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Revision 2785 by tim, Mon Apr 24 18:49:32 2006 UTC vs.
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1	<	@string{jcp = "J. Chem. Phys."}
2	<	@string{cpl = "Chem. Phys. Lett."}
3	<	@string{jpc = "J. Phys. Chem."}
4	<	@string{jpcA = "J. Phys. Chem. A"}
5	<	@string{jpcB = "J. Phys. Chem. B"}
6	<	@string{cp  = "Chem. Phys."}
7	<	@string{acp = "Adv. Chem. Phys."}
8	<	@string{pra = "Phys. Rev. A"}
9	<	@string{prb = "Phys. Rev. B"}
10	<	@string{pre = "Phys. Rev. E"}
11	<	@string{prl = "Phys. Rev. Lett."}
12	<	@string{rmp = "Rev. Mod. Phys."}
13	<	@string{jml = "J. Mol. Liq."}
14	<	@string{mp = "Mol. Phys."}
15	<	@string{pnas = "Proc. Natl. Acad. Sci. USA"}
16	<	@string{jacs = "J. Am. Chem. Soc."}
17	<	@string{jmb = "J. Mol. Biol."}
18	<
19	<
20	<	@Book{Berne90,
21	<	author =       {B.~J. Berne and R. Pecora},
22	<	title =        {Dynamic Light Scattering},
23	<	publisher =    {Robert E. Krieger Publishing Company, Inc.},
24	<	year =         1990,
25	<	address =      {Malabar, Florida}
26	<	}
27	<
28	<	@Article{Evans77,
29	<	author =       {D.~J. Evans},
30	<	title =        {On the representation of orientation space},
31	<	journal =      {Mol. Phys.},
32	<	year =         1977,
33	<	volume =       34,
34	<	pages =        {317-325}
35	<	}
36	<
37	<	@Article{Tuckerman92,
38	<	author =       {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
39	<	title =        {Reversible multiple time scale molecular dynamics},
40	<	journal =      jcp,
41	<	year =         1992,
42	<	volume =       97,
43	<	pages =        {1990-2001}
44	<	}
45	<
46	<	@Book{Hansen86,
47	<	author =       {J.~P. Hansen and I.~R. McDonald},
48	<	title =        {Theory of Simple Liquids},
49	<	chapter =      7,
50	<	publisher =    {Academic Press},
51	<	year =         1986,
52	<	address =      {London},
53	<	pages =        {199-206}
54	<	}
55	<
56	<	@Article{Angelani98,
57	<	author =       {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
58	<	title =        {Connected Network of Minima as a Model Glass: Long
59	<	Time Dynamics},
60	<	journal =      prl,
61	<	year =         1998,
62	<	volume =       81,
63	<	number =       21,
64	<	pages =        {4648-4651}
65	<	}
66	<
67	<	@Article{Stillinger82,
68	<	author =       {F.~H. Stillinger and T.~A. Weber},
69	<	title =        {Hidden structure in liquids},
70	<	journal =      pra,
71	<	year =         1982,
72	<	volume =       25,
73	<	number =       2,
74	<	pages =        {978-989}
75	<	}
76	<
77	<	@Article{Stillinger83,
78	<	author =       {F.~H. Stillinger and T.~A. Weber},
79	<	title =        {Dynamics of structural transitions in liquids},
80	<	journal =      pra,
81	<	year =         1983,
82	<	volume =       28,
83	<	number =       4,
84	<	pages =        {2408-2416}
85	<	}
86	<
87	<	@Article{Weber84,
88	<	author =       {T.~A. Weber and F.~H. Stillinger},
89	<	title =        {The effect of density on the inherent structure in
90	<	liquids},
91	<	journal =      jcp,
92	<	year =         1984,
93	<	volume =       80,
94	<	number =       6,
95	<	pages =        {2742-2746}
96	<	}
97	<
98	<	@Article{Stillinger85,
99	<	author =       {F.~H. Stillinger and T.~A. Weber},
100	<	title =        {Inherent structure theory of liquids in the
101	<	hard-sphere limit},
102	<	journal =      jcp,
103	<	year =         1985,
104	<	volume =       83,
105	<	number =       9,
106	<	pages =        {4767-4775}
107	<	}
108	<
109	<	@Article{Stillinger98,
110	<	author =       {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
111	<	title =        {Signatures of distinct dynamical regimes in the
112	<	energy landscape of a glass-forming liquid},
113	<	journal =      {Nature},
114	<	year =         1998,
115	<	volume =       393,
116	<	pages =        {554-557}
117	<	}
118	<
119	<
120	<	@Article{Parkhurst75a,
121	<	author =       {H.~J. {Parkhurst, Jr.} and J. Jonas},
122	<	title =        {Dense liquids. I. The effect of density and
123	<	temperature on viscosity of tetramethylsilane and
124	<	benzene-$\mbox{D}_6$},
125	<	journal =      jcp,
126	<	year =         1975,
127	<	volume =       63,
128	<	number =       6,
129	<	pages =        {2698-2704}
130	<	}
131	<
132	<	@Article{Parkhurst75b,
133	<	author =       {H.~J. {Parkhurst, Jr.} and J. Jonas},
134	<	title =        {Dense liquids. II. The effect of density and
135	<	temperature on viscosity of tetramethylsilane and
136	<	benzene },
137	<	journal =      jcp,
138	<	year =         1975,
139	<	volume =       63,
140	<	number =       6,
141	<	pages =        {2705-2709}
142	<	}
143	<
144	<	@Article{Forester97,
145	<	author =       {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
146	<	title =        {Antibiotic activity of valinomycin - Molecular
147	<	dynamics simulations involving the water/membrane
148	<	interface},
149	<	journal =      {J. Chem. Soc. - Faraday Transactions},
150	<	year =         1997,
151	<	volume =       93,
152	<	pages =        {613-619}
153	<	}
154	<
155	<	@Article{Tieleman98,
156	<	author =       {D.~P. Tieleman and H.~J.~C. Berendsen},
157	<	title =        {A molecular dynamics study of the pores formed by
158	<	Escherichia coli OmpF porin in a fully hydrated
159	<	palmitoyloleoylphosphatidylcholine bilayer},
160	<	journal =      {Biophys. J.},
161	<	year =         1998,
162	<	volume =       74,
163	<	pages =        {2786-2801}
164	<	}
165	<
166	<	@Article{Cascales98,
167	<	author =       {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
168	<	title =        {Anaesthetic mechanism on a model biological
169	<	membrane: A molecular dynamics simulation study},
170	<	journal =      {J. Phys. Chem. B},
171	<	year =         1998,
172	<	volume =       102,
173	<	pages =        {625-631}
174	<	}
175	<
176	<	@Article{Bassolino95,
177	<	author =       {D. Bassolino and H.~E. Alper and T.~R. Stouch},
178	<	title =        {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID
179	<	BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
180	<	journal =      {J. Am. Chem. Soc.},
181	<	year =         1995,
182	<	volume =       117,
183	<	pages =        {4118-4129}
184	<	}
185	<
186	<	@Article{Alper95,
187	<	author =       {H.~E. Alper and T.~R. Stouch},
188	<	title =        {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN
189	<	BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
190	<	journal =      {J. Phys. Chem.},
191	<	year =         1995,
192	<	volume =       99,
193	<	pages =        {5724-5731}
194	<	}
195	<
196	<	@Article{Sok92,
197	<	author =       {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
198	<	title =        {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF
199	<	SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
200	<	journal =      {J. Chem. Phys.},
201	<	year =         1992,
202	<	volume =       96,
203	<	pages =        {4699-4704}
204	<	}
205	<
206	<	@Article{Rabani99,
207	<	author =       {E. Rabani and J.~D. Gezelter and B.~J. Berne},
208	<	title =        {Direct Observation of Stretched-Exponential
209	<	Relaxation in Low-Temperature Lennard-Jones Systems
210	<	Using the Cage Correlation Function},
211	<	journal =      prl,
212	<	year =         {1999},
213	<	volume =       82,
214	<	pages =        {3649}
215	<	}
216	<
217	<	@Article{Rabani97,
218	<	author =       {E. Rabani and J.~D. Gezelter and B.~J. Berne},
219	<	title =        {Calculating the hopping rate for self-diffusion on
220	<	rough potential energy surfaces: Cage correlations},
221	<	journal =      {J. Chem. Phys.},
222	<	year =         1997,
223	<	volume =       107,
224	<	pages =        {6867-6876}
225	<	}
226	<
227	<	@Article{Gezelter99,
228	<	author =       {J.~D. Gezelter and E. Rabani and B.~J. Berne},
229	<	title =        {Methods for calculating the hopping rate for
230	<	orientational and spatial diffusion in a molecular
231	<	liquid: $\mbox{CS}_{2}$},
232	<	journal =      jcp,
233	<	year =         1999,
234	<	volume =       110,
235	<	pages =        3444
236	<	}
237	<
238	<	@Article{Gezelter98a,
239	<	author =       {J.~D. Gezelter and E. Rabani and B.~J. Berne},
240	<	title =        {Response to 'Comment on a Critique of the
241	<	Instantaneous Normal Mode (INM) Approach to
242	<	Diffusion'},
243	<	journal =      jcp,
244	<	year =         1998,
245	<	volume =       109,
246	<	pages =        4695
247	<	}
248	<
249	<	@Article{Gezelter97,
250	<	author =       {J.~D. Gezelter and E. Rabani and B.~J. Berne},
251	<	title =        {Can imaginary instantaneous normal mode frequencies
252	<	predict barriers to self-diffusion?},
253	<	journal =      jcp,
254	<	year =         1997,
255	<	volume =       107,
256	<	pages =        4618
257	<	}
258	<
259	<	@Article{Zwanzig83,
260	<	author =       {R. Zwanzig},
261	<	title =        {On the relation between self-diffusion and viscosity
262	<	of liquids},
263	<	journal =      jcp,
264	<	year =         1983,
265	<	volume =       79,
266	<	pages =        {4507-4508}
267	<	}
268	<
269	<	@Article{Zwanzig88,
270	<	author =       {R. Zwanzig},
271	<	title =        {Diffusion in rough potential},
272	<	journal =      {Proc. Natl. Acad. Sci. USA},
273	<	year =         1988,
274	<	volume =       85,
275	<	pages =        2029
276	<	}
277	<
278	<	@Article{Stillinger95,
279	<	author =       {F.~H. Stillinger},
280	<	title =        {A Topographic View of Supercooled Liquids and Glass
281	<	Formation},
282	<	journal =      {Science},
283	<	year =         1995,
284	<	volume =       267,
285	<	pages =        {1935-1939}
286	<	}
287	<
288	<	@InCollection{Angell85,
289	<	author =       {C.~A. Angell},
290	<	title =        {unknown},
291	<	booktitle =    {Relaxations in Complex Systems},
292	<	publisher =    {National Technical Information Service,
293	<	U.S. Department of Commerce},
294	<	year =         1985,
295	<	editor =       {K.~Ngai and G.~B. Wright},
296	<	address =      {Springfield, VA},
297	<	pages =        1
298	<	}
299	<
300	<	@Article{Bembenek96,
301	<	author =       {S.~D. Bembenek and B.~B. Laird},
302	<	title =        {The role of localization in glasses and supercooled liquids},
303	<	journal =      jcp,
304	<	year =         1996,
305	<	volume =       104,
306	<	pages =        5199
307	<	}
308	<
309	<	@Article{Sun97,
310	<	author =       {X. Sun and W.~H. Miller},
311	<	title =        {Semiclassical initial value representation for
312	<	electronically nonadiabatic molecular dynamics},
313	<	journal =      jcp,
314	<	year =         1997,
315	<	volume =       106,
316	<	pages =        6346
317	<	}
318	<
319	<	@Article{Spath96,
320	<	author =       {B.~W. Spath and W.~H. Miller},
321	<	title =        {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION
322	<	PROBABILITIES},
323	<	journal =      jcp,
324	<	year =         1996,
325	<	volume =       104,
326	<	pages =        95
327	<	}
328	<
329	<	@Book{Warshel91,
330	<	author =       {Arieh Warshel},
331	<	title =        {Computer modeling of chemical reactions in enzymes
332	<	and solutions},
333	<	publisher =    {Wiley},
334	<	year =         1991,
335	<	address =      {New York}
336	<	}
337	<
338	<	@Article{Vuilleumier97,
339	<	author =       {Rodolphe Vuilleumier and Daniel Borgis},
340	<	title =        {Molecular Dynamics of an excess proton in water
341	<	using a non-additive valence bond force field},
342	<	journal =      jpc,
343	<	year =         1997,
344	<	volume =       {in press}
345	<	}
346	<
347	<	@Article{Kob95a,
348	<	author =       {W. Kob and H.~C. Andersen},
349	<	title =        {Testing mode-coupling theory for a supercooled
350	<	binary Lennard-Jones mixtures: The van Hove
351	<	corraltion function},
352	<	journal =      pre,
353	<	year =         1995,
354	<	volume =       51,
355	<	pages =        {4626-4641}
356	<	}
357	<
358	<	@Article{Kob95b,
359	<	author =       {W. Kob and H.~C. Andersen},
360	<	title =        {Testing mode-coupling theory for a supercooled
361	<	binary Lennard-Jones mixtures. II. Intermediate
362	<	scattering function and dynamic susceptibility},
363	<	journal =      pre,
364	<	year =         1995,
365	<	volume =       52,
366	<	pages =        {4134-4153}
367	<	}
368	<
369	<	@InProceedings{Gotze89,
370	<	author =       "W. G{\"{o}}tze",
371	<	title =        "Aspects of Structural Glass Transitions",
372	<	editor =       "J.~P. Hansen and D. Levesque and J. Zinn-Justin",
373	<	volume =       "I",
374	<	pages =        "287-503",
375	<	booktitle =    "Liquids, Freezing and Glass Transitions",
376	<	year =         1989,
377	<	publisher =    "North-Holland",
378	<	address =      "Amsterdam"
379	<	}
380	<
381	<	@Article{Sun97a,
382	<	author =       "X. Sun and W.~H. Miller",
383	<	title =        {Mixed semiclassical-classical approaches to the
384	<	dynamics of complex molecular systems},
385	<	journal =      jcp,
386	<	year =         1997,
387	<	pages =        916
388	<	}
389	<
390	<	@Article{Keshavamurthy94,
391	<	author =       "S. Keshavamurthy and W.~H. Miller",
392	<	title =        "ivr",
393	<	journal =      cpl,
394	<	year =         1994,
395	<	volume =       218,
396	<	pages =        189
397	<	}
398	<
399	<	@Article{Billing75,
400	<	author =       "G.~D. Billing",
401	<	title =        "ehrenfest",
402	<	journal =      cpl,
403	<	year =         1975,
404	<	volume =       30,
405	<	pages =        391
406	<	}
407	<
408	<	@Article{Chang90,
409	<	author =       {Y.-T. Chang and W.~H. Miller},
410	<	title =        {An Empirical Valence Bond Model for Constructing
411	<	Global Potential Energy Surfaces for Chemical
412	<	Reactions of Polyatomic Molecular Systems},
413	<	journal =      jpc,
414	<	year =         1990,
415	<	volume =       94,
416	<	pages =        {5884-5888}
417	<	}
418	<
419	<	@Article{Shor94,
420	<	author =       {P.W. Shor},
421	<	title =        {Algorithms for quantum computation: discrete
422	<	logarithms and factoring},
423	<	journal =      {Proceedings of the 35th Annual Symposium
424	<	on Foundations of Computer Science},
425	<	year =         1994,
426	<	pages =        {124-134}
427	<	}
428	<
429	<	@Article{Feynman82,
430	<	author =       {R.~P. Feynman},
431	<	title =        {Simulating physics with computers},
432	<	journal =      {Int. J. Theor. Phys.},
433	<	year =         1982,
434	<	volume =       21,
435	<	pages =        {467-488}
436	<	}
437	<
438	<	@Article{Grover97,
439	<	author =       {L.~K. Grover},
440	<	title =        {Quantum computers can search arbitrarily large
441	<	databases by a single query},
442	<	journal =      prl,
443	<	year =         1997,
444	<	volume =       79,
445	<	pages =        {4709-4712}
446	<	}
447	<
448	<	@Article{Chuang98,
449	<	author =       {I. Chuang and N. Gershenfeld and M. Kubinec},
450	<	title =        {Experimental Implementation of Fast Quantum Searching},
451	<	journal =      prl,
452	<	year =         1998,
453	<	volume =       80,
454	<	pages =        {3408-3411}
455	<	}
456	<
457	<	@Article{Monroe95,
458	<	author =       "C. Monroe and D.~M. Meekhof and B.~E. King and
459	<	W.~M. Itano and D.~J. Wineland",
460	<	title =        {Demonstration of a fundamental quantum logic gate},
461	<	journal =      prl,
462	<	year =         1995,
463	<	volume =       75,
464	<	pages =        4714
465	<	}
466	<
467	<	@Article{Lent93,
468	<	author =       "C.~S. Lent and P.~D. Tougaw and W.~Porod and
469	<	G.~H. Bernstein",
470	<	title =        {Quantum Cellular Automata},
471	<	journal =      {Nanotechnology},
472	<	year =         1993,
473	<	volume =       4,
474	<	pages =        {49-57}
475	<	}
476	<
477	<	@Article{Barenco95,
478	<	author =       "A. Barenco and C.~H. Bennett and R. Cleve and
479	<	D.~P. DiVincenzo and N. Margolus and P. Shor and
480	<	T. Sleator and J.~A. Smolin and H. Weinfurter",
481	<	title =        {elementary gates for quantum computation},
482	<	journal =      {Phys. Rev. A},
483	<	year =         1995,
484	<	volume =       52,
485	<	pages =        {3457-3467}
486	<	}
487	<
488	<	@Article{Small97,
489	<	author =       {T. Reinot and J.~M. Hayes and G.~J. Small},
490	<	title =        {Electronic dephasing and electron-phonon coupling of
491	<	aluminum phthalocyanine tetrasulphonate in
492	<	hyperquenched and annealed glassy films of ethanol
493	<	and methanol over a broad temperature range},
494	<	journal =      jcp,
495	<	year =         1997,
496	<	volume =       106,
497	<	pages =        {457-466}
498	<	}
499	<
500	<	@Article{Laflamme96,
501	<	author =       {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
502	<	title =        {A perfect quantum error correcting code: 5 bit code
503	<	correcting a general 1 qubit error to encode 1 qubit
504	<	of information},
505	<	journal =      prl,
506	<	year =         1996,
507	<	volume =       98,
508	<	pages =        77
509	<	}
510	<
511	<	@Article{Shor95,
512	<	author =       {P.~W. Shor},
513	<	title =        {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY},
514	<	journal =      {Phys. Rev. A},
515	<	year =         1995,
516	<	volume =       52,
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1536	<	}
1537	<
1538	<	@Article{chandra99:ssd_md,
1539	<	author =   {A. Chandra and T. Ichiye},
1540	<	title =    {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation},
1541	<	journal =      {Journal of Chemical Physics},
1542	<	year =     1999,
1543	<	volume =   111,
1544	<	number =   6,
1545	<	pages =    {2701-2709}
1	>	This file was created with JabRef 2.0.1.
