in [Numer. Math.,
2750	+	76 (1997), pp. 441-462]. In this paper we aim at providing a unifying
2751	+	framework and a simplification of the existing results and corresponding
2752	+	proofs. Our approach to backward error analysis is based on a simple
2753	+	recursive definition of the modified vector fields that does not
2754	+	require explicit Taylor series expansion of the numerical method
2755	+	and the corresponding flow maps as in the above-cited works. As
2756	+	an application we discuss the long time integration of chaotic Hamiltonian
2757	+	systems and the approximation of time averages along numerically
2758	+	computed trajectories.},
2759	+	annote = {237HV Times Cited:43 Cited References Count:41},
2760	+	issn = {0036-1429},
2761	+	uri = {<Go to ISI>://000082650600010},
2762	+	}
2763	+
2764		@ARTICLE{Ros2005,
2765		author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
2766		title = {Banana-shaped liquid crystals: a new field to explore},
#	Line 1939 | Line 2770 | Encoding: GBK
2770		pages = {5093-5098},
2771		number = {48},
2772		abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
2773	<	mesogenic materials represent a bewitching and stimulating field
2774	<	of research that is interesting both academically and in terms of
2775	<	applications. Numerous topics are open to investigation in this
2776	<	area because of the rich phenomenology and new possibilities that
2777	<	these materials offer. The principal concepts in this area are reviewed
2778	<	along with recent results. In addition, new directions to stimulate
2779	<	further research activities are highlighted.},
2773	>	mesogenic materials represent a bewitching and stimulating field
2774	>	of research that is interesting both academically and in terms of
2775	>	applications. Numerous topics are open to investigation in this
2776	>	area because of the rich phenomenology and new possibilities that
2777	>	these materials offer. The principal concepts in this area are reviewed
2778	>	along with recent results. In addition, new directions to stimulate
2779	>	further research activities are highlighted.},
2780		annote = {990XA Times Cited:3 Cited References Count:72},
2781		issn = {0959-9428},
2782		uri = {<Go to ISI>://000233775500001},
2783	+	}
2784	+
2785	+	@ARTICLE{Roux1991,
2786	+	author = {B. Roux and M. Karplus},
2787	+	title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
2788	+	journal = {Journal of Physical Chemistry},
2789	+	year = {1991},
2790	+	volume = {95},
2791	+	pages = {4856-4868},
2792	+	number = {12},
2793	+	month = {Jun 13},
2794	+	abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
2795	+	poly-(L,D)-alanine beta-helix, a model for the interior of the gramicidin
2796	+	channel. Because of the different dynamical regimes for the three
2797	+	species (high barrier for Na+, low barrier for K+, almost free diffusion
2798	+	for water), different methods are used to calculate the mobilities.
2799	+	By use of activated dynamics and a potential of mean force determined
2800	+	previously (Roux, B.; Karplus, M. Biophys. J. 1991, 59, 961), the
2801	+	barrier crossing rate of Na+ ion is determined. The motion of Na+
2802	+	at the transition state is controlled by local interactions and
2803	+	collisions with the neighboring carbonyls and the two nearest water
2804	+	molecules. There are significant deviations from transition-state
2805	+	theory; the transmission coefficient is equal to 0.11. The water
2806	+	and K+ motions are found to be well described by a diffusive model;
2807	+	the motion of K+ appears to be controlled by the diffusion of water.
2808	+	The time-dependent friction functions of Na+ and K+ ions in the
2809	+	periodic beta-helix are calculated and analyzed by using a generalized
2810	+	Langevin equation approach. Both Na+ and K+ suffer many rapid collisions,
2811	+	and their dynamics is overdamped and noninertial. Thus, the selectivity
2812	+	sequence of ions in the beta-helix is not influenced strongly by
2813	+	their masses.},
2814	+	annote = {Fr756 Times Cited:97 Cited References Count:65},
2815	+	issn = {0022-3654},
2816	+	uri = {<Go to ISI>://A1991FR75600049},
2817		}
2818
2819		@ARTICLE{Roy2005,
2820		author = {A. Roy and N. V. Madhusudana},
2821		title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases
2822	<	in banana shaped molecules},
2822	>	in banana shaped molecules},
2823		journal = {European Physical Journal E},
2824		year = {2005},
2825		volume = {18},
#	Line 1962 | Line 2827 | Encoding: GBK
2827		number = {3},
2828		month = {Nov},
2829		abstract = {A vast majority of compounds with bent core or banana shaped molecules
2830	<	exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased
2831	<	in a homologous series. The B-6 phase has an intercalated fluid
2832	<	lamellar structure with a layer spacing of half the molecular length.
2833	<	The B-1 phase has a two dimensionally periodic rectangular columnar
2834	<	structure. The B-2 phase has a monolayer fluid lamellar structure
2835	<	with molecules tilted with respect to the layer normal. Neglecting
2836	<	the tilt order of the molecules in the B-2 phase, we have developed
2837	<	a frustrated packing model to describe this phase sequence qualitatively.
2838	<	The model has some analogy with that of the frustrated smectics
2839	<	exhibited by highly polar rod like molecules.},
2830	>	exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased
2831	>	in a homologous series. The B-6 phase has an intercalated fluid
2832	>	lamellar structure with a layer spacing of half the molecular length.
2833	>	The B-1 phase has a two dimensionally periodic rectangular columnar
2834	>	structure. The B-2 phase has a monolayer fluid lamellar structure
2835	>	with molecules tilted with respect to the layer normal. Neglecting
2836	>	the tilt order of the molecules in the B-2 phase, we have developed
2837	>	a frustrated packing model to describe this phase sequence qualitatively.
2838	>	The model has some analogy with that of the frustrated smectics
2839	>	exhibited by highly polar rod like molecules.},
2840		annote = {985FW Times Cited:0 Cited References Count:30},
2841		issn = {1292-8941},
2842		uri = {<Go to ISI>://000233363300002},
2843		}
2844
2845	+	@ARTICLE{Ryckaert1977,
2846	+	author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
2847	+	title = {Numerical-Integration of Cartesian Equations of Motion of a System
2848	+	with Constraints - Molecular-Dynamics of N-Alkanes},
2849	+	journal = {Journal of Computational Physics},
2850	+	year = {1977},
2851	+	volume = {23},
2852	+	pages = {327-341},
2853	+	number = {3},
2854	+	annote = {Cz253 Times Cited:3680 Cited References Count:7},
2855	+	issn = {0021-9991},
2856	+	uri = {<Go to ISI>://A1977CZ25300007},
2857	+	}
2858	+
2859	+	@ARTICLE{Sagui1999,
2860	+	author = {C. Sagui and T. A. Darden},
2861	+	title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic
2862	+	effects},
2863	+	journal = {Annual Review of Biophysics and Biomolecular Structure},
2864	+	year = {1999},
2865	+	volume = {28},
2866	+	pages = {155-179},
2867	+	abstract = {Current computer simulations of biomolecules typically make use of
2868	+	classical molecular dynamics methods, as a very large number (tens
2869	+	to hundreds of thousands) of atoms are involved over timescales
2870	+	of many nanoseconds. The methodology for treating short-range bonded
2871	+	and van der Waals interactions has matured. However, long-range
2872	+	electrostatic interactions still represent a bottleneck in simulations.
2873	+	In this article, we introduce the basic issues for an accurate representation
2874	+	of the relevant electrostatic interactions. In spite of the huge
2875	+	computational time demanded by most biomolecular systems, it is
2876	+	no longer necessary to resort to uncontrolled approximations such
2877	+	as the use of cutoffs. In particular, we discuss the Ewald summation
2878	+	methods, the fast particle mesh methods, and the fast multipole
2879	+	methods. We also review recent efforts to understand the role of
2880	+	boundary conditions in systems with long-range interactions, and
2881	+	conclude with a short perspective on future trends.},
2882	+	annote = {213KJ Times Cited:126 Cited References Count:73},
2883	+	issn = {1056-8700},
2884	+	uri = {<Go to ISI>://000081271400008},
2885	+	}
2886	+
2887		@ARTICLE{Sandu1999,
2888		author = {A. Sandu and T. Schlick},
2889		title = {Masking resonance artifacts in force-splitting methods for biomolecular
2890	<	simulations by extrapolative Langevin dynamics},
2890	>	simulations by extrapolative Langevin dynamics},
2891		journal = {Journal of Computational Physics},
2892		year = {1999},
2893		volume = {151},
#	Line 1988 | Line 2895 | Encoding: GBK
2895		number = {1},
2896		month = {May 1},
2897		abstract = {Numerical resonance artifacts have become recognized recently as a
2898	<	limiting factor to increasing the timestep in multiple-timestep
2899	<	(MTS) biomolecular dynamics simulations. At certain timesteps correlated
2900	<	to internal motions (e.g., 5 fs, around half the period of the fastest
2901	<	bond stretch, T-min), visible inaccuracies or instabilities can
2902	<	occur. Impulse-MTS schemes are vulnerable to these resonance errors
2903	<	since large energy pulses are introduced to the governing dynamics
2904	<	equations when the slow forces are evaluated. We recently showed
2905	<	that such resonance artifacts can be masked significantly by applying
2906	<	extrapolative splitting to stochastic dynamics. Theoretical and
2907	<	numerical analyses of force-splitting integrators based on the Verlet
2908	<	discretization are reported here for linear models to explain these
2909	<	observations and to suggest how to construct effective integrators
2910	<	for biomolecular dynamics that balance stability with accuracy.
2911	<	Analyses for Newtonian dynamics demonstrate the severe resonance
2912	<	patterns of the Impulse splitting, with this severity worsening
2913	<	with the outer timestep. Delta t: Constant Extrapolation is generally
2914	<	unstable, but the disturbances do not grow with Delta t. Thus. the
2915	<	stochastic extrapolative combination can counteract generic instabilities
2916	<	and largely alleviate resonances with a sufficiently strong Langevin
2917	<	heat-bath coupling (gamma), estimates for which are derived here
2918	<	based on the fastest and slowest motion periods. These resonance
2919	<	results generally hold for nonlinear test systems: a water tetramer
2920	<	and solvated protein. Proposed related approaches such as Extrapolation/Correction
2921	<	and Midpoint Extrapolation work better than Constant Extrapolation
2922	<	only for timesteps less than T-min/2. An effective extrapolative
2923	<	stochastic approach for biomolecules that balances long-timestep
2924	<	stability with good accuracy for the fast subsystem is then applied
2925	<	to a biomolecule using a three-class partitioning: the medium forces
2926	<	are treated by Midpoint Extrapolation via position Verlet, and the
2927	<	slow forces are incorporated by Constant Extrapolation. The resulting
2928	<	algorithm (LN) performs well on a solvated protein system in terms
2929	<	of thermodynamic properties and yields an order of magnitude speedup
2930	<	with respect to single-timestep Langevin trajectories. Computed
2931	<	spectral density functions also show how the Newtonian modes can
2932	<	be approximated by using a small gamma in the range Of 5-20 ps(-1).
2933	<	(C) 1999 Academic Press.},
2898	>	limiting factor to increasing the timestep in multiple-timestep
2899	>	(MTS) biomolecular dynamics simulations. At certain timesteps correlated
2900	>	to internal motions (e.g., 5 fs, around half the period of the fastest
2901	>	bond stretch, T-min), visible inaccuracies or instabilities can
2902	>	occur. Impulse-MTS schemes are vulnerable to these resonance errors
2903	>	since large energy pulses are introduced to the governing dynamics
2904	>	equations when the slow forces are evaluated. We recently showed
2905	>	that such resonance artifacts can be masked significantly by applying
2906	>	extrapolative splitting to stochastic dynamics. Theoretical and
2907	>	numerical analyses of force-splitting integrators based on the Verlet
2908	>	discretization are reported here for linear models to explain these
2909	>	observations and to suggest how to construct effective integrators
2910	>	for biomolecular dynamics that balance stability with accuracy.