2	>	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},
7	>	title = {Calculation of the solution properties of flexible macromolecules:
8	>	methods and applications},
9	>	journal = {European Biophysics Journal with Biophysics Letters},
10	>	year = {2003},
11	>	volume = {32},
12	>	pages = {477-486},
13	>	number = {5},
14	>	month = {Aug},
15	>	abstract = {While the prediction of hydrodynamic properties of rigid particles
16	>	is nowadays feasible using simple and efficient computer programs,
17	>	the calculation of such properties and, in general, the dynamic
18	>	behavior of flexible macromolecules has not reached a similar situation.
19	>	Although the theories are available, usually the computational work
20	>	is done using solutions specific for each problem. We intend to
21	>	develop computer programs that would greatly facilitate the task
22	>	of predicting solution behavior of flexible macromolecules. In this
23	>	paper, we first present an overview of the two approaches that are
24	>	most practical: the Monte Carlo rigid-body treatment, and the Brownian
25	>	dynamics simulation technique. The Monte Carlo procedure is based
26	>	on the calculation of properties for instantaneous conformations
27	>	of the macromolecule that are regarded as if they were instantaneously
28	>	rigid. We describe how a Monte Carlo program can be interfaced to
29	>	the programs in the HYDRO suite for rigid particles, and provide
30	>	an example of such calculation, for a hypothetical particle: a protein
31	>	with two domains connected by a flexible linker. We also describe
32	>	briefly the essentials of Brownian dynamics, and propose a general
33	>	mechanical model that includes several kinds of intramolecular interactions,
34	>	such as bending, internal rotation, excluded volume effects, etc.
35	>	We provide an example of the application of this methodology to
36	>	the dynamics of a semiflexible, wormlike DNA.},
37	>	annote = {724XK Times Cited:6 Cited References Count:64},
38	>	issn = {0175-7571},
39	>	uri = {<Go to ISI>://000185513400011},
40	>	}
41	>
42	>	@ARTICLE{Alakent2005,
43	>	author = {B. Alakent and M. C. Camurdan and P. Doruker},
44	>	title = {Hierarchical structure of the energy landscape of proteins revisited
45	>	by time series analysis. II. Investigation of explicit solvent effects},
46	>	journal = {Journal of Chemical Physics},
47	>	year = {2005},
48	>	volume = {123},
49	>	pages = {-},
50	>	number = {14},
51	>	month = {Oct 8},
52	>	abstract = {Time series analysis tools are employed on the principal modes obtained
53	>	from the C-alpha trajectories from two independent molecular-dynamics
54	>	simulations of alpha-amylase inhibitor (tendamistat). Fluctuations
55	>	inside an energy minimum (intraminimum motions), transitions between
56	>	minima (interminimum motions), and relaxations in different hierarchical
57	>	energy levels are investigated and compared with those encountered
58	>	in vacuum by using different sampling window sizes and intervals.
59	>	The low-frequency low-indexed mode relationship, established in
60	>	vacuum, is also encountered in water, which shows the reliability
61	>	of the important dynamics information offered by principal components
62	>	analysis in water. It has been shown that examining a short data
63	>	collection period (100 ps) may result in a high population of overdamped
64	>	modes, while some of the low-frequency oscillations (< 10 cm(-1))
65	>	can be captured in water by using a longer data collection period
66	>	(1200 ps). Simultaneous analysis of short and long sampling window
67	>	sizes gives the following picture of the effect of water on protein
68	>	dynamics. Water makes the protein lose its memory: future conformations
69	>	are less dependent on previous conformations due to the lowering
70	>	of energy barriers in hierarchical levels of the energy landscape.
71	>	In short-time dynamics (< 10 ps), damping factors extracted from
72	>	time series model parameters are lowered. For tendamistat, the friction
73	>	coefficient in the Langevin equation is found to be around 40-60
74	>	cm(-1) for the low-indexed modes, compatible with literature. The
75	>	fact that water has increased the friction and that on the other
76	>	hand has lubrication effect at first sight contradicts. However,
77	>	this comes about because water enhances the transitions between
78	>	minima and forces the protein to reduce its already inherent inability
79	>	to maintain oscillations observed in vacuum. Some of the frequencies
80	>	lower than 10 cm(-1) are found to be overdamped, while those higher
81	>	than 20 cm(-1) are slightly increased. As for the long-time dynamics
82	>	in water, it is found that random-walk motion is maintained for
83	>	approximately 200 ps (about five times of that in vacuum) in the
84	>	low-indexed modes, showing the lowering of energy barriers between
85	>	the higher-level minima.},
86	>	annote = {973OH Times Cited:1 Cited References Count:33},
87	>	issn = {0021-9606},
88	>	uri = {<Go to ISI>://000232532000064},
89	>	}
90	>
91	>	@BOOK{Allen1987,
92	>	title = {Computer Simulations of Liquids},
93	>	publisher = {Oxford University Press},
94	>	year = {1987},
95	>	author = {M.~P. Allen and D.~J. Tildesley},
96	>	address = {New York},
97	>	}
98	>
99	>	@ARTICLE{Allison1991,
100	>	author = {S. A. Allison},
101	>	title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application
102	>	to Polarized Dynamic Light-Scattering},
103	>	journal = {Macromolecules},
104	>	year = {1991},
105	>	volume = {24},
106	>	pages = {530-536},
107	>	number = {2},
108	>	month = {Jan 21},
109	>	abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
110	>	of rigid macromolecules. It is applied to polarized dynamic light
111	>	scattering from rodlike sturctures and from a model of a DNA fragment
112	>	(762 base pairs). A number of rod cases are examined in which the
113	>	translational anisotropy is increased form zero to a large value.
114	>	Simulated first cumulants as well as amplitudes and lifetimes of
115	>	the dynamic form factor are compared with predictions of analytic
116	>	theories and found to be in very good agreement with them. For DNA
117	>	fragments 762 base pairs in length or longer, translational anisotropy
118	>	does not contribute significantly to dynamic light scattering. In
119	>	a comparison of rigid and flexible simulations on semistiff models
120	>	of this fragment, it is shown directly that flexing contributes
121	>	to the faster decay processes probed by light scattering and that
122	>	the flexible model studies are in good agreement with experiment.},
123	>	annote = {Eu814 Times Cited:8 Cited References Count:32},
124	>	issn = {0024-9297},
125	>	uri = {<Go to ISI>://A1991EU81400029},
126	>	}
127	>
128	>	@ARTICLE{Auerbach2005,
129	>	author = {A. Auerbach},
130	>	title = {Gating of acetylcholine receptor channels: Brownian motion across
131	>	a broad transition state},
132	>	journal = {Proceedings of the National Academy of Sciences of the United States
133	>	of America},
134	>	year = {2005},
135	>	volume = {102},
136	>	pages = {1408-1412},
137	>	number = {5},
138	>	month = {Feb 1},
139	>	abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
140	>	stable #closed# and #open# conformations. In patch clamp recordings,
141	>	diliganded AChR gating appears to be a simple, two-state reaction.
142	>	However, mutagenesis studies indicate that during gating dozens
143	>	of residues across the protein move asynchronously and are organized
144	>	into rigid body gating domains (#blocks#). Moreover, there is an
145	>	upper limit to the apparent channel opening rate constant. These
146	>	observations suggest that the gating reaction has a broad, corrugated
147	>	transition state region, with the maximum opening rate reflecting,
148	>	in part, the mean first-passage time across this ensemble. Simulations
149	>	reveal that a flat, isotropic energy profile for the transition
150	>	state can account for many of the essential features of AChR gating.
151	>	With this mechanism, concerted, local structural transitions that
152	>	occur on the broad transition state ensemble give rise to fractional
153	>	measures of reaction progress (Phi values) determined by rate-equilibrium
154	>	free energy relationship analysis. The results suggest that the
155	>	coarse-grained AChR gating conformational change propagates through
156	>	the protein with dynamics that are governed by the Brownian motion
157	>	of individual gating blocks.},
158	>	annote = {895QF Times Cited:9 Cited References Count:33},
159	>	issn = {0027-8424},
160	>	uri = {<Go to ISI>://000226877300030},
161	>	}
162	>
163	>	@ARTICLE{Baber1995,
164	>	author = {J. Baber and J. F. Ellena and D. S. Cafiso},
165	>	title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined
166	>	Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
167	>	journal = {Biochemistry},
168	>	year = {1995},
169	>	volume = {34},
170	>	pages = {6533-6539},
171	>	number = {19},
172	>	month = {May 16},
173	>	abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
174	>	on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine
175	>	membranes in the liquid crystalline phase was investigated using
176	>	H-2 NMR. Upon the addition of the anesthetics, the first five methylene
177	>	units near the interface generally show a very small increase in
178	>	segmental order, while segments deeper within the bilayer show a
179	>	small decrease in segmental order. From the H-2 NMR results, the
180	>	chain length for the perdeuterated palmitoyl chain in the absence
181	>	of anesthetic was found to be 12.35 Angstrom. Upon the addition
182	>	of halothane enflurane, or isoflurane, the acyl chain undergoes
183	>	slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively,
184	>	at 50 mol % anesthetic. A simple model was used to estimate the
185	>	relative amounts of anesthetic located near the interface and deeper
186	>	in the bilayer hydrocarbon region, and only a slight preference
187	>	for an interfacial location was observed. Intermolecular H-1-H-1
188	>	nuclear Overhauser effects (NOEs) were measured between phospholipid
189	>	and halothane protons. These NOEs are consistent with the intramembrane
190	>	location of the anesthetics suggested by the H-2 NMR data. In addition,
191	>	the NOE data indicate that anesthetics prefer the interfacial and
192	>	hydrocarbon regions of the membrane and are not found in high concentrations
193	>	in the phospholipid headgroup.},
194	>	annote = {Qz716 Times Cited:38 Cited References Count:37},
195	>	issn = {0006-2960},
196	>	uri = {<Go to ISI>://A1995QZ71600035},
197	>	}
198	>
199	>	@ARTICLE{Banerjee2004,
200	>	author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
201	>	title = {Solution of quantum Langevin equation: Approximations, theoretical
202	>	and numerical aspects},
203	>	journal = {Journal of Chemical Physics},
204	>	year = {2004},
205	>	volume = {120},
206	>	pages = {8960-8972},
207	>	number = {19},
208	>	month = {May 15},
209	>	abstract = {Based on a coherent state representation of noise operator and an
210	>	ensemble averaging procedure using Wigner canonical thermal distribution
211	>	for harmonic oscillators, a generalized quantum Langevin equation
212	>	has been recently developed [Phys. Rev. E 65, 021109 (2002); 66,
213	>	051106 (2002)] to derive the equations of motion for probability
214	>	distribution functions in c-number phase-space. We extend the treatment
215	>	to explore several systematic approximation schemes for the solutions
216	>	of the Langevin equation for nonlinear potentials for a wide range
217	>	of noise correlation, strength and temperature down to the vacuum
218	>	limit. The method is exemplified by an analytic application to harmonic
219	>	oscillator for arbitrary memory kernel and with the help of a numerical
220	>	calculation of barrier crossing, in a cubic potential to demonstrate
221	>	the quantum Kramers' turnover and the quantum Arrhenius plot. (C)
222	>	2004 American Institute of Physics.},
223	>	annote = {816YY Times Cited:8 Cited References Count:35},
224	>	issn = {0021-9606},
225	>	uri = {<Go to ISI>://000221146400009},
226	>	}
227	>
228	>	@ARTICLE{Barth1998,
229	>	author = {E. Barth and T. Schlick},
230	>	title = {Overcoming stability limitations in biomolecular dynamics. I. Combining
231	>	force splitting via extrapolation with Langevin dynamics in LN},
232	>	journal = {Journal of Chemical Physics},
233	>	year = {1998},
234	>	volume = {109},
235	>	pages = {1617-1632},
236	>	number = {5},
237	>	month = {Aug 1},
238	>	abstract = {We present an efficient new method termed LN for propagating biomolecular
239	>	dynamics according to the Langevin equation that arose fortuitously
240	>	upon analysis of the range of harmonic validity of our normal-mode
241	>	scheme LIN. LN combines force linearization with force splitting
242	>	techniques and disposes of LIN'S computationally intensive minimization
243	>	(anharmonic correction) component. Unlike the competitive multiple-timestepping
244	>	(MTS) schemes today-formulated to be symplectic and time-reversible-LN
245	>	merges the slow and fast forces via extrapolation rather than impulses;
246	>	the Langevin heat bath prevents systematic energy drifts. This combination
247	>	succeeds in achieving more significant speedups than these MTS methods
248	>	which are Limited by resonance artifacts to an outer timestep less
249	>	than some integer multiple of half the period of the fastest motion
250	>	(around 4-5 fs for biomolecules). We show that LN achieves very
251	>	good agreement with small-timestep solutions of the Langevin equation
252	>	in terms of thermodynamics (energy means and variances), geometry,
253	>	and dynamics (spectral densities) for two proteins in vacuum and
254	>	a large water system. Significantly, the frequency of updating the
255	>	slow forces extends to 48 fs or more, resulting in speedup factors
256	>	exceeding 10. The implementation of LN in any program that employs
257	>	force-splitting computations is straightforward, with only partial
258	>	second-derivative information required, as well as sparse Hessian/vector
259	>	multiplication routines. The linearization part of LN could even
260	>	be replaced by direct evaluation of the fast components. The application
261	>	of LN to biomolecular dynamics is well suited for configurational
262	>	sampling, thermodynamic, and structural questions. (C) 1998 American
263	>	Institute of Physics.},
264	>	annote = {105HH Times Cited:29 Cited References Count:49},
265	>	issn = {0021-9606},
266	>	uri = {<Go to ISI>://000075066300006},
267	>	}
268	>
269	>	@ARTICLE{Batcho2001,
270	>	author = {P. F. Batcho and T. Schlick},
271	>	title = {Special stability advantages of position-Verlet over velocity-Verlet
272	>	in multiple-time step integration},
273	>	journal = {Journal of Chemical Physics},
274	>	year = {2001},
275	>	volume = {115},
276	>	pages = {4019-4029},
277	>	number = {9},
278	>	month = {Sep 1},
279	>	abstract = {We present an analysis for a simple two-component harmonic oscillator
280	>	that compares the use of position-Verlet to velocity-Verlet for
281	>	multiple-time step integration. The numerical stability analysis
282	>	based on the impulse-Verlet splitting shows that position-Verlet
283	>	has enhanced stability, in terms of the largest allowable time step,
284	>	for cases where an ample separation of time scales exists. Numerical
285	>	investigations confirm the advantages of the position-Verlet scheme
286	>	when used for the fastest time scales of the system. Applications
287	>	to a biomolecule. a solvated protein, for both Newtonian and Langevin
288	>	dynamics echo these trends over large outer time-step regimes. (C)
289	>	2001 American Institute of Physics.},
290	>	annote = {469KV Times Cited:6 Cited References Count:30},
291	>	issn = {0021-9606},
292	>	uri = {<Go to ISI>://000170813800005},
293	>	}
294	>
295	>	@ARTICLE{Bates2005,
296	>	author = {M. A. Bates and G. R. Luckhurst},
297	>	title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation
298	>	study},
299	>	journal = {Physical Review E},
300	>	year = {2005},
301	>	volume = {72},
302	>	pages = {-},
303	>	number = {5},
304	>	month = {Nov},
305	>	abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
306	>	can exhibit the elusive biaxial nematic phase, we have developed
307	>	a generic simulation model for such systems. This contains the features
308	>	of the molecule that are essential to its liquid crystal behavior,
309	>	namely the anisotropies of the two arms and the angle between them.
310	>	The behavior of the model has been investigated using Monte Carlo
311	>	simulations for a wide range of these structural parameters. This
312	>	allows us to establish the relationship between the V-shaped molecule
313	>	and its ability to form a biaxial nematic phase. Of particular importance
314	>	are the criteria of geometry and the relative anisotropy necessary
315	>	for the system to exhibit a Landau point, at which the biaxial nematic
316	>	is formed directly from the isotropic phase. The simulations have
317	>	also been used to determine the orientational order parameters for
318	>	a selection of molecular axes. These are especially important because
319	>	they reveal the phase symmetry and are connected to the experimental
320	>	determination of this. The simulation results show that, whereas
321	>	some positions are extremely sensitive to the phase biaxiality,
322	>	others are totally blind to this.},
323	>	annote = {Part 1 988LQ Times Cited:0 Cited References Count:38},
324	>	issn = {1539-3755},
325	>	uri = {<Go to ISI>://000233603100030},
326	>	}
327	>
328	>	@ARTICLE{Beard2003,
329	>	author = {D. A. Beard and T. Schlick},
330	>	title = {Unbiased rotational moves for rigid-body dynamics},
331	>	journal = {Biophysical Journal},
332	>	year = {2003},
333	>	volume = {85},
334	>	pages = {2973-2976},
335	>	number = {5},
336	>	month = {Nov 1},
337	>	abstract = {We introduce an unbiased protocol for performing rotational moves
338	>	in rigid-body dynamics simulations. This approach - based on the
339	>	analytic solution for the rotational equations of motion for an
340	>	orthogonal coordinate system at constant angular velocity - removes
341	>	deficiencies that have been largely ignored in Brownian dynamics
342	>	simulations, namely errors for finite rotations that result from
343	>	applying the noncommuting rotational matrices in an arbitrary order.