2911	>	Analyses for Newtonian dynamics demonstrate the severe resonance
2912	>	patterns of the Impulse splitting, with this severity worsening
2913	>	with the outer timestep. Delta t: Constant Extrapolation is generally
2914	>	unstable, but the disturbances do not grow with Delta t. Thus. the
2915	>	stochastic extrapolative combination can counteract generic instabilities
2916	>	and largely alleviate resonances with a sufficiently strong Langevin
2917	>	heat-bath coupling (gamma), estimates for which are derived here
2918	>	based on the fastest and slowest motion periods. These resonance
2919	>	results generally hold for nonlinear test systems: a water tetramer
2920	>	and solvated protein. Proposed related approaches such as Extrapolation/Correction
2921	>	and Midpoint Extrapolation work better than Constant Extrapolation
2922	>	only for timesteps less than T-min/2. An effective extrapolative
2923	>	stochastic approach for biomolecules that balances long-timestep
2924	>	stability with good accuracy for the fast subsystem is then applied
2925	>	to a biomolecule using a three-class partitioning: the medium forces
2926	>	are treated by Midpoint Extrapolation via position Verlet, and the
2927	>	slow forces are incorporated by Constant Extrapolation. The resulting
2928	>	algorithm (LN) performs well on a solvated protein system in terms
2929	>	of thermodynamic properties and yields an order of magnitude speedup
2930	>	with respect to single-timestep Langevin trajectories. Computed
2931	>	spectral density functions also show how the Newtonian modes can
2932	>	be approximated by using a small gamma in the range Of 5-20 ps(-1).
2933	>	(C) 1999 Academic Press.},
2934		annote = {194FM Times Cited:14 Cited References Count:32},
2935		issn = {0021-9991},
2936		uri = {<Go to ISI>://000080181500004},
2937		}
2938
2939	+	@ARTICLE{Sasaki2004,
2940	+	author = {Y. Sasaki and R. Shukla and B. D. Smith},
2941	+	title = {Facilitated phosphatidylserine flip-flop across vesicle and cell
2942	+	membranes using urea-derived synthetic translocases},
2943	+	journal = {Organic \& Biomolecular Chemistry},
2944	+	year = {2004},
2945	+	volume = {2},
2946	+	pages = {214-219},
2947	+	number = {2},
2948	+	abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
2949	+	groups are shown to facilitate the translocation of fluorescent
2950	+	phospholipid probes and endogenous phosphatidylserine across vesicle
2951	+	and erythrocyte cell membranes. The synthetic translocases appear
2952	+	to operate by binding to the phospholipid head groups and forming
2953	+	lipophilic supramolecular complexes which diffuse through the non-polar
2954	+	interior of the bilayer membrane.},
2955	+	annote = {760PX Times Cited:8 Cited References Count:25},
2956	+	issn = {1477-0520},
2957	+	uri = {<Go to ISI>://000187843800012},
2958	+	}
2959	+
2960		@ARTICLE{Satoh1996,
2961		author = {K. Satoh and S. Mita and S. Kondo},
2962		title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect
2963	<	of terminal dipole moment on mesophase formation},
2963	>	of terminal dipole moment on mesophase formation},
2964		journal = {Chemical Physics Letters},
2965		year = {1996},
2966		volume = {255},
#	Line 2040 | Line 2968 | Encoding: GBK
2968		number = {1-3},
2969		month = {Jun 7},
2970		abstract = {The effects of dipole-dipole interaction on mesophase formation are
2971	<	investigated with a Monte Carlo simulation using the dipolar Gay-Berne
2972	<	potential. It is shown that the dipole moment at the end of a molecule
2973	<	causes a shift in the nematic-isotropic transition toward higher
2974	<	temperature and a spread of the temperature range of the nematic
2975	<	phase and that layer structures with various interdigitations are
2976	<	formed in the smectic phase.},
2971	>	investigated with a Monte Carlo simulation using the dipolar Gay-Berne
2972	>	potential. It is shown that the dipole moment at the end of a molecule
2973	>	causes a shift in the nematic-isotropic transition toward higher
2974	>	temperature and a spread of the temperature range of the nematic
2975	>	phase and that layer structures with various interdigitations are
2976	>	formed in the smectic phase.},
2977		annote = {Uq975 Times Cited:32 Cited References Count:33},
2978		issn = {0009-2614},
2979		uri = {<Go to ISI>://A1996UQ97500017},
2980		}
2981
2982	+	@ARTICLE{Schaps1999,
2983	+	author = {G. L. Schaps},
2984	+	title = {Compiler construction with ANTLR and Java - Tools for building tools},
2985	+	journal = {Dr Dobbs Journal},
2986	+	year = {1999},
2987	+	volume = {24},
2988	+	pages = {84-+},
2989	+	number = {3},
2990	+	month = {Mar},
2991	+	annote = {163EC Times Cited:0 Cited References Count:0},
2992	+	issn = {1044-789X},
2993	+	uri = {<Go to ISI>://000078389200023},
2994	+	}
2995	+
2996		@ARTICLE{Shen2002,
2997		author = {M. Y. Shen and K. F. Freed},
2998		title = {Long time dynamics of met-enkephalin: Comparison of explicit and
2999	<	implicit solvent models},
2999	>	implicit solvent models},
3000		journal = {Biophysical Journal},
3001		year = {2002},
3002		volume = {82},
#	Line 2062 | Line 3004 | Encoding: GBK
3004		number = {4},
3005		month = {Apr},
3006		abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
3007	<	structure and receptor docking mechanism are still not well understood.