344	>	Our algorithm should thus replace standard approaches to rotate
345	>	local coordinate frames in Langevin and Brownian dynamics simulations.},
346	>	annote = {736UA Times Cited:0 Cited References Count:11},
347	>	issn = {0006-3495},
348	>	uri = {<Go to ISI>://000186190500018},
349	>	}
350	>
351	>	@ARTICLE{Beloborodov1998,
352	>	author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev},
353	>	title = {Effect of coupling between rotational and translational Brownian
354	>	motions on NMR spin relaxation: Consideration using green function
355	>	of rigid body diffusion},
356	>	journal = {Journal of Magnetic Resonance},
357	>	year = {1998},
358	>	volume = {132},
359	>	pages = {328-329},
360	>	number = {2},
361	>	month = {Jun},
362	>	abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
363	>	Biopolymers 33, 409-436, 1993), it was analytically shown that coupling
364	>	between translation and rotation diffusion degrees of freedom does
365	>	not affect the correlation functions relevant to the NMR intramolecular
366	>	relaxation. It follows that spectral densities usually used for
367	>	the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37,
368	>	647-654, 1962) can be regarded as exact in respect to the rotation-translation
369	>	coupling for the spin system connected with a rigid body. (C) 1998
370	>	Academic Press.},
371	>	annote = {Zu605 Times Cited:2 Cited References Count:6},
372	>	issn = {1090-7807},
373	>	uri = {<Go to ISI>://000074214800017},
374	>	}
375	>
376	>	@ARTICLE{Berardi1996,
377	>	author = {R. Berardi and S. Orlandi and C. Zannoni},
378	>	title = {Antiphase structures in polar smectic liquid crystals and their molecular
379	>	origin},
380	>	journal = {Chemical Physics Letters},
381	>	year = {1996},
382	>	volume = {261},
383	>	pages = {357-362},
384	>	number = {3},
385	>	month = {Oct 18},
386	>	abstract = {We demonstrate that the overall molecular dipole organization in a
387	>	smectic liquid crystal formed of polar molecules can be strongly
388	>	influenced by the position of the dipole in the molecule. We study
389	>	by large scale Monte Carlo simulations systems of attractive-repulsive
390	>	''Gay-Berne'' elongated ellipsoids with an axial dipole at the center
391	>	or near the end of the molecule and we show that monolayer smectic
392	>	liquid crystals and modulated antiferroelectric bilayer stripe domains
393	>	similar to the experimentally observed ''antiphase'' structures
394	>	are obtained in the two cases.},
395	>	annote = {Vn637 Times Cited:49 Cited References Count:26},
396	>	issn = {0009-2614},
397	>	uri = {<Go to ISI>://A1996VN63700023},
398	>	}
399	>
400	>	@ARTICLE{Berkov2005,
401	>	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},
431	>	title = {Magnetization precession due to a spin-polarized current in a thin
432	>	nanoelement: Numerical simulation study},
433	>	journal = {Physical Review B},
434	>	year = {2005},
435	>	volume = {72},
436	>	pages = {-},
437	>	number = {9},
438	>	month = {Sep},
439	>	abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
440	>	formalism) of magnetization oscillations driven by a spin-polarized
441	>	current through a thin elliptical nanoelement is presented. We show
442	>	that a sophisticated micromagnetic model, where a polycrystalline
443	>	structure of a nanoelement is taken into account, can explain qualitatively
444	>	all most important features of the magnetization oscillation spectra
445	>	recently observed experimentally [S. I. Kiselev , Nature 425, 380
446	>	(2003)], namely, existence of several equidistant spectral bands,
447	>	sharp onset and abrupt disappearance of magnetization oscillations
448	>	with increasing current, absence of the out-of-plane regime predicted
449	>	by a macrospin model, and the relation between frequencies of so-called
450	>	small-angle and quasichaotic oscillations. However, a quantitative
451	>	agreement with experimental results (especially concerning the frequency
452	>	of quasichaotic oscillations) could not be achieved in the region
453	>	of reasonable parameter values, indicating that further model refinement
454	>	is necessary for a complete understanding of the spin-driven magnetization
455	>	precession even in this relatively simple experimental situation.},
456	>	annote = {969IT Times Cited:2 Cited References Count:55},
457	>	issn = {1098-0121},
458	>	uri = {<Go to ISI>://000232228500058},
459	>	}
460	>
461	>	@ARTICLE{Berkov2002,
462	>	author = {D. V. Berkov and N. L. Gorn and P. Gornert},
463	>	title = {Magnetization dynamics in nanoparticle systems: Numerical simulation
464	>	using Langevin dynamics},
465	>	journal = {Physica Status Solidi a-Applied Research},
466	>	year = {2002},
467	>	volume = {189},
468	>	pages = {409-421},
469	>	number = {2},
470	>	month = {Feb 16},
471	>	abstract = {We report on recent progress achieved by the development of numerical
472	>	methods based on the stochastic (Langevin) dynamics applied to systems
473	>	of interacting magnetic nanoparticles. The method enables direct
474	>	simulations of the trajectories of magnetic moments taking into
475	>	account (i) all relevant interactions, (ii) precession dynamics,
476	>	and (iii) temperature fluctuations included via the random (thermal)
477	>	field. We present several novel results obtained using new methods
478	>	developed for the solution of the Langevin equations. In particular,
479	>	we have investigated magnetic nanodots and disordered granular systems
480	>	of single-domain magnetic particles. For the first case we have
481	>	calculated the spectrum and the spatial distribution of spin excitations.
482	>	For the second system the complex ac susceptibility chi(omega, T)
483	>	for various particle concentrations and particle anisotropies were
484	>	computed and compared with numerous experimental results.},
485	>	annote = {526TF Times Cited:4 Cited References Count:37},
486	>	issn = {0031-8965},
487	>	uri = {<Go to ISI>://000174145200026},
488	>	}
489	>
490	>	@ARTICLE{Bernal1980,
491	>	author = {J.M. Bernal and J. G. {de la Torre}},
492	>	title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules
493	>	with Arbitrary Shape},
494	>	journal = {Biopolymers},
495	>	year = {1980},
496	>	volume = {19},
497	>	pages = {751-766},
498	>	}
499	>
500	>	@ARTICLE{Brunger1984,
501	>	author = {A. Brunger and C. L. Brooks and M. Karplus},
502	>	title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations
503	>	of St2 Water},
504	>	journal = {Chemical Physics Letters},
505	>	year = {1984},
506	>	volume = {105},
507	>	pages = {495-500},
508	>	number = {5},
509	>	annote = {Sm173 Times Cited:143 Cited References Count:22},
510	>	issn = {0009-2614},
511	>	uri = {<Go to ISI>://A1984SM17300007},
512	>	}
513	>
514	>	@ARTICLE{Camp1999,
515	>	author = {P. J. Camp and M. P. Allen and A. J. Masters},
516	>	title = {Theory and computer simulation of bent-core molecules},
517	>	journal = {Journal of Chemical Physics},
518	>	year = {1999},
519	>	volume = {111},
520	>	pages = {9871-9881},
521	>	number = {21},
522	>	month = {Dec 1},
523	>	abstract = {Fluids of hard bent-core molecules have been studied using theory
524	>	and computer simulation. The molecules are composed of two hard
525	>	spherocylinders, with length-to-breadth ratio L/D, joined by their
526	>	ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20
527	>	degrees, the simulations show isotropic, nematic, smectic, and solid
528	>	phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic,
529	>	and solid phases are in evidence, which suggests that there is a
530	>	nematic-smectic-solid triple point at an angle in the range 20 degrees
531	>	< gamma < 30 degrees. In all of the orientationally ordered fluid
532	>	phases the order is purely uniaxial. For gamma = 10 degrees and
533	>	20 degrees, at the studied densities, the solid is also uniaxially
534	>	ordered, whilst for gamma = 30 degrees the solid layers are biaxially
535	>	ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find
536	>	no spontaneous orientational ordering. This is shown to be due to
537	>	the interlocking of dimer pairs which precludes alignment. We find
538	>	similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial
539	>	nematic transition is predicted by Onsager theory. Simulations in
540	>	the biaxial nematic phase show it to be at least mechanically stable
541	>	with respect to the isotropic phase, however. We have compared the
542	>	quasi-exact simulation results in the isotropic phase with the predicted
543	>	equations of state from three theories: the virial expansion containing
544	>	the second and third virial coefficients; the Parsons-Lee equation
545	>	of state; an application of Wertheim's theory of associating fluids
546	>	in the limit of infinite attractive association energy. For all
547	>	of the molecule elongations and geometries we have simulated, the
548	>	Wertheim theory proved to be the most accurate. Interestingly, the
549	>	isotropic equation of state is virtually independent of the dimer
550	>	bond angle-a feature that is also reflected in the lack of variation
551	>	with angle of the calculated second and third virial coefficients.
552	>	(C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].},
553	>	annote = {255TC Times Cited:24 Cited References Count:38},
554	>	issn = {0021-9606},
555	>	uri = {<Go to ISI>://000083685400056},
556	>	}
557	>
558	>	@ARTICLE{Care2005,
559	>	author = {C. M. Care and D. J. Cleaver},
560	>	title = {Computer simulation of liquid crystals},
561	>	journal = {Reports on Progress in Physics},
562	>	year = {2005},
563	>	volume = {68},
564	>	pages = {2665-2700},
565	>	number = {11},
566	>	month = {Nov},
567	>	abstract = {A review is presented of molecular and mesoscopic computer simulations
568	>	of liquid crystalline systems. Molecular simulation approaches applied
569	>	to such systems are described, and the key findings for bulk phase
570	>	behaviour are reported. Following this, recently developed lattice
571	>	Boltzmann approaches to the mesoscale modelling of nemato-dynanics
572	>	are reviewed. This paper concludes with a discussion of possible
573	>	areas for future development in this field.},
574	>	annote = {989TU Times Cited:2 Cited References Count:258},
575	>	issn = {0034-4885},
576	>	uri = {<Go to ISI>://000233697600004},
577	>	}
578	>
579	>	@ARTICLE{Carrasco1999,
580	>	author = {B. Carrasco and J. G. {de la Torre}},
581	>	title = {Hydrodynamic properties of rigid particles: Comparison of different
582	>	modeling and computational procedures},
583	>	journal = {Biophysical Journal},
584	>	year = {1999},
585	>	volume = {76},
586	>	pages = {3044-3057},
587	>	number = {6},
588	>	month = {Jun},
589	>	abstract = {The hydrodynamic properties of rigid particles are calculated from
590	>	models composed of spherical elements (beads) using theories developed
591	>	by Kirkwood, Bloomfield, and their coworkers. Bead models have usually
592	>	been built in such a way that the beads fill the volume occupied
593	>	by the particles. Sometimes the beads are few and of varying sizes
594	>	(bead models in the strict sense), and other times there are many
595	>	small beads (filling models). Because hydrodynamic friction takes
596	>	place at the molecular surface, another possibility is to use shell
597	>	models, as originally proposed by Bloomfield. In this work, we have
598	>	developed procedures to build models of the various kinds, and we
599	>	describe the theory and methods for calculating their hydrodynamic
600	>	properties, including approximate methods that may be needed to
601	>	treat models with a very large number of elements. By combining
602	>	the various possibilities of model building and hydrodynamic calculation,
603	>	several strategies can be designed. We have made a quantitative
604	>	comparison of the performance of the various strategies by applying
605	>	them to some test cases, for which the properties are known a priori.
606	>	We provide guidelines and computational tools for bead modeling.},
607	>	annote = {200TT Times Cited:46 Cited References Count:57},
608	>	issn = {0006-3495},
609	>	uri = {<Go to ISI>://000080556700016},
610	>	}
611	>
612	>	@ARTICLE{Chandra1999,
613	>	author = {A. Chandra and T. Ichiye},
614	>	title = {Dynamical properties of the soft sticky dipole model of water: Molecular
615	>	dynamics simulations},
616	>	journal = {Journal of Chemical Physics},
617	>	year = {1999},
618	>	volume = {111},
619	>	pages = {2701-2709},
620	>	number = {6},
621	>	month = {Aug 8},
622	>	abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
623	>	are calculated by means of molecular dynamics simulations. Since
624	>	this is not a simple point model, the forces and torques arising
625	>	from the SSD potential are derived here. Simulations are carried
626	>	out in the microcanonical ensemble employing the Ewald method for
627	>	the electrostatic interactions. Various time correlation functions
628	>	and dynamical quantities associated with the translational and rotational
629	>	motion of water molecules are evaluated and compared with those
630	>	of two other commonly used models of liquid water, namely the transferable
631	>	intermolecular potential-three points (TIP3P) and simple point charge/extended
632	>	(SPC/E) models, and also with experiments. The dynamical properties
633	>	of the SSD water model are found to be in good agreement with the
634	>	experimental results and appear to be better than the TIP3P and
635	>	SPC/E models in most cases, as has been previously shown for its
636	>	thermodynamic, structural, and dielectric properties. Also, molecular
637	>	dynamics simulations of the SSD model are found to run much faster
638	>	than TIP3P, SPC/E, and other multisite models. (C) 1999 American
639	>	Institute of Physics. [S0021-9606(99)51430-X].},
640	>	annote = {221EN Times Cited:14 Cited References Count:66},
641	>	issn = {0021-9606},
642	>	uri = {<Go to ISI>://000081711200038},
643		}
644
645	<	@Book{allen87:csl,
646	<	author =   {M.~P. Allen and D.~J. Tildesley},
647	<	title =    {Computer Simulations of Liquids},
648	<	publisher =    {Oxford University Press},
649	<	year =     1987,
650	<	address =  {New York}
645	>	@ARTICLE{Cheung2004,
646	>	author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
647	>	title = {Calculation of flexoelectric coefficients for a nematic liquid crystal
648	>	by atomistic simulation},
649	>	journal = {Journal of Chemical Physics},
650	>	year = {2004},
651	>	volume = {121},
652	>	pages = {9131-9139},
653	>	number = {18},
654	>	month = {Nov 8},
655	>	abstract = {Equilibrium molecular dynamics calculations have been performed for
656	>	the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile
657	>	(PCH5) using a fully atomistic model. Simulation data have been
658	>	obtained for a series of temperatures in the nematic phase. The
659	>	simulation data have been used to calculate the flexoelectric coefficients
660	>	e(s) and e(b) using the linear response formalism of Osipov and
661	>	Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr.
662	>	31, 125 (1986)]. The temperature and order parameter dependence
663	>	of e(s) and e(b) are examined, as are separate contributions from
664	>	different intermolecular interactions. Values of e(s) and e(b) calculated
665	>	from simulation are consistent with those found from experiment.
666	>	(C) 2004 American Institute of Physics.},
667	>	annote = {866UM Times Cited:4 Cited References Count:61},
668	>	issn = {0021-9606},
669	>	uri = {<Go to ISI>://000224798900053},
670		}
671
672	<	@Book{leach01:mm,
673	<	author =   {A. Leach},
674	<	title =    {Molecular Modeling: Principles and Applications},
675	<	publisher =    {Pearson Educated Limited},
676	<	year =     2001,
677	<	address =  {Harlow, England},
678	<	edition =  {2nd}
672	>	@ARTICLE{Cheung2002,
673	>	author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
674	>	title = {Calculation of the rotational viscosity of a nematic liquid crystal},
675	>	journal = {Chemical Physics Letters},
676	>	year = {2002},
677	>	volume = {356},
678	>	pages = {140-146},
679	>	number = {1-2},
680	>	month = {Apr 15},
681	>	abstract = {Equilibrium molecular dynamics calculations have been performed for
682	>	the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile
683	>	(PCH5) using a fully atomistic model. Simulation data has been obtained
684	>	for a series of temperatures in the nematic phase. The rotational
685	>	viscosity co-efficient gamma(1), has been calculated using the angular
686	>	velocity correlation function of the nematic director, n, the mean
687	>	squared diffusion of n and statistical mechanical methods based
688	>	on the rotational diffusion co-efficient. We find good agreement
689	>	between the first two methods and experimental values. (C) 2002
690	>	Published by Elsevier Science B.V.},
691	>	annote = {547KF Times Cited:8 Cited References Count:31},
692	>	issn = {0009-2614},
693	>	uri = {<Go to ISI>://000175331000020},
694		}
695
696	<
697	<	@Article{katsaras00,
698	<	author =   {J. Katsaras and S. Tristram-Nagle and Y. Liu and R.~L. Headrick and E. Fontes and P.~C. Mason and J.~F. Nagle},
699	<	title =    {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples},
700	<	journal =      {Physical Review E},
701	<	year =     2000,
702	<	volume =   61,
703	<	number =   5,
704	<	pages =    {5668-5677}
696	>	@ARTICLE{Chin2004,
697	>	author = {S. A. Chin},
698	>	title = {Dynamical multiple-time stepping methods for overcoming resonance
699	>	instabilities},
700	>	journal = {Journal of Chemical Physics},
701	>	year = {2004},
702	>	volume = {120},
703	>	pages = {8-13},
704	>	number = {1},
705	>	month = {Jan 1},
706	>	abstract = {Current molecular dynamics simulations of biomolecules using multiple
707	>	time steps to update the slowly changing force are hampered by instabilities
708	>	beginning at time steps near the half period of the fastest vibrating
709	>	mode. These #resonance# instabilities have became a critical barrier
710	>	preventing the long time simulation of biomolecular dynamics. Attempts
711	>	to tame these instabilities by altering the slowly changing force
712	>	and efforts to damp them out by Langevin dynamics do not address
713	>	the fundamental cause of these instabilities. In this work, we trace
714	>	the instability to the nonanalytic character of the underlying spectrum
715	>	and show that a correct splitting of the Hamiltonian, which renders
716	>	the spectrum analytic, restores stability. The resulting Hamiltonian
717	>	dictates that in addition to updating the momentum due to the slowly
718	>	changing force, one must also update the position with a modified
719	>	mass. Thus multiple-time stepping must be done dynamically. (C)
720	>	2004 American Institute of Physics.},
721	>	annote = {757TK Times Cited:1 Cited References Count:22},
722	>	issn = {0021-9606},
723	>	uri = {<Go to ISI>://000187577400003},
724		}
725
726	<	@Article{sengupta00,
727	<	author =   {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
728	<	title =    {Novel structural Features of the ripple phase of phospholipids},
729	<	journal =      {Europhysics Letters},
730	<	year =     2000,
731	<	volume =   49,
732	<	number =   6,
733	<	pages =    {722-728}
726	>	@ARTICLE{Cook2000,
727	>	author = {M. J. Cook and M. R. Wilson},
728	>	title = {Simulation studies of dipole correlation in the isotropic liquid
729	>	phase},
730	>	journal = {Liquid Crystals},
731	>	year = {2000},
732	>	volume = {27},
733	>	pages = {1573-1583},
734	>	number = {12},
735	>	month = {Dec},
736	>	abstract = {The Kirkwood correlation factor g(1) determines the preference for
737	>	local parallel or antiparallel dipole association in the isotropic
738	>	phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood
739	>	factors greater than 1 have an enhanced effective dipole moment
740	>	along the molecular long axis. This leads to higher values of Delta
741	>	epsilon in the nematic phase. This paper describes state-of-the-art
742	>	molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile
743	>	(PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl)
744	>	in the isotropic liquid phase using an all-atom force field and
745	>	taking long range electrostatics into account using an Ewald summation.
746	>	Using this methodology, PCH5 is seen to prefer antiparallel dipole
747	>	alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel
748	>	dipole alignment with a positive g(1); this is in accordance with
749	>	experimental dielectric measurements. Analysis of the molecular
750	>	dynamics trajectories allows an assessment of why these molecules
751	>	behave differently.},
752	>	annote = {376BF Times Cited:10 Cited References Count:16},
753	>	issn = {0267-8292},
754	>	uri = {<Go to ISI>://000165437800002},
755		}
756
757	<	@Article{venable00,
758	<	author =   {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
759	<	title =    {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
760	<	journal =      jcp,
761	<	year =     2000,
762	<	volume =   112,
763	<	number =   10,
764	<	pages =    {4822-4832}
757	>	@ARTICLE{Cui2003,
758	>	author = {B. X. Cui and M. Y. Shen and K. F. Freed},
759	>	title = {Folding and misfolding of the papillomavirus E6 interacting peptide
760	>	E6ap},
761	>	journal = {Proceedings of the National Academy of Sciences of the United States
762	>	of America},
763	>	year = {2003},
764	>	volume = {100},
765	>	pages = {7087-7092},
766	>	number = {12},
767	>	month = {Jun 10},
768	>	abstract = {All-atom Langevin dynamics simulations have been performed to study
769	>	the folding pathways of the 18-residue binding domain fragment E6ap
770	>	of the human papillomavirus E6 interacting peptide. Six independent
771	>	folding trajectories, with a total duration of nearly 2 mus, all
772	>	lead to the same native state in which the E6ap adopts a fluctuating
773	>	a-helix structure in the central portion (Ser-4-Leu-13) but with
774	>	very flexible N and C termini. Simulations starting from different
775	>	core configurations exhibit the E6ap folding dynamics as either
776	>	a two- or three-state folder with an intermediate misfolded state.