3008	<	The conformational dynamics of this neuron peptide in liquid water
3009	<	are studied here by using all-atom molecular dynamics (MID) and
3010	<	implicit water Langevin dynamics (LD) simulations with AMBER potential
3011	<	functions and the three-site transferable intermolecular potential
3012	<	(TIP3P) model for water. To achieve the same simulation length in
3013	<	physical time, the full MID simulations require 200 times as much
3014	<	CPU time as the implicit water LID simulations. The solvent hydrophobicity
3015	<	and dielectric behavior are treated in the implicit solvent LD simulations
3016	<	by using a macroscopic solvation potential, a single dielectric
3017	<	constant, and atomic friction coefficients computed using the accessible
3018	<	surface area method with the TIP3P model water viscosity as determined
3019	<	here from MID simulations for pure TIP3P water. Both the local and
3020	<	the global dynamics obtained from the implicit solvent LD simulations
3021	<	agree very well with those from the explicit solvent MD simulations.
3022	<	The simulations provide insights into the conformational restrictions
3023	<	that are associated with the bioactivity of the opiate peptide dermorphin
3024	<	for the delta-receptor.},
3007	>	structure and receptor docking mechanism are still not well understood.
3008	>	The conformational dynamics of this neuron peptide in liquid water
3009	>	are studied here by using all-atom molecular dynamics (MID) and
3010	>	implicit water Langevin dynamics (LD) simulations with AMBER potential
3011	>	functions and the three-site transferable intermolecular potential
3012	>	(TIP3P) model for water. To achieve the same simulation length in
3013	>	physical time, the full MID simulations require 200 times as much
3014	>	CPU time as the implicit water LID simulations. The solvent hydrophobicity
3015	>	and dielectric behavior are treated in the implicit solvent LD simulations
3016	>	by using a macroscopic solvation potential, a single dielectric
3017	>	constant, and atomic friction coefficients computed using the accessible
3018	>	surface area method with the TIP3P model water viscosity as determined
3019	>	here from MID simulations for pure TIP3P water. Both the local and
3020	>	the global dynamics obtained from the implicit solvent LD simulations
3021	>	agree very well with those from the explicit solvent MD simulations.
3022	>	The simulations provide insights into the conformational restrictions
3023	>	that are associated with the bioactivity of the opiate peptide dermorphin
3024	>	for the delta-receptor.},
3025		annote = {540MH Times Cited:36 Cited References Count:45},
3026		issn = {0006-3495},
3027		uri = {<Go to ISI>://000174932400010},
#	Line 2099 | Line 3041 | Encoding: GBK
3041		uri = {<Go to ISI>://000227296700019},
3042		}
3043
3044	+	@ARTICLE{Shimada1993,
3045	+	author = {J. Shimada and H. Kaneko and T. Takada},
3046	+	title = {Efficient Calculations of Coulombic Interactions in Biomolecular
3047	+	Simulations with Periodic Boundary-Conditions},
3048	+	journal = {Journal of Computational Chemistry},
3049	+	year = {1993},
3050	+	volume = {14},
3051	+	pages = {867-878},
3052	+	number = {7},
3053	+	month = {Jul},
3054	+	abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
3055	+	simulations, two possibilities are considered. The first is the
3056	+	famous particle-particle and particle-mesh (PPPM) method developed
3057	+	by Hockney and Eastwood, and the second is a new one developed here
3058	+	in their spirit but by the use of the multipole expansion technique
3059	+	suggested by Ladd. It is then numerically found that the new PPPM
3060	+	method gives more accurate results for a two-particle system at
3061	+	small separation of particles. Preliminary numerical examination
3062	+	of the various computational methods for a single configuration
3063	+	of a model BPTI-water system containing about 24,000 particles indicates
3064	+	that both of the PPPM methods give far more accurate values with
3065	+	reasonable computational cost than do the conventional truncation
3066	+	methods. It is concluded the two PPPM methods are nearly comparable
3067	+	in overall performance for the many-particle systems, although the
3068	+	first method has the drawback that the accuracy in the total electrostatic
3069	+	energy is not high for configurations of charged particles randomly
3070	+	generated.},
3071	+	annote = {Lh164 Times Cited:27 Cited References Count:47},
3072	+	issn = {0192-8651},
3073	+	uri = {<Go to ISI>://A1993LH16400011},
3074	+	}
3075	+
3076		@ARTICLE{Skeel2002,
3077		author = {R. D. Skeel and J. A. Izaguirre},
3078		title = {An impulse integrator for Langevin dynamics},
#	Line 2109 | Line 3083 | Encoding: GBK
3083		number = {24},
3084		month = {Dec 20},
3085		abstract = {The best simple method for Newtonian molecular dynamics is indisputably
3086	<	the leapfrog Stormer-Verlet method. The appropriate generalization
3087	<	to simple Langevin dynamics is unclear. An analysis is presented
3088	<	comparing an 'impulse method' (kick; fluctuate; kick), the 1982
3089	<	method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus
3090	<	(BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen
3091	<	methods can be implemented as efficiently as the BBK method. Other
3092	<	considerations suggest that the impulse method is the best basic
3093	<	method for simple Langevin dynamics, with the van Gunsteren-Berendsen
3094	<	method a close contender.},
3086	>	the leapfrog Stormer-Verlet method. The appropriate generalization
3087	>	to simple Langevin dynamics is unclear. An analysis is presented
3088	>	comparing an 'impulse method' (kick; fluctuate; kick), the 1982
3089	>	method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus
3090	>	(BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen
3091	>	methods can be implemented as efficiently as the BBK method. Other
3092	>	considerations suggest that the impulse method is the best basic
3093	>	method for simple Langevin dynamics, with the van Gunsteren-Berendsen
3094	>	method a close contender.},
3095		annote = {633RX Times Cited:8 Cited References Count:22},
3096		issn = {0026-8976},
3097		uri = {<Go to ISI>://000180297200014},
#	Line 2126 | Line 3100 | Encoding: GBK
3100		@ARTICLE{Skeel1997,
3101		author = {R. D. Skeel and G. H. Zhang and T. Schlick},
3102		title = {A family of symplectic integrators: Stability, accuracy, and molecular
3103	<	dynamics applications},
3103	>	dynamics applications},
3104		journal = {Siam Journal on Scientific Computing},
3105		year = {1997},
3106		volume = {18},
#	Line 2134 | Line 3108 | Encoding: GBK
3108		number = {1},
3109		month = {Jan},
3110		abstract = {The following integration methods for special second-order ordinary
3111	<	differential equations are studied: leapfrog, implicit midpoint,
3112	<	trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all
3113	<	are members, or equivalent to members, of a one-parameter family
3114	<	of schemes. Some methods have more than one common form, and we
3115	<	discuss a systematic enumeration of these forms. We also present
3116	<	a stability and accuracy analysis based on the idea of ''modified
3117	<	equations'' and a proof of symplecticness. It follows that Cowell-Numerov
3118	<	and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic.