777	>	The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13)
778	>	is well conserved in the native-state structure but absent in the
779	>	intermediate structure, suggesting that the leucine core is not
780	>	only essential for the binding activity of E6ap but also important
781	>	for the stability of the native structure. The free energy landscape
782	>	reveals a significant barrier between the basins separating the
783	>	native and misfolded states. We also discuss the various underlying
784	>	forces that drive the peptide into its native state.},
785	>	annote = {689LC Times Cited:3 Cited References Count:48},
786	>	issn = {0027-8424},
787	>	uri = {<Go to ISI>://000183493500037},
788		}
789
790	<	@Article{lindahl00,
791	<	author =   {E. Lindahl and O. Edholm},
792	<	title =    {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
793	<	journal =      {Biophysical Journal},
794	<	year =     2000,
795	<	volume =   79,
796	<	pages =    {426-433},
797	<	month =    {July}
790	>	@ARTICLE{Denisov2003,
791	>	author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou},
792	>	title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
793	>	journal = {Physical Review B},
794	>	year = {2003},
795	>	volume = {67},
796	>	pages = {-},
797	>	number = {1},
798	>	month = {Jan 1},
799	>	abstract = {We study the slow phase of thermally activated magnetic relaxation
800	>	in finite two-dimensional ensembles of dipolar interacting ferromagnetic
801	>	nanoparticles whose easy axes of magnetization are perpendicular
802	>	to the distribution plane. We develop a method to numerically simulate
803	>	the magnetic relaxation for the case that the smallest heights of
804	>	the potential barriers between the equilibrium directions of the
805	>	nanoparticle magnetic moments are much larger than the thermal energy.
806	>	Within this framework, we analyze in detail the role that the correlations
807	>	of the nanoparticle magnetic moments and the finite size of the
808	>	nanoparticle ensemble play in magnetic relaxation.},
809	>	annote = {642XH Times Cited:11 Cited References Count:31},
810	>	issn = {1098-0121},
811	>	uri = {<Go to ISI>://000180830400056},
812		}
813
814	<
815	<	@Article{saiz02,
816	<	author =   {L. Saiz and M. Klein},
817	<	title =    {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
818	<	journal =      jcp,
819	<	year =     2002,
820	<	volume =   116,
821	<	number =   7,
822	<	pages =    {3052-3057}
814	>	@ARTICLE{Derreumaux1998,
815	>	author = {P. Derreumaux and T. Schlick},
816	>	title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
817	>	journal = {Biophysical Journal},
818	>	year = {1998},
819	>	volume = {74},
820	>	pages = {72-81},
821	>	number = {1},
822	>	month = {Jan},
823	>	abstract = {To explore the origin of the large-scale motion of triosephosphate
824	>	isomerase's flexible loop (residues 166 to 176) at the active site,
825	>	several simulation protocols are employed both for the free enzyme
826	>	in vacuo and for the free enzyme with some solvent modeling: high-temperature
827	>	Langevin dynamics simulations, sampling by a #dynamics##driver#
828	>	approach, and potential-energy surface calculations. Our focus is
829	>	on obtaining the energy barrier to the enzyme's motion and establishing
830	>	the nature of the loop movement. Previous calculations did not determine
831	>	this energy barrier and the effect of solvent on the barrier. High-temperature
832	>	molecular dynamics simulations and crystallographic studies have
833	>	suggested a rigid-body motion with two hinges located at both ends
834	>	of the loop; Brownian dynamics simulations at room temperature pointed
835	>	to a very flexible behavior. The present simulations and analyses
836	>	reveal that although solute/solvent hydrogen bonds play a crucial
837	>	role in lowering the energy along the pathway, there still remains
838	>	a high activation barrier, This finding clearly indicates that,
839	>	if the loop opens and closes in the absence of a substrate at standard
840	>	conditions (e.g., room temperature, appropriate concentration of
841	>	isomerase), the time scale for transition is not in the nanosecond
842	>	but rather the microsecond range. Our results also indicate that
843	>	in the context of spontaneous opening in the free enzyme, the motion
844	>	is of rigid-body type and that the specific interaction between
845	>	residues Ala(176) and Tyr(208) plays a crucial role in the loop
846	>	opening/closing mechanism.},
847	>	annote = {Zl046 Times Cited:30 Cited References Count:29},
848	>	issn = {0006-3495},
849	>	uri = {<Go to ISI>://000073393400009},
850		}
851
852	<	@Article{stevens95,
853	<	author =   {M.~J. Stevens and G.~S. Grest},
854	<	title =    {Phase coexistence of a Stockmayer fluid in an aplied field},
855	<	journal =      {Physical Review E},
856	<	year =     1995,
857	<	volume =   51,
858	<	number =   6,
859	<	pages =    {5976-5983}
852	>	@ARTICLE{Dullweber1997,
853	>	author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
854	>	title = {Symplectic splitting methods for rigid body molecular dynamics},
855	>	journal = {Journal of Chemical Physics},
856	>	year = {1997},
857	>	volume = {107},
858	>	pages = {5840-5851},
859	>	number = {15},
860	>	month = {Oct 15},
861	>	abstract = {Rigid body molecular models possess symplectic structure and time-reversal
862	>	symmetry. Standard numerical integration methods destroy both properties,
863	>	introducing nonphysical dynamical behavior such as numerically induced
864	>	dissipative states and drift in the energy during long term simulations.
865	>	This article describes the construction, implementation, and practical
866	>	application of fast explicit symplectic-reversible integrators for
867	>	multiple rigid body molecular simulations, These methods use a reduction
868	>	to Euler equations for the free rigid body, together with a symplectic
869	>	splitting technique. In every time step, the orientational dynamics
870	>	of each rigid body is integrated by a sequence of planar rotations.
871	>	Besides preserving the symplectic and reversible structures of the
872	>	flow, this scheme accurately conserves the total angular momentum
873	>	of a system of interacting rigid bodies. Excellent energy conservation
874	>	fan be obtained relative to traditional methods, especially in long-time
875	>	simulations. The method is implemented in a research code, ORIENT
876	>	and compared with a quaternion/extrapolation scheme for the TIP4P
877	>	model of water. Our experiments show that the symplectic-reversible
878	>	scheme is far superior to the more traditional quaternion method.
879	>	(C) 1997 American Institute of Physics.},
880	>	annote = {Ya587 Times Cited:35 Cited References Count:32},
881	>	issn = {0021-9606},
882	>	uri = {<Go to ISI>://A1997YA58700024},
883		}
884
885	<	@Article{darden93:pme,
886	<	author =   {T. Darden and D. York and L. Pedersen},
887	<	title =    {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
888	<	journal =      {Journal of Chemical Physics},
889	<	year =     1993,
890	<	volume =   98,
891	<	number =   12,
892	<	pages =    {10089-10092}
885	>	@ARTICLE{Edwards2005,
886	>	author = {S. A. Edwards and D. R. M. Williams},
887	>	title = {Stretching a single diblock copolymer in a selective solvent: Langevin
888	>	dynamics simulations},
889	>	journal = {Macromolecules},
890	>	year = {2005},
891	>	volume = {38},
892	>	pages = {10590-10595},
893	>	number = {25},
894	>	month = {Dec 13},
895	>	abstract = {Using the Langevin dynamics technique, we have carried out simulations
896	>	of a single-chain flexible diblock copolymer. The polymer consists
897	>	of two blocks of equal length, one very poorly solvated and the
898	>	other close to theta-conditions. We study what happens when such
899	>	a polymer is stretched, for a range of different stretching speeds,
900	>	and correlate our observations with features in the plot of force
901	>	vs extension. We find that at slow speeds this force profile does
902	>	not increase monotonically, in disagreement with earlier predictions,
903	>	and that at high speeds there is a strong dependence on which end
904	>	of the polymer is pulled, as well as a high level of hysteresis.},
905	>	annote = {992EC Times Cited:0 Cited References Count:13},
906	>	issn = {0024-9297},
907	>	uri = {<Go to ISI>://000233866200035},
908		}
909
910	<
911	<
912	<	@Article{goetz98,
913	<	author =   {R. Goetz and R. Lipowsky},
914	<	title =    {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
915	<	journal =      {Journal of Chemical Physics},
916	<	year =     1998,
917	<	volume =   108,
918	<	number =   17,
919	<	pages =    7397
910	>	@ARTICLE{Egberts1988,
911	>	author = {E. Egberts and H. J. C. Berendsen},
912	>	title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic
913	>	Detail},
914	>	journal = {Journal of Chemical Physics},
915	>	year = {1988},
916	>	volume = {89},
917	>	pages = {3718-3732},
918	>	number = {6},
919	>	month = {Sep 15},
920	>	annote = {Q0188 Times Cited:219 Cited References Count:43},
921	>	issn = {0021-9606},
922	>	uri = {<Go to ISI>://A1988Q018800036},
923		}
924
925	<	@Article{marrink01:undulation,
926	<	author =   {S.~J. Marrink and A.~E. Mark},
927	<	title =    {Effect of undulations on surface tension in simulated bilayers},
928	<	journal =      {Journal of Physical Chemistry B},
929	<	year =     2001,
930	<	volume =   105,
931	<	pages =    {6122-6127}
925	>	@ARTICLE{Ermak1978,
926	>	author = {D. L. Ermak and J. A. Mccammon},
927	>	title = {Brownian Dynamics with Hydrodynamic Interactions},
928	>	journal = {Journal of Chemical Physics},
929	>	year = {1978},
930	>	volume = {69},
931	>	pages = {1352-1360},
932	>	number = {4},
933	>	annote = {Fp216 Times Cited:785 Cited References Count:42},
934	>	issn = {0021-9606},
935	>	uri = {<Go to ISI>://A1978FP21600004},
936		}
937
938	<	@Article{lindahl00:undulation,
939	<	author =   {E. Lindahl and O. Edholm},
940	<	title =    {Mesoscopic undulation and thickness fluctuations in lipid bilayers from molecular dynamics simulation},
941	<	journal =      {Biophysical Journal},
942	<	year =     2000,
943	<	volume =   79,
944	<	pages =    {426-433}
938	>	@ARTICLE{Fennell2004,
939	>	author = {C. J. Fennell and J. D. Gezelter},
940	>	title = {On the structural and transport properties of the soft sticky dipole
941	>	and related single-point water models},
942	>	journal = {Journal of Chemical Physics},
943	>	year = {2004},
944	>	volume = {120},
945	>	pages = {9175-9184},
946	>	number = {19},
947	>	month = {May 15},
948	>	abstract = {The density maximum and temperature dependence of the self-diffusion
949	>	constant were investigated for the soft sticky dipole (SSD) water
950	>	model and two related reparametrizations of this single-point model.
951	>	A combination of microcanonical and isobaric-isothermal molecular
952	>	dynamics simulations was used to calculate these properties, both
953	>	with and without the use of reaction field to handle long-range
954	>	electrostatics. The isobaric-isothermal simulations of the melting
955	>	of both ice-I-h and ice-I-c showed a density maximum near 260 K.
956	>	In most cases, the use of the reaction field resulted in calculated
957	>	densities which were significantly lower than experimental densities.
958	>	Analysis of self-diffusion constants shows that the original SSD
959	>	model captures the transport properties of experimental water very
960	>	well in both the normal and supercooled liquid regimes. We also
961	>	present our reparametrized versions of SSD for use both with the
962	>	reaction field or without any long-range electrostatic corrections.
963	>	These are called the SSD/RF and SSD/E models, respectively. These
964	>	modified models were shown to maintain or improve upon the experimental
965	>	agreement with the structural and transport properties that can
966	>	be obtained with either the original SSD or the density-corrected
967	>	version of the original model (SSD1). Additionally, a novel low-density
968	>	ice structure is presented which appears to be the most stable ice
969	>	structure for the entire SSD family. (C) 2004 American Institute
970	>	of Physics.},
971	>	annote = {816YY Times Cited:5 Cited References Count:39},
972	>	issn = {0021-9606},
973	>	uri = {<Go to ISI>://000221146400032},
974		}
975
976	<	@Article{metropolis:1949,
977	<	author =   {N. Metropolis and S. Ulam},
978	<	title =    {The $\mbox{Monte Carlo}$ Method},
979	<	journal =      {J. Am. Stat. Ass.},
980	<	year =     1949,
981	<	volume =   44,
982	<	pages =    {335-341}
976	>	@ARTICLE{Fernandes2002,
977	>	author = {M. X. Fernandes and J. G. {de la Torre}},
978	>	title = {Brownian dynamics simulation of rigid particles of arbitrary shape
979	>	in external fields},
980	>	journal = {Biophysical Journal},
981	>	year = {2002},
982	>	volume = {83},
983	>	pages = {3039-3048},
984	>	number = {6},
985	>	month = {Dec},
986	>	abstract = {We have developed a Brownian dynamics simulation algorithm to generate
987	>	Brownian trajectories of an isolated, rigid particle of arbitrary
988	>	shape in the presence of electric fields or any other external agents.
989	>	Starting from the generalized diffusion tensor, which can be calculated
990	>	with the existing HYDRO software, the new program BROWNRIG (including
991	>	a case-specific subprogram for the external agent) carries out a
992	>	simulation that is analyzed later to extract the observable dynamic
993	>	properties. We provide a variety of examples of utilization of this
994	>	method, which serve as tests of its performance, and also illustrate
995	>	its applicability. Examples include free diffusion, transport in
996	>	an electric field, and diffusion in a restricting environment.},
997	>	annote = {633AD Times Cited:2 Cited References Count:43},
998	>	issn = {0006-3495},
999	>	uri = {<Go to ISI>://000180256300012},
1000		}
1001
1002	<	@Article{metropolis:1953,
1003	<	author =   {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
1004	<	title =    {Equation of State Calculations by Fast Computing Machines},
1005	<	journal =      {J. Chem. Phys.},
1006	<	year =     1953,
1007	<	volume =   21,
1008	<	pages =    {1087-1092}
1002	>	@ARTICLE{Gay1981,
1003	>	author = {J. G. Gay and B. J. Berne},
1004	>	title = {Modification of the Overlap Potential to Mimic a Linear Site-Site
1005	>	Potential},
1006	>	journal = {Journal of Chemical Physics},
1007	>	year = {1981},
1008	>	volume = {74},
1009	>	pages = {3316-3319},
1010	>	number = {6},
1011	>	annote = {Lj347 Times Cited:482 Cited References Count:13},
1012	>	issn = {0021-9606},
1013	>	uri = {<Go to ISI>://A1981LJ34700029},
1014		}
1015
1016	<	@Article{born:1912,
1017	<	author =   {M. Born and Th. Von~Karman},
1018	<	title =    {Uber Schwingungen in Raumgittern},
1019	<	journal =      {Physik Z.},
1020	<	year =     1912,
1021	<	volume =   13,
1022	<	number =   {297-309}
1016	>	@ARTICLE{Gelin1999,
1017	>	author = {M. F. Gelin},
1018	>	title = {Inertial effects in the Brownian dynamics with rigid constraints},
1019	>	journal = {Macromolecular Theory and Simulations},
1020	>	year = {1999},
1021	>	volume = {8},
1022	>	pages = {529-543},
1023	>	number = {6},
1024	>	month = {Nov},
1025	>	abstract = {To investigate the influence of inertial effects on the dynamics of
1026	>	an assembly of beads subjected to rigid constraints and placed in
1027	>	a buffer medium, a convenient method to introduce suitable generalized
1028	>	coordinates is presented. Without any restriction on the nature
1029	>	of the soft forces involved (both stochastic and deterministic),
1030	>	pertinent Langevin equations are derived. Provided that the Brownian
1031	>	forces are Gaussian and Markovian, the corresponding Fokker-Planck
1032	>	equation (FPE) is obtained in the complete phase space of generalized
1033	>	coordinates and momenta. The correct short time behavior for correlation
1034	>	functions (CFs) of generalized coordinates is established, and the
1035	>	diffusion equation with memory (DEM) is deduced from the FPE in
1036	>	the high friction Limit. The DEM is invoked to perform illustrative
1037	>	calculations in two dimensions of the orientational CFs for once
1038	>	broken nonrigid rods immobilized on a surface. These calculations
1039	>	reveal that the CFs under certain conditions exhibit an oscillatory
1040	>	behavior, which is irreproducible within the standard diffusion
1041	>	equation. Several methods are considered for the approximate solution
1042	>	of the DEM, and their application to three dimensional DEMs is discussed.},
1043	>	annote = {257MM Times Cited:2 Cited References Count:82},
1044	>	issn = {1022-1344},
1045	>	uri = {<Go to ISI>://000083785700002},
1046		}
1047
1048	<	@Book{chandler:1987,
1049	<	author =   {David Chandler},
1050	<	title =    {Introduction to Modern Statistical Mechanics},
1051	<	publisher =    {Oxford University Press},
1052	<	year =     1987
1048	>	@BOOK{Goldstein2001,
1049	>	title = {Classical Mechanics},
1050	>	publisher = {Addison Wesley},
1051	>	year = {2001},
1052	>	author = {H. Goldstein and C. Poole and J. Safko},
1053	>	address = {San Francisco},
1054	>	edition = {3rd},
1055		}
1056
1057	<
1058	<	@Article{pearlman:1995,
1059	<	author =   {David~A. Pearlman and David~A. Case and James~W. Caldwell and Wilson~S. Ross and Thomas~E. Cheatham~III and Steve DeBolt and David Ferguson and George Seibel and Peter Kollman},
1060	<	title =    {{\sc amber}, a package of computer programs for applying molecular mechanics. normal mode analysis, molecular dynamics, and free energy calculations to simulate the structural and energetic properties of molecules},
1061	<	journal =      {Computer Physics Communications},
1062	<	year =     1995,
1063	<	volume =   91,
1064	<	pages =    {1-41}
1065	<	}
1066	<
1067	<	@Book{Goldstein01,
1068	<	author =   {H. Goldstein and C. Poole and J. Safko},
1069	<	title =    {Classical Mechanics},
1070	<	publisher =    {Addison Wesley},
1071	<	year =     2001,
1072	<	address =  {San Francisco},
1073	<	edition =  {3rd}
1057	>	@ARTICLE{Gray2003,
1058	>	author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and
1059	>	B. Kuhlman and C. A. Rohl and D. Baker},
1060	>	title = {Protein-protein docking with simultaneous optimization of rigid-body
1061	>	displacement and side-chain conformations},
1062	>	journal = {Journal of Molecular Biology},
1063	>	year = {2003},
1064	>	volume = {331},
1065	>	pages = {281-299},
1066	>	number = {1},
1067	>	month = {Aug 1},
1068	>	abstract = {Protein-protein docking algorithms provide a means to elucidate structural
1069	>	details for presently unknown complexes. Here, we present and evaluate
1070	>	a new method to predict protein-protein complexes from the coordinates
1071	>	of the unbound monomer components. The method employs a low-resolution,
1072	>	rigid-body, Monte Carlo search followed by simultaneous optimization
1073	>	of backbone displacement and side-chain conformations using Monte
1074	>	Carlo minimization. Up to 10(5) independent simulations are carried
1075	>	out, and the resulting #decoys# are ranked using an energy function
1076	>	dominated by van der Waals interactions, an implicit solvation model,
1077	>	and an orientation-dependent hydrogen bonding potential. Top-ranking
1078	>	decoys are clustered to select the final predictions. Small-perturbation
1079	>	studies reveal the formation of binding funnels in 42 of 54 cases
1080	>	using coordinates derived from the bound complexes and in 32 of
1081	>	54 cases using independently determined coordinates of one or both
1082	>	monomers. Experimental binding affinities correlate with the calculated
1083	>	score function and explain the predictive success or failure of
1084	>	many targets. Global searches using one or both unbound components
1085	>	predict at least 25% of the native residue-residue contacts in 28
1086	>	of the 32 cases where binding funnels exist. The results suggest
1087	>	that the method may soon be useful for generating models of biologically
1088	>	important complexes from the structures of the isolated components,
1089	>	but they also highlight the challenges that must be met to achieve
1090	>	consistent and accurate prediction of protein-protein interactions.