3119	<	A different interpretation of the values used by these integrators
3120	<	leads to higher accuracy and better energy conservation. Hence,
3121	<	we suggest that the straightforward analysis of energy conservation
3122	<	is misleading.},
3111	>	differential equations are studied: leapfrog, implicit midpoint,
3112	>	trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all
3113	>	are members, or equivalent to members, of a one-parameter family
3114	>	of schemes. Some methods have more than one common form, and we
3115	>	discuss a systematic enumeration of these forms. We also present
3116	>	a stability and accuracy analysis based on the idea of ''modified
3117	>	equations'' and a proof of symplecticness. It follows that Cowell-Numerov
3118	>	and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic.
3119	>	A different interpretation of the values used by these integrators
3120	>	leads to higher accuracy and better energy conservation. Hence,
3121	>	we suggest that the straightforward analysis of energy conservation
3122	>	is misleading.},
3123		annote = {We981 Times Cited:30 Cited References Count:35},
3124		issn = {1064-8275},
3125		uri = {<Go to ISI>://A1997WE98100012},
#	Line 2153 | Line 3127 | Encoding: GBK
3127
3128		@ARTICLE{Tao2005,
3129		author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont
3130	<	and W. J. Briels},
3130	>	and W. J. Briels},
3131		title = {Brownian dynamics simulations of the self- and collective rotational
3132	<	diffusion coefficients of rigid long thin rods},
3132	>	diffusion coefficients of rigid long thin rods},
3133		journal = {Journal of Chemical Physics},
3134		year = {2005},
3135		volume = {122},
#	Line 2163 | Line 3137 | Encoding: GBK
3137		number = {24},
3138		month = {Jun 22},
3139		abstract = {Recently a microscopic theory for the dynamics of suspensions of long
3140	<	thin rigid rods was presented, confirming and expanding the well-known
3141	<	theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon,
3142	<	Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here
3143	<	this theory is put to the test by comparing it against computer
3144	<	simulations. A Brownian dynamics simulation program was developed
3145	<	to follow the dynamics of the rods, with a length over a diameter
3146	<	ratio of 60, on the Smoluchowski time scale. The model accounts
3147	<	for excluded volume interactions between rods, but neglects hydrodynamic
3148	<	interactions. The self-rotational diffusion coefficients D-r(phi)
3149	<	of the rods were calculated by standard methods and by a new, more
3150	<	efficient method based on calculating average restoring torques.
3151	<	Collective decay of orientational order was calculated by means
3152	<	of equilibrium and nonequilibrium simulations. Our results show
3153	<	that, for the currently accessible volume fractions, the decay times
3154	<	in both cases are virtually identical. Moreover, the observed decay
3155	<	of diffusion coefficients with volume fraction is much quicker than
3156	<	predicted by the theory, which is attributed to an oversimplification
3157	<	of dynamic correlations in the theory. (c) 2005 American Institute
3158	<	of Physics.},
3140	>	thin rigid rods was presented, confirming and expanding the well-known
3141	>	theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon,
3142	>	Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here
3143	>	this theory is put to the test by comparing it against computer
3144	>	simulations. A Brownian dynamics simulation program was developed
3145	>	to follow the dynamics of the rods, with a length over a diameter
3146	>	ratio of 60, on the Smoluchowski time scale. The model accounts
3147	>	for excluded volume interactions between rods, but neglects hydrodynamic
3148	>	interactions. The self-rotational diffusion coefficients D-r(phi)
3149	>	of the rods were calculated by standard methods and by a new, more
3150	>	efficient method based on calculating average restoring torques.