1091	>	(C) 2003 Elsevier Ltd. All rights reserved.},
1092	>	annote = {704QL Times Cited:48 Cited References Count:60},
1093	>	issn = {0022-2836},
1094	>	uri = {<Go to ISI>://000184351300022},
1095		}
1096
1097	<	@Article{Bratko85,
1098	<	author =   {D. Bratko and L. Blum and A. Luzar},
1099	<	title =    {A simple model for the intermolecular potential of water},
1100	<	journal =      jcp,
1101	<	year =     1985,
1102	<	volume =   83,
1103	<	number =   12,
1104	<	pages =    {6367-6370}
1097	>	@ARTICLE{Hao1993,
1098	>	author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga},
1099	>	title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic
1100	>	Trypsin-Inhibitor Studied by Computer-Simulations},
1101	>	journal = {Biochemistry},
1102	>	year = {1993},
1103	>	volume = {32},
1104	>	pages = {9614-9631},
1105	>	number = {37},
1106	>	month = {Sep 21},
1107	>	abstract = {A new procedure for studying the folding and unfolding of proteins,
1108	>	with an application to bovine pancreatic trypsin inhibitor (BPTI),
1109	>	is reported. The unfolding and refolding of the native structure
1110	>	of the protein are characterized by the dimensions of the protein,
1111	>	expressed in terms of the three principal radii of the structure
1112	>	considered as an ellipsoid. A dynamic equation, describing the variations
1113	>	of the principal radii on the unfolding path, and a numerical procedure
1114	>	to solve this equation are proposed. Expanded and distorted conformations
1115	>	are refolded to the native structure by a dimensional-constraint
1116	>	energy minimization procedure. A unique and reproducible unfolding
1117	>	pathway for an intermediate of BPTI lacking the [30,51] disulfide
1118	>	bond is obtained. The resulting unfolded conformations are extended;
1119	>	they contain near-native local structure, but their longest principal
1120	>	radii are more than 2.5 times greater than that of the native structure.
1121	>	The most interesting finding is that the majority of expanded conformations,
1122	>	generated under various conditions, can be refolded closely to the
1123	>	native structure, as measured by the correct overall chain fold,
1124	>	by the rms deviations from the native structure of only 1.9-3.1
1125	>	angstrom, and by the energy differences of about 10 kcal/mol from
1126	>	the native structure. Introduction of the [30,51] disulfide bond
1127	>	at this stage, followed by minimization, improves the closeness
1128	>	of the refolded structures to the native structure, reducing the
1129	>	rms deviations to 0.9-2.0 angstrom. The unique refolding of these
1130	>	expanded structures over such a large conformational space implies
1131	>	that the folding is strongly dictated by the interactions in the
1132	>	amino acid sequence of BPTI. The simulations indicate that, under
1133	>	conditions that favor a compact structure as mimicked by the volume
1134	>	constraints in our algorithm; the expanded conformations have a
1135	>	strong tendency to move toward the native structure; therefore,
1136	>	they probably would be favorable folding intermediates. The results
1137	>	presented here support a general model for protein folding, i.e.,
1138	>	progressive formation of partially folded structural units, followed
1139	>	by collapse to the compact native structure. The general applicability
1140	>	of the procedure is also discussed.},
1141	>	annote = {Ly294 Times Cited:27 Cited References Count:57},
1142	>	issn = {0006-2960},
1143	>	uri = {<Go to ISI>://A1993LY29400014},
1144		}
1145
1146	<	@Article{Bratko95,
1147	<	author =   {L. Blum and F. Vericat and D. Bratko},
1148	<	title =    {Towards an analytical model of water: The octupolar model},
1149	<	journal =      jcp,
1150	<	year =     1995,
1151	<	volume =   102,
1152	<	number =   3,
1153	<	pages =    {1461-1462}
1146	>	@ARTICLE{Hinsen2000,
1147	>	author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel
1148	>	and G. R. Kneller},
1149	>	title = {Harmonicity in slow protein dynamics},
1150	>	journal = {Chemical Physics},
1151	>	year = {2000},
1152	>	volume = {261},
1153	>	pages = {25-37},
1154	>	number = {1-2},
1155	>	month = {Nov 1},
1156	>	abstract = {The slow dynamics of proteins around its native folded state is usually
1157	>	described by diffusion in a strongly anharmonic potential. In this
1158	>	paper, we try to understand the form and origin of the anharmonicities,
1159	>	with the principal aim of gaining a better understanding of the
1160	>	principal motion types, but also in order to develop more efficient
1161	>	numerical methods for simulating neutron scattering spectra of large
1162	>	proteins. First, we decompose a molecular dynamics (MD) trajectory
1163	>	of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water
1164	>	into three contributions that we expect to be independent: the global
1165	>	motion of the residues, the rigid-body motion of the sidechains
1166	>	relative to the backbone, and the internal deformations of the sidechains.
1167	>	We show that they are indeed almost independent by verifying the
1168	>	factorization of the incoherent intermediate scattering function.
1169	>	Then, we show that the global residue motions, which include all
1170	>	large-scale backbone motions, can be reproduced by a simple harmonic
1171	>	model which contains two contributions: a short-time vibrational
1172	>	term, described by a standard normal mode calculation in a local
1173	>	minimum, and a long-time diffusive term, described by Brownian motion
1174	>	in an effective harmonic potential. The potential and the friction
1175	>	constants were fitted to the MD data. The major anharmonic contribution
1176	>	to the incoherent intermediate scattering function comes from the
1177	>	rigid-body diffusion of the sidechains. This model can be used to
1178	>	calculate scattering functions for large proteins and for long-time
1179	>	scales very efficiently, and thus provides a useful complement to
1180	>	MD simulations, which are best suited for detailed studies on smaller
1181	>	systems or for shorter time scales. (C) 2000 Elsevier Science B.V.
1182	>	All rights reserved.},
1183	>	annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31},
1184	>	issn = {0301-0104},
1185	>	uri = {<Go to ISI>://000090121700003},
1186		}
1187
1188	<	@Article{Ichiye03,
1189	<	author =   {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks
1190	<	and T. Ichiye},
1191	<	title =    {A temperature of maximum density in soft sticky dipole
1192	<	water},
1193	<	journal =      cpl,
1194	<	year =     2003,
1195	<	volume =   376,
1196	<	pages =    {646-652},
1188	>	@ARTICLE{Ho1992,
1189	>	author = {C. Ho and C. D. Stubbs},
1190	>	title = {Hydration at the Membrane Protein-Lipid Interface},
1191	>	journal = {Biophysical Journal},
1192	>	year = {1992},
1193	>	volume = {63},
1194	>	pages = {897-902},
1195	>	number = {4},
1196	>	month = {Oct},
1197	>	abstract = {Evidence has been found for the existence water at the protein-lipid
1198	>	hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome
1199	>	C, using two related fluorescence spectroscopic approaches. The
1200	>	first approach exploited the fact that the presence of water in
1201	>	the excited state solvent cage of a fluorophore increases the rate
1202	>	of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl)
1203	>	phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores
1204	>	are located in the hydrophobic core of the lipid bilayer, the introduction
1205	>	of gramicidin reduced the fluorescence lifetime, indicative of an
1206	>	increased presence of water in the bilayer. Since a high protein:lipid
1207	>	ratio was used, the fluorophores were forced to be adjacent to the
1208	>	protein hydrophobic surface, hence the presence of water in this
1209	>	region could be inferred. Cholesterol is known to reduce the water
1210	>	content of lipid bilayers and this effect was maintained at the
1211	>	protein-lipid interface with both gramicidin and apocytochrome C,
1212	>	again suggesting hydration in this region. The second approach was
1213	>	to use the fluorescence enhancement induced by exchanging deuterium
1214	>	oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH,
1215	>	located in the lipid head group region, and of the gramicidin intrinsic
1216	>	tryptophans were greater in a D2O buffer compared with H2O, showing
1217	>	that the fluorophores were exposed to water in the bilayer at the
1218	>	protein-lipid interface. In the presence of cholesterol the fluorescence
1219	>	intensity ratio of D2O to H2O decreased, indicating a removal of
1220	>	water by the cholesterol, in keeping with the lifetime data. Altered
1221	>	hydration at the protein-lipid interface could affect conformation,
1222	>	thereby offering a new route by which membrane protein functioning
1223	>	may be modified.},
1224	>	annote = {Ju251 Times Cited:55 Cited References Count:44},
1225	>	issn = {0006-3495},
1226	>	uri = {<Go to ISI>://A1992JU25100002},
1227		}
1228
1229	<
1230	<	@Article{Soper86,
1231	<	author =   {A.~K. Soper and M.~G. Phillips},
1232	<	title =    {A new determination of the structure of water at 298K},
1233	<	journal =      cp,
1234	<	year =     1986,
1235	<	volume =   107,
1236	<	number =   1,
1237	<	pages =    {47-60},
1229	>	@ARTICLE{Huh2004,
1230	>	author = {Y. Huh and N. M. Cann},
1231	>	title = {Discrimination in isotropic, nematic, and smectic phases of chiral
1232	>	calamitic molecules: A computer simulation study},
1233	>	journal = {Journal of Chemical Physics},
1234	>	year = {2004},
1235	>	volume = {121},
1236	>	pages = {10299-10308},
1237	>	number = {20},
1238	>	month = {Nov 22},
1239	>	abstract = {Racemic fluids of chiral calamitic molecules are investigated with
1240	>	molecular dynamics simulations. In particular, the phase behavior
1241	>	as a function of density is examined for eight racemates. The relationship
1242	>	between chiral discrimination and orientational order in the phase
1243	>	is explored. We find that the transition from the isotropic phase
1244	>	to a liquid crystal phase is accompanied by an increase in chiral
1245	>	discrimination, as measured by differences in radial distributions.
1246	>	Among ordered phases, discrimination is largest for smectic phases
1247	>	with a significant preference for heterochiral contact within the
1248	>	layers. (C) 2004 American Institute of Physics.},
1249	>	annote = {870FJ Times Cited:0 Cited References Count:63},
1250	>	issn = {0021-9606},
1251	>	uri = {<Go to ISI>://000225042700059},
1252		}
1253
1254	<	@Article{plimpton95,
1255	<	author =   {S. Plimpton},
1256	<	title =    {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
1257	<	journal =      {J. Comp. Phys.},
1258	<	year =     1995,
1259	<	volume =   117,
1260	<	pages =    {1-19},
1254	>	@ARTICLE{Izaguirre2001,
1255	>	author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
1256	>	title = {Langevin stabilization of molecular dynamics},
1257	>	journal = {Journal of Chemical Physics},
1258	>	year = {2001},
1259	>	volume = {114},
1260	>	pages = {2090-2098},
1261	>	number = {5},
1262	>	month = {Feb 1},
1263	>	abstract = {In this paper we show the possibility of using very mild stochastic
1264	>	damping to stabilize long time step integrators for Newtonian molecular
1265	>	dynamics. More specifically, stable and accurate integrations are
1266	>	obtained for damping coefficients that are only a few percent of
1267	>	the natural decay rate of processes of interest, such as the velocity
1268	>	autocorrelation function. Two new multiple time stepping integrators,
1269	>	Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are
1270	>	introduced in this paper. Both use the mollified impulse method
1271	>	for the Newtonian term. LM uses a discretization of the Langevin
1272	>	equation that is exact for the constant force, and BBK-M uses the
1273	>	popular Brunger-Brooks-Karplus integrator (BBK). These integrators,
1274	>	along with an extrapolative method called LN, are evaluated across
1275	>	a wide range of damping coefficient values. When large damping coefficients
1276	>	are used, as one would for the implicit modeling of solvent molecules,
1277	>	the method LN is superior, with LM closely following. However, with
1278	>	mild damping of 0.2 ps(-1), LM produces the best results, allowing
1279	>	long time steps of 14 fs in simulations containing explicitly modeled
1280	>	flexible water. With BBK-M and the same damping coefficient, time
1281	>	steps of 12 fs are possible for the same system. Similar results
1282	>	are obtained for a solvated protein-DNA simulation of estrogen receptor
1283	>	ER with estrogen response element ERE. A parallel version of BBK-M
1284	>	runs nearly three times faster than the Verlet-I/r-RESPA (reversible
1285	>	reference system propagator algorithm) when using the largest stable
1286	>	time step on each one, and it also parallelizes well. The computation
1287	>	of diffusion coefficients for flexible water and ER/ERE shows that
1288	>	when mild damping of up to 0.2 ps-1 is used the dynamics are not
1289	>	significantly distorted. (C) 2001 American Institute of Physics.},
1290	>	annote = {397CQ Times Cited:14 Cited References Count:36},
1291	>	issn = {0021-9606},
1292	>	uri = {<Go to ISI>://000166676100020},
1293		}
1294
1295	<	@Article{plimpton93,
1296	<	author =   {S.~J. Plimpton and B.~A. Hendrickson},
1297	<	title =    {Parallel Molecular Dynamics with the Embedded Atom Method},
1298	<	journal =      {MRS Proceedings},
1299	<	year =     1993,
1300	<	volume =   291,
1301	<	pages =    37
1295	>	@ARTICLE{Gray2003,
1296	>	author = {J.~J Gray,S. Moughon, C. Wang },
1297	>	title = {Protein-protein docking with simultaneous optimization of rigid-body
1298	>	displacement and side-chain conformations},
1299	>	journal = {jmb},
1300	>	year = {2003},
1301	>	volume = {331},
1302	>	pages = {281-299},
1303		}
1304
1305	<
1306	<	@Article{Ercolessi02,
1307	<	author =   {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
1308	<	title =    {Bending strain-driven modification of surface resconstructions: Au(111)},
1309	<	journal =      prb,
1310	<	year =     2002,
1311	<	volume =   65,
1312	<	pages =    241406
1305	>	@ARTICLE{Klimov1997,
1306	>	author = {D. K. Klimov and D. Thirumalai},
1307	>	title = {Viscosity dependence of the folding rates of proteins},
1308	>	journal = {Physical Review Letters},
1309	>	year = {1997},
1310	>	volume = {79},
1311	>	pages = {317-320},
1312	>	number = {2},
1313	>	month = {Jul 14},
1314	>	abstract = {The viscosity (eta) dependence of the folding rates for four sequences
1315	>	(the native state of three sequences is a beta sheet, while the
1316	>	fourth forms an alpha helix) is calculated for off-lattice models
1317	>	of proteins. Assuming that the dynamics is given by the Langevin
1318	>	equation, we show that the folding rates increase linearly at low
1319	>	viscosities eta, decrease as 1/eta at large eta, and have a maximum
1320	>	at intermediate values. The Kramers' theory of barrier crossing
1321	>	provides a quantitative fit of the numerical results. By mapping
1322	>	the simulation results to real proteins we estimate that for optimized
1323	>	sequences the time scale for forming a four turn alpha-helix topology
1324	>	is about 500 ns, whereas for beta sheet it is about 10 mu s.},
1325	>	annote = {Xk293 Times Cited:77 Cited References Count:17},
1326	>	issn = {0031-9007},
1327	>	uri = {<Go to ISI>://A1997XK29300035},
1328		}
1329
1330	<	@Article{Ercolessi88,
1331	<	author =   {F. Ercolessi  and M. Parrinello  and E. Tosatti},
1332	<	title =    {Simulation of Gold in the Glue Model.},
1333	<	journal =      {Philosophical Magazine A},
1334	<	year =     1988,
1335	<	volume =   58,
1336	<	pages =    {213-226}
1330	>	@ARTICLE{Lansac2001,
1331	>	author = {Y. Lansac and M. A. Glaser and N. A. Clark},
1332	>	title = {Microscopic structure and dynamics of a partial bilayer smectic liquid
1333	>	crystal},
1334	>	journal = {Physical Review E},
1335	>	year = {2001},
1336	>	volume = {6405},
1337	>	pages = {-},
1338	>	number = {5},
1339	>	month = {Nov},
1340	>	abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
1341	>	class of mesogens. Many of the peculiar properties of nCB's (e.g.,
1342	>	the occurence of the partial bilayer smectic-A(d) phase) are thought
1343	>	to be a manifestation of short-range antiparallel association of
1344	>	neighboring molecules, resulting from strong dipole-dipole interactions
1345	>	between cyano groups. To test and extend existing models of microscopic
1346	>	ordering in nCB's, we carry out large-scale atomistic simulation
1347	>	studies of the microscopic structure and dynamics of the Sm-A(d)
1348	>	phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of
1349	>	thermodynamic, structural, and dynamical properties for this material,
1350	>	and make a detailed comparison of our results with experimental
1351	>	measurements in order to validate our molecular model. Semiquantitative
1352	>	agreement with experiment is found: the smectic layer spacing and
1353	>	mass density are well reproduced, translational diffusion constants
1354	>	are similar to experiment, but the orientational ordering of alkyl
1355	>	chains is overestimated. This simulation provides a detailed picture
1356	>	of molecular conformation, smectic layer structure, and intermolecular
1357	>	correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range
1358	>	antiparallel association of molecules arising from dipole-dipole
1359	>	interactions plays a dominant role in determining the molecular-scale
1360	>	structure of 8CB.},
1361	>	annote = {Part 1 496QF Times Cited:10 Cited References Count:60},
1362	>	issn = {1063-651X},
1363	>	uri = {<Go to ISI>://000172406900063},
1364		}
1365
1366	<	@Article{Finnis84,
1367	<	author =   {M.~W Finnis and J.~E. Sinclair },
1368	<	title =    {A Simple Empirical N-Body Potential for Transition-Metals},
1369	<	journal =      {Phil. Mag. A},
1370	<	year =     1984,
1371	<	volume =   50,
1372	<	pages =    {45-55}
1366	>	@ARTICLE{Lansac2003,
1367	>	author = {Y. Lansac and P. K. Maiti and N. A. Clark and M. A. Glaser},
1368	>	title = {Phase behavior of bent-core molecules},
1369	>	journal = {Physical Review E},
1370	>	year = {2003},
1371	>	volume = {67},
1372	>	pages = {-},
1373	>	number = {1},
1374	>	month = {Jan},
1375	>	abstract = {Recently, a new class of smectic liquid crystal phases characterized
1376	>	by the spontaneous formation of macroscopic chiral domains from
1377	>	achiral bent-core molecules has been discovered. We have carried
1378	>	out Monte Carlo simulations of a minimal hard spherocylinder dimer
1379	>	model to investigate the role of excluded volume interactions in
1380	>	determining the phase behavior of bent-core materials and to probe
1381	>	the molecular origins of polar and chiral symmetry breaking. We
1382	>	present the phase diagram of hard spherocylinder dimers of length-diameter
1383	>	ratio of 5 as a function of pressure or density and dimer opening
1384	>	angle psi. With decreasing psi, a transition from a nonpolar to
1385	>	a polar smectic A phase is observed near psi=167degrees, and the
1386	>	nematic phase becomes thermodynamically unstable for psi<135degrees.