3151	>	Collective decay of orientational order was calculated by means
3152	>	of equilibrium and nonequilibrium simulations. Our results show
3153	>	that, for the currently accessible volume fractions, the decay times
3154	>	in both cases are virtually identical. Moreover, the observed decay
3155	>	of diffusion coefficients with volume fraction is much quicker than
3156	>	predicted by the theory, which is attributed to an oversimplification
3157	>	of dynamic correlations in the theory. (c) 2005 American Institute
3158	>	of Physics.},
3159		annote = {943DN Times Cited:3 Cited References Count:26},
3160		issn = {0021-9606},
3161		uri = {<Go to ISI>://000230332400077},
#	Line 2200 | Line 3174 | Encoding: GBK
3174		@ARTICLE{Tu1995,
3175		author = {K. Tu and D. J. Tobias and M. L. Klein},
3176		title = {Constant pressure and temperature molecular dynamics simulation of
3177	<	a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine
3178	<	bilayer},
3177	>	a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine
3178	>	bilayer},
3179		journal = {Biophysical Journal},
3180		year = {1995},
3181		volume = {69},
#	Line 2209 | Line 3183 | Encoding: GBK
3183		number = {6},
3184		month = {Dec},
3185		abstract = {We report a constant pressure and temperature molecular dynamics simulation
3186	<	of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine
3187	<	at 50 degrees C and 28 water molecules/lipid. We have shown that
3188	<	the bilayer is stable throughout the 1550-ps simulation and have
3189	<	demonstrated convergence of the system dimensions. Several important
3190	<	aspects of the bilayer structure have been investigated and compared
3191	<	favorably with experimental results. For example, the average positions
3192	<	of specific carbon atoms along the bilayer normal agree well with
3193	<	neutron diffraction data, and the electron density profile is in
3194	<	accord with x-ray diffraction results. The hydrocarbon chain deuterium
3195	<	order parameters agree reasonably well with NMR results for the
3196	<	middles of the chains, but the simulation predicts too much order
3197	<	at the chain ends. In spite of the deviations in the order parameters,
3198	<	the hydrocarbon chain packing density appears to be essentially
3199	<	correct, inasmuch as the area/lipid and bilayer thickness are in
3200	<	agreement with the most refined experimental estimates. The deuterium
3201	<	order parameters for the glycerol and choline groups, as well as
3202	<	the phosphorus chemical shift anisotropy, are in qualitative agreement
3203	<	with those extracted from NMR measurements.},
3186	>	of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine
3187	>	at 50 degrees C and 28 water molecules/lipid. We have shown that
3188	>	the bilayer is stable throughout the 1550-ps simulation and have
3189	>	demonstrated convergence of the system dimensions. Several important
3190	>	aspects of the bilayer structure have been investigated and compared
3191	>	favorably with experimental results. For example, the average positions
3192	>	of specific carbon atoms along the bilayer normal agree well with
3193	>	neutron diffraction data, and the electron density profile is in
3194	>	accord with x-ray diffraction results. The hydrocarbon chain deuterium
3195	>	order parameters agree reasonably well with NMR results for the
3196	>	middles of the chains, but the simulation predicts too much order
3197	>	at the chain ends. In spite of the deviations in the order parameters,
3198	>	the hydrocarbon chain packing density appears to be essentially
3199	>	correct, inasmuch as the area/lipid and bilayer thickness are in
3200	>	agreement with the most refined experimental estimates. The deuterium
3201	>	order parameters for the glycerol and choline groups, as well as
3202	>	the phosphorus chemical shift anisotropy, are in qualitative agreement
3203	>	with those extracted from NMR measurements.},
3204		annote = {Tv018 Times Cited:108 Cited References Count:34},
3205		issn = {0006-3495},
3206		uri = {<Go to ISI>://A1995TV01800037},
#	Line 2242 | Line 3216 | Encoding: GBK
3216		number = {3},
3217		month = {Aug 1},
3218		abstract = {The Trotter factorization of the Liouville propagator is used to generate
3219	<	new reversible molecular dynamics integrators. This strategy is
3220	<	applied to derive reversible reference system propagator algorithms
3221	<	(RESPA) that greatly accelerate simulations of systems with a separation
3222	<	of time scales or with long range forces. The new algorithms have
3223	<	all of the advantages of previous RESPA integrators but are reversible,
3224	<	and more stable than those methods. These methods are applied to
3225	<	a set of paradigmatic systems and are shown to be superior to earlier
3226	<	methods. It is shown how the new RESPA methods are related to predictor-corrector
3227	<	integrators. Finally, we show how these methods can be used to accelerate
3228	<	the integration of the equations of motion of systems with Nose
3229	<	thermostats.},
3219	>	new reversible molecular dynamics integrators. This strategy is
3220	>	applied to derive reversible reference system propagator algorithms
3221	>	(RESPA) that greatly accelerate simulations of systems with a separation
3222	>	of time scales or with long range forces. The new algorithms have
3223	>	all of the advantages of previous RESPA integrators but are reversible,
3224	>	and more stable than those methods. These methods are applied to
3225	>	a set of paradigmatic systems and are shown to be superior to earlier
3226	>	methods. It is shown how the new RESPA methods are related to predictor-corrector
3227	>	integrators. Finally, we show how these methods can be used to accelerate
3228	>	the integration of the equations of motion of systems with Nose
3229	>	thermostats.},
3230		annote = {Je891 Times Cited:680 Cited References Count:19},
3231		issn = {0021-9606},
3232		uri = {<Go to ISI>://A1992JE89100044},
3233		}
3234
3235	+	@BOOK{Varadarajan1974,
3236	+	title = {Lie groups, Lie algebras, and their representations},
3237	+	publisher = {Prentice-Hall},
3238	+	year = {1974},
3239	+	author = {V.S. Varadarajan},
3240	+	address = {New York},
3241	+	}
3242	+
3243	+	@ARTICLE{Vincent1995,
3244	+	author = {J. J. Vincent and K. M. Merz},
3245	+	title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing
3246	+	Interface Standard},
3247	+	journal = {Journal of Computational Chemistry},
3248	+	year = {1995},
3249	+	volume = {16},
3250	+	pages = {1420-1427},
3251	+	number = {11},
3252	+	month = {Nov},
3253	+	abstract = {We have implemented a portable parallel version of the macromolecular
3254	+	modeling package AMBER4. The message passing paradigm was used.
3255	+	All message passing constructs are compliant with the Message Passing
3256	+	Interface (MPI) standard. The molecular dynamics/minimization module
3257	+	MINMD and the free-energy perturbation module Gibbs have been implemented
3258	+	in parallel on a number of machines, including a Gray T3D, an IBM
3259	+	SP1/SP2, and a collection of networked workstations. In addition,
3260	+	the code has been tested with an MPI implementation from Argonne
3261	+	National Laboratories/Mississippi State University which runs on
3262	+	many parallel machines. The goal of this work is to decrease the
3263	+	amount of time required to perform molecular dynamics simulations.