1387	>	Free energy calculations indicate that the antipolar smectic A (SmAP(A))
1388	>	phase is more stable than the polar smectic A phase (SmAP(F)). No
1389	>	chiral smectic or biaxial nematic phases were found.},
1390	>	annote = {Part 1 646CM Times Cited:15 Cited References Count:38},
1391	>	issn = {1063-651X},
1392	>	uri = {<Go to ISI>://000181017300042},
1393		}
1394
1395	<	@Article{FBD86,
1396	<	author =       {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
1397	<	title =        {Embedded-atom-method functions for the fcc metals
1398	<	$\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1399	<	journal =      prb,
1400	<	year =         1986,
1401	<	volume =       33,
1815	<	number =       12,
1816	<	pages =        7983
1395	>	@BOOK{Leach2001,
1396	>	title = {Molecular Modeling: Principles and Applications},
1397	>	publisher = {Pearson Educated Limited},
1398	>	year = {2001},
1399	>	author = {A. Leach},
1400	>	address = {Harlow, England},
1401	>	edition = {2nd},
1402		}
1403
1404	<	@Article{johnson89,
1405	<	author =   {R.~A. Johnson},
1406	<	title =    {Alloy models with the embedded-atom method},
1407	<	journal =      prb,
1408	<	year =     1989,
1409	<	volume =   39,
1825	<	number =   17,
1826	<	pages =    12554
1404	>	@BOOK{Leimkuhler2004,
1405	>	title = {Simulating Hamiltonian Dynamics},
1406	>	publisher = {Cambridge University Press},
1407	>	year = {2004},
1408	>	author = {B. Leimkuhler and S. Reich},
1409	>	address = {Cambridge},
1410		}
1411
1412	<	@Article{Laird97,
1413	<	author =   {A. Kol and B.~B. Laird and B.~J. Leimkuhler},
1414	<	title =    {A symplectic method for rigid-body molecular simulation},
1415	<	journal =      jcp,
1416	<	year =     1997,
1417	<	volume =   107,
1418	<	number =   7,
1419	<	pages =    {2580-2588}
1412	>	@ARTICLE{Levelut1981,
1413	>	author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard
1414	>	and G. Sigaud},
1415	>	title = {Number of Sa Phases},
1416	>	journal = {Physical Review A},
1417	>	year = {1981},
1418	>	volume = {24},
1419	>	pages = {2180-2186},
1420	>	number = {4},
1421	>	annote = {Ml751 Times Cited:96 Cited References Count:16},
1422	>	issn = {1050-2947},
1423	>	uri = {<Go to ISI>://A1981ML75100057},
1424		}
1425
1426	<
1427	<	@Article{hoover85,
1428	<	author =   {W.~G. Hoover},
1429	<	title =    {Canonical dynamics: Equilibrium phase-space distributions},
1430	<	journal =      pra,
1431	<	year =     1985,
1432	<	volume =   31,
1433	<	pages =    1695
1426	>	@ARTICLE{Lieb1982,
1427	>	author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
1428	>	title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers -
1429	>	Evidence from Raman-Scattering},
1430	>	journal = {Biochimica Et Biophysica Acta},
1431	>	year = {1982},
1432	>	volume = {688},
1433	>	pages = {388-398},
1434	>	number = {2},
1435	>	annote = {Nu461 Times Cited:40 Cited References Count:28},
1436	>	issn = {0006-3002},
1437	>	uri = {<Go to ISI>://A1982NU46100012},
1438		}
1439
1440	<	@Article{Roux91,
1441	<	author =   {B. Roux and M. Karplus},
1442	<	title =    {Ion transport in a Gramicidin-like channel: dynamics and mobility},
1443	<	journal =      jpc,
1444	<	year =     1991,
1445	<	volume =   95,
1446	<	number =   15,
1447	<	pages =    {4856-4868}
1440	>	@ARTICLE{Link1997,
1441	>	author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A.
1442	>	Clark and E. Korblova and D. M. Walba},
1443	>	title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic
1444	>	phase of achiral molecules},
1445	>	journal = {Science},
1446	>	year = {1997},
1447	>	volume = {278},
1448	>	pages = {1924-1927},
1449	>	number = {5345},
1450	>	month = {Dec 12},
1451	>	abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
1452	>	cores was found to have fluid layers that exhibit two spontaneous
1453	>	symmetry-breaking instabilities: polar molecular orientational ordering
1454	>	about the layer normal and molecular tilt. These instabilities combine
1455	>	to form a chiral layer structure with a handedness that depends
1456	>	on the sign of the tilt. The bulk states are either antiferroelectric-racemic,
1457	>	with the layer polar direction and handedness alternating in sign
1458	>	from layer to layer, or antiferroelectric-chiral, which is of uniform
1459	>	layer handedness. Both states exhibit an electric field-induced
1460	>	transition from antiferroelectric to ferroelectric.},
1461	>	annote = {Yl002 Times Cited:407 Cited References Count:25},
1462	>	issn = {0036-8075},
1463	>	uri = {<Go to ISI>://A1997YL00200028},
1464		}
1465
1466	<
1467	<	@Article{Marrink94,
1468	<	author =   {S.~J Marrink and H.~J.~C. Berendsen},
1469	<	title =    {Simulation of water transport through a lipid membrane},
1470	<	journal =      jpc,
1471	<	year =     1994,
1472	<	volume =   98,
1473	<	number =   15,
1474	<	pages =    {4155-4168}
1466	>	@ARTICLE{Liwo2005,
1467	>	author = {A. Liwo and M. Khalili and H. A. Scheraga},
1468	>	title = {Ab initio simulations of protein folding pathways by molecular dynamics
1469	>	with the united-residue (UNRES) model of polypeptide chains},
1470	>	journal = {Febs Journal},
1471	>	year = {2005},
1472	>	volume = {272},
1473	>	pages = {359-360},
1474	>	month = {Jul},
1475	>	annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
1476	>	issn = {1742-464X},
1477	>	uri = {<Go to ISI>://000234826102043},
1478		}
1479
1480	<
1481	<	@Article{Daw89,
1482	<	author =   {Murray~S. Daw},
1483	<	title =    {Model of metallic cohesion: The embedded-atom method},
1484	<	journal =      {Physical Review B},
1485	<	year =     1989,
1486	<	volume =   39,
1877	<	pages =    {7441-7452}
1480	>	@BOOK{Marion1990,
1481	>	title = {Classical Dynamics of Particles and Systems},
1482	>	publisher = {Academic Press},
1483	>	year = {1990},
1484	>	author = {J.~B. Marion},
1485	>	address = {New York},
1486	>	edition = {2rd},
1487		}
1488
1489	<	@InBook{voter,
1490	<	author =   {A.~F. Voter},
1491	<	editor =   {J.~H. Westbrook and R.~L. Fleischer},
1492	<	title =    {Intermetallic Compounds: Principles and Practice},
1493	<	chapter =      4,
1494	<	publisher =    {John Wiley and Sons Ltd},
1495	<	year =     1995,
1887	<	volume =   1,
1888	<	pages =    77
1489	>	@ARTICLE{McLachlan1993,
1490	>	author = {R.~I McLachlan},
1491	>	title = {Explicit Lie-Poisson integration and the Euler equations},
1492	>	journal = {prl},
1493	>	year = {1993},
1494	>	volume = {71},
1495	>	pages = {3043-3046},
1496		}
1497
1498	<	@Article{marrink:2002,
1499	<	author =   {S.~J. Marrink and D.~P. Teileman},
1500	<	title =    {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1501	<	journal =      {Biophysical Journal},
1502	<	year =     2002,
1503	<	volume =   83,
1504	<	pages =    {2386-2392}
1498	>	@ARTICLE{McLachlan2005,
1499	>	author = {R. I. McLachlan and A. Zanna},
1500	>	title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
1501	>	journal = {Foundations of Computational Mathematics},
1502	>	year = {2005},
1503	>	volume = {5},
1504	>	pages = {87-123},
1505	>	number = {1},
1506	>	month = {Feb},
1507	>	abstract = {In this paper we revisit the Moser-Veselov description of the free
1508	>	rigid body in body coordinates, which, in the 3 x 3 case, can be
1509	>	implemented as an explicit, second-order, integrable approximation
1510	>	of the continuous solution. By backward error analysis, we study
1511	>	the modified vector field which is integrated exactly by the discrete
1512	>	algorithm. We deduce that the discrete Moser-Veselov (DMV) is well
1513	>	approximated to higher order by time reparametrizations of the continuous
1514	>	equations (modified vector field). We use the modified vector field
1515	>	to scale the initial data of the DMV to improve the order of the
1516	>	approximation and show the equivalence of the DMV and the RATTLE
1517	>	algorithm. Numerical integration with these preprocessed initial
1518	>	data is several orders of magnitude more accurate than the original
1519	>	DMV and RATTLE approach.},
1520	>	annote = {911NS Times Cited:0 Cited References Count:14},
1521	>	issn = {1615-3375},
1522	>	uri = {<Go to ISI>://000228011900003},
1523		}
1524
1525	<	@Article{sum:2003,
1526	<	author =   {A.~K. Sum and J.~J. de~Pablo},
1527	<	title =    {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
1528	<	journal =      {Biophysical Journal},
1529	<	year =     2003,
1530	<	volume =   85,
1531	<	pages =    {3636-3645}
1525	>	@ARTICLE{Memmer2002,
1526	>	author = {R. Memmer},
1527	>	title = {Liquid crystal phases of achiral banana-shaped molecules: a computer
1528	>	simulation study},
1529	>	journal = {Liquid Crystals},
1530	>	year = {2002},
1531	>	volume = {29},
1532	>	pages = {483-496},
1533	>	number = {4},
1534	>	month = {Apr},
1535	>	abstract = {The phase behaviour of achiral banana-shaped molecules was studied
1536	>	by computer simulation. The banana-shaped molecules were described
1537	>	by model intermolecular interactions based on the Gay-Berne potential.
1538	>	The characteristic molecular structure was considered by joining
1539	>	two calamitic Gay-Berne particles through a bond to form a biaxial
1540	>	molecule of point symmetry group C-2v with a suitable bending angle.
1541	>	The dependence on temperature of systems of N=1024 rigid banana-shaped
1542	>	molecules with bending angle phi=140degrees has been studied by
1543	>	means of Monte Carlo simulations in the isobaric-isothermal ensemble
1544	>	(NpT). On cooling an isotropic system, two phase transitions characterized
1545	>	by phase transition enthalpy, entropy and relative volume change
1546	>	have been observed. For the first time by computer simulation of
1547	>	a many-particle system of banana-shaped molecules, at low temperature
1548	>	an untilted smectic phase showing a global phase biaxiality and
1549	>	a spontaneous local polarization in the layers, i.e. a local polar
1550	>	arrangement of the steric dipoles, with an antiferroelectric-like
1551	>	superstructure could be proven, a phase structure which recently
1552	>	has been discovered experimentally. Additionally, at intermediate
1553	>	temperature a nematic-like phase has been proved, whereas close
1554	>	to the transition to the smectic phase hints of a spontaneous achiral
1555	>	symmetry breaking have been determined. Here, in the absence of
1556	>	a layered structure a helical superstructure has been formed. All
1557	>	phases have been characterized by visual representations of selected
1558	>	configurations, scalar and pseudoscalar correlation functions, and
1559	>	order parameters.},
1560	>	annote = {531HT Times Cited:12 Cited References Count:37},
1561	>	issn = {0267-8292},
1562	>	uri = {<Go to ISI>://000174410500001},
1563		}
1564
1565	<	@Article{gomez:2003,
1566	<	author =   {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom},
1567	<	title =    {Setting up and optimization of membrane protein simulations},
1568	<	journal =      {Eur. Biophys. J.},
1569	<	year =     2002,
1570	<	volume =   31,
1571	<	pages =    {217-227}
1565	>	@ARTICLE{Metropolis1949,
1566	>	author = {N. Metropolis and S. Ulam},
1567	>	title = {The $\mbox{Monte Carlo}$ Method},
1568	>	journal = {J. Am. Stat. Ass.},
1569	>	year = {1949},
1570	>	volume = {44},
1571	>	pages = {335-341},
1572		}
1573
1574	<
1575	<	@Article{smondyrev:1999,
1576	<	author =   {A.~M. Smondyrev and M.~L. Berkowitz},
1577	<	title =    {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1578	<	journal =      {Biophysical Journal},
1579	<	year =     1999,
1580	<	volume =   76,
1581	<	pages =    {2472-2478}
1574	>	@ARTICLE{Mielke2004,
1575	>	author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen
1576	>	and C. J. Benham},
1577	>	title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian
1578	>	dynamics study},
1579	>	journal = {Journal of Chemical Physics},
1580	>	year = {2004},
1581	>	volume = {121},
1582	>	pages = {8104-8112},
1583	>	number = {16},
1584	>	month = {Oct 22},
1585	>	abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
1586	>	DNA can potentially induce long-range structural deformations integral
1587	>	to mechanisms of biological significance in both prokaryotes and
1588	>	eukaryotes. In this paper, we introduce a dynamic computer model
1589	>	for investigating this phenomenon. Duplex DNA is represented as
1590	>	a chain of hydrodynamic beads interacting through potentials of
1591	>	linearly elastic stretching, bending, and twisting, as well as excluded
1592	>	volume. The chain, linear when relaxed, is looped to form two open
1593	>	but topologically constrained subdomains. This permits the dynamic
1594	>	introduction of torsional stress via a centrally applied torque.
1595	>	We simulate by Brownian dynamics the 100 mus response of a 477-base
1596	>	pair B-DNA template to the localized torque generated by the prokaryotic
1597	>	transcription ensemble. Following a sharp rise at early times, the
1598	>	distributed twist assumes a nearly constant value in both subdomains,
1599	>	and a succession of supercoiling deformations occurs as superhelical
1600	>	stress is increasingly partitioned to writhe. The magnitude of writhe
1601	>	surpasses that of twist before also leveling off when the structure
1602	>	reaches mechanical equilibrium with the torsional load. Superhelicity
1603	>	is simultaneously right handed in one subdomain and left handed
1604	>	in the other, as predicted by the #transcription-induced##twin-supercoiled-domain#
1605	>	model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84,
1606	>	7024 (1987)]. The properties of the chain at the onset of writhing
1607	>	agree well with predictions from theory, and the generated stress
1608	>	is ample for driving secondary structural transitions in physiological
1609	>	DNA. (C) 2004 American Institute of Physics.},
1610	>	annote = {861ZF Times Cited:3 Cited References Count:34},
1611	>	issn = {0021-9606},
1612	>	uri = {<Go to ISI>://000224456500064},
1613		}
1614
1615	<	@Article{nina:2002,
1616	<	author =   {M. Nina and T. Simonson},
1617	<	title =    {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments},
1618	<	journal =      {J. Phys. Chem. B},
1619	<	year =     2002,
1620	<	volume =   106,
1621	<	pages =    {3696-3705}
1615	>	@ARTICLE{Naess2001,
1616	>	author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter},
1617	>	title = {Brownian dynamics simulation of rigid bodies and segmented polymer
1618	>	chains. Use of Cartesian rotation vectors as the generalized coordinates
1619	>	describing angular orientations},
1620	>	journal = {Physica A},
1621	>	year = {2001},
1622	>	volume = {294},
1623	>	pages = {323-339},
1624	>	number = {3-4},
1625	>	month = {May 15},
1626	>	abstract = {The three Eulerian angles constitute the classical choice of generalized
1627	>	coordinates used to describe the three degrees of rotational freedom
1628	>	of a rigid body, but it has long been known that this choice yields
1629	>	singular equations of motion. The latter is also true when Eulerian
1630	>	angles are used in Brownian dynamics analyses of the angular orientation
1631	>	of single rigid bodies and segmented polymer chains. Starting from
1632	>	kinetic theory we here show that by instead employing the three
1633	>	components of Cartesian rotation vectors as the generalized coordinates
1634	>	describing angular orientation, no singularity appears in the configuration
1635	>	space diffusion equation and the associated Brownian dynamics algorithm.
1636	>	The suitability of Cartesian rotation vectors in Brownian dynamics
1637	>	simulations of segmented polymer chains with spring-like or ball-socket
1638	>	joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.},
1639	>	annote = {433TA Times Cited:7 Cited References Count:19},
1640	>	issn = {0378-4371},
1641	>	uri = {<Go to ISI>://000168774800005},
1642		}
1643
1644	<	@Article{norberg:2000,
1645	<	author =   {J. Norberg and L. Nilsson},
1646	<	title =    {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
1647	<	journal =      {Biophysical Journal},
1648	<	year =     2000,
1649	<	volume =   79,
1650	<	pages =    {1537-1553}
1644	>	@ARTICLE{Niori1996,
1645	>	author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe},
1646	>	title = {Distinct ferroelectric smectic liquid crystals consisting of banana
1647	>	shaped achiral molecules},
1648	>	journal = {Journal of Materials Chemistry},
1649	>	year = {1996},
1650	>	volume = {6},
1651	>	pages = {1231-1233},
1652	>	number = {7},
1653	>	month = {Jul},
1654	>	abstract = {The synthesis of a banana-shaped molecule is reported and it is found
1655	>	that the smectic phase which it forms is biaxial with the molecules
1656	>	packed in the best,direction into a layer. Because of this characteristic
1657	>	packing, spontaneous polarization appears parallel to the layer
1658	>	and switches on reversal of an applied electric field. This is the
1659	>	first obvious example of ferroelectricity in an achiral smectic
1660	>	phase and is ascribed to the C-2v symmetry of the molecular packing.},
1661	>	annote = {Ux855 Times Cited:447 Cited References Count:18},
1662	>	issn = {0959-9428},
1663	>	uri = {<Go to ISI>://A1996UX85500025},
1664		}
1665
1666	<	@Article{patra:2003,
1667	<	author =   {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
1668	<	title =    {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
1669	<	journal =      {Biophysical Journal},
1670	<	year =     2003,
1671	<	volume =   84,
1672	<	pages =    {3636-3645}
1666	>	@ARTICLE{Noguchi2002,
1667	>	author = {H. Noguchi and M. Takasu},
1668	>	title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
1669	>	journal = {Physical Review E},
1670	>	year = {2002},
1671	>	volume = {65},
1672	>	pages = {-},
1673	>	number = {5},
1674	>	month = {may},
1675	>	abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
1676	>	forces using a Brownian dynamics simulation. Two nanoparticles,
1677	>	which interact repulsively with amphiphilic molecules, are put inside
1678	>	a vesicle. The position of one nanoparticle is fixed, and the other
1679	>	is moved by a constant force as in optical-trapping experiments.