3264	+	Performance results for a Lipid bilayer molecular dynamics simulation
3265	+	on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995
3266	+	by John Wiley & Sons, Inc.},
3267	+	annote = {Ta403 Times Cited:16 Cited References Count:23},
3268	+	issn = {0192-8651},
3269	+	uri = {<Go to ISI>://A1995TA40300009},
3270	+	}
3271	+
3272		@ARTICLE{Wegener1979,
3273		author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
3274		title = {A general ellipsoid can not always serve as a modle for the rotational
3275	<	diffusion properties of arbitrary shaped rigid molecules},
3275	>	diffusion properties of arbitrary shaped rigid molecules},
3276		journal = {Proc. Natl. Acad. Sci.},
3277		year = {1979},
3278		volume = {76},
#	Line 2269 | Line 3280 | Encoding: GBK
3280		number = {12},
3281		}
3282
3283	+	@ARTICLE{Wilson2006,
3284	+	author = {G.~V. Wilson },
3285	+	title = {Where's the Real Bottleneck in Scientific Computing?},
3286	+	journal = {American Scientist},
3287	+	year = {2006},
3288	+	volume = {94},
3289	+	}
3290	+
3291		@ARTICLE{Withers2003,
3292		author = {I. M. Withers},
3293		title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne
3294	<	fluid},
3294	>	fluid},
3295		journal = {Journal of Chemical Physics},
3296		year = {2003},
3297		volume = {119},
#	Line 2280 | Line 3299 | Encoding: GBK
3299		number = {19},
3300		month = {Nov 15},
3301		abstract = {The effects of longitudinal quadrupole moments on the formation of
3302	<	liquid crystalline phases are studied by means of constant NPT Monte
3303	<	Carlo simulation methods. The popular Gay-Berne model mesogen is
3304	<	used as the reference fluid, which displays the phase sequences
3305	<	isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0)
3306	<	and low (T*=1.5) temperatures, respectively. With increasing quadrupole
3307	<	magnitude the smectic phases are observed to be stabilized with
3308	<	respect to the isotropic liquid, while the smectic B is destabilized
3309	<	with respect to the smectic A. At the lower temperature, a sufficiently
3310	<	large quadrupole magnitude results in the injection of the smectic
3311	<	A phase into the phase sequence and the replacement of the smectic
3312	<	B phase by the tilted smectic J phase. The nematic phase is also
3313	<	injected into the phase sequence at both temperatures considered,
3314	<	and ultimately for sufficiently large quadrupole magnitudes no coherent
3315	<	layered structures were observed. The stabilization of the smectic
3316	<	A phase supports the commonly held belief that, while the inclusion
3317	<	of polar groups is not a prerequisite for the formation of the smectic
3318	<	A phase, quadrupolar interactions help to increase the temperature
3319	<	and pressure range for which the smectic A phase is observed. The
3320	<	quality of the layered structure is worsened with increasing quadrupole
3321	<	magnitude. This behavior, along with the injection of the nematic
3322	<	phase into the phase sequence, indicate that the general tendency
3323	<	of the quadrupolar interactions is to destabilize the layered structure.
3324	<	A pressure dependence upon the smectic layer spacing is observed.
3325	<	This behavior is in much closer agreement with experimental findings
3326	<	than has been observed previously for nonpolar Gay-Berne and hard
3327	<	spherocylinder models. (C) 2003 American Institute of Physics.},
3302	>	liquid crystalline phases are studied by means of constant NPT Monte
3303	>	Carlo simulation methods. The popular Gay-Berne model mesogen is
3304	>	used as the reference fluid, which displays the phase sequences
3305	>	isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0)
3306	>	and low (T*=1.5) temperatures, respectively. With increasing quadrupole
3307	>	magnitude the smectic phases are observed to be stabilized with
3308	>	respect to the isotropic liquid, while the smectic B is destabilized
3309	>	with respect to the smectic A. At the lower temperature, a sufficiently
3310	>	large quadrupole magnitude results in the injection of the smectic
3311	>	A phase into the phase sequence and the replacement of the smectic
3312	>	B phase by the tilted smectic J phase. The nematic phase is also
3313	>	injected into the phase sequence at both temperatures considered,
3314	>	and ultimately for sufficiently large quadrupole magnitudes no coherent
3315	>	layered structures were observed. The stabilization of the smectic
3316	>	A phase supports the commonly held belief that, while the inclusion
3317	>	of polar groups is not a prerequisite for the formation of the smectic
3318	>	A phase, quadrupolar interactions help to increase the temperature
3319	>	and pressure range for which the smectic A phase is observed. The
3320	>	quality of the layered structure is worsened with increasing quadrupole
3321	>	magnitude. This behavior, along with the injection of the nematic
3322	>	phase into the phase sequence, indicate that the general tendency
3323	>	of the quadrupolar interactions is to destabilize the layered structure.
3324	>	A pressure dependence upon the smectic layer spacing is observed.
3325	>	This behavior is in much closer agreement with experimental findings
3326	>	than has been observed previously for nonpolar Gay-Berne and hard
3327	>	spherocylinder models. (C) 2003 American Institute of Physics.},
3328		annote = {738EF Times Cited:3 Cited References Count:43},
3329		issn = {0021-9606},
3330		uri = {<Go to ISI>://000186273200027},
3331		}
3332
3333	+	@ARTICLE{Wolf1999,
3334	+	author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
3335	+	title = {Exact method for the simulation of Coulombic systems by spherically
3336	+	truncated, pairwise r(-1) summation},
3337	+	journal = {Journal of Chemical Physics},
3338	+	year = {1999},
3339	+	volume = {110},
3340	+	pages = {8254-8282},
3341	+	number = {17},
3342	+	month = {May 1},
3343	+	abstract = {Based on a recent result showing that the net Coulomb potential in
3344	+	condensed ionic systems is rather short ranged, an exact and physically
3345	+	transparent method permitting the evaluation of the Coulomb potential
3346	+	by direct summation over the r(-1) Coulomb pair potential is presented.
3347	+	The key observation is that the problems encountered in determining
3348	+	the Coulomb energy by pairwise, spherically truncated r(-1) summation
3349	+	are a direct consequence of the fact that the system summed over
3350	+	is practically never neutral. A simple method is developed that
3351	+	achieves charge neutralization wherever the r(-1) pair potential
3352	+	is truncated. This enables the extraction of the Coulomb energy,
3353	+	forces, and stresses from a spherically truncated, usually charged
3354	+	environment in a manner that is independent of the grouping of the
3355	+	pair terms. The close connection of our approach with the Ewald
3356	+	method is demonstrated and exploited, providing an efficient method
3357	+	for the simulation of even highly disordered ionic systems by direct,
3358	+	pairwise r(-1) summation with spherical truncation at rather short
3359	+	range, i.e., a method which fully exploits the short-ranged nature
3360	+	of the interactions in ionic systems. The method is validated by
3361	+	simulations of crystals, liquids, and interfacial systems, such
3362	+	as free surfaces and grain boundaries. (C) 1999 American Institute
3363	+	of Physics. [S0021-9606(99)51517-1].},
3364	+	annote = {189PD Times Cited:70 Cited References Count:34},
3365	+	issn = {0021-9606},
3366	+	uri = {<Go to ISI>://000079913000008},
3367	+	}
3368	+
3369	+	@ARTICLE{Yoshida1990,
3370	+	author = {H. Yoshida},
3371	+	title = {Construction of Higher-Order Symplectic Integrators},
3372	+	journal = {Physics Letters A},
3373	+	year = {1990},
3374	+	volume = {150},
3375	+	pages = {262-268},
3376	+	number = {5-7},
3377	+	month = {Nov 12},
3378	+	annote = {Ej798 Times Cited:492 Cited References Count:9},
3379	+	issn = {0375-9601},
3380	+	uri = {<Go to ISI>://A1990EJ79800009},
3381	+	}
3382	+
3383	+	@Article{Blum1972,
3384	+	author =   {L. Blum and A.~J. Torruella},
3385	+	title =    {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
3386	+	journal =  {Journal of Chemical Physics},
3387	+	year =     1972,
3388	+	volume =   56,
3389	+	number =   1,
3390	+	pages =    {303-309}
3391	+	}
3392	+
3393	+	@Article{Stone1978,
3394	+	author =   {A.~J. Stone},
3395	+	title =    {The description of bimolecular potentials, forces and torques: the S and V function expansions},
3396	+	journal =  {Molecular Physics},
3397	+	year =     1978,
3398	+	volume =   36,
3399	+	number =   1,
3400	+	pages =    {241-256}
3401	+	}
3402	+
3403	+	@Article{Berardi2003,
3404	+	author =   {R. Berardi, M. Cecchini and C. Zannoni},
3405	+	title =    {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
3406	+	journal =  {Journal of Chemical Physics},
3407	+	year =     2003,
3408	+	volume =   119,
3409	+	number =   18,
3410	+	pages =    {9933-9946}
3411	+	}
3412	+
3413	+	@Article{Beard2000,
3414	+	author =   {D. A. Beard and T. Schlick},
3415	+	title =    {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
3416	+	journal =  {Journal of Chemical Physics},
3417	+	year =     2000,
3418	+	volume =   112,
3419	+	number =   17,
3420	+	pages =    {7313-7322}
3421	+	}
3422	+
3423	+	@BOOK{Hirsch1997,
3424	+	title = {Differential Topology},
3425	+	publisher = {Springer},
3426	+	year = {1997},
3427	+	author = {M.W. Hirsch},
3428	+	address = {New York}
3429	+	}
3430	+
3431	+	@BOOK{Jost2002,
3432	+	title = {Riemannian Geometry and Geometric Analysis},
3433	+	publisher = {Springer-Verlag},
3434	+	year = {2002},
3435	+	author = {J. Jost},
3436	+	address = {Berlin}
3437	+	}
3438	+
3439	+	@BOOK{McDuff1998,
3440	+	title = {Introduction to Symplectic Topology },
3441	+	publisher = {Oxford Mathematical Monographs},
3442	+	year = {1998},
3443	+	author = {D. McDuff and D. Salamon},
3444	+	address = {Oxford}
3445	+	}
3446	+
3447	+	@Article{Matubayasi1999,
3448	+	author =   {N. Matubayasi and M. Nakahara},
3449	+	title =    {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
3450	+	journal =  {Journal of Chemical Physics},
3451	+	year =     1999,
3452	+	volume =   110,
3453	+	number =   7,
3454	+	pages =    {3291-3301}
3455	+	}
3456	+
3457	+	@Article{Miller2002,
3458	+	author =   {T.F. Miller III, M. Eleftheriou},
3459	+	title =    {Symplectic quaternion scheme for biophysical molecular dynamics},
3460	+	journal =  {Journal of Chemical Physics},
3461	+	year =     1999,
3462	+	volume =   116,
3463	+	number =   20,
3464	+	pages =    {8649-8659}
3465	+	}
3466	+
3467	+	@Article{McMillan1971,
3468	+	author =   {W.L. McMillan},
3469	+	title =    {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},
3470	+	journal =  {Journal of Chemical Physics},
3471	+	year =     1971,
3472	+	volume =   4,
3473	+	number =   3,
3474	+	pages =    {1238¨C1246 }
3475	+	}
3476	+
3477	+	@Article{Gilmore1974,
3478	+	author =   {R. Gilmore},
3479	+	title =    {Baker-Campbell-Hausdorff Formulas},
3480	+	journal =  {Journal of Mathematical Physics},
3481	+	year =     1974,
3482	+	volume =   15,
3483	+	number =   12,
3484	+	pages =    {2090-2092}
3485	+	}
3486	+
3487	+	@Article{Strang1968,
3488	+	author =   {G. Strang},
3489	+	title =    {On the construction and comparision of difference schemes},
3490	+	journal =  {SIAM Journal on Numerical Analysis},
3491	+	year =     1968,
3492	+	volume =   5,
3493	+	number =   3,
3494	+	pages =    {506-517}
3495	+	}

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