1680	>	First, the pulled vesicle stretches into a pear or tube shape. Then
1681	>	the inner monolayer in the tube-shaped region is deformed, and a
1682	>	cylindrical structure is formed between two vesicles. After stretching
1683	>	the cylindrical region, fission occurs near the moved vesicle. Soon
1684	>	after this the cylindrical region shrinks. The trapping force similar
1685	>	to 100 pN is needed to induce the formation of the cylindrical structure
1686	>	and fission.},
1687	>	annote = {Part 1 568PX Times Cited:5 Cited References Count:39},
1688	>	issn = {1063-651X},
1689	>	uri = {<Go to ISI>://000176552300084},
1690		}
1691
1692	<	@Article{marrink04,
1693	<	author =   {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
1694	<	title =    {Coarse Grained Model for Semiquantitative Lipid Simulations},
1695	<	journal =      {J. Phys. Chem. B},
1696	<	year =     2004,
1697	<	volume =   108,
1698	<	pages =    {750-760}
1692	>	@ARTICLE{Noguchi2001,
1693	>	author = {H. Noguchi and M. Takasu},
1694	>	title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
1695	>	journal = {Journal of Chemical Physics},
1696	>	year = {2001},
1697	>	volume = {115},
1698	>	pages = {9547-9551},
1699	>	number = {20},
1700	>	month = {Nov 22},
1701	>	abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
1702	>	simulation. Amphiphilic molecules spontaneously form vesicles with
1703	>	a bilayer structure. Two vesicles come into contact and form a stalk
1704	>	intermediate, in which a necklike structure only connects the outer
1705	>	monolayers, as predicted by the stalk hypothesis. We have found
1706	>	a new pathway of pore opening from stalks at high temperature: the
1707	>	elliptic stalk bends and contact between the ends of the arc-shaped
1708	>	stalk leads to pore opening. On the other hand, we have clarified
1709	>	that the pore-opening process at low temperature agrees with the
1710	>	modified stalk model: a pore is induced by contact between the inner
1711	>	monolayers inside the stalk. (C) 2001 American Institute of Physics.},
1712	>	annote = {491UW Times Cited:48 Cited References Count:25},
1713	>	issn = {0021-9606},
1714	>	uri = {<Go to ISI>://000172129300049},
1715		}
1716
1717	<	@Article{andersen83,
1718	<	author =   {H.~C. Andersen},
1719	<	title =    {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
1720	<	journal =      {Journal of Computational Physics},
1721	<	year =     1983,
1722	<	volume =   52,
1723	<	pages =    {24-34}
1717	>	@ARTICLE{Orlandi2006,
1718	>	author = {S. Orlandi and R. Berardi and J. Steltzer and C. Zannoni},
1719	>	title = {A Monte Carlo study of the mesophases formed by polar bent-shaped
1720	>	molecules},
1721	>	journal = {Journal of Chemical Physics},
1722	>	year = {2006},
1723	>	volume = {124},
1724	>	pages = {-},
1725	>	number = {12},
1726	>	month = {Mar 28},
1727	>	abstract = {Liquid crystal phases formed by bent-shaped (or #banana#) molecules
1728	>	are currently of great interest. Here we investigate by Monte Carlo
1729	>	computer simulations the phases formed by rigid banana molecules
1730	>	modeled combining three Gay-Berne sites and containing either one
1731	>	central or two lateral and transversal dipoles. We show that changing
1732	>	the dipole position and orientation has a profound effect on the
1733	>	mesophase stability and molecular organization. In particular, we
1734	>	find a uniaxial nematic phase only for off-center dipolar models
1735	>	and tilted phases only for the one with terminal dipoles. (c) 2006
1736	>	American Institute of Physics.},
1737	>	annote = {028CP Times Cited:0 Cited References Count:42},
1738	>	issn = {0021-9606},
1739	>	uri = {<Go to ISI>://000236464000072},
1740		}
1741
1742	<	@Article{hura00,
1743	<	author =   {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
1744	<	title =    {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
1745	<	journal =      {J. Chem. Phys.},
1746	<	year =     2000,
1747	<	volume =   113,
1748	<	pages =    {9140-9148}
1742	>	@ARTICLE{Palacios1998,
1743	>	author = {J. L. Garcia-Palacios and F. J. Lazaro},
1744	>	title = {Langevin-dynamics study of the dynamical properties of small magnetic
1745	>	particles},
1746	>	journal = {Physical Review B},
1747	>	year = {1998},
1748	>	volume = {58},
1749	>	pages = {14937-14958},
1750	>	number = {22},
1751	>	month = {Dec 1},
1752	>	abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
1753	>	magnetic moment is numerically solved (properly observing the customary
1754	>	interpretation of it as a Stratonovich stochastic differential equation),
1755	>	in order to study the dynamics of magnetic nanoparticles. The corresponding
1756	>	Langevin-dynamics approach allows for the study of the fluctuating
1757	>	trajectories of individual magnetic moments, where we have encountered
1758	>	remarkable phenomena in the overbarrier rotation process, such as
1759	>	crossing-back or multiple crossing of the potential barrier, rooted
1760	>	in the gyromagnetic nature of the system. Concerning averaged quantities,
1761	>	we study the linear dynamic response of the archetypal ensemble
1762	>	of noninteracting classical magnetic moments with axially symmetric
1763	>	magnetic anisotropy. The results are compared with different analytical
1764	>	expressions used to model the relaxation of nanoparticle ensembles,
1765	>	assessing their accuracy. It has been found that, among a number
1766	>	of heuristic expressions for the linear dynamic susceptibility,
1767	>	only the simple formula proposed by Shliomis and Stepanov matches
1768	>	the coarse features of the susceptibility reasonably. By comparing
1769	>	the numerical results with the asymptotic formula of Storonkin {Sov.
1770	>	Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]},
1771	>	the effects of the intra-potential-well relaxation modes on the
1772	>	low-temperature longitudinal dynamic response have been assessed,
1773	>	showing their relatively small reflection in the susceptibility
1774	>	curves but their dramatic influence on the phase shifts. Comparison
1775	>	of the numerical results with the exact zero-damping expression
1776	>	for the transverse susceptibility by Garanin, Ishchenko, and Panina
1777	>	{Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242
1778	>	(1990)]}, reveals a sizable contribution of the spread of the precession
1779	>	frequencies of the magnetic moment in the anisotropy field to the
1780	>	dynamic response at intermediate-to-high temperatures. [S0163-1829
1781	>	(98)00446-9].},
1782	>	annote = {146XW Times Cited:66 Cited References Count:45},
1783	>	issn = {0163-1829},
1784	>	uri = {<Go to ISI>://000077460000052},
1785		}
1786
1787	<
1788	<	@Article{ryckaert77,
1789	<	author =   {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
1790	<	title =    {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
1791	<	journal =      {Journal of Computational Physics},
1792	<	year =     1977,
1793	<	volume =   23,
1794	<	pages =    {327-341}
1787	>	@ARTICLE{Pastor1988,
1788	>	author = {R. W. Pastor and B. R. Brooks and A. Szabo},
1789	>	title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
1790	>	journal = {Molecular Physics},
1791	>	year = {1988},
1792	>	volume = {65},
1793	>	pages = {1409-1419},
1794	>	number = {6},
1795	>	month = {Dec 20},
1796	>	annote = {T1302 Times Cited:61 Cited References Count:26},
1797	>	issn = {0026-8976},
1798	>	uri = {<Go to ISI>://A1988T130200011},
1799		}
1800
1801	<
1802	<	@InBook{fowles99:lagrange,
1803	<	author =   {G.~R. Fowles and G.~L. Cassiday},
1804	<	title =    {Analytical Mechanics},
1805	<	chapter =      10,
1806	<	publisher =    {Saunders College Publishing},
1807	<	year =     1999,
1808	<	edition =  {6th}
1801	>	@ARTICLE{Pelzl1999,
1802	>	author = {G. Pelzl and S. Diele and W. Weissflog},
1803	>	title = {Banana-shaped compounds - A new field of liquid crystals},
1804	>	journal = {Advanced Materials},
1805	>	year = {1999},
1806	>	volume = {11},
1807	>	pages = {707-724},
1808	>	number = {9},
1809	>	month = {Jul 5},
1810	>	annote = {220RC Times Cited:313 Cited References Count:49},
1811	>	issn = {0935-9648},
1812	>	uri = {<Go to ISI>://000081680400007},
1813		}
1814
1815	<	@Article{petrache00,
1816	<	author =   {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
1817	<	title =    {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
1818	<	journal =      {Biophysical Journal},
1819	<	year =     2000,
1820	<	volume =   79,
1821	<	pages =    {3172-3192}
1815	>	@ARTICLE{Perram1985,
1816	>	author = {J. W. Perram and M. S. Wertheim},
1817	>	title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and
1818	>	the Contact Function},
1819	>	journal = {Journal of Computational Physics},
1820	>	year = {1985},
1821	>	volume = {58},
1822	>	pages = {409-416},
1823	>	number = {3},
1824	>	annote = {Akb93 Times Cited:71 Cited References Count:12},
1825	>	issn = {0021-9991},
1826	>	uri = {<Go to ISI>://A1985AKB9300008},
1827		}
1828
1829	<	@Article{egberts88,
1830	<	author =   {E. Egberts and H.~J.~C. Berendsen},
1831	<	title =    {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
1832	<	journal =      {J. Chem. Phys.},
1833	<	year =     1988,
1834	<	volume =   89,
1835	<	pages =    {3718-3732}
1829	>	@ARTICLE{Petrache1998,
1830	>	author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle},
1831	>	title = {Fluid phase structure of EPC and DMPC bilayers},
1832	>	journal = {Chemistry and Physics of Lipids},
1833	>	year = {1998},
1834	>	volume = {95},
1835	>	pages = {83-94},
1836	>	number = {1},
1837	>	month = {Sep},
1838	>	abstract = {X-ray diffraction data taken at high instrumental resolution were
1839	>	obtained for EPC and DMPC under various osmotic pressures, primarily
1840	>	at T = 30 degrees C. The headgroup thickness D-HH was obtained from
1841	>	relative electron density profiles. By using volumetric results
1842	>	and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4
1843	>	+/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The
1844	>	analysis also gives estimates for the areal compressibility K-A.
1845	>	The A(F) results lead to other structural results regarding membrane
1846	>	thickness and associated waters. Using the recently determined absolute
1847	>	electrons density profile of DPPC, the AF results also lead to absolute
1848	>	electron density profiles and absolute continuous transforms \F(q)\
1849	>	for EPC and DMPC, Limited measurements of temperature dependence
1850	>	show directly that fluctuations increase with increasing temperature
1851	>	and that a small decrease in bending modulus K-c accounts for the
1852	>	increased water spacing reported by Simon et al. (1995) Biophys.
1853	>	J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights
1854	>	reserved.},
1855	>	annote = {130AT Times Cited:98 Cited References Count:39},
1856	>	issn = {0009-3084},
1857	>	uri = {<Go to ISI>://000076497600007},
1858		}
1859
1860	<	@Article{Holz00,
1861	<	author =       {M. Holz and S.~R. Heil and A. Sacco},
1862	<	title =        {Temperature-dependent self-diffusion coefficients of
1863	<	water and six selected molecular liquids for calibration
1864	<	in accurate $^1${\sc h} {\sc nmr pfg} measurements},
1865	<	journal =      {Phys. Chem. Chem. Phys.},
1866	<	year =         2000,
1867	<	volume =       2,
2028	<	pages =        {4740-4742},
1860	>	@ARTICLE{Powles1973,
1861	>	author = {J.~G. Powles},
1862	>	title = {A general ellipsoid can not always serve as a modle for the rotational
1863	>	diffusion properties of arbitrary shaped rigid molecules},
1864	>	journal = {Advan. Phys.},
1865	>	year = {1973},
1866	>	volume = {22},
1867	>	pages = {1-56},
1868		}
1869
1870	<	@InCollection{zannoni94,
1871	<	author =   {C. Zannoni},
1872	<	title =    {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
1873	<	booktitle =    {The Molecular Dynamics of Liquid Crstals},
1874	<	pages =    {139-169},
1875	<	publisher =    {Kluwer Academic Publishers},
1876	<	year =     1994,
1877	<	editor =   {G.~R. Luckhurst and C.~A. Veracini},
1878	<	chapter =  6
1870	>	@ARTICLE{Recio2004,
1871	>	author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
1872	>	title = {Identification of protein-protein interaction sites from docking
1873	>	energy landscapes},
1874	>	journal = {Journal of Molecular Biology},
1875	>	year = {2004},
1876	>	volume = {335},
1877	>	pages = {843-865},
1878	>	number = {3},
1879	>	month = {Jan 16},
1880	>	abstract = {Protein recognition is one of the most challenging and intriguing
1881	>	problems in structural biology. Despite all the available structural,
1882	>	sequence and biophysical information about protein-protein complexes,
1883	>	the physico-chemical patterns, if any, that make a protein surface
1884	>	likely to be involved in protein-protein interactions, remain elusive.
1885	>	Here, we apply protein docking simulations and analysis of the interaction
1886	>	energy landscapes to identify protein-protein interaction sites.
1887	>	The new protocol for global docking based on multi-start global
1888	>	energy optimization of an allatom model of the ligand, with detailed
1889	>	receptor potentials and atomic solvation parameters optimized in
1890	>	a training set of 24 complexes, explores the conformational space
1891	>	around the whole receptor without restrictions. The ensembles of
1892	>	the rigid-body docking solutions generated by the simulations were
1893	>	subsequently used to project the docking energy landscapes onto
1894	>	the protein surfaces. We found that highly populated low-energy
1895	>	regions consistently corresponded to actual binding sites. The procedure
1896	>	was validated on a test set of 21 known protein-protein complexes
1897	>	not used in the training set. As much as 81% of the predicted high-propensity
1898	>	patch residues were located correctly in the native interfaces.
1899	>	This approach can guide the design of mutations on the surfaces
1900	>	of proteins, provide geometrical details of a possible interaction,
1901	>	and help to annotate protein surfaces in structural proteomics.
1902	>	(C) 2003 Elsevier Ltd. All rights reserved.},
1903	>	annote = {763GQ Times Cited:21 Cited References Count:59},
1904	>	issn = {0022-2836},
1905	>	uri = {<Go to ISI>://000188066900016},
1906		}
1907
1908	+	@ARTICLE{Reddy2006,
1909	+	author = {R. A. Reddy and C. Tschierske},
1910	+	title = {Bent-core liquid crystals: polar order, superstructural chirality
1911	+	and spontaneous desymmetrisation in soft matter systems},
1912	+	journal = {Journal of Materials Chemistry},
1913	+	year = {2006},
1914	+	volume = {16},
1915	+	pages = {907-961},
1916	+	number = {10},
1917	+	abstract = {An overview on the recent developments in the field of liquid crystalline
1918	+	bent-core molecules (so-called banana liquid crystals) is given.
1919	+	After some basic issues, dealing with general aspects of the systematisation
1920	+	of the mesophases, development of polar order and chirality in this
1921	+	class of LC systems and explaining some general structure-property
1922	+	relationships, we focus on fascinating new developments in this
1923	+	field, such as modulated, undulated and columnar phases, so-called
1924	+	B7 phases, phase biaxiality, ferroelectric and antiferroelectric
1925	+	polar order in smectic and columnar phases, amplification and switching
1926	+	of chirality and the spontaneous formation of superstructural and
1927	+	supramolecular chirality.},
1928	+	annote = {021NS Times Cited:2 Cited References Count:316},
1929	+	issn = {0959-9428},
1930	+	uri = {<Go to ISI>://000235990500001},
1931	+	}
1932
1933	<	@Article{melchionna93,
1934	<	author =   {S. Melchionna and G. Ciccotti and B.~L. Holian},
1935	<	title =    {Hoover {\sc npt} dynamics for systems varying in shape and size},
1936	<	journal =      {Molecular Physics},
1937	<	year =     1993,
1938	<	volume =   78,
1939	<	pages =    {533-544}
1933	>	@ARTICLE{Ros2005,
1934	>	author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
1935	>	title = {Banana-shaped liquid crystals: a new field to explore},
1936	>	journal = {Journal of Materials Chemistry},
1937	>	year = {2005},
1938	>	volume = {15},
1939	>	pages = {5093-5098},
1940	>	number = {48},
1941	>	abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
1942	>	mesogenic materials represent a bewitching and stimulating field
1943	>	of research that is interesting both academically and in terms of
1944	>	applications. Numerous topics are open to investigation in this
1945	>	area because of the rich phenomenology and new possibilities that
1946	>	these materials offer. The principal concepts in this area are reviewed
1947	>	along with recent results. In addition, new directions to stimulate
1948	>	further research activities are highlighted.},
1949	>	annote = {990XA Times Cited:3 Cited References Count:72},
1950	>	issn = {0959-9428},
1951	>	uri = {<Go to ISI>://000233775500001},
1952		}
1953
1954	<	@Article{fennell04,
1955	<	author =   {C.~J. Fennell and J.~D. Gezelter},
1956	<	title =    {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models},
1957	<	journal =      {J. Chem. Phys},
1958	<	year =     {in press 2004}
1954	>	@ARTICLE{Roy2005,
1955	>	author = {A. Roy and N. V. Madhusudana},
1956	>	title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases
1957	>	in banana shaped molecules},
1958	>	journal = {European Physical Journal E},
1959	>	year = {2005},
1960	>	volume = {18},
1961	>	pages = {253-258},
1962	>	number = {3},
1963	>	month = {Nov},
1964	>	abstract = {A vast majority of compounds with bent core or banana shaped molecules
1965	>	exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased
1966	>	in a homologous series. The B-6 phase has an intercalated fluid
1967	>	lamellar structure with a layer spacing of half the molecular length.
1968	>	The B-1 phase has a two dimensionally periodic rectangular columnar
1969	>	structure. The B-2 phase has a monolayer fluid lamellar structure
1970	>	with molecules tilted with respect to the layer normal. Neglecting
1971	>	the tilt order of the molecules in the B-2 phase, we have developed
1972	>	a frustrated packing model to describe this phase sequence qualitatively.
1973	>	The model has some analogy with that of the frustrated smectics
1974	>	exhibited by highly polar rod like molecules.},
1975	>	annote = {985FW Times Cited:0 Cited References Count:30},
1976	>	issn = {1292-8941},
1977	>	uri = {<Go to ISI>://000233363300002},
1978		}
1979
1980	<	@Article{klein01,
1981	<	author =   {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
1982	<	title =    {A coarse Grain Model for Phospholipid Simulations},
1983	<	journal =      {J. Phys. Chem. B},
1984	<	year =     2001,
1985	<	volume =   105,
1986	<	pages =    {4464-4470}
1980	>	@ARTICLE{Sandu1999,
1981	>	author = {A. Sandu and T. Schlick},
1982	>	title = {Masking resonance artifacts in force-splitting methods for biomolecular
1983	>	simulations by extrapolative Langevin dynamics},
1984	>	journal = {Journal of Computational Physics},
1985	>	year = {1999},
1986	>	volume = {151},
1987	>	pages = {74-113},
1988	>	number = {1},
1989	>	month = {May 1},
1990	>	abstract = {Numerical resonance artifacts have become recognized recently as a
1991	>	limiting factor to increasing the timestep in multiple-timestep
1992	>	(MTS) biomolecular dynamics simulations. At certain timesteps correlated
1993	>	to internal motions (e.g., 5 fs, around half the period of the fastest
1994	>	bond stretch, T-min), visible inaccuracies or instabilities can
1995	>	occur. Impulse-MTS schemes are vulnerable to these resonance errors
1996	>	since large energy pulses are introduced to the governing dynamics
1997	>	equations when the slow forces are evaluated. We recently showed
1998	>	that such resonance artifacts can be masked significantly by applying
1999	>	extrapolative splitting to stochastic dynamics. Theoretical and
2000	>	numerical analyses of force-splitting integrators based on the Verlet
2001	>	discretization are reported here for linear models to explain these
2002	>	observations and to suggest how to construct effective integrators
2003	>	for biomolecular dynamics that balance stability with accuracy.
2004	>	Analyses for Newtonian dynamics demonstrate the severe resonance
2005	>	patterns of the Impulse splitting, with this severity worsening
2006	>	with the outer timestep. Delta t: Constant Extrapolation is generally
2007	>	unstable, but the disturbances do not grow with Delta t. Thus. the
2008	>	stochastic extrapolative combination can counteract generic instabilities
2009	>	and largely alleviate resonances with a sufficiently strong Langevin
2010	>	heat-bath coupling (gamma), estimates for which are derived here
2011	>	based on the fastest and slowest motion periods. These resonance
2012	>	results generally hold for nonlinear test systems: a water tetramer
2013	>	and solvated protein. Proposed related approaches such as Extrapolation/Correction
2014	>	and Midpoint Extrapolation work better than Constant Extrapolation
2015	>	only for timesteps less than T-min/2. An effective extrapolative
2016	>	stochastic approach for biomolecules that balances long-timestep
2017	>	stability with good accuracy for the fast subsystem is then applied
2018	>	to a biomolecule using a three-class partitioning: the medium forces
2019	>	are treated by Midpoint Extrapolation via position Verlet, and the
2020	>	slow forces are incorporated by Constant Extrapolation. The resulting
2021	>	algorithm (LN) performs well on a solvated protein system in terms
2022	>	of thermodynamic properties and yields an order of magnitude speedup
2023	>	with respect to single-timestep Langevin trajectories. Computed
2024	>	spectral density functions also show how the Newtonian modes can
2025	>	be approximated by using a small gamma in the range Of 5-20 ps(-1).
2026	>	(C) 1999 Academic Press.},
2027	>	annote = {194FM Times Cited:14 Cited References Count:32},
2028	>	issn = {0021-9991},
2029	>	uri = {<Go to ISI>://000080181500004},
2030		}
2031
2032	<
2033	<	@Article{marrink03:vesicles,
2034	<	author =   {S.~J. Marrink and A.~E. Mark},
2035	<	title =    {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
2036	<	journal =      {J. Am. Chem. Soc.},
2037	<	year =     2003,
2038	<	volume =   125,
2039	<	pages =    {15233-15242}
2032	>	@ARTICLE{Satoh1996,
2033	>	author = {K. Satoh and S. Mita and S. Kondo},
2034	>	title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect
2035	>	of terminal dipole moment on mesophase formation},
2036	>	journal = {Chemical Physics Letters},
2037	>	year = {1996},
2038	>	volume = {255},
2039	>	pages = {99-104},
2040	>	number = {1-3},
2041	>	month = {Jun 7},
2042	>	abstract = {The effects of dipole-dipole interaction on mesophase formation are
2043	>	investigated with a Monte Carlo simulation using the dipolar Gay-Berne
2044	>	potential. It is shown that the dipole moment at the end of a molecule
2045	>	causes a shift in the nematic-isotropic transition toward higher
2046	>	temperature and a spread of the temperature range of the nematic
2047	>	phase and that layer structures with various interdigitations are
2048	>	formed in the smectic phase.},
2049	>	annote = {Uq975 Times Cited:32 Cited References Count:33},
2050	>	issn = {0009-2614},
2051	>	uri = {<Go to ISI>://A1996UQ97500017},
2052		}
2053
2054	<	@Book{gamma94,
2055	<	author =       {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
2056	<	title =        {Design Patterns: Elements of Reusable Object-Oriented Software},
2057	<	chapter =      7,
2058	<	publisher =    {Perason Education},
2059	<	year =         1994,
2060	<	address =      {London},
2054	>	@ARTICLE{Shen2002,
2055	>	author = {M. Y. Shen and K. F. Freed},
2056	>	title = {Long time dynamics of met-enkephalin: Comparison of explicit and
2057	>	implicit solvent models},
2058	>	journal = {Biophysical Journal},
2059	>	year = {2002},
2060	>	volume = {82},
2061	>	pages = {1791-1808},
2062	>	number = {4},
2063	>	month = {Apr},
2064	>	abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
2065	>	structure and receptor docking mechanism are still not well understood.
2066	>	The conformational dynamics of this neuron peptide in liquid water
2067	>	are studied here by using all-atom molecular dynamics (MID) and
2068	>	implicit water Langevin dynamics (LD) simulations with AMBER potential
2069	>	functions and the three-site transferable intermolecular potential
2070	>	(TIP3P) model for water. To achieve the same simulation length in
2071	>	physical time, the full MID simulations require 200 times as much
2072	>	CPU time as the implicit water LID simulations. The solvent hydrophobicity
2073	>	and dielectric behavior are treated in the implicit solvent LD simulations
2074	>	by using a macroscopic solvation potential, a single dielectric
2075	>	constant, and atomic friction coefficients computed using the accessible
2076	>	surface area method with the TIP3P model water viscosity as determined
2077	>	here from MID simulations for pure TIP3P water. Both the local and
2078	>	the global dynamics obtained from the implicit solvent LD simulations
2079	>	agree very well with those from the explicit solvent MD simulations.
2080	>	The simulations provide insights into the conformational restrictions
2081	>	that are associated with the bioactivity of the opiate peptide dermorphin
2082	>	for the delta-receptor.},
2083	>	annote = {540MH Times Cited:36 Cited References Count:45},
2084	>	issn = {0006-3495},
2085	>	uri = {<Go to ISI>://000174932400010},
2086		}
2087
2088	<	@Book{alexander,
2089	<	author =       {C. Alexander},
2090	<	title =        {A Pattern Language: Towns, Buildings, Construction},
2091	<	publisher =    {Oxford University Press},
2092	<	year =         1987,
2093	<	address =      {New York}
2088	>	@ARTICLE{Shillcock2005,
2089	>	author = {J. C. Shillcock and R. Lipowsky},
2090	>	title = {Tension-induced fusion of bilayer membranes and vesicles},
2091	>	journal = {Nature Materials},
2092	>	year = {2005},
2093	>	volume = {4},
2094	>	pages = {225-228},
2095	>	number = {3},
2096	>	month = {Mar},
2097	>	annote = {901QJ Times Cited:9 Cited References Count:23},
2098	>	issn = {1476-1122},
2099	>	uri = {<Go to ISI>://000227296700019},
2100		}
2101
2102	<	@Article{wilson,
2103	<	author =   {G.~V. Wilson },
2104	<	title =    {Where's the Real Bottleneck in Scientific Computing?},
2105	<	journal =      {American Scientist},
2106	<	year =     2006,
2107	<	volume =   94
2102	>	@ARTICLE{Skeel2002,
2103	>	author = {R. D. Skeel and J. A. Izaguirre},
2104	>	title = {An impulse integrator for Langevin dynamics},
2105	>	journal = {Molecular Physics},
2106	>	year = {2002},
2107	>	volume = {100},
2108	>	pages = {3885-3891},
2109	>	number = {24},
2110	>	month = {Dec 20},
2111	>	abstract = {The best simple method for Newtonian molecular dynamics is indisputably
2112	>	the leapfrog Stormer-Verlet method. The appropriate generalization
2113	>	to simple Langevin dynamics is unclear. An analysis is presented
2114	>	comparing an 'impulse method' (kick; fluctuate; kick), the 1982
2115	>	method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus
2116	>	(BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen
2117	>	methods can be implemented as efficiently as the BBK method. Other
2118	>	considerations suggest that the impulse method is the best basic
2119	>	method for simple Langevin dynamics, with the van Gunsteren-Berendsen
2120	>	method a close contender.},
2121	>	annote = {633RX Times Cited:8 Cited References Count:22},
2122	>	issn = {0026-8976},
2123	>	uri = {<Go to ISI>://000180297200014},
2124		}
2125
2126	<	@article{Meineke05,
2127	<	Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
2128	<	Date-Modified = {2006-03-05 12:37:31 -0500},
2129	<	Journal = {J. Comp. Chem.},
2130	<	Pages = {252-271},
2131	<	Title = {OOPSE: An Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
2132	<	Volume = 26,
2133	<	Year = 2005
2126	>	@ARTICLE{Skeel1997,
2127	>	author = {R. D. Skeel and G. H. Zhang and T. Schlick},
2128	>	title = {A family of symplectic integrators: Stability, accuracy, and molecular
2129	>	dynamics applications},
2130	>	journal = {Siam Journal on Scientific Computing},
2131	>	year = {1997},
2132	>	volume = {18},
2133	>	pages = {203-222},
2134	>	number = {1},
2135	>	month = {Jan},
2136	>	abstract = {The following integration methods for special second-order ordinary
2137	>	differential equations are studied: leapfrog, implicit midpoint,
2138	>	trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all
2139	>	are members, or equivalent to members, of a one-parameter family
2140	>	of schemes. Some methods have more than one common form, and we
2141	>	discuss a systematic enumeration of these forms. We also present
2142	>	a stability and accuracy analysis based on the idea of ''modified
2143	>	equations'' and a proof of symplecticness. It follows that Cowell-Numerov
2144	>	and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic.
2145	>	A different interpretation of the values used by these integrators
2146	>	leads to higher accuracy and better energy conservation. Hence,
2147	>	we suggest that the straightforward analysis of energy conservation
2148	>	is misleading.},
2149	>	annote = {We981 Times Cited:30 Cited References Count:35},
2150	>	issn = {1064-8275},
2151	>	uri = {<Go to ISI>://A1997WE98100012},
2152		}
2153
2154	<	@article{Matthey05,
2155	<	Author = {T. Matthey, T. Cickovski and \textit{et al}},
2156	<	Date-Modified = {2006-03-05 12:37:31 -0500},
2157	<	Journal = {ACM Transactions on Mathematical Software},
2158	<	Pages = {237-265},
2159	<	Title = {ProtoMol, an Object-Oriented Framework for Prototyping Novel Algorithms for Molecular Dynamics},
2160	<	Volume = 20,
2161	<	Year = 2004
2154	>	@ARTICLE{Tao2005,
2155	>	author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont
2156	>	and W. J. Briels},
2157	>	title = {Brownian dynamics simulations of the self- and collective rotational
2158	>	diffusion coefficients of rigid long thin rods},
2159	>	journal = {Journal of Chemical Physics},
2160	>	year = {2005},
2161	>	volume = {122},
2162	>	pages = {-},
2163	>	number = {24},
2164	>	month = {Jun 22},
2165	>	abstract = {Recently a microscopic theory for the dynamics of suspensions of long
2166	>	thin rigid rods was presented, confirming and expanding the well-known
2167	>	theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon,
2168	>	Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here
2169	>	this theory is put to the test by comparing it against computer
2170	>	simulations. A Brownian dynamics simulation program was developed
2171	>	to follow the dynamics of the rods, with a length over a diameter
2172	>	ratio of 60, on the Smoluchowski time scale. The model accounts
2173	>	for excluded volume interactions between rods, but neglects hydrodynamic
2174	>	interactions. The self-rotational diffusion coefficients D-r(phi)
2175	>	of the rods were calculated by standard methods and by a new, more
2176	>	efficient method based on calculating average restoring torques.
2177	>	Collective decay of orientational order was calculated by means
2178	>	of equilibrium and nonequilibrium simulations. Our results show
2179	>	that, for the currently accessible volume fractions, the decay times
2180	>	in both cases are virtually identical. Moreover, the observed decay
2181	>	of diffusion coefficients with volume fraction is much quicker than
2182	>	predicted by the theory, which is attributed to an oversimplification
2183	>	of dynamic correlations in the theory. (c) 2005 American Institute
2184	>	of Physics.},
2185	>	annote = {943DN Times Cited:3 Cited References Count:26},
2186	>	issn = {0021-9606},
2187	>	uri = {<Go to ISI>://000230332400077},
2188		}
2189
2190	<	@Book{tolman79,
2191	<	author =       {R.~C. Tolman},
2192	<	title =        {The Principles of Statistical Mechanics},
2193	<	chapter =      2,
2194	<	publisher =    {Dover Publications, Inc.},
2195	<	year =         1979,
2196	<	address =      {New York},
2197	<	pages =        {19-22}
2190	>	@BOOK{Tolman1979,
2191	>	title = {The Principles of Statistical Mechanics},
2192	>	publisher = {Dover Publications, Inc.},
2193	>	year = {1979},
2194	>	author = {R.~C. Tolman},
2195	>	address = {New York},
2196	>	chapter = {2},
2197	>	pages = {19-22},
2198		}
2199
2200	<	@Book{Marion90,
2201	<	author =   {J.~B. Marion},
2202	<	title =    {Classical Dynamics of Particles and Systems},
2203	<	publisher =    {Academic Press},
2204	<	year =     1990,
2205	<	address =  {New York},
2206	<	edition =  {2rd}
2200	>	@ARTICLE{Tu1995,
2201	>	author = {K. Tu and D. J. Tobias and M. L. Klein},
2202	>	title = {Constant pressure and temperature molecular dynamics simulation of
2203	>	a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine
2204	>	bilayer},
2205	>	journal = {Biophysical Journal},
2206	>	year = {1995},
2207	>	volume = {69},
2208	>	pages = {2558-2562},
2209	>	number = {6},
2210	>	month = {Dec},
2211	>	abstract = {We report a constant pressure and temperature molecular dynamics simulation
2212	>	of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine
2213	>	at 50 degrees C and 28 water molecules/lipid. We have shown that
2214	>	the bilayer is stable throughout the 1550-ps simulation and have
2215	>	demonstrated convergence of the system dimensions. Several important
2216	>	aspects of the bilayer structure have been investigated and compared
2217	>	favorably with experimental results. For example, the average positions
2218	>	of specific carbon atoms along the bilayer normal agree well with
2219	>	neutron diffraction data, and the electron density profile is in
2220	>	accord with x-ray diffraction results. The hydrocarbon chain deuterium
2221	>	order parameters agree reasonably well with NMR results for the
2222	>	middles of the chains, but the simulation predicts too much order
2223	>	at the chain ends. In spite of the deviations in the order parameters,
2224	>	the hydrocarbon chain packing density appears to be essentially
2225	>	correct, inasmuch as the area/lipid and bilayer thickness are in
2226	>	agreement with the most refined experimental estimates. The deuterium
2227	>	order parameters for the glycerol and choline groups, as well as
2228	>	the phosphorus chemical shift anisotropy, are in qualitative agreement
2229	>	with those extracted from NMR measurements.},
2230	>	annote = {Tv018 Times Cited:108 Cited References Count:34},
2231	>	issn = {0006-3495},
2232	>	uri = {<Go to ISI>://A1995TV01800037},
2233		}
2234
2235	<	@Book{Leimkuhler04,
2236	<	author =   {B. Leimkuhler and S. Reich},
2237	<	title =    {Simulating Hamiltonian Dynamics},
2238	<	publisher =    {Cambridge University Press},
2239	<	year =     2004,
2240	<	address =  {Cambridge}
2235	>	@ARTICLE{Tuckerman1992,
2236	>	author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
2237	>	title = {Reversible Multiple Time Scale Molecular-Dynamics},
2238	>	journal = {Journal of Chemical Physics},
2239	>	year = {1992},
2240	>	volume = {97},
2241	>	pages = {1990-2001},
2242	>	number = {3},
2243	>	month = {Aug 1},
2244	>	abstract = {The Trotter factorization of the Liouville propagator is used to generate
2245	>	new reversible molecular dynamics integrators. This strategy is
2246	>	applied to derive reversible reference system propagator algorithms
2247	>	(RESPA) that greatly accelerate simulations of systems with a separation
2248	>	of time scales or with long range forces. The new algorithms have
2249	>	all of the advantages of previous RESPA integrators but are reversible,
2250	>	and more stable than those methods. These methods are applied to
2251	>	a set of paradigmatic systems and are shown to be superior to earlier
2252	>	methods. It is shown how the new RESPA methods are related to predictor-corrector
2253	>	integrators. Finally, we show how these methods can be used to accelerate
2254	>	the integration of the equations of motion of systems with Nose
2255	>	thermostats.},
2256	>	annote = {Je891 Times Cited:680 Cited References Count:19},
2257	>	issn = {0021-9606},
2258	>	uri = {<Go to ISI>://A1992JE89100044},
2259		}
2260
2261	<	@Article{Gray03,
2262	<	author =       {J.~J Gray,S. Moughon, C. Wang },
2263	<	title =        {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations},
2264	<	journal =      {jmb},
2265	<	year =         2003,
2266	<	volume =       331,
2267	<	pages =        {281-299}
2261	>	@ARTICLE{Wegener1979,
2262	>	author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
2263	>	title = {A general ellipsoid can not always serve as a modle for the rotational
2264	>	diffusion properties of arbitrary shaped rigid molecules},
2265	>	journal = {Proc. Natl. Acad. Sci.},
2266	>	year = {1979},
2267	>	volume = {76},
2268	>	pages = {6356-6360},
2269	>	number = {12},
2270		}
2271
2272	<	@Article{McLachlan93,
2273	<	author =       {R.~I McLachlan},
2274	<	title =        {Explicit Lie-Poisson integration and the Euler equations},
2275	<	journal =      {prl},
2276	<	year =         1993,
2277	<	volume =       71,
2278	<	pages =        {3043-3046}
2272	>	@ARTICLE{Withers2003,
2273	>	author = {I. M. Withers},
2274	>	title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne
2275	>	fluid},
2276	>	journal = {Journal of Chemical Physics},
2277	>	year = {2003},
2278	>	volume = {119},
2279	>	pages = {10209-10223},
2280	>	number = {19},
2281	>	month = {Nov 15},
2282	>	abstract = {The effects of longitudinal quadrupole moments on the formation of
2283	>	liquid crystalline phases are studied by means of constant NPT Monte
2284	>	Carlo simulation methods. The popular Gay-Berne model mesogen is
2285	>	used as the reference fluid, which displays the phase sequences
2286	>	isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0)
2287	>	and low (T*=1.5) temperatures, respectively. With increasing quadrupole
2288	>	magnitude the smectic phases are observed to be stabilized with
2289	>	respect to the isotropic liquid, while the smectic B is destabilized
2290	>	with respect to the smectic A. At the lower temperature, a sufficiently
2291	>	large quadrupole magnitude results in the injection of the smectic
2292	>	A phase into the phase sequence and the replacement of the smectic
2293	>	B phase by the tilted smectic J phase. The nematic phase is also
2294	>	injected into the phase sequence at both temperatures considered,
2295	>	and ultimately for sufficiently large quadrupole magnitudes no coherent
2296	>	layered structures were observed. The stabilization of the smectic
2297	>	A phase supports the commonly held belief that, while the inclusion
2298	>	of polar groups is not a prerequisite for the formation of the smectic
2299	>	A phase, quadrupolar interactions help to increase the temperature
2300	>	and pressure range for which the smectic A phase is observed. The
2301	>	quality of the layered structure is worsened with increasing quadrupole
2302	>	magnitude. This behavior, along with the injection of the nematic
2303	>	phase into the phase sequence, indicate that the general tendency
2304	>	of the quadrupolar interactions is to destabilize the layered structure.
2305	>	A pressure dependence upon the smectic layer spacing is observed.
2306	>	This behavior is in much closer agreement with experimental findings
2307	>	than has been observed previously for nonpolar Gay-Berne and hard
2308	>	spherocylinder models. (C) 2003 American Institute of Physics.},
2309	>	annote = {738EF Times Cited:3 Cited References Count:43},
2310	>	issn = {0021-9606},
2311	>	uri = {<Go to ISI>://000186273200027},
2312		}
2167	–	@ARTICLE{Wegener79,
2168	–	AUTHOR =       {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
2169	–	TITLE =        {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
2170	–	JOURNAL =      {Proc. Natl. Acad. Sci.},
2171	–	YEAR =         {1979},
2172	–	volume =       {76},
2173	–	number =       {12},
2174	–	pages =        {6356-6360}
2175	–	}
2313
2177	–	@ARTICLE{Powles73,
2178	–	AUTHOR =       {J.~G. Powles},
2179	–	TITLE =        {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
2180	–	JOURNAL =      {Advan. Phys.},
2181	–	YEAR =         {1973},
2182	–	volume =       {22},
2183	–	pages =        {1-56}
2184	–	}

